Daily Papers

When reading a document, glancing at the spatial layout of a document is an initial step to understand it roughly. Traditional document layout analysis (DLA) methods, however, offer only a superficial parsing of documents, focusing on basic instance detection and often failing to capture the nuanced spatial and logical relations between instances. These limitations hinder DLA-based models from achieving a gradually deeper comprehension akin to human reading. In this work, we propose a novel graph-based Document Structure Analysis (gDSA) task. This task requires that model not only detects document elements but also generates spatial and logical relations in form of a graph structure, allowing to understand documents in a holistic and intuitive manner. For this new task, we construct a relation graph-based document structure analysis dataset (GraphDoc) with 80K document images and 4.13M relation annotations, enabling training models to complete multiple tasks like reading order, hierarchical structures analysis, and complex inter-element relation inference. Furthermore, a document relation graph generator (DRGG) is proposed to address the gDSA task, which achieves performance with 57.6% at mAP_g@0.5 for a strong benchmark baseline on this novel task and dataset. We hope this graphical representation of document structure can mark an innovative advancement in document structure analysis and understanding. The new dataset and code will be made publicly available at https://yufanchen96.github.io/projects/GraphDoc.

Solving math word problems requires deductive reasoning over the quantities in the text. Various recent research efforts mostly relied on sequence-to-sequence or sequence-to-tree models to generate mathematical expressions without explicitly performing relational reasoning between quantities in the given context. While empirically effective, such approaches typically do not provide explanations for the generated expressions. In this work, we view the task as a complex relation extraction problem, proposing a novel approach that presents explainable deductive reasoning steps to iteratively construct target expressions, where each step involves a primitive operation over two quantities defining their relation. Through extensive experiments on four benchmark datasets, we show that the proposed model significantly outperforms existing strong baselines. We further demonstrate that the deductive procedure not only presents more explainable steps but also enables us to make more accurate predictions on questions that require more complex reasoning.

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

Discovering novel high-entropy alloys (HEAs) with desirable properties is challenging due to the vast compositional space and complex phase formation mechanisms. Efficient exploration of this space requires a strategic approach that integrates heterogeneous knowledge sources. Here, we propose a framework that systematically combines knowledge extracted from computational material datasets with domain knowledge distilled from scientific literature using large language models (LLMs). A central feature of this approach is the explicit consideration of element substitutability, identifying chemically similar elements that can be interchanged to potentially stabilize desired HEAs. Dempster-Shafer theory, a mathematical framework for reasoning under uncertainty, is employed to model and combine substitutabilities based on aggregated evidence from multiple sources. The framework predicts the phase stability of candidate HEA compositions and is systematically evaluated on both quaternary alloy systems, demonstrating superior performance compared to baseline machine learning models and methods reliant on single-source evidence in cross-validation experiments. By leveraging multi-source knowledge, the framework retains robust predictive power even when key elements are absent from the training data, underscoring its potential for knowledge transfer and extrapolation. Furthermore, the enhanced interpretability of the methodology offers insights into the fundamental factors governing HEA formation. Overall, this work provides a promising strategy for accelerating HEA discovery by integrating computational and textual knowledge sources, enabling efficient exploration of vast compositional spaces with improved generalization and interpretability.

Embedding-based methods for reasoning in knowledge hypergraphs learn a representation for each entity and relation. Current methods do not capture the procedural rules underlying the relations in the graph. We propose a simple embedding-based model called ReAlE that performs link prediction in knowledge hypergraphs (generalized knowledge graphs) and can represent high-level abstractions in terms of relational algebra operations. We show theoretically that ReAlE is fully expressive and provide proofs and empirical evidence that it can represent a large subset of the primitive relational algebra operations, namely renaming, projection, set union, selection, and set difference. We also verify experimentally that ReAlE outperforms state-of-the-art models in knowledge hypergraph completion, and in representing each of these primitive relational algebra operations. For the latter experiment, we generate a synthetic knowledge hypergraph, for which we design an algorithm based on the Erdos-R'enyi model for generating random graphs.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

The drive for predictable LLM reasoning in their integration with compound systems has popularized structured outputs, yet concerns remain about performance trade-offs compared to unconstrained natural language. At the same time, training on unconstrained Chain of Thought (CoT) traces has brought about a new class of strong reasoning models that nevertheless present novel compute budget and faithfulness challenges. This paper introduces iSelf-Discover, an instance-level adaptation of the Self-Discover framework, and using it compares dynamically generated structured JSON reasoning with its unstructured counterpart. Our empirical evaluation across diverse benchmarks using state-of-the-art open-source models supports a consistent advantage for unstructured reasoning. Notably, on the complex MATH benchmark, unstructured plans achieved relative performance improvements of up to 18.90\% over structured approaches. Zero-shot unstructured iSelf-Discover variants are also shown to outperform their five-shot structured counterparts, underscoring the significance of this gap, even when structured plans are dynamically generated to ensure reasoning precedes the final answer. We further demonstrate that the optimal granularity of plan generation (instance-level vs. task-level) is context-dependent. These findings invite re-evaluation of the reliance on structured formats for complex problem-solving and how compound systems should be organized.

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated a fully automated pipeline, verified by subject matter experts, to facilitate this task. Our approach integrates OpenAI reasoning models with named entity recognition (NER) systems to extract chemical entities from recent literature, which are then augmented with external knowledge bases to form a comprehensive knowledge graph. By generating multi-hop questions across these graphs, we assess LLM performance in both context-augmented and non-context augmented settings. Our experiments reveal that even state-of-the-art models face significant challenges in multi-hop compositional reasoning. The results reflect the importance of augmenting LLMs with document retrieval, which can have a substantial impact on improving their performance. However, even perfect retrieval accuracy with full context does not eliminate reasoning errors, underscoring the complexity of compositional reasoning. This work not only benchmarks and highlights the limitations of current LLMs but also presents a novel data generation pipeline capable of producing challenging reasoning datasets across various domains. Overall, this research advances our understanding of reasoning in computational linguistics.

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

Relation extraction has the potential for large-scale knowledge graph construction, but current methods do not consider the qualifier attributes for each relation triplet, such as time, quantity or location. The qualifiers form hyper-relational facts which better capture the rich and complex knowledge graph structure. For example, the relation triplet (Leonard Parker, Educated At, Harvard University) can be factually enriched by including the qualifier (End Time, 1967). Hence, we propose the task of hyper-relational extraction to extract more specific and complete facts from text. To support the task, we construct HyperRED, a large-scale and general-purpose dataset. Existing models cannot perform hyper-relational extraction as it requires a model to consider the interaction between three entities. Hence, we propose CubeRE, a cube-filling model inspired by table-filling approaches and explicitly considers the interaction between relation triplets and qualifiers. To improve model scalability and reduce negative class imbalance, we further propose a cube-pruning method. Our experiments show that CubeRE outperforms strong baselines and reveal possible directions for future research. Our code and data are available at github.com/declare-lab/HyperRED.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

We consider learning representations of entities and relations in KBs using the neural-embedding approach. We show that most existing models, including NTN (Socher et al., 2013) and TransE (Bordes et al., 2013b), can be generalized under a unified learning framework, where entities are low-dimensional vectors learned from a neural network and relations are bilinear and/or linear mapping functions. Under this framework, we compare a variety of embedding models on the link prediction task. We show that a simple bilinear formulation achieves new state-of-the-art results for the task (achieving a top-10 accuracy of 73.2% vs. 54.7% by TransE on Freebase). Furthermore, we introduce a novel approach that utilizes the learned relation embeddings to mine logical rules such as "BornInCity(a,b) and CityInCountry(b,c) => Nationality(a,c)". We find that embeddings learned from the bilinear objective are particularly good at capturing relational semantics and that the composition of relations is characterized by matrix multiplication. More interestingly, we demonstrate that our embedding-based rule extraction approach successfully outperforms a state-of-the-art confidence-based rule mining approach in mining Horn rules that involve compositional reasoning.

Retrieving relevant documents from a corpus is typically based on the semantic similarity between the document content and query text. The inclusion of structural relationship between documents can benefit the retrieval mechanism by addressing semantic gaps. However, incorporating these relationships requires tractable mechanisms that balance structure with semantics and take advantage of the prevalent pre-train/fine-tune paradigm. We propose here a holistic approach to learning document representations by integrating intra-document content with inter-document relations. Our deep metric learning solution analyzes the complex neighborhood structure in the relationship network to efficiently sample similar/dissimilar document pairs and defines a novel quintuplet loss function that simultaneously encourages document pairs that are semantically relevant to be closer and structurally unrelated to be far apart in the representation space. Furthermore, the separation margins between the documents are varied flexibly to encode the heterogeneity in relationship strengths. The model is fully fine-tunable and natively supports query projection during inference. We demonstrate that it outperforms competing methods on multiple datasets for document retrieval tasks.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

This paper studies the problem of solving complex chemistry problems with large language models (LLMs). Despite the extensive general knowledge in LLMs (such as GPT-4), they struggle with chemistry reasoning that requires faithful grounded reasoning with diverse chemical knowledge and an integrative understanding of chemical interactions. We propose InstructChem, a new structured reasoning approach that substantially boosts the LLMs' chemical reasoning capabilities. InstructChem explicitly decomposes the reasoning into three critical phrases, including chemical formulae generation by LLMs that offers the basis for subsequent grounded reasoning, step-by-step reasoning that makes multi-step derivations with the identified formulae for a preliminary answer, and iterative review-and-refinement that steers LLMs to progressively revise the previous phases for increasing confidence, leading to the final high-confidence answer. We conduct extensive experiments on four different chemistry challenges, including quantum chemistry, quantum mechanics, physical chemistry, and chemistry kinetics. Our approach significantly enhances GPT-4 on chemistry reasoning, yielding an 8% average absolute improvement and a 30% peak improvement. We further use the generated reasoning by GPT-4 to fine-tune smaller LMs (e.g., Vicuna) and observe strong improvement of the smaller LMs. This validates our approach and enables LLMs to generate high-quality reasoning.

Answering complex queries on incomplete knowledge graphs is a challenging task where a model needs to answer complex logical queries in the presence of missing knowledge. Prior work in the literature has proposed to address this problem by designing architectures trained end-to-end for the complex query answering task with a reasoning process that is hard to interpret while requiring data and resource-intensive training. Other lines of research have proposed re-using simple neural link predictors to answer complex queries, reducing the amount of training data by orders of magnitude while providing interpretable answers. The neural link predictor used in such approaches is not explicitly optimised for the complex query answering task, implying that its scores are not calibrated to interact together. We propose to address these problems via CQD^{A}, a parameter-efficient score adaptation model optimised to re-calibrate neural link prediction scores for the complex query answering task. While the neural link predictor is frozen, the adaptation component -- which only increases the number of model parameters by 0.03% -- is trained on the downstream complex query answering task. Furthermore, the calibration component enables us to support reasoning over queries that include atomic negations, which was previously impossible with link predictors. In our experiments, CQD^{A} produces significantly more accurate results than current state-of-the-art methods, improving from 34.4 to 35.1 Mean Reciprocal Rank values averaged across all datasets and query types while using leq 30% of the available training query types. We further show that CQD^{A} is data-efficient, achieving competitive results with only 1% of the training complex queries, and robust in out-of-domain evaluations.

Reasoning on knowledge graphs is a challenging task because it utilizes observed information to predict the missing one. Particularly, answering complex queries based on first-order logic is one of the crucial tasks to verify learning to reason abilities for generalization and composition. Recently, the prevailing method is query embedding which learns the embedding of a set of entities and treats logic operations as set operations and has shown great empirical success. Though there has been much research following the same formulation, many of its claims lack a formal and systematic inspection. In this paper, we rethink this formulation and justify many of the previous claims by characterizing the scope of queries investigated previously and precisely identifying the gap between its formulation and its goal, as well as providing complexity analysis for the currently investigated queries. Moreover, we develop a new dataset containing ten new types of queries with features that have never been considered and therefore can provide a thorough investigation of complex queries. Finally, we propose a new neural-symbolic method, Fuzzy Inference with Truth value (FIT), where we equip the neural link predictors with fuzzy logic theory to support end-to-end learning using complex queries with provable reasoning capability. Empirical results show that our method outperforms previous methods significantly in the new dataset and also surpasses previous methods in the existing dataset at the same time.

Formulating and answering logical queries is a standard communication interface for knowledge graphs (KGs). Alleviating the notorious incompleteness of real-world KGs, neural methods achieved impressive results in link prediction and complex query answering tasks by learning representations of entities, relations, and queries. Still, most existing query answering methods rely on transductive entity embeddings and cannot generalize to KGs containing new entities without retraining the entity embeddings. In this work, we study the inductive query answering task where inference is performed on a graph containing new entities with queries over both seen and unseen entities. To this end, we devise two mechanisms leveraging inductive node and relational structure representations powered by graph neural networks (GNNs). Experimentally, we show that inductive models are able to perform logical reasoning at inference time over unseen nodes generalizing to graphs up to 500% larger than training ones. Exploring the efficiency--effectiveness trade-off, we find the inductive relational structure representation method generally achieves higher performance, while the inductive node representation method is able to answer complex queries in the inference-only regime without any training on queries and scales to graphs of millions of nodes. Code is available at https://github.com/DeepGraphLearning/InductiveQE.

Recent advancements in large language models (LLMs) have led to significant improvements in various natural language processing tasks, but it is still challenging for LLMs to perform knowledge-intensive complex question answering due to LLMs' inefficacy in reasoning planning and the hallucination problem. A typical solution is to employ retrieval-augmented generation (RAG) coupled with chain-of-thought (CoT) reasoning, which decomposes complex questions into chain-like sub-questions and applies iterative RAG at each sub-question. However, prior works exhibit sub-optimal reasoning planning and overlook dynamic knowledge retrieval from heterogeneous sources. In this paper, we propose AtomR, a novel heterogeneous knowledge reasoning framework that conducts multi-source reasoning at the atomic level. Drawing inspiration from the graph modeling of knowledge, AtomR leverages large language models (LLMs) to decompose complex questions into combinations of three atomic knowledge operators, significantly enhancing the reasoning process at both the planning and execution stages. We also introduce BlendQA, a novel evaluation benchmark tailored to assess complex heterogeneous knowledge reasoning. Experiments show that AtomR significantly outperforms state-of-the-art baselines across three single-source and two multi-source reasoning benchmarks, with notable performance gains of 9.4% on 2WikiMultihop and 9.5% on BlendQA.

Text-to-image (T2I) generation aims to synthesize images from textual prompts, which jointly specify what must be shown and imply what can be inferred, thereby corresponding to two core capabilities: composition and reasoning. However, with the emerging advances of T2I models in reasoning beyond composition, existing benchmarks reveal clear limitations in providing comprehensive evaluations across and within these capabilities. Meanwhile, these advances also enable models to handle more complex prompts, whereas current benchmarks remain limited to low scene density and simplified one-to-one reasoning. To address these limitations, we propose T2I-CoReBench, a comprehensive and complex benchmark that evaluates both composition and reasoning capabilities of T2I models. To ensure comprehensiveness, we structure composition around scene graph elements (instance, attribute, and relation) and reasoning around the philosophical framework of inference (deductive, inductive, and abductive), formulating a 12-dimensional evaluation taxonomy. To increase complexity, driven by the inherent complexities of real-world scenarios, we curate each prompt with high compositional density for composition and multi-step inference for reasoning. We also pair each prompt with a checklist that specifies individual yes/no questions to assess each intended element independently to facilitate fine-grained and reliable evaluation. In statistics, our benchmark comprises 1,080 challenging prompts and around 13,500 checklist questions. Experiments across 27 current T2I models reveal that their composition capability still remains limited in complex high-density scenarios, while the reasoning capability lags even further behind as a critical bottleneck, with all models struggling to infer implicit elements from prompts. Our project page: https://t2i-corebench.github.io/.

Retrieving external knowledge and prompting large language models with relevant information is an effective paradigm to enhance the performance of question-answering tasks. Previous research typically handles paragraphs from external documents in isolation, resulting in a lack of context and ambiguous references, particularly in multi-document and complex tasks. To overcome these challenges, we propose a new retrieval framework IIER, that leverages Inter-chunk Interactions to Enhance Retrieval. This framework captures the internal connections between document chunks by considering three types of interactions: structural, keyword, and semantic. We then construct a unified Chunk-Interaction Graph to represent all external documents comprehensively. Additionally, we design a graph-based evidence chain retriever that utilizes previous paths and chunk interactions to guide the retrieval process. It identifies multiple seed nodes based on the target question and iteratively searches for relevant chunks to gather supporting evidence. This retrieval process refines the context and reasoning chain, aiding the large language model in reasoning and answer generation. Extensive experiments demonstrate that IIER outperforms strong baselines across four datasets, highlighting its effectiveness in improving retrieval and reasoning capabilities.

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

Property prediction accuracy has long been a key parameter of machine learning in materials informatics. Accordingly, advanced models showing state-of-the-art performance turn into highly parameterized black boxes missing interpretability. Here, we present an elegant way to make their reasoning transparent. Human-readable text-based descriptions automatically generated within a suite of open-source tools are proposed as materials representation. Transformer language models pretrained on 2 million peer-reviewed articles take as input well-known terms, e.g., chemical composition, crystal symmetry, and site geometry. Our approach outperforms crystal graph networks by classifying four out of five analyzed properties if one considers all available reference data. Moreover, fine-tuned text-based models show high accuracy in the ultra-small data limit. Explanations of their internal machinery are produced using local interpretability techniques and are faithful and consistent with domain expert rationales. This language-centric framework makes accurate property predictions accessible to people without artificial-intelligence expertise.

Logical reasoning task has attracted great interest since it was proposed. Faced with such a task, current competitive models, even large language models (e.g., ChatGPT and PaLM 2), still perform badly. Previous promising LMs struggle in logical consistency modeling and logical structure perception. To this end, we model the logical reasoning task by transforming each logical sample into reasoning paths and propose an architecture PathReasoner. It addresses the task from the views of both data and model. To expand the diversity of the logical samples, we propose an atom extension strategy supported by equivalent logical formulas, to form new reasoning paths. From the model perspective, we design a stack of transformer-style blocks. In particular, we propose a path-attention module to joint model in-atom and cross-atom relations with the high-order diffusion strategy. Experiments show that PathReasoner achieves competitive performances on two logical reasoning benchmarks and great generalization abilities.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

The pursuit of automated scientific discovery has fueled progress from symbolic logic to modern AI, forging new frontiers in reasoning and pattern recognition. Transformers function as potential systems, where every possible relationship remains latent potentiality until tasks impose constraints, akin to measurement. Yet, refining their sampling requires more than probabilistic selection: solutions must conform to specific structures or rules, ensuring consistency and the invocation of general principles. We present Graph-PReFLexOR (Graph-based Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning), a framework that combines graph reasoning with symbolic abstraction to dynamically expand domain knowledge. Inspired by reinforcement learning, Graph-PReFLexOR defines reasoning as a structured mapping, where tasks yield knowledge graphs, abstract patterns, and ultimately, final answers. Inspired by category theory, it encodes concepts as nodes and their relationships as edges, supporting hierarchical inference and adaptive learning through isomorphic representations. Demonstrations include hypothesis generation, materials design, and creative reasoning, such as discovering relationships between mythological concepts like 'thin places' with materials science. We propose a 'knowledge garden growth' strategy that integrates insights across domains, promoting interdisciplinary connections. Results with a 3-billion-parameter Graph-PReFLexOR model show superior reasoning depth and adaptability, underscoring the potential for transparent, multidisciplinary AI-driven discovery. It lays the groundwork for general autonomous reasoning solutions.

Joint entity and relation extraction plays a pivotal role in various applications, notably in the construction of knowledge graphs. Despite recent progress, existing approaches often fall short in two key aspects: richness of representation and coherence in output structure. These models often rely on handcrafted heuristics for computing entity and relation representations, potentially leading to loss of crucial information. Furthermore, they disregard task and/or dataset-specific constraints, resulting in output structures that lack coherence. In our work, we introduce EnriCo, which mitigates these shortcomings. Firstly, to foster rich and expressive representation, our model leverage attention mechanisms that allow both entities and relations to dynamically determine the pertinent information required for accurate extraction. Secondly, we introduce a series of decoding algorithms designed to infer the highest scoring solutions while adhering to task and dataset-specific constraints, thus promoting structured and coherent outputs. Our model demonstrates competitive performance compared to baselines when evaluated on Joint IE datasets.

Answering complex real-world questions often requires accurate retrieval from textual knowledge graphs (TKGs). The scarcity of annotated data, along with intricate topological structures, makes this task particularly challenging. As the nature of relational path information could enhance the inference ability of Large Language Models (LLMs), efficiently retrieving more complex relational path information from TKGs presents another key challenge. To tackle these challenges, we first develop a Dataset for LLMs Complex Reasoning over Textual Knowledge Graphs (RiTeK) with a broad topological structure coverage.We synthesize realistic user queries that integrate diverse topological structures, relational information, and complex textual descriptions. We conduct rigorous expert evaluation to validate the quality of our synthesized queries. And then, we introduce an enhanced Monte Carlo Tree Search (MCTS) method, Relational MCTS, to automatically extract relational path information from textual graphs for specific queries. Our dataset mainly covers the medical domain as the relation types and entity are complex and publicly available. Experimental results indicate that RiTeK poses significant challenges for current retrieval and LLM systems, while the proposed Relational MCTS method enhances LLM inference ability and achieves state-of-the-art performance on RiTeK.

We propose a fully spectral, neuro\-symbolic reasoning architecture that leverages Graph Signal Processing (GSP) as the primary computational backbone for integrating symbolic logic and neural inference. Unlike conventional reasoning models that treat spectral graph methods as peripheral components, our approach formulates the entire reasoning pipeline in the graph spectral domain. Logical entities and relationships are encoded as graph signals, processed via learnable spectral filters that control multi-scale information propagation, and mapped into symbolic predicates for rule-based inference. We present a complete mathematical framework for spectral reasoning, including graph Fourier transforms, band-selective attention, and spectral rule grounding. Experiments on benchmark reasoning datasets (ProofWriter, EntailmentBank, bAbI, CLUTRR, and ARC-Challenge) demonstrate improvements in logical consistency, interpretability, and computational efficiency over state\-of\-the\-art neuro\-symbolic models. Our results suggest that GSP provides a mathematically grounded and computationally efficient substrate for robust and interpretable reasoning systems.

Many learning algorithms such as kernel machines, nearest neighbors, clustering, or anomaly detection, are based on the concept of 'distance' or 'similarity'. Before similarities are used for training an actual machine learning model, we would like to verify that they are bound to meaningful patterns in the data. In this paper, we propose to make similarities interpretable by augmenting them with an explanation in terms of input features. We develop BiLRP, a scalable and theoretically founded method to systematically decompose similarity scores on pairs of input features. Our method can be expressed as a composition of LRP explanations, which were shown in previous works to scale to highly nonlinear functions. Through an extensive set of experiments, we demonstrate that BiLRP robustly explains complex similarity models, e.g. built on VGG-16 deep neural network features. Additionally, we apply our method to an open problem in digital humanities: detailed assessment of similarity between historical documents such as astronomical tables. Here again, BiLRP provides insight and brings verifiability into a highly engineered and problem-specific similarity model.

Many mathematical models have been leveraged to design embeddings for representing Knowledge Graph (KG) entities and relations for link prediction and many downstream tasks. These mathematically-inspired models are not only highly scalable for inference in large KGs, but also have many explainable advantages in modeling different relation patterns that can be validated through both formal proofs and empirical results. In this paper, we make a comprehensive overview of the current state of research in KG completion. In particular, we focus on two main branches of KG embedding (KGE) design: 1) distance-based methods and 2) semantic matching-based methods. We discover the connections between recently proposed models and present an underlying trend that might help researchers invent novel and more effective models. Next, we delve into CompoundE and CompoundE3D, which draw inspiration from 2D and 3D affine operations, respectively. They encompass a broad spectrum of techniques including distance-based and semantic-based methods. We will also discuss an emerging approach for KG completion which leverages pre-trained language models (PLMs) and textual descriptions of entities and relations and offer insights into the integration of KGE embedding methods with PLMs for KG completion.

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

Representation learning on heterogeneous graphs aims to obtain meaningful node representations to facilitate various downstream tasks, such as node classification and link prediction. Existing heterogeneous graph learning methods are primarily developed by following the propagation mechanism of node representations. There are few efforts on studying the role of relations for improving the learning of more fine-grained node representations. Indeed, it is important to collaboratively learn the semantic representations of relations and discern node representations with respect to different relation types. To this end, in this paper, we propose a novel Relation-aware Heterogeneous Graph Neural Network, namely R-HGNN, to learn node representations on heterogeneous graphs at a fine-grained level by considering relation-aware characteristics. Specifically, a dedicated graph convolution component is first designed to learn unique node representations from each relation-specific graph separately. Then, a cross-relation message passing module is developed to improve the interactions of node representations across different relations. Also, the relation representations are learned in a layer-wise manner to capture relation semantics, which are used to guide the node representation learning process. Moreover, a semantic fusing module is presented to aggregate relation-aware node representations into a compact representation with the learned relation representations. Finally, we conduct extensive experiments on a variety of graph learning tasks, and experimental results demonstrate that our approach consistently outperforms existing methods among all the tasks.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

In-context Learning (ICL) enables large language models (LLMs) to tackle downstream tasks through sophisticated prompting and high-quality demonstrations. However, this traditional ICL paradigm shows limitations when facing complex mathematical reasoning tasks, primarily due to its heavy dependence on example quality and the necessity for human intervention in challenging scenarios. To address these limitations, this paper presents HiAR-ICL, a High-level Automated Reasoning paradigm in ICL that shifts focus from specific examples to abstract thinking patterns, extending the conventional concept of context in ICL. HiAR-ICL introduces five atomic reasoning actions as fundamental components for constructing chain-structured patterns. Using Monte Carlo Tree Search, we explore reasoning paths and construct thought cards to guide subsequent inference. We then develop a cognitive complexity framework that dynamically matches problems with appropriate thought cards. Experimental results demonstrate HiAR-ICL's effectiveness, achieving state-of-the-art accuracy (79.6%) on the MATH benchmark with Qwen2.5-7B-Instruct, surpassing GPT-4o (76.6%) and Claude 3.5 (71.1%).

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the necessity of navigating extremely high-dimensional combinatorial and nonlinear hypothesis spaces. Traditional methods of equation discovery largely focus on extracting equations from data alone, often neglecting the rich domain-specific prior knowledge that scientists typically depend on. To bridge this gap, we introduce LLM-SR, a novel approach that leverages the extensive scientific knowledge and robust code generation capabilities of Large Language Models (LLMs) to discover scientific equations from data in an efficient manner. Specifically, LLM-SR treats equations as programs with mathematical operators and combines LLMs' scientific priors with evolutionary search over equation programs. The LLM iteratively proposes new equation skeletons, drawing from its physical understanding, which are then optimized against data to estimate skeleton parameters. We demonstrate LLM-SR's effectiveness across three diverse scientific domains, where it discovers physically accurate equations that provide significantly better fits to in-domain and out-of-domain data compared to the well-established equation discovery baselines

Hypergraphs offer a powerful framework for modeling higher-order interactions that traditional pairwise graphs cannot fully capture. However, practical constraints often lead to their simplification into projected graphs, resulting in substantial information loss and ambiguity in representing higher-order relationships. In this work, we propose MARIOH, a supervised approach for reconstructing the original hypergraph from its projected graph by leveraging edge multiplicity. To overcome the difficulties posed by the large search space, MARIOH integrates several key ideas: (a) identifying provable size-2 hyperedges, which reduces the candidate search space, (b) predicting the likelihood of candidates being hyperedges by utilizing both structural and multiplicity-related features, and (c) not only targeting promising hyperedge candidates but also examining less confident ones to explore alternative possibilities. Together, these ideas enable MARIOH to efficiently and effectively explore the search space. In our experiments using 10 real-world datasets, MARIOH achieves up to 74.51% higher reconstruction accuracy compared to state-of-the-art methods.

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and rich resource of such data. However, manual dataset creation from these resources is challenging due to issues in maintaining quality and consistency, scalability limitations, and the risk of human error and bias. Therefore, in this work, we develop a chemist AI agent, powered by large language models (LLMs), to overcome these challenges by autonomously creating structured datasets from natural language text, ranging from sentences and paragraphs to extensive scientific research articles. Our chemist AI agent, Eunomia, can plan and execute actions by leveraging the existing knowledge from decades of scientific research articles, scientists, the Internet and other tools altogether. We benchmark the performance of our approach in three different information extraction tasks with various levels of complexity, including solid-state impurity doping, metal-organic framework (MOF) chemical formula, and property relations. Our results demonstrate that our zero-shot agent, with the appropriate tools, is capable of attaining performance that is either superior or comparable to the state-of-the-art fine-tuned materials information extraction methods. This approach simplifies compilation of machine learning-ready datasets for various materials discovery applications, and significantly ease the accessibility of advanced natural language processing tools for novice users in natural language. The methodology in this work is developed as an open-source software on https://github.com/AI4ChemS/Eunomia.

Solving complex mathematical problems via system-2 reasoning is a natural human skill, yet it remains a significant challenge for current large language models (LLMs). We identify the scarcity of deliberate multi-step reasoning data as a primary limiting factor. To this end, we introduce Enriched Instruction Tuning (EIT), a method that enriches existing human-annotated mathematical datasets by synergizing human and AI feedback to create fine-grained reasoning trajectories. These datasets are then used to fine-tune open-source LLMs, enhancing their mathematical reasoning abilities without reliance on any symbolic verification program. Concretely, EIT is composed of two critical steps: Enriching with Reasoning Plan (ERP) and Enriching with Reasoning Step (ERS). The former generates a high-level plan that breaks down complex instructions into a sequence of simpler objectives, while ERS fills in reasoning contexts often overlooked by human annotators, creating a smoother reasoning trajectory for LLM fine-tuning. Unlike existing CoT prompting methods that generate reasoning chains only depending on LLM's internal knowledge, our method leverages human-annotated initial answers as ``meta-knowledge'' to help LLMs generate more detailed and precise reasoning processes, leading to a more trustworthy LLM expert for complex mathematical problems. In experiments, EIT achieves an accuracy of 84.1% on GSM8K and 32.5% on MATH, surpassing state-of-the-art fine-tuning and prompting methods, and even matching the performance of tool-augmented methods.

Hyper-relational knowledge graphs (HKGs) extend standard knowledge graphs by associating attribute-value qualifiers to triples, which effectively represent additional fine-grained information about its associated triple. Hyper-relational knowledge graph completion (HKGC) aims at inferring unknown triples while considering its qualifiers. Most existing approaches to HKGC exploit a global-level graph structure to encode hyper-relational knowledge into the graph convolution message passing process. However, the addition of multi-hop information might bring noise into the triple prediction process. To address this problem, we propose HyperFormer, a model that considers local-level sequential information, which encodes the content of the entities, relations and qualifiers of a triple. More precisely, HyperFormer is composed of three different modules: an entity neighbor aggregator module allowing to integrate the information of the neighbors of an entity to capture different perspectives of it; a relation qualifier aggregator module to integrate hyper-relational knowledge into the corresponding relation to refine the representation of relational content; a convolution-based bidirectional interaction module based on a convolutional operation, capturing pairwise bidirectional interactions of entity-relation, entity-qualifier, and relation-qualifier. realize the depth perception of the content related to the current statement. Furthermore, we introduce a Mixture-of-Experts strategy into the feed-forward layers of HyperFormer to strengthen its representation capabilities while reducing the amount of model parameters and computation. Extensive experiments on three well-known datasets with four different conditions demonstrate HyperFormer's effectiveness. Datasets and code are available at https://github.com/zhiweihu1103/HKGC-HyperFormer.

Network embedding, which maps graphs to distributed representations, is a unified framework for various graph inference tasks. According to the topology properties (e.g., structural roles and community memberships of nodes) to be preserved, it can be categorized into the identity and position embedding. However, existing methods can only capture one type of property. Some approaches can support the inductive inference that generalizes the embedding model to new nodes or graphs but relies on the availability of attributes. Due to the complicated correlations between topology and attributes, it is unclear for some inductive methods which type of property they can capture. In this study, we explore a unified framework for the joint inductive inference of identity and position embeddings without attributes. An inductive random walk embedding (IRWE) method is proposed, which combines multiple attention units to handle the random walk on graph topology and simultaneously derives identity and position embeddings that are jointly optimized. In particular, we demonstrate that some random walk statistics can be informative features to characterize node identities and positions while supporting the inductive embedding inference. Experiments validate the superior performance of IRWE beyond various baselines for the transductive and inductive inference of identity and position embeddings.

Despite the success of large vision and language models (VLMs) in many downstream applications, it is unclear how well they encode compositional information. Here, we create the Attribution, Relation, and Order (ARO) benchmark to systematically evaluate the ability of VLMs to understand different types of relationships, attributes, and order. ARO consists of Visual Genome Attribution, to test the understanding of objects' properties; Visual Genome Relation, to test for relational understanding; and COCO & Flickr30k-Order, to test for order sensitivity. ARO is orders of magnitude larger than previous benchmarks of compositionality, with more than 50,000 test cases. We show where state-of-the-art VLMs have poor relational understanding, can blunder when linking objects to their attributes, and demonstrate a severe lack of order sensitivity. VLMs are predominantly trained and evaluated on large datasets with rich compositional structure in the images and captions. Yet, training on these datasets has not been enough to address the lack of compositional understanding, and evaluating on these datasets has failed to surface this deficiency. To understand why these limitations emerge and are not represented in the standard tests, we zoom into the evaluation and training procedures. We demonstrate that it is possible to perform well on retrieval over existing datasets without using the composition and order information. Given that contrastive pretraining optimizes for retrieval on datasets with similar shortcuts, we hypothesize that this can explain why the models do not need to learn to represent compositional information. This finding suggests a natural solution: composition-aware hard negative mining. We show that a simple-to-implement modification of contrastive learning significantly improves the performance on tasks requiring understanding of order and compositionality.

Hypergraph neural networks (HNNs) using neural networks to encode hypergraphs provide a promising way to model higher-order relations in data and further solve relevant prediction tasks built upon such higher-order relations. However, higher-order relations in practice contain complex patterns and are often highly irregular. So, it is often challenging to design an HNN that suffices to express those relations while keeping computational efficiency. Inspired by hypergraph diffusion algorithms, this work proposes a new HNN architecture named ED-HNN, which provably represents any continuous equivariant hypergraph diffusion operators that can model a wide range of higher-order relations. ED-HNN can be implemented efficiently by combining star expansions of hypergraphs with standard message passing neural networks. ED-HNN further shows great superiority in processing heterophilic hypergraphs and constructing deep models. We evaluate ED-HNN for node classification on nine real-world hypergraph datasets. ED-HNN uniformly outperforms the best baselines over these nine datasets and achieves more than 2\%uparrow in prediction accuracy over four datasets therein.

We consider higher-order linear-chain conditional random fields (HO-LC-CRFs) for sequence modelling, and use sum-product networks (SPNs) for representing higher-order input- and output-dependent factors. SPNs are a recently introduced class of deep models for which exact and efficient inference can be performed. By combining HO-LC-CRFs with SPNs, expressive models over both the output labels and the hidden variables are instantiated while still enabling efficient exact inference. Furthermore, the use of higher-order factors allows us to capture relations of multiple input segments and multiple output labels as often present in real-world data. These relations can not be modelled by the commonly used first-order models and higher-order models with local factors including only a single output label. We demonstrate the effectiveness of our proposed models for sequence labeling. In extensive experiments, we outperform other state-of-the-art methods in optical character recognition and achieve competitive results in phone classification.

Recent advances in large language models (LLMs) have intensified efforts to fuse heterogeneous open-source models into a unified system that inherits their complementary strengths. Existing logit-based fusion methods maintain inference efficiency but treat vocabulary dimensions independently, overlooking semantic dependencies encoded by cross-dimension interactions. These dependencies reflect how token types interact under a model's internal reasoning and are essential for aligning models with diverse generation behaviors. To explicitly model these dependencies, we propose InfiGFusion, the first structure-aware fusion framework with a novel Graph-on-Logits Distillation (GLD) loss. Specifically, we retain the top-k logits per output and aggregate their outer products across sequence positions to form a global co-activation graph, where nodes represent vocabulary channels and edges quantify their joint activations. To ensure scalability and efficiency, we design a sorting-based closed-form approximation that reduces the original O(n^4) cost of Gromov-Wasserstein distance to O(n log n), with provable approximation guarantees. Experiments across multiple fusion settings show that GLD consistently improves fusion quality and stability. InfiGFusion outperforms SOTA models and fusion baselines across 11 benchmarks spanning reasoning, coding, and mathematics. It shows particular strength in complex reasoning tasks, with +35.6 improvement on Multistep Arithmetic and +37.06 on Causal Judgement over SFT, demonstrating superior multi-step and relational inference.

E-commerce platforms should provide detailed product descriptions (attribute values) for effective product search and recommendation. However, attribute value information is typically not available for new products. To predict unseen attribute values, large quantities of labeled training data are needed to train a traditional supervised learning model. Typically, it is difficult, time-consuming, and costly to manually label large quantities of new product profiles. In this paper, we propose a novel method to efficiently and effectively extract unseen attribute values from new products in the absence of labeled data (zero-shot setting). We propose HyperPAVE, a multi-label zero-shot attribute value extraction model that leverages inductive inference in heterogeneous hypergraphs. In particular, our proposed technique constructs heterogeneous hypergraphs to capture complex higher-order relations (i.e. user behavior information) to learn more accurate feature representations for graph nodes. Furthermore, our proposed HyperPAVE model uses an inductive link prediction mechanism to infer future connections between unseen nodes. This enables HyperPAVE to identify new attribute values without the need for labeled training data. We conduct extensive experiments with ablation studies on different categories of the MAVE dataset. The results demonstrate that our proposed HyperPAVE model significantly outperforms existing classification-based, generation-based large language models for attribute value extraction in the zero-shot setting.

Relation extraction (RE) has achieved remarkable progress with the help of pre-trained language models. However, existing RE models are usually incapable of handling two situations: implicit expressions and long-tail relation classes, caused by language complexity and data sparsity. Further, these approaches and models are largely inaccessible to users who don't have direct access to large language models (LLMs) and/or infrastructure for supervised training or fine-tuning. Rule-based systems also struggle with implicit expressions. Apart from this, Real world financial documents such as various 10-X reports (including 10-K, 10-Q, etc.) of publicly traded companies pose another challenge to rule-based systems in terms of longer and complex sentences. In this paper, we introduce a simple approach that consults training relations at test time through a nearest-neighbor search over dense vectors of lexico-syntactic patterns and provides a simple yet effective means to tackle the above issues. We evaluate our approach on REFinD and show that our method achieves state-of-the-art performance. We further show that it can provide a good start for human in the loop setup when a small number of annotations are available and it is also beneficial when domain experts can provide high quality patterns.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Much of the knowledge encoded in transformer language models (LMs) may be expressed in terms of relations: relations between words and their synonyms, entities and their attributes, etc. We show that, for a subset of relations, this computation is well-approximated by a single linear transformation on the subject representation. Linear relation representations may be obtained by constructing a first-order approximation to the LM from a single prompt, and they exist for a variety of factual, commonsense, and linguistic relations. However, we also identify many cases in which LM predictions capture relational knowledge accurately, but this knowledge is not linearly encoded in their representations. Our results thus reveal a simple, interpretable, but heterogeneously deployed knowledge representation strategy in transformer LMs.

Foundation models have demonstrated remarkable capabilities across various domains, but developing analogous models for knowledge graphs presents unique challenges due to their dynamic nature and the need for cross-domain reasoning. To address these issues, we introduce \textsc{GraphOracle}, a relation-centric foundation model that unifies reasoning across knowledge graphs by converting them into Relation-Dependency Graphs (RDG), explicitly encoding compositional patterns with fewer edges than prior methods. A query-dependent attention mechanism is further developed to learn inductive representations for both relations and entities. Pre-training on diverse knowledge graphs, followed by minutes-level fine-tuning, enables effective generalization to unseen entities, relations, and entire graphs. Through comprehensive experiments on 31 diverse benchmarks spanning transductive, inductive, and cross-domain settings, we demonstrate consistent state-of-the-art performance with minimal adaptation, improving the prediction performance by up to 35\% compared to the strongest baselines.

Automated theorem proving (ATP) has become an appealing domain for exploring the reasoning ability of the recent successful generative language models. However, current ATP benchmarks mainly focus on symbolic inference, but rarely involve the understanding of complex number combination reasoning. In this work, we propose TRIGO, an ATP benchmark that not only requires a model to reduce a trigonometric expression with step-by-step proofs but also evaluates a generative LM's reasoning ability on formulas and its capability to manipulate, group, and factor number terms. We gather trigonometric expressions and their reduced forms from the web, annotate the simplification process manually, and translate it into the Lean formal language system. We then automatically generate additional examples from the annotated samples to expand the dataset. Furthermore, we develop an automatic generator based on Lean-Gym to create dataset splits of varying difficulties and distributions in order to thoroughly analyze the model's generalization ability. Our extensive experiments show our proposed TRIGO poses a new challenge for advanced generative LM's including GPT-4 which is pre-trained on a considerable amount of open-source formal theorem-proving language data, and provide a new tool to study the generative LM's ability on both formal and mathematical reasoning.

Synthesis procedures play a critical role in materials research, as they directly affect material properties. With data-driven approaches increasingly accelerating materials discovery, there is growing interest in extracting synthesis procedures from scientific literature as structured data. However, existing studies often rely on rigid, domain-specific schemas with predefined fields for structuring synthesis procedures or assume that synthesis procedures are linear sequences of operations, which limits their ability to capture the structural complexity of real-world procedures. To address these limitations, we adopt PROV-DM, an international standard for provenance information, which supports flexible, graph-based modeling of procedures. We present MatPROV, a dataset of PROV-DM-compliant synthesis procedures extracted from scientific literature using large language models. MatPROV captures structural complexities and causal relationships among materials, operations, and conditions through visually intuitive directed graphs. This representation enables machine-interpretable synthesis knowledge, opening opportunities for future research such as automated synthesis planning and optimization.

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

We present an approach to modifying Transformer architectures by integrating graph-aware relational reasoning into the attention mechanism, merging concepts from graph neural networks and language modeling. Building on the inherent connection between attention and graph theory, we reformulate the Transformer's attention mechanism as a graph operation and propose Graph-Aware Isomorphic Attention. This method leverages advanced graph modeling strategies, including Graph Isomorphism Networks (GIN) and Principal Neighborhood Aggregation (PNA), to enrich the representation of relational structures. Our approach captures complex dependencies and generalizes across tasks, as evidenced by a reduced generalization gap and improved learning performance. Additionally, we expand the concept of graph-aware attention to introduce Sparse GIN-Attention, a fine-tuning approach that employs sparse GINs. By interpreting attention matrices as sparse adjacency graphs, this technique enhances the adaptability of pre-trained foundational models with minimal computational overhead, endowing them with graph-aware capabilities. Sparse GIN-Attention fine-tuning achieves improved training dynamics and better generalization compared to alternative methods like low-rank adaption (LoRA). We discuss latent graph-like structures within traditional attention mechanisms, offering a new lens through which Transformers can be understood. By evolving Transformers as hierarchical GIN models for relational reasoning. This perspective suggests profound implications for foundational model development, enabling the design of architectures that dynamically adapt to both local and global dependencies. Applications in bioinformatics, materials science, language modeling, and beyond could benefit from this synthesis of relational and sequential data modeling, setting the stage for interpretable and generalizable modeling strategies.

Integer sequences are of central importance to the modeling of concepts admitting complete finitary descriptions. We introduce a novel view on the learning of such concepts and lay down a set of benchmarking tasks aimed at conceptual understanding by machine learning models. These tasks indirectly assess model ability to abstract, and challenge them to reason both interpolatively and extrapolatively from the knowledge gained by observing representative examples. To further aid research in knowledge representation and reasoning, we present FACT, the Finitary Abstraction Comprehension Toolkit. The toolkit surrounds a large dataset of integer sequences comprising both organic and synthetic entries, a library for data pre-processing and generation, a set of model performance evaluation tools, and a collection of baseline model implementations, enabling the making of the future advancements with ease.

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message passing networks layers and train it in a end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.

It is crucial to automatically construct knowledge graphs (KGs) of diverse new relations to support knowledge discovery and broad applications. Previous KG construction methods, based on either crowdsourcing or text mining, are often limited to a small predefined set of relations due to manual cost or restrictions in text corpus. Recent research proposed to use pretrained language models (LMs) as implicit knowledge bases that accept knowledge queries with prompts. Yet, the implicit knowledge lacks many desirable properties of a full-scale symbolic KG, such as easy access, navigation, editing, and quality assurance. In this paper, we propose a new approach of harvesting massive KGs of arbitrary relations from pretrained LMs. With minimal input of a relation definition (a prompt and a few shot of example entity pairs), the approach efficiently searches in the vast entity pair space to extract diverse accurate knowledge of the desired relation. We develop an effective search-and-rescore mechanism for improved efficiency and accuracy. We deploy the approach to harvest KGs of over 400 new relations from different LMs. Extensive human and automatic evaluations show our approach manages to extract diverse accurate knowledge, including tuples of complex relations (e.g., "A is capable of but not good at B"). The resulting KGs as a symbolic interpretation of the source LMs also reveal new insights into the LMs' knowledge capacities.

The goal of this paper is to detect objects by exploiting their interrelationships. Contrary to existing methods, which learn objects and relations separately, our key idea is to learn the object-relation distribution jointly. We first propose a novel way of creating a graphical representation of an image from inter-object relation priors and initial class predictions, we call a context-likelihood graph. We then learn the joint distribution with an energy-based modeling technique which allows to sample and refine the context-likelihood graph iteratively for a given image. Our formulation of jointly learning the distribution enables us to generate a more accurate graph representation of an image which leads to a better object detection performance. We demonstrate the benefits of our context-likelihood graph formulation and the energy-based graph refinement via experiments on the Visual Genome and MS-COCO datasets where we achieve a consistent improvement over object detectors like DETR and Faster-RCNN, as well as alternative methods modeling object interrelationships separately. Our method is detector agnostic, end-to-end trainable, and especially beneficial for rare object classes.

Information Extraction (IE) is crucial for converting unstructured data into structured formats like Knowledge Graphs (KGs). A key task within IE is Relation Extraction (RE), which identifies relationships between entities in text. Various RE methods exist, including supervised, unsupervised, weakly supervised, and rule-based approaches. Recent studies leveraging pre-trained language models (PLMs) have shown significant success in this area. In the current era dominated by Large Language Models (LLMs), fine-tuning these models can overcome limitations associated with zero-shot LLM prompting-based RE methods, especially regarding domain adaptation challenges and identifying implicit relations between entities in sentences. These implicit relations, which cannot be easily extracted from a sentence's dependency tree, require logical inference for accurate identification. This work explores the performance of fine-tuned LLMs and their integration into the Retrieval Augmented-based (RAG) RE approach to address the challenges of identifying implicit relations at the sentence level, particularly when LLMs act as generators within the RAG framework. Empirical evaluations on the TACRED, TACRED-Revisited (TACREV), Re-TACRED, and SemEVAL datasets show significant performance improvements with fine-tuned LLMs, including Llama2-7B, Mistral-7B, and T5 (Large). Notably, our approach achieves substantial gains on SemEVAL, where implicit relations are common, surpassing previous results on this dataset. Additionally, our method outperforms previous works on TACRED, TACREV, and Re-TACRED, demonstrating exceptional performance across diverse evaluation scenarios.

A key to knowledge graph embedding (KGE) is to choose a proper representation space, e.g., point-wise Euclidean space and complex vector space. In this paper, we propose a unified perspective of embedding and introduce uncertainty into KGE from the view of group theory. Our model can incorporate existing models (i.e., generality), ensure the computation is tractable (i.e., efficiency) and enjoy the expressive power of complex random variables (i.e., expressiveness). The core idea is that we embed entities/relations as elements of a symmetric group, i.e., permutations of a set. Permutations of different sets can reflect different properties of embedding. And the group operation of symmetric groups is easy to compute. In specific, we show that the embedding of many existing models, point vectors, can be seen as elements of a symmetric group. To reflect uncertainty, we first embed entities/relations as permutations of a set of random variables. A permutation can transform a simple random variable into a complex random variable for greater expressiveness, called a normalizing flow. We then define scoring functions by measuring the similarity of two normalizing flows, namely NFE. We construct several instantiating models and prove that they are able to learn logical rules. Experimental results demonstrate the effectiveness of introducing uncertainty and our model. The code is available at https://github.com/changyi7231/NFE.

Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry -- from educational foundations to specialized expertise -- spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code) -- mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

Leveraging new data sources is a key step in accelerating the pace of materials design and discovery. To complement the strides in synthesis planning driven by historical, experimental, and computed data, we present an automated method for connecting scientific literature to synthesis insights. Starting from natural language text, we apply word embeddings from language models, which are fed into a named entity recognition model, upon which a conditional variational autoencoder is trained to generate syntheses for arbitrary materials. We show the potential of this technique by predicting precursors for two perovskite materials, using only training data published over a decade prior to their first reported syntheses. We demonstrate that the model learns representations of materials corresponding to synthesis-related properties, and that the model's behavior complements existing thermodynamic knowledge. Finally, we apply the model to perform synthesizability screening for proposed novel perovskite compounds.

In self-supervised learning, a system is tasked with achieving a surrogate objective by defining alternative targets on a set of unlabeled data. The aim is to build useful representations that can be used in downstream tasks, without costly manual annotation. In this work, we propose a novel self-supervised formulation of relational reasoning that allows a learner to bootstrap a signal from information implicit in unlabeled data. Training a relation head to discriminate how entities relate to themselves (intra-reasoning) and other entities (inter-reasoning), results in rich and descriptive representations in the underlying neural network backbone, which can be used in downstream tasks such as classification and image retrieval. We evaluate the proposed method following a rigorous experimental procedure, using standard datasets, protocols, and backbones. Self-supervised relational reasoning outperforms the best competitor in all conditions by an average 14% in accuracy, and the most recent state-of-the-art model by 3%. We link the effectiveness of the method to the maximization of a Bernoulli log-likelihood, which can be considered as a proxy for maximizing the mutual information, resulting in a more efficient objective with respect to the commonly used contrastive losses.

In this paper, we study the problem of inference in high-order structured prediction tasks. In the context of Markov random fields, the goal of a high-order inference task is to maximize a score function on the space of labels, and the score function can be decomposed into sum of unary and high-order potentials. We apply a generative model approach to study the problem of high-order inference, and provide a two-stage convex optimization algorithm for exact label recovery. We also provide a new class of hypergraph structural properties related to hyperedge expansion that drives the success in general high-order inference problems. Finally, we connect the performance of our algorithm and the hyperedge expansion property using a novel hypergraph Cheeger-type inequality.

Exploiting large language models (LLMs) to tackle deductive reasoning has garnered growing attention. It still remains highly challenging to achieve satisfactory results in complex deductive problems, characterized by plenty of premises (i.e., facts or rules) entailing intricate relationships among entities and requiring multi-hop reasoning. One intuitive solution is to decompose the original task into smaller sub-tasks, and then chain the multiple casual reasoning steps together in a forward (e.g., Selection-Inference) or backward (e.g., LAMBADA) direction. However, these techniques inevitably necessitate a large number of overall stages, leading to computationally expensive operations and a higher possibility of making misleading steps. In addition to stage-by-stage decomposition, we draw inspiration from another aspect of human problem-solving. Humans tend to distill the most relevant information and organize their thoughts systematically (e.g., creating mind maps), which assists them in answering questions or drawing conclusions precisely and quickly. In light of this, we propose a novel reasoning approach named Concise and Organized Perception (COP). COP carefully analyzes the given statements to efficiently identify the most pertinent information while eliminating redundancy. It then prompts the LLMs in a more organized form that adapts to the model's inference process. By perceiving concise and organized proofs, the deductive reasoning abilities of LLMs can be better elicited, and the risk of acquiring errors caused by excessive reasoning stages is mitigated. Furthermore, our approach can be combined with the aforementioned ones to further boost their performance. Extensive experimental results on three popular deductive benchmarks (i.e., ProofWriter, PrOntoQA and PrOntoQA-OOD) show that COP significantly outperforms previous state-of-the-art methods.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

Open-domain complex Question Answering (QA) is a difficult task with challenges in evidence retrieval and reasoning. The complexity of such questions could stem from questions being compositional, hybrid evidence, or ambiguity in questions. While retrieval performance for classical QA tasks is well explored, their capabilities for heterogeneous complex retrieval tasks, especially in an open-domain setting, and the impact on downstream QA performance, are relatively unexplored. To address this, in this work, we propose a benchmark composing diverse complex QA tasks and provide a toolkit to evaluate state-of-the-art pre-trained dense and sparse retrieval models in an open-domain setting. We observe that late interaction models and surprisingly lexical models like BM25 perform well compared to other pre-trained dense retrieval models. In addition, since context-based reasoning is critical for solving complex QA tasks, we also evaluate the reasoning capabilities of LLMs and the impact of retrieval performance on their reasoning capabilities. Through experiments, we observe that much progress is to be made in retrieval for complex QA to improve downstream QA performance. Our software and related data can be accessed at https://github.com/VenkteshV/DEXTER

We present IBR, an Iterative Backward Reasoning model to solve the proof generation tasks on rule-based Question Answering (QA), where models are required to reason over a series of textual rules and facts to find out the related proof path and derive the final answer. We handle the limitations of existed works in two folds: 1) enhance the interpretability of reasoning procedures with detailed tracking, by predicting nodes and edges in the proof path iteratively backward from the question; 2) promote the efficiency and accuracy via reasoning on the elaborate representations of nodes and history paths, without any intermediate texts that may introduce external noise during proof generation. There are three main modules in IBR, QA and proof strategy prediction to obtain the answer and offer guidance for the following procedure; parent node prediction to determine a node in the existing proof that a new child node will link to; child node prediction to find out which new node will be added to the proof. Experiments on both synthetic and paraphrased datasets demonstrate that IBR has better in-domain performance as well as cross-domain transferability than several strong baselines. Our code and models are available at https://github.com/find-knowledge/IBR .

Denoising diffusion models enable conditional generation and density modeling of complex relationships like images and text. However, the nature of the learned relationships is opaque making it difficult to understand precisely what relationships between words and parts of an image are captured, or to predict the effect of an intervention. We illuminate the fine-grained relationships learned by diffusion models by noticing a precise relationship between diffusion and information decomposition. Exact expressions for mutual information and conditional mutual information can be written in terms of the denoising model. Furthermore, pointwise estimates can be easily estimated as well, allowing us to ask questions about the relationships between specific images and captions. Decomposing information even further to understand which variables in a high-dimensional space carry information is a long-standing problem. For diffusion models, we show that a natural non-negative decomposition of mutual information emerges, allowing us to quantify informative relationships between words and pixels in an image. We exploit these new relations to measure the compositional understanding of diffusion models, to do unsupervised localization of objects in images, and to measure effects when selectively editing images through prompt interventions.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of "slow thinking" into multimodal large language models (MLLMs). Our core idea is that different levels of reasoning abilities can be combined dynamically to tackle questions with different complexity. To this end, we propose a paradigm of Self-structured Chain of Thought (SCoT), which is composed of minimal semantic atomic steps. Different from existing methods that rely on structured templates or free-form paradigms, our method can not only generate cognitive CoT structures for various complex tasks but also mitigates the phenomenon of overthinking. To introduce structured reasoning capabilities into visual understanding models, we further design a novel AtomThink framework with four key modules, including (i) a data engine to generate high-quality multimodal reasoning paths; (ii) a supervised fine-tuning process with serialized inference data; (iii) a policy-guided multi-turn inference method; and (iv) an atomic capability metric to evaluate the single step utilization rate. We conduct extensive experiments to show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving more than 10\% average accuracy gains on MathVista and MathVerse. Compared to state-of-the-art structured CoT approaches, our method not only achieves higher accuracy but also improves data utilization by 5 times and boosts inference efficiency by 85.3\%. Our code is now public available in https://github.com/Quinn777/AtomThink.

Answering complex questions is a time-consuming activity for humans that requires reasoning and integration of information. Recent work on reading comprehension made headway in answering simple questions, but tackling complex questions is still an ongoing research challenge. Conversely, semantic parsers have been successful at handling compositionality, but only when the information resides in a target knowledge-base. In this paper, we present a novel framework for answering broad and complex questions, assuming answering simple questions is possible using a search engine and a reading comprehension model. We propose to decompose complex questions into a sequence of simple questions, and compute the final answer from the sequence of answers. To illustrate the viability of our approach, we create a new dataset of complex questions, ComplexWebQuestions, and present a model that decomposes questions and interacts with the web to compute an answer. We empirically demonstrate that question decomposition improves performance from 20.8 precision@1 to 27.5 precision@1 on this new dataset.

Understanding the relations between entities denoted by NPs in a text is a critical part of human-like natural language understanding. However, only a fraction of such relations is covered by standard NLP tasks and benchmarks nowadays. In this work, we propose a novel task termed text-based NP enrichment (TNE), in which we aim to enrich each NP in a text with all the preposition-mediated relations -- either explicit or implicit -- that hold between it and other NPs in the text. The relations are represented as triplets, each denoted by two NPs related via a preposition. Humans recover such relations seamlessly, while current state-of-the-art models struggle with them due to the implicit nature of the problem. We build the first large-scale dataset for the problem, provide the formal framing and scope of annotation, analyze the data, and report the results of fine-tuned language models on the task, demonstrating the challenge it poses to current technology. A webpage with a data-exploration UI, a demo, and links to the code, models, and leaderboard, to foster further research into this challenging problem can be found at: yanaiela.github.io/TNE/.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

Multimodal relation extraction (MRE) is a crucial task in the fields of Knowledge Graph and Multimedia, playing a pivotal role in multimodal knowledge graph construction. However, existing methods are typically limited to extracting a single type of relational triplet, which restricts their ability to extract triplets beyond the specified types. Directly combining these methods fails to capture dynamic cross-modal interactions and introduces significant computational redundancy. Therefore, we propose a novel unified multimodal Relation Extraction framework with Multilevel Optimal Transport and mixture-of-Experts, termed REMOTE, which can simultaneously extract intra-modal and inter-modal relations between textual entities and visual objects. To dynamically select optimal interaction features for different types of relational triplets, we introduce mixture-of-experts mechanism, ensuring the most relevant modality information is utilized. Additionally, considering that the inherent property of multilayer sequential encoding in existing encoders often leads to the loss of low-level information, we adopt a multilevel optimal transport fusion module to preserve low-level features while maintaining multilayer encoding, yielding more expressive representations. Correspondingly, we also create a Unified Multimodal Relation Extraction (UMRE) dataset to evaluate the effectiveness of our framework, encompassing diverse cases where the head and tail entities can originate from either text or image. Extensive experiments show that REMOTE effectively extracts various types of relational triplets and achieves state-of-the-art performanc on almost all metrics across two other public MRE datasets. We release our resources at https://github.com/Nikol-coder/REMOTE.

The digitization of complex technical systems, such as Piping and Instrumentation Diagrams (P&IDs), is crucial for efficient maintenance and operation of complex systems in hydraulic and process engineering. Previous approaches often rely on separate modules that analyze diagram elements individually, neglecting the diagram's overall structure. We address this limitation by proposing a novel approach that utilizes the Relationformer, a state-of-the-art deep learning architecture, to extract graphs from P&IDs. Our method leverages the ability of the Relationformer to simultaneously detect objects and their relationships in images, making it suitable for the task of graph extraction from engineering diagrams. We apply our proposed approach to both real-world and synthetically created P&ID datasets, and evaluate its effectiveness by comparing it with a modular digitization approach based on recent literature. We present PID2Graph, the first publicly accessible P&ID dataset featuring comprehensive labels for the graph structure, including symbols, nodes and their connections that is used for evaluation. To understand the effect of patching and stitching of both of the approaches, we compare values before and after merging the patches. For the real-world data, the Relationformer achieves convincing results, outperforming the modular digitization approach for edge detection by more than 25%. Our work provides a comprehensive framework for assessing the performance of P&ID digitization methods and opens up new avenues for research in this area using transformer architectures. The P&ID dataset used for evaluation will be published and publicly available upon acceptance of the paper.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

We propose a novel interpretation technique to explain the behavior of structured output models, which learn mappings between an input vector to a set of output variables simultaneously. Because of the complex relationship between the computational path of output variables in structured models, a feature can affect the value of output through other ones. We focus on one of the outputs as the target and try to find the most important features utilized by the structured model to decide on the target in each locality of the input space. In this paper, we assume an arbitrary structured output model is available as a black box and argue how considering the correlations between output variables can improve the explanation performance. The goal is to train a function as an interpreter for the target output variable over the input space. We introduce an energy-based training process for the interpreter function, which effectively considers the structural information incorporated into the model to be explained. The effectiveness of the proposed method is confirmed using a variety of simulated and real data sets.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

Symbolic regression plays a crucial role in modern scientific research thanks to its capability of discovering concise and interpretable mathematical expressions from data. A grand challenge lies in the arduous search for parsimonious and generalizable mathematical formulas, in an infinite search space, while intending to fit the training data. Existing algorithms have faced a critical bottleneck of accuracy and efficiency over a decade when handling problems of complexity, which essentially hinders the pace of applying symbolic regression for scientific exploration across interdisciplinary domains. To this end, we introduce a parallelized tree search (PTS) model to efficiently distill generic mathematical expressions from limited data. Through a series of extensive experiments, we demonstrate the superior accuracy and efficiency of PTS for equation discovery, which greatly outperforms the state-of-the-art baseline models on over 80 synthetic and experimental datasets (e.g., lifting its performance by up to 99% accuracy improvement and one-order of magnitude speed up). PTS represents a key advance in accurate and efficient data-driven discovery of symbolic, interpretable models (e.g., underlying physical laws) and marks a pivotal transition towards scalable symbolic learning.

Markov processes are widely used mathematical models for describing dynamic systems in various fields. However, accurately simulating large-scale systems at long time scales is computationally expensive due to the short time steps required for accurate integration. In this paper, we introduce an inference process that maps complex systems into a simplified representational space and models large jumps in time. To achieve this, we propose Time-lagged Information Bottleneck (T-IB), a principled objective rooted in information theory, which aims to capture relevant temporal features while discarding high-frequency information to simplify the simulation task and minimize the inference error. Our experiments demonstrate that T-IB learns information-optimal representations for accurately modeling the statistical properties and dynamics of the original process at a selected time lag, outperforming existing time-lagged dimensionality reduction methods.

Effectively representing materials as text has the potential to leverage the vast advancements of large language models (LLMs) for discovering new materials. While LLMs have shown remarkable success in various domains, their application to materials science remains underexplored. A fundamental challenge is the lack of understanding of how to best utilize text-based representations for materials modeling. This challenge is further compounded by the absence of a comprehensive benchmark to rigorously evaluate the capabilities and limitations of these text representations in capturing the complexity of material systems. To address this gap, we propose MatText, a suite of benchmarking tools and datasets designed to systematically evaluate the performance of language models in modeling materials. MatText encompasses nine distinct text-based representations for material systems, including several novel representations. Each representation incorporates unique inductive biases that capture relevant information and integrate prior physical knowledge about materials. Additionally, MatText provides essential tools for training and benchmarking the performance of language models in the context of materials science. These tools include standardized dataset splits for each representation, probes for evaluating sensitivity to geometric factors, and tools for seamlessly converting crystal structures into text. Using MatText, we conduct an extensive analysis of the capabilities of language models in modeling materials. Our findings reveal that current language models consistently struggle to capture the geometric information crucial for materials modeling across all representations. Instead, these models tend to leverage local information, which is emphasized in some of our novel representations. Our analysis underscores MatText's ability to reveal shortcomings of text-based methods for materials design.

We study the problem of learning representations of entities and relations in knowledge graphs for predicting missing links. The success of such a task heavily relies on the ability of modeling and inferring the patterns of (or between) the relations. In this paper, we present a new approach for knowledge graph embedding called RotatE, which is able to model and infer various relation patterns including: symmetry/antisymmetry, inversion, and composition. Specifically, the RotatE model defines each relation as a rotation from the source entity to the target entity in the complex vector space. In addition, we propose a novel self-adversarial negative sampling technique for efficiently and effectively training the RotatE model. Experimental results on multiple benchmark knowledge graphs show that the proposed RotatE model is not only scalable, but also able to infer and model various relation patterns and significantly outperform existing state-of-the-art models for link prediction.

Hyperbolic space has proven to be well-suited for capturing hierarchical relations in data, such as trees and directed acyclic graphs. Prior work introduced the concept of entailment cones, which uses partial orders defined by nested cones in the Poincar\'e ball to model hierarchies. Here, we introduce the ``shadow cones" framework, a physics-inspired entailment cone construction. Specifically, we model partial orders as subset relations between shadows formed by a light source and opaque objects in hyperbolic space. The shadow cones framework generalizes entailment cones to a broad class of formulations and hyperbolic space models beyond the Poincar\'e ball. This results in clear advantages over existing constructions: for example, shadow cones possess better optimization properties over constructions limited to the Poincar\'e ball. Our experiments on datasets of various sizes and hierarchical structures show that shadow cones consistently and significantly outperform existing entailment cone constructions. These results indicate that shadow cones are an effective way to model partial orders in hyperbolic space, offering physically intuitive and novel insights about the nature of such structures.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

Advanced reasoning in large language models has achieved remarkable performance on challenging tasks, but the prevailing long-context reasoning paradigm faces critical limitations: quadratic computational scaling with sequence length, reasoning constrained by maximum context boundaries, and performance degradation beyond pre-training context windows. Existing approaches primarily compress reasoning chains without addressing the fundamental scaling problem. To overcome these challenges, we introduce InftyThink, a paradigm that transforms monolithic reasoning into an iterative process with intermediate summarization. By interleaving short reasoning segments with concise progress summaries, our approach enables unbounded reasoning depth while maintaining bounded computational costs. This creates a characteristic sawtooth memory pattern that significantly reduces computational complexity compared to traditional approaches. Furthermore, we develop a methodology for reconstructing long-context reasoning datasets into our iterative format, transforming OpenR1-Math into 333K training instances. Experiments across multiple model architectures demonstrate that our approach reduces computational costs while improving performance, with Qwen2.5-Math-7B showing 3-13% improvements across MATH500, AIME24, and GPQA_diamond benchmarks. Our work challenges the assumed trade-off between reasoning depth and computational efficiency, providing a more scalable approach to complex reasoning without architectural modifications.

Despite the recent advancements in Multi-modal Large Language Models (MLLMs), understanding inter-object relations, i.e., interactions or associations between distinct objects, remains a major challenge for such models. This issue significantly hinders their advanced reasoning capabilities and is primarily due to the lack of large-scale, high-quality, and diverse multi-modal data essential for training and evaluating MLLMs. In this paper, we provide a taxonomy of inter-object relations and introduce Multi-Modal Relation Understanding (MMRel), a comprehensive dataset designed to bridge this gap by providing large-scale, high-quality and diverse data for studying inter-object relations with MLLMs. MMRel features three distinctive attributes: (i) It includes over 15K question-answer pairs, which are sourced from three distinct domains, ensuring large scale and high diversity; (ii) It contains a subset featuring highly unusual relations, on which MLLMs often fail due to hallucinations, thus are very challenging; (iii) It provides manually verified high-quality labels for inter-object relations. Thanks to these features, MMRel is ideal for evaluating MLLMs on relation understanding, as well as being used to fine-tune MLLMs to enhance relation understanding and even benefit overall performance in various vision-language tasks. Extensive experiments on various popular MLLMs validate the effectiveness of MMRel. Both MMRel dataset and the complete labeling scripts have been made publicly available.

For supervised learning with tabular data, decision tree ensembles produced via boosting techniques generally dominate real-world applications involving iid training/test sets. However for graph data where the iid assumption is violated due to structured relations between samples, it remains unclear how to best incorporate this structure within existing boosting pipelines. To this end, we propose a generalized framework for iterating boosting with graph propagation steps that share node/sample information across edges connecting related samples. Unlike previous efforts to integrate graph-based models with boosting, our approach is anchored in a principled meta loss function such that provable convergence can be guaranteed under relatively mild assumptions. Across a variety of non-iid graph datasets with tabular node features, our method achieves comparable or superior performance than both tabular and graph neural network models, as well as existing hybrid strategies that combine the two. Beyond producing better predictive performance than recently proposed graph models, our proposed techniques are easy to implement, computationally more efficient, and enjoy stronger theoretical guarantees (which make our results more reproducible).

Circuits based on sum-product structure have become a ubiquitous representation to compactly encode knowledge, from Boolean functions to probability distributions. By imposing constraints on the structure of such circuits, certain inference queries become tractable, such as model counting and most probable configuration. Recent works have explored analyzing probabilistic and causal inference queries as compositions of basic operators to derive tractability conditions. In this paper, we take an algebraic perspective for compositional inference, and show that a large class of queries - including marginal MAP, probabilistic answer set programming inference, and causal backdoor adjustment - correspond to a combination of basic operators over semirings: aggregation, product, and elementwise mapping. Using this framework, we uncover simple and general sufficient conditions for tractable composition of these operators, in terms of circuit properties (e.g., marginal determinism, compatibility) and conditions on the elementwise mappings. Applying our analysis, we derive novel tractability conditions for many such compositional queries. Our results unify tractability conditions for existing problems on circuits, while providing a blueprint for analysing novel compositional inference queries.

Heterogeneous graph learning aims to capture complex relationships and diverse relational semantics among entities in a heterogeneous graph to obtain meaningful representations for nodes and edges. Recent advancements in heterogeneous graph neural networks (HGNNs) have achieved state-of-the-art performance by considering relation heterogeneity and using specialized message functions and aggregation rules. However, existing frameworks for heterogeneous graph learning have limitations in generalizing across diverse heterogeneous graph datasets. Most of these frameworks follow the "pre-train" and "fine-tune" paradigm on the same dataset, which restricts their capacity to adapt to new and unseen data. This raises the question: "Can we generalize heterogeneous graph models to be well-adapted to diverse downstream learning tasks with distribution shifts in both node token sets and relation type heterogeneity?'' To tackle those challenges, we propose HiGPT, a general large graph model with Heterogeneous graph instruction-tuning paradigm. Our framework enables learning from arbitrary heterogeneous graphs without the need for any fine-tuning process from downstream datasets. To handle distribution shifts in heterogeneity, we introduce an in-context heterogeneous graph tokenizer that captures semantic relationships in different heterogeneous graphs, facilitating model adaptation. We incorporate a large corpus of heterogeneity-aware graph instructions into our HiGPT, enabling the model to effectively comprehend complex relation heterogeneity and distinguish between various types of graph tokens. Furthermore, we introduce the Mixture-of-Thought (MoT) instruction augmentation paradigm to mitigate data scarcity by generating diverse and informative instructions. Through comprehensive evaluations, our proposed framework demonstrates exceptional performance in terms of generalization performance.

Despite the recent successes of vanilla Graph Neural Networks (GNNs) on many tasks, their foundation on pairwise interaction networks inherently limits their capacity to discern latent higher-order interactions in complex systems. To bridge this capability gap, we propose a novel approach exploiting the rich mathematical theory of simplicial complexes (SCs) - a robust tool for modeling higher-order interactions. Current SC-based GNNs are burdened by high complexity and rigidity, and quantifying higher-order interaction strengths remains challenging. Innovatively, we present a higher-order Flower-Petals (FP) model, incorporating FP Laplacians into SCs. Further, we introduce a Higher-order Graph Convolutional Network (HiGCN) grounded in FP Laplacians, capable of discerning intrinsic features across varying topological scales. By employing learnable graph filters, a parameter group within each FP Laplacian domain, we can identify diverse patterns where the filters' weights serve as a quantifiable measure of higher-order interaction strengths. The theoretical underpinnings of HiGCN's advanced expressiveness are rigorously demonstrated. Additionally, our empirical investigations reveal that the proposed model accomplishes state-of-the-art (SOTA) performance on a range of graph tasks and provides a scalable and flexible solution to explore higher-order interactions in graphs.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

Networks of atom-centered coordination octahedra commonly occur in inorganic and hybrid solid-state materials. Characterizing their spatial arrangements and characteristics is crucial for relating structures to properties for many materials families. The traditional method using case-by-case inspection becomes prohibitive for discovering trends and similarities in large datasets. Here, we operationalize chemical intuition to automate the geometric parsing, quantification, and classification of coordination octahedral networks. We find axis-resolved tilting trends in ABO_{3} perovskite polymorphs, which assist in detecting oxidation state changes. Moreover, we develop a scale-invariant encoding scheme to represent these networks, which, combined with human-assisted unsupervised machine learning, allows us to taxonomize the inorganic framework polytypes in hybrid iodoplumbates (A_xPb_yI_z). Consequently, we uncover a violation of Pauling's third rule and the design principles underpinning their topological diversity. Our results offer a glimpse into the vast design space of atomic octahedral networks and inform high-throughput, targeted screening of specific structure types.

Materials discovery and development are critical for addressing global challenges. Yet, the exponential growth in materials science literature comprising vast amounts of textual data has created significant bottlenecks in knowledge extraction, synthesis, and scientific reasoning. Large Language Models (LLMs) offer unprecedented opportunities to accelerate materials research through automated analysis and prediction. Still, their effective deployment requires domain-specific adaptation for understanding and solving domain-relevant tasks. Here, we present LLaMat, a family of foundational models for materials science developed through continued pretraining of LLaMA models on an extensive corpus of materials literature and crystallographic data. Through systematic evaluation, we demonstrate that LLaMat excels in materials-specific NLP and structured information extraction while maintaining general linguistic capabilities. The specialized LLaMat-CIF variant demonstrates unprecedented capabilities in crystal structure generation, predicting stable crystals with high coverage across the periodic table. Intriguingly, despite LLaMA-3's superior performance in comparison to LLaMA-2, we observe that LLaMat-2 demonstrates unexpectedly enhanced domain-specific performance across diverse materials science tasks, including structured information extraction from text and tables, more particularly in crystal structure generation, a potential adaptation rigidity in overtrained LLMs. Altogether, the present work demonstrates the effectiveness of domain adaptation towards developing practically deployable LLM copilots for materials research. Beyond materials science, our findings reveal important considerations for domain adaptation of LLMs, such as model selection, training methodology, and domain-specific performance, which may influence the development of specialized scientific AI systems.

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Aiming at better representing multivariate relationships, this paper investigates a motif dimensional framework for higher-order graph learning. The graph learning effectiveness can be improved through OFFER. The proposed framework mainly aims at accelerating and improving higher-order graph learning results. We apply the acceleration procedure from the dimensional of network motifs. Specifically, the refined degree for nodes and edges are conducted in two stages: (1) employ motif degree of nodes to refine the adjacency matrix of the network; and (2) employ motif degree of edges to refine the transition probability matrix in the learning process. In order to assess the efficiency of the proposed framework, four popular network representation algorithms are modified and examined. By evaluating the performance of OFFER, both link prediction results and clustering results demonstrate that the graph representation learning algorithms enhanced with OFFER consistently outperform the original algorithms with higher efficiency.

Mathematical reasoning represents a critical frontier in advancing large language models (LLMs). While step-by-step approaches have emerged as the dominant paradigm for mathematical problem-solving in LLMs, the quality of reasoning steps in training data fundamentally constrains the performance of the models. Recent studies has demonstrated that more detailed intermediate steps can enhance model performance, yet existing methods for step expansion either require more powerful external models or incur substantial computational costs. In this paper, we introduce MathFimer, a novel framework for mathematical reasoning step expansion inspired by the "Fill-in-the-middle" task from code completion. By decomposing solution chains into prefix-suffix pairs and training models to reconstruct missing intermediate steps, we develop a specialized model, MathFimer-7B, on our carefully curated NuminaMath-FIM dataset. We then apply these models to enhance existing mathematical reasoning datasets by inserting detailed intermediate steps into their solution chains, creating MathFimer-expanded versions. Through comprehensive experiments on multiple mathematical reasoning datasets, including MathInstruct, MetaMathQA and etc., we demonstrate that models trained on MathFimer-expanded data consistently outperform their counterparts trained on original data across various benchmarks such as GSM8K and MATH. Our approach offers a practical, scalable solution for enhancing mathematical reasoning capabilities in LLMs without relying on powerful external models or expensive inference procedures.

Predicting physical properties of materials from their crystal structures is a fundamental problem in materials science. In peripheral areas such as the prediction of molecular properties, fully connected attention networks have been shown to be successful. However, unlike these finite atom arrangements, crystal structures are infinitely repeating, periodic arrangements of atoms, whose fully connected attention results in infinitely connected attention. In this work, we show that this infinitely connected attention can lead to a computationally tractable formulation, interpreted as neural potential summation, that performs infinite interatomic potential summations in a deeply learned feature space. We then propose a simple yet effective Transformer-based encoder architecture for crystal structures called Crystalformer. Compared to an existing Transformer-based model, the proposed model requires only 29.4% of the number of parameters, with minimal modifications to the original Transformer architecture. Despite the architectural simplicity, the proposed method outperforms state-of-the-art methods for various property regression tasks on the Materials Project and JARVIS-DFT datasets.

Compositional relational reasoning (CRR) is a hallmark of human intelligence, but we lack a clear understanding of whether and how existing transformer large language models (LLMs) can solve CRR tasks. To enable systematic exploration of the CRR capability of LLMs, we first propose a new synthetic benchmark called Generalized Associative Recall (GAR) by integrating and generalizing the essence of several tasks in mechanistic interpretability (MI) study in a unified framework. Evaluation shows that GAR is challenging enough for existing LLMs, revealing their fundamental deficiency in CRR. Meanwhile, it is easy enough for systematic MI study. Then, to understand how LLMs solve GAR tasks, we use attribution patching to discover the core circuits reused by Vicuna-33B across different tasks and a set of vital attention heads. Intervention experiments show that the correct functioning of these heads significantly impacts task performance. Especially, we identify two classes of heads whose activations represent the abstract notion of true and false in GAR tasks respectively. They play a fundamental role in CRR across various models and tasks. The dataset and code are available at https://github.com/Caiyun-AI/GAR.

Customized image generation is crucial for delivering personalized content based on user-provided image prompts, aligning large-scale text-to-image diffusion models with individual needs. However, existing models often overlook the relationships between customized objects in generated images. Instead, this work addresses that gap by focusing on relation-aware customized image generation, which aims to preserve the identities from image prompts while maintaining the predicate relations described in text prompts. Specifically, we introduce RelationBooth, a framework that disentangles identity and relation learning through a well-curated dataset. Our training data consists of relation-specific images, independent object images containing identity information, and text prompts to guide relation generation. Then, we propose two key modules to tackle the two main challenges: generating accurate and natural relations, especially when significant pose adjustments are required, and avoiding object confusion in cases of overlap. First, we introduce a keypoint matching loss that effectively guides the model in adjusting object poses closely tied to their relationships. Second, we incorporate local features from the image prompts to better distinguish between objects, preventing confusion in overlapping cases. Extensive results on three benchmarks demonstrate the superiority of RelationBooth in generating precise relations while preserving object identities across a diverse set of objects and relations. The source code and trained models will be made available to the public.

This paper introduces Grounded Image Text Matching with Mismatched Relation (GITM-MR), a novel visual-linguistic joint task that evaluates the relation understanding capabilities of transformer-based pre-trained models. GITM-MR requires a model to first determine if an expression describes an image, then localize referred objects or ground the mismatched parts of the text. We provide a benchmark for evaluating pre-trained models on this task, with a focus on the challenging settings of limited data and out-of-distribution sentence lengths. Our evaluation demonstrates that pre-trained models lack data efficiency and length generalization ability. To address this, we propose the Relation-sensitive Correspondence Reasoning Network (RCRN), which incorporates relation-aware reasoning via bi-directional message propagation guided by language structure. RCRN can be interpreted as a modular program and delivers strong performance in both length generalization and data efficiency.

Mathematical geometric reasoning is essential for scientific discovery and educational development, requiring precise logic and rigorous formal verification. While recent advances in Multimodal Large Language Models (MLLMs) have improved reasoning tasks, existing models typically struggle with formal geometric reasoning, particularly when dynamically constructing and verifying auxiliary geometric elements. To address these challenges, we introduce Geoint-R1, a multimodal reasoning framework designed to generate formally verifiable geometric solutions from textual descriptions and visual diagrams. Geoint-R1 uniquely integrates auxiliary elements construction, formal reasoning represented via Lean4, and interactive visualization. To systematically evaluate and advance formal geometric reasoning, we propose the Geoint benchmark, comprising 1,885 rigorously annotated geometry problems across diverse topics such as plane, spatial, and solid geometry. Each problem includes structured textual annotations, precise Lean4 code for auxiliary constructions, and detailed solution steps verified by experts. Extensive experiments demonstrate that Geoint-R1 significantly surpasses existing multimodal and math-specific reasoning models, particularly on challenging problems requiring explicit auxiliary element constructions.

Large language models have been extensively studied as neural knowledge bases for their knowledge access, editability, reasoning, and explainability. However, few works focus on the structural patterns of their knowledge. Motivated by this gap, we investigate these structural patterns from a graph perspective. We quantify the knowledge of LLMs at both the triplet and entity levels, and analyze how it relates to graph structural properties such as node degree. Furthermore, we uncover the knowledge homophily, where topologically close entities exhibit similar levels of knowledgeability, which further motivates us to develop graph machine learning models to estimate entity knowledge based on its local neighbors. This model further enables valuable knowledge checking by selecting triplets less known to LLMs. Empirical results show that using selected triplets for fine-tuning leads to superior performance.

The integration of knowledge extracted from diverse models, whether described by domain experts or generated by machine learning algorithms, has historically been challenged by the absence of a suitable framework for specifying and integrating structures, learning processes, data transformations, and data models or rules. In this work, we extend algebraic specification methods to address these challenges within such a framework. In our work, we tackle the challenging task of developing a comprehensive framework for defining and analyzing deep learning architectures. We believe that previous efforts have fallen short by failing to establish a clear connection between the constraints a model must adhere to and its actual implementation. Our methodology employs graphical structures that resemble Ehresmann's sketches, interpreted within a universe of fuzzy sets. This approach offers a unified theory that elegantly encompasses both deterministic and non-deterministic neural network designs. Furthermore, we highlight how this theory naturally incorporates fundamental concepts from computer science and automata theory. Our extended algebraic specification framework, grounded in graphical structures akin to Ehresmann's sketches, offers a promising solution for integrating knowledge across disparate models and domains. By bridging the gap between domain-specific expertise and machine-generated insights, we pave the way for more comprehensive, collaborative, and effective approaches to knowledge integration and modeling.

Large Language Models (LLMs) have shown impressive progress in mathematical reasoning. While data augmentation is promising to enhance mathematical problem-solving ability, current approaches are predominantly limited to instance-level modifications-such as rephrasing or generating syntactic variations-which fail to capture and leverage the intrinsic relational structures inherent in mathematical knowledge. Inspired by human learning processes, where mathematical proficiency develops through systematic exposure to interconnected concepts, we introduce MathFusion, a novel framework that enhances mathematical reasoning through cross-problem instruction synthesis. MathFusion implements this through three fusion strategies: (1) sequential fusion, which chains related problems to model solution dependencies; (2) parallel fusion, which combines analogous problems to reinforce conceptual understanding; and (3) conditional fusion, which creates context-aware selective problems to enhance reasoning flexibility. By applying these strategies, we generate a new dataset, MathFusionQA, followed by fine-tuning models (DeepSeekMath-7B, Mistral-7B, Llama3-8B) on it. Experimental results demonstrate that MathFusion achieves substantial improvements in mathematical reasoning while maintaining high data efficiency, boosting performance by 18.0 points in accuracy across diverse benchmarks while requiring only 45K additional synthetic instructions, representing a substantial improvement over traditional single-instruction approaches. Our datasets, models, and code are publicly available at https://github.com/QizhiPei/mathfusion.

Multi-hop logical reasoning is an established problem in the field of representation learning on knowledge graphs (KGs). It subsumes both one-hop link prediction as well as other more complex types of logical queries. Existing algorithms operate only on classical, triple-based graphs, whereas modern KGs often employ a hyper-relational modeling paradigm. In this paradigm, typed edges may have several key-value pairs known as qualifiers that provide fine-grained context for facts. In queries, this context modifies the meaning of relations, and usually reduces the answer set. Hyper-relational queries are often observed in real-world KG applications, and existing approaches for approximate query answering cannot make use of qualifier pairs. In this work, we bridge this gap and extend the multi-hop reasoning problem to hyper-relational KGs allowing to tackle this new type of complex queries. Building upon recent advancements in Graph Neural Networks and query embedding techniques, we study how to embed and answer hyper-relational conjunctive queries. Besides that, we propose a method to answer such queries and demonstrate in our experiments that qualifiers improve query answering on a diverse set of query patterns.

A prominent challenge for modern language understanding systems is the ability to answer implicit reasoning questions, where the required reasoning steps for answering the question are not mentioned in the text explicitly. In this work, we investigate why current models struggle with implicit reasoning question answering (QA) tasks, by decoupling inference of reasoning steps from their execution. We define a new task of implicit relation inference and construct a benchmark, IMPLICITRELATIONS, where given a question, a model should output a list of concept-relation pairs, where the relations describe the implicit reasoning steps required for answering the question. Using IMPLICITRELATIONS, we evaluate models from the GPT-3 family and find that, while these models struggle on the implicit reasoning QA task, they often succeed at inferring implicit relations. This suggests that the challenge in implicit reasoning questions does not stem from the need to plan a reasoning strategy alone, but to do it while also retrieving and reasoning over relevant information.

Temporal hypergraphs provide a powerful paradigm for modeling time-dependent, higher-order interactions in complex systems. Representation learning for hypergraphs is essential for extracting patterns of the higher-order interactions that are critically important in real-world problems in social network analysis, neuroscience, finance, etc. However, existing methods are typically designed only for specific tasks or static hypergraphs. We present CAT-Walk, an inductive method that learns the underlying dynamic laws that govern the temporal and structural processes underlying a temporal hypergraph. CAT-Walk introduces a temporal, higher-order walk on hypergraphs, SetWalk, that extracts higher-order causal patterns. CAT-Walk uses a novel adaptive and permutation invariant pooling strategy, SetMixer, along with a set-based anonymization process that hides the identity of hyperedges. Finally, we present a simple yet effective neural network model to encode hyperedges. Our evaluation on 10 hypergraph benchmark datasets shows that CAT-Walk attains outstanding performance on temporal hyperedge prediction benchmarks in both inductive and transductive settings. It also shows competitive performance with state-of-the-art methods for node classification. (https://github.com/ubc-systopia/CATWalk)

In this paper, we propose Neural-Symbolic Collaborative Distillation (NesyCD), a novel knowledge distillation method for learning the complex reasoning abilities of Large Language Models (LLMs, e.g., \textgreater 13B). We argue that complex reasoning tasks are difficult for Small Language Models (SLMs, e.g., leq 7B), as these tasks demand not only general cognitive abilities but also specialized knowledge, which is often sparse and difficult for these neural-based SLMs to effectively capture. Therefore, NesyCD distills the general capabilities and specialized knowledge in LLMs using different manners. On the one hand, we distill only general abilities from teacher LLMs into the student SLMs of parameterized neural networks. On the other hand, for the specialized abilities and uncommon knowledge of a complex reasoning task, we employ a symbolic knowledge distillation approach to obtain and store the specialized knowledge within a symbolic knowledge base (KB). By decoupling general and specialized capabilities, the proposed NesyCD can achieve superior performance cost-effectively, utilizing smaller models and blending parameterized neural networks with symbolic KB. Moreover, the specialized KB generalizes well and is comprehended and manipulated by humans. Our experiments show that NesyCD significantly boosts SLMs' complex reasoning performance on in-domain (BBH, GSM8K) and out-of-domain (AGIEval, ARC) datasets. Notably, our approach enabled the LLaMA3-8B and Qwen2-7B to surpass GPT-3.5-turbo in performance and come close to matching LLaMA3-70B, despite the latter having nine times more parameters. Our code will be available at https://github.com/Xnhyacinth/NesyCD.

Reasoning over visual relationships-spatial, functional, interactional, social, etc.-is considered to be a fundamental component of human cognition. Yet, despite the major advances in visual comprehension in multimodal language models (MLMs), precise reasoning over relationships and their generations remains a challenge. We introduce ROBIN: an MLM instruction-tuned with densely annotated relationships capable of constructing high-quality dense scene graphs at scale. To train ROBIN, we curate SVG, a synthetic scene graph dataset by completing the missing relations of selected objects in existing scene graphs using a teacher MLM and a carefully designed filtering process to ensure high-quality. To generate more accurate and rich scene graphs at scale for any image, we introduce SG-EDIT: a self-distillation framework where GPT-4o further refines ROBIN's predicted scene graphs by removing unlikely relations and/or suggesting relevant ones. In total, our dataset contains 146K images and 5.6M relationships for 2.6M objects. Results show that our ROBIN-3B model, despite being trained on less than 3 million instances, outperforms similar-size models trained on over 300 million instances on relationship understanding benchmarks, and even surpasses larger models up to 13B parameters. Notably, it achieves state-of-the-art performance in referring expression comprehension with a score of 88.9, surpassing the previous best of 87.4. Our results suggest that training on the refined scene graph data is crucial to maintaining high performance across diverse visual reasoning task.

While large language models (LLMs) have achieved impressive progress, their application in scientific domains such as chemistry remains hindered by shallow domain understanding and limited reasoning capabilities. In this work, we focus on the specific field of chemistry and develop a Chemical Reasoner LLM, ChemDFM-R. We first construct a comprehensive dataset of atomized knowledge points to enhance the model's understanding of the fundamental principles and logical structure of chemistry. Then, we propose a mix-sourced distillation strategy that integrates expert-curated knowledge with general-domain reasoning skills, followed by domain-specific reinforcement learning to enhance chemical reasoning. Experiments on diverse chemical benchmarks demonstrate that ChemDFM-R achieves state-of-the-art performance while providing interpretable, rationale-driven outputs. Further case studies illustrate how explicit reasoning chains significantly improve the reliability, transparency, and practical utility of the model in real-world human-AI collaboration scenarios.

This paper is concerned with learning to solve tasks that require a chain of interdependent steps of relational inference, like answering complex questions about the relationships between objects, or solving puzzles where the smaller elements of a solution mutually constrain each other. We introduce the recurrent relational network, a general purpose module that operates on a graph representation of objects. As a generalization of Santoro et al. [2017]'s relational network, it can augment any neural network model with the capacity to do many-step relational reasoning. We achieve state of the art results on the bAbI textual question-answering dataset with the recurrent relational network, consistently solving 20/20 tasks. As bAbI is not particularly challenging from a relational reasoning point of view, we introduce Pretty-CLEVR, a new diagnostic dataset for relational reasoning. In the Pretty-CLEVR set-up, we can vary the question to control for the number of relational reasoning steps that are required to obtain the answer. Using Pretty-CLEVR, we probe the limitations of multi-layer perceptrons, relational and recurrent relational networks. Finally, we show how recurrent relational networks can learn to solve Sudoku puzzles from supervised training data, a challenging task requiring upwards of 64 steps of relational reasoning. We achieve state-of-the-art results amongst comparable methods by solving 96.6% of the hardest Sudoku puzzles.

As a vital stage of automated rule checking (ARC), rule interpretation of regulatory texts requires considerable effort. However, interpreting regulatory clauses with implicit properties or complex computational logic is still challenging due to the lack of domain knowledge and limited expressibility of conventional logic representations. Thus, LLM-FuncMapper, an approach to identifying predefined functions needed to interpret various regulatory clauses based on the large language model (LLM), is proposed. First, by systematically analysis of building codes, a series of atomic functions are defined to capture shared computational logics of implicit properties and complex constraints, creating a database of common blocks for interpreting regulatory clauses. Then, a prompt template with the chain of thought is developed and further enhanced with a classification-based tuning strategy, to enable common LLMs for effective function identification. Finally, the proposed approach is validated with statistical analysis, experiments, and proof of concept. Statistical analysis reveals a long-tail distribution and high expressibility of the developed function database, with which almost 100% of computer-processible clauses can be interpreted and represented as computer-executable codes. Experiments show that LLM-FuncMapper achieve promising results in identifying relevant predefined functions for rule interpretation. Further proof of concept in automated rule interpretation also demonstrates the possibility of LLM-FuncMapper in interpreting complex regulatory clauses. To the best of our knowledge, this study is the first attempt to introduce LLM for understanding and interpreting complex regulatory clauses, which may shed light on further adoption of LLM in the construction domain.

Transformer language models (LMs) have been shown to represent concepts as directions in the latent space of hidden activations. However, for any given human-interpretable concept, how can we find its direction in the latent space? We present a technique called linear relational concepts (LRC) for finding concept directions corresponding to human-interpretable concepts at a given hidden layer in a transformer LM by first modeling the relation between subject and object as a linear relational embedding (LRE). While the LRE work was mainly presented as an exercise in understanding model representations, we find that inverting the LRE while using earlier object layers results in a powerful technique to find concept directions that both work well as a classifier and causally influence model outputs.

This report overviews our ongoing work in enriching chain-of-thoughts datasets requiring arithmetical reasoning with the integration of non-parametric components, such as a calculator. We conduct an analysis of prominent relevant datasets such as GSM8K, Ape210K, AQuA-RAT, and MathQA and propose a machine-processable HTML-like format specifically tailored for working with semi-structured chains. By converting the datasets into this unified format, we enable the effective integration of large language models and symbolic systems, empowering them to tackle arithmetical reasoning tasks more efficiently.

Chain-of-thought prompting~(CoT) and tool augmentation have been validated in recent work as effective practices for improving large language models~(LLMs) to perform step-by-step reasoning on complex math-related tasks. However, most existing math reasoning datasets may be not able to fully evaluate and analyze the ability of LLMs in manipulating tools and performing reasoning, as they may only require very few invocations of tools or miss annotations for evaluating intermediate reasoning steps. To address the issue, we construct CARP, a new Chinese dataset consisting of 4,886 computation-intensive algebra problems with formulated annotations on intermediate steps. In CARP, we test four LLMs with CoT prompting, and find that they are all prone to make mistakes at the early steps of the solution, leading to wrong answers. Based on this finding, we propose a new approach that can deliberate the reasoning steps with tool interfaces, namely DELI. In DELI, we first initialize a step-by-step solution based on retrieved exemplars, then iterate two deliberation procedures that check and refine the intermediate steps of the generated solution, from the perspectives of tool manipulation and natural language reasoning, until obtaining converged solutions or reaching the maximum turn. Experimental results on CARP and six other datasets show that the proposed DELI mostly outperforms competitive baselines, and can further boost the performance of existing CoT methods. Our data and code are available in https://github.com/RUCAIBox/CARP.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we present a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph in an unsupervised scenario, so that it helps learn the multiplex association. Our method is the first to combine Graph Neural Network with the task of intestinal flora disease prediction. We employ complex relation-types to construct the Original-Graph and disrupt the relationships among nodes to generate corresponding Shuffled-Graph. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five classical OTU gut microbiome datasets demonstrate the effectiveness and stability of our method. (We will release our code soon.)

In this study, we focus on the graph representation learning (a.k.a. network embedding) in attributed graphs. Different from existing embedding methods that treat the incorporation of graph structure and semantic as the simple combination of two optimization objectives, we propose a novel semantic graph representation (SGR) method to formulate the joint optimization of the two heterogeneous sources into a common high-order proximity based framework. Concretely, we first construct an auxiliary weighted graph, where the complex homogeneous and heterogeneous relations among nodes and attributes in the original graph are comprehensively encoded. Conventional embedding methods that consider high-order topology proximities can then be easily applied to the newly constructed graph to learn the representations of both node and attribute while capturing the nonlinear high-order intrinsic correlation inside or among graph structure and semantic. The learned attribute embeddings can also effectively support some semantic-oriented inference tasks (e.g., semantic community detection), helping to reveal the graph's deep semantic. The effectiveness of SGR is further verified on a series of real graphs, where it achieves impressive performance over other baselines.

Information extraction (IE) is an important task in Natural Language Processing (NLP), involving the extraction of named entities and their relationships from unstructured text. In this paper, we propose a novel approach to this task by formulating it as graph structure learning (GSL). By formulating IE as GSL, we enhance the model's ability to dynamically refine and optimize the graph structure during the extraction process. This formulation allows for better interaction and structure-informed decisions for entity and relation prediction, in contrast to previous models that have separate or untied predictions for these tasks. When compared against state-of-the-art baselines on joint entity and relation extraction benchmarks, our model, GraphER, achieves competitive results.

Recent advances in text-to-image (T2I) generation have shown remarkable success in producing high-quality images from text. However, existing T2I models show decayed performance in compositional image generation involving multiple objects and intricate relationships. We attribute this problem to limitations in existing datasets of image-text pairs, which lack precise inter-object relationship annotations with prompts only. To address this problem, we construct LAION-SG, a large-scale dataset with high-quality structural annotations of scene graphs (SG), which precisely describe attributes and relationships of multiple objects, effectively representing the semantic structure in complex scenes. Based on LAION-SG, we train a new foundation model SDXL-SG to incorporate structural annotation information into the generation process. Extensive experiments show advanced models trained on our LAION-SG boast significant performance improvements in complex scene generation over models on existing datasets. We also introduce CompSG-Bench, a benchmark that evaluates models on compositional image generation, establishing a new standard for this domain.

Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.

Image retrieval, i.e., finding desired images given a reference image, inherently encompasses rich, multi-faceted search intents that are difficult to capture solely using image-based measures. Recent work leverages text instructions to allow users to more freely express their search intents. However, existing work primarily focuses on image pairs that are visually similar and/or can be characterized by a small set of pre-defined relations. The core thesis of this paper is that text instructions can enable retrieving images with richer relations beyond visual similarity. To show this, we introduce MagicLens, a series of self-supervised image retrieval models that support open-ended instructions. MagicLens is built on a key novel insight: image pairs that naturally occur on the same web pages contain a wide range of implicit relations (e.g., inside view of), and we can bring those implicit relations explicit by synthesizing instructions via large multimodal models (LMMs) and large language models (LLMs). Trained on 36.7M (query image, instruction, target image) triplets with rich semantic relations mined from the web, MagicLens achieves comparable or better results on eight benchmarks of various image retrieval tasks than prior state-of-the-art (SOTA) methods. Remarkably, it outperforms previous SOTA but with a 50X smaller model size on multiple benchmarks. Additional human analyses on a 1.4M-image unseen corpus further demonstrate the diversity of search intents supported by MagicLens.

Complex chemical space and limited knowledge scope with biases holds immense challenge for human scientists, yet in automated materials discovery. Existing intelligent methods relies more on numerical computation, leading to inefficient exploration and results with hard-interpretability. To bridge this gap, we introduce a principles-guided material discovery system powered by language inferential multi-agent system (MAS), namely PriM. Our framework integrates automated hypothesis generation with experimental validation in a roundtable system of MAS, enabling systematic exploration while maintaining scientific rigor. Based on our framework, the case study of nano helix demonstrates higher materials exploration rate and property value while providing transparent reasoning pathways. This approach develops an automated-and-transparent paradigm for material discovery, with broad implications for rational design of functional materials. Code is publicly available at our https://github.com/amair-lab/PriM{GitHub}.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

Two important aspects of semantic parsing for question answering are the breadth of the knowledge source and the depth of logical compositionality. While existing work trades off one aspect for another, this paper simultaneously makes progress on both fronts through a new task: answering complex questions on semi-structured tables using question-answer pairs as supervision. The central challenge arises from two compounding factors: the broader domain results in an open-ended set of relations, and the deeper compositionality results in a combinatorial explosion in the space of logical forms. We propose a logical-form driven parsing algorithm guided by strong typing constraints and show that it obtains significant improvements over natural baselines. For evaluation, we created a new dataset of 22,033 complex questions on Wikipedia tables, which is made publicly available.

This paper studies the topic modeling problem of tagged documents and images. Higher-order relations among tagged documents and images are major and ubiquitous characteristics, and play positive roles in extracting reliable and interpretable topics. In this paper, we propose the tag-topic models (TTM) to depict such higher-order topic structural dependencies within the Markov random field (MRF) framework. First, we use the novel factor graph representation of latent Dirichlet allocation (LDA)-based topic models from the MRF perspective, and present an efficient loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Second, we propose the factor hypergraph representation of TTM, and focus on both pairwise and higher-order relation modeling among tagged documents and images. Efficient loopy BP algorithm is developed to learn TTM, which encourages the topic labeling smoothness among tagged documents and images. Extensive experimental results confirm the incorporation of higher-order relations to be effective in enhancing the overall topic modeling performance, when compared with current state-of-the-art topic models, in many text and image mining tasks of broad interests such as word and link prediction, document classification, and tag recommendation.

Embedding knowledge graphs (KGs) into continuous vector spaces is a focus of current research. Early works performed this task via simple models developed over KG triples. Recent attempts focused on either designing more complicated triple scoring models, or incorporating extra information beyond triples. This paper, by contrast, investigates the potential of using very simple constraints to improve KG embedding. We examine non-negativity constraints on entity representations and approximate entailment constraints on relation representations. The former help to learn compact and interpretable representations for entities. The latter further encode regularities of logical entailment between relations into their distributed representations. These constraints impose prior beliefs upon the structure of the embedding space, without negative impacts on efficiency or scalability. Evaluation on WordNet, Freebase, and DBpedia shows that our approach is simple yet surprisingly effective, significantly and consistently outperforming competitive baselines. The constraints imposed indeed improve model interpretability, leading to a substantially increased structuring of the embedding space. Code and data are available at https://github.com/iieir-km/ComplEx-NNE_AER.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Reasoning-enhanced large language models (RLLMs), whether explicitly trained for reasoning or prompted via chain-of-thought (CoT), have achieved state-of-the-art performance on many complex reasoning tasks. However, we uncover a surprising and previously overlooked phenomenon: explicit CoT reasoning can significantly degrade instruction-following accuracy. Evaluating 15 models on two benchmarks: IFEval (with simple, rule-verifiable constraints) and ComplexBench (with complex, compositional constraints), we consistently observe performance drops when CoT prompting is applied. Through large-scale case studies and an attention-based analysis, we identify common patterns where reasoning either helps (e.g., with formatting or lexical precision) or hurts (e.g., by neglecting simple constraints or introducing unnecessary content). We propose a metric, constraint attention, to quantify model focus during generation and show that CoT reasoning often diverts attention away from instruction-relevant tokens. To mitigate these effects, we introduce and evaluate four strategies: in-context learning, self-reflection, self-selective reasoning, and classifier-selective reasoning. Our results demonstrate that selective reasoning strategies, particularly classifier-selective reasoning, can substantially recover lost performance. To our knowledge, this is the first work to systematically expose reasoning-induced failures in instruction-following and offer practical mitigation strategies.

The rapid advancement of perovskite solar cells (PSCs) has led to an exponential growth in research publications, creating an urgent need for efficient knowledge management and reasoning systems in this domain. We present a comprehensive knowledge-enhanced system for PSCs that integrates three key components. First, we develop Perovskite-KG, a domain-specific knowledge graph constructed from 1,517 research papers, containing 23,789 entities and 22,272 relationships. Second, we create two complementary datasets: Perovskite-Chat, comprising 55,101 high-quality question-answer pairs generated through a novel multi-agent framework, and Perovskite-Reasoning, containing 2,217 carefully curated materials science problems. Third, we introduce two specialized large language models: Perovskite-Chat-LLM for domain-specific knowledge assistance and Perovskite-Reasoning-LLM for scientific reasoning tasks. Experimental results demonstrate that our system significantly outperforms existing models in both domain-specific knowledge retrieval and scientific reasoning tasks, providing researchers with effective tools for literature review, experimental design, and complex problem-solving in PSC research.

Multi-hop reasoning (i.e., reasoning across two or more documents) is a key ingredient for NLP models that leverage large corpora to exhibit broad knowledge. To retrieve evidence passages, multi-hop models must contend with a fast-growing search space across the hops, represent complex queries that combine multiple information needs, and resolve ambiguity about the best order in which to hop between training passages. We tackle these problems via Baleen, a system that improves the accuracy of multi-hop retrieval while learning robustly from weak training signals in the many-hop setting. To tame the search space, we propose condensed retrieval, a pipeline that summarizes the retrieved passages after each hop into a single compact context. To model complex queries, we introduce a focused late interaction retriever that allows different parts of the same query representation to match disparate relevant passages. Lastly, to infer the hopping dependencies among unordered training passages, we devise latent hop ordering, a weak-supervision strategy in which the trained retriever itself selects the sequence of hops. We evaluate Baleen on retrieval for two-hop question answering and many-hop claim verification, establishing state-of-the-art performance.

Pre-trained language models have been found to capture a surprisingly rich amount of lexical knowledge, ranging from commonsense properties of everyday concepts to detailed factual knowledge about named entities. Among others, this makes it possible to distill high-quality word vectors from pre-trained language models. However, it is currently unclear to what extent it is possible to distill relation embeddings, i.e. vectors that characterize the relationship between two words. Such relation embeddings are appealing because they can, in principle, encode relational knowledge in a more fine-grained way than is possible with knowledge graphs. To obtain relation embeddings from a pre-trained language model, we encode word pairs using a (manually or automatically generated) prompt, and we fine-tune the language model such that relationally similar word pairs yield similar output vectors. We find that the resulting relation embeddings are highly competitive on analogy (unsupervised) and relation classification (supervised) benchmarks, even without any task-specific fine-tuning. Source code to reproduce our experimental results and the model checkpoints are available in the following repository: https://github.com/asahi417/relbert

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model.

Relational reasoning is a central component of generally intelligent behavior, but has proven difficult for neural networks to learn. In this paper we describe how to use Relation Networks (RNs) as a simple plug-and-play module to solve problems that fundamentally hinge on relational reasoning. We tested RN-augmented networks on three tasks: visual question answering using a challenging dataset called CLEVR, on which we achieve state-of-the-art, super-human performance; text-based question answering using the bAbI suite of tasks; and complex reasoning about dynamic physical systems. Then, using a curated dataset called Sort-of-CLEVR we show that powerful convolutional networks do not have a general capacity to solve relational questions, but can gain this capacity when augmented with RNs. Our work shows how a deep learning architecture equipped with an RN module can implicitly discover and learn to reason about entities and their relations.

Language models pretrained on large collections of tabular data have demonstrated their effectiveness in several downstream tasks. However, many of these models do not take into account the row/column permutation invariances, hierarchical structure, etc. that exist in tabular data. To alleviate these limitations, we propose HYTREL, a tabular language model, that captures the permutation invariances and three more structural properties of tabular data by using hypergraphs - where the table cells make up the nodes and the cells occurring jointly together in each row, column, and the entire table are used to form three different types of hyperedges. We show that HYTREL is maximally invariant under certain conditions for tabular data, i.e., two tables obtain the same representations via HYTREL iff the two tables are identical up to permutations. Our empirical results demonstrate that HYTREL consistently outperforms other competitive baselines on four downstream tasks with minimal pretraining, illustrating the advantages of incorporating the inductive biases associated with tabular data into the representations. Finally, our qualitative analyses showcase that HYTREL can assimilate the table structures to generate robust representations for the cells, rows, columns, and the entire table.

Inductive Reasoning (IR), the ability to summarize rules from examples and apply on new ones, has long been viewed as a primal ability for general intelligence and widely studied by cognitive science and AI researchers. Many benchmarks have been proposed to measure such ability for Large Language Models (LLMs); however, they focus on few-shot (usually <10) setting and lack evaluation for aggregating many pieces of information from long contexts. On the other hand, the ever-growing context length of LLMs have brought forth the novel paradigm of many-shot In-Context Learning (ICL), which addresses new tasks with hundreds to thousands of examples without expensive and inefficient fine-tuning. However, many-shot evaluations are mostly focused on classification (a very limited aspect of IR), and popular long-context LLM tasks such as Needle-In-A-Haystack (NIAH) seldom require complicated intelligence for integrating many pieces of information. To fix the issues from both worlds, we propose MIR-Bench, the first many-shot in-context inductive reasoning benchmark that asks LLM to induce output via input-output examples from underlying functions with diverse data format. Based on MIR-Bench, we study many novel problems for inductive reasoning and many-shot ICL, including robustness against erroneous shots and the effect of Chain-of-Thought (CoT), and acquired insightful findings.

The chain-of-though (CoT) prompting methods were successful in various natural language processing (NLP) tasks thanks to their ability to unveil the underlying complex reasoning processes. Such reasoning processes typically exhibit implicitly structured steps. Recent efforts also started investigating methods to encourage more explicitly structured reasoning procedures to be captured. In this work, we propose Tab-CoT, a novel tabular-format CoT prompting method, which allows the complex reasoning process to be explicitly modelled in a highly structured manner. Despite its simplicity, we show that our approach is capable of performing reasoning across multiple dimensions (i.e., both rows and columns). We demonstrate our approach's strong zero-shot and few-shot capabilities through extensive experiments on a range of reasoning tasks.

Complex reasoning is an impressive ability shown by large language models (LLMs). Most LLMs are skilled in deductive reasoning, such as chain-of-thought prompting or iterative tool-using to solve challenging tasks step-by-step. In this paper, we hope to focus on evaluating and teaching LLMs to conduct inductive reasoning, that is, LLMs are supposed to infer underlying rules by observing examples or sequential transformations. However, collecting large-scale and diverse human-generated inductive data is challenging. We focus on data synthesis in the code domain and propose a Case2Code task by exploiting the expressiveness and correctness of programs. Specifically, we collect a diverse set of executable programs, synthesize input-output transformations for each program, and force LLMs to infer the underlying code implementations based on the synthetic I/O cases. We first evaluate representative LLMs on the synthesized Case2Code task and demonstrate that the Case-to-code induction is challenging for LLMs. Then, we synthesize large-scale Case2Code training samples to train LLMs to perform inductive reasoning. Experimental results show that such induction training benefits not only in distribution Case2Code performance but also enhances various coding abilities of trained LLMs, demonstrating the great potential of learning inductive reasoning via synthetic data.

Answering real-world user queries, such as product search, often requires accurate retrieval of information from semi-structured knowledge bases or databases that involve blend of unstructured (e.g., textual descriptions of products) and structured (e.g., entity relations of products) information. However, previous works have mostly studied textual and relational retrieval tasks as separate topics. To address the gap, we develop STARK, a large-scale Semi-structure retrieval benchmark on Textual and Relational Knowledge Bases. We design a novel pipeline to synthesize natural and realistic user queries that integrate diverse relational information and complex textual properties, as well as their ground-truth answers. Moreover, we rigorously conduct human evaluation to validate the quality of our benchmark, which covers a variety of practical applications, including product recommendations, academic paper searches, and precision medicine inquiries. Our benchmark serves as a comprehensive testbed for evaluating the performance of retrieval systems, with an emphasis on retrieval approaches driven by large language models (LLMs). Our experiments suggest that the STARK datasets present significant challenges to the current retrieval and LLM systems, indicating the demand for building more capable retrieval systems that can handle both textual and relational aspects.

Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.

Human cognition exhibits systematic compositionality, the algebraic ability to generate infinite novel combinations from finite learned components, which is the key to understanding and reasoning about complex logic. In this work, we investigate the compositionality of large language models (LLMs) in mathematical reasoning. Specifically, we construct a new dataset MathTrap by introducing carefully designed logical traps into the problem descriptions of MATH and GSM8K. Since problems with logical flaws are quite rare in the real world, these represent "unseen" cases to LLMs. Solving these requires the models to systematically compose (1) the mathematical knowledge involved in the original problems with (2) knowledge related to the introduced traps. Our experiments show that while LLMs possess both components of requisite knowledge, they do not spontaneously combine them to handle these novel cases. We explore several methods to mitigate this deficiency, such as natural language prompts, few-shot demonstrations, and fine-tuning. Additionally, we test the recently released OpenAI o1 model and find that human-like `slow thinking' helps improve the compositionality of LLMs. Overall, systematic compositionality remains an open challenge for large language models.

Continuous latent variables (LVs) are a key ingredient of many generative models, as they allow modelling expressive mixtures with an uncountable number of components. In contrast, probabilistic circuits (PCs) are hierarchical discrete mixtures represented as computational graphs composed of input, sum and product units. Unlike continuous LV models, PCs provide tractable inference but are limited to discrete LVs with categorical (i.e. unordered) states. We bridge these model classes by introducing probabilistic integral circuits (PICs), a new language of computational graphs that extends PCs with integral units representing continuous LVs. In the first place, PICs are symbolic computational graphs and are fully tractable in simple cases where analytical integration is possible. In practice, we parameterise PICs with light-weight neural nets delivering an intractable hierarchical continuous mixture that can be approximated arbitrarily well with large PCs using numerical quadrature. On several distribution estimation benchmarks, we show that such PIC-approximating PCs systematically outperform PCs commonly learned via expectation-maximization or SGD.

Large Language Models (LLMs) are general-purpose tools with wide-ranging applications, including in materials science. In this work, we introduce aLLoyM, a fine-tuned LLM specifically trained on alloy compositions, temperatures, and their corresponding phase information. To develop aLLoyM, we curated question-and-answer (Q&A) pairs for binary and ternary phase diagrams using the open-source Computational Phase Diagram Database (CPDDB) and assessments based on CALPHAD (CALculation of PHAse Diagrams). We fine-tuned Mistral, an open-source pre-trained LLM, for two distinct Q&A formats: multiple-choice and short-answer. Benchmark evaluations demonstrate that fine-tuning substantially enhances performance on multiple-choice phase diagram questions. Moreover, the short-answer model of aLLoyM exhibits the ability to generate novel phase diagrams from its components alone, underscoring its potential to accelerate the discovery of previously unexplored materials systems. To promote further research and adoption, we have publicly released the short-answer fine-tuned version of aLLoyM, along with the complete benchmarking Q&A dataset, on Hugging Face.

Relational databases (RDBs) are composed of interconnected tables, where relationships between them are defined through foreign keys. Recent research on applying machine learning to RDBs has explored graph-based representations of RDBs, where rows of tables are modeled as nodes, and foreign key relationships are modeled as edges. RDB-to-graph modeling helps capture cross-table dependencies, ultimately leading to enhanced performance across diverse tasks. However, there are numerous ways to model RDBs as graphs, and performance varies significantly depending on the chosen graph model. In our analysis, applying a common heuristic rule for graph modeling leads to up to a 10% drop in performance compared to the best-performing graph model, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph-performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 9 automatic RDB-to-graph modeling methods on the 12 tasks over 600x faster than on-the-fly evaluation, which requires repeated model training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling.

Complex question-answering (QA) systems face significant challenges in retrieving and reasoning over information that addresses multi-faceted queries. While large language models (LLMs) have advanced the reasoning capabilities of these systems, the bounded-recall problem persists, where procuring all relevant documents in first-stage retrieval remains a challenge. Missing pertinent documents at this stage leads to performance degradation that cannot be remedied in later stages, especially given the limited context windows of LLMs which necessitate high recall at smaller retrieval depths. In this paper, we introduce SUNAR, a novel approach that leverages LLMs to guide a Neighborhood Aware Retrieval process. SUNAR iteratively explores a neighborhood graph of documents, dynamically promoting or penalizing documents based on uncertainty estimates from interim LLM-generated answer candidates. We validate our approach through extensive experiments on two complex QA datasets. Our results show that SUNAR significantly outperforms existing retrieve-and-reason baselines, achieving up to a 31.84% improvement in performance over existing state-of-the-art methods for complex QA.

Large language models (LLMs), especially Explicit Long Chain-of-Thought (CoT) reasoning models like DeepSeek-R1 and QWQ, have demonstrated powerful reasoning capabilities, achieving impressive performance in commonsense reasoning and mathematical inference. Despite their effectiveness, Long-CoT reasoning models are often criticized for their limited ability and low efficiency in knowledge-intensive domains such as molecule discovery. Success in this field requires a precise understanding of domain knowledge, including molecular structures and chemical principles, which is challenging due to the inherent complexity of molecular data and the scarcity of high-quality expert annotations. To bridge this gap, we introduce Mol-R1, a novel framework designed to improve explainability and reasoning performance of R1-like Explicit Long-CoT reasoning LLMs in text-based molecule generation. Our approach begins with a high-quality reasoning dataset curated through Prior Regulation via In-context Distillation (PRID), a dedicated distillation strategy to effectively generate paired reasoning traces guided by prior regulations. Building upon this, we introduce MoIA, Molecular Iterative Adaptation, a sophisticated training strategy that iteratively combines Supervised Fine-tuning (SFT) with Reinforced Policy Optimization (RPO), tailored to boost the reasoning performance of R1-like reasoning models for molecule discovery. Finally, we examine the performance of Mol-R1 in the text-based molecule reasoning generation task, showing superior performance against existing baselines.

Recent studies suggest that deep learning models inductive bias towards favoring simpler features may be one of the sources of shortcut learning. Yet, there has been limited focus on understanding the complexity of the myriad features that models learn. In this work, we introduce a new metric for quantifying feature complexity, based on V-information and capturing whether a feature requires complex computational transformations to be extracted. Using this V-information metric, we analyze the complexities of 10,000 features, represented as directions in the penultimate layer, that were extracted from a standard ImageNet-trained vision model. Our study addresses four key questions: First, we ask what features look like as a function of complexity and find a spectrum of simple to complex features present within the model. Second, we ask when features are learned during training. We find that simpler features dominate early in training, and more complex features emerge gradually. Third, we investigate where within the network simple and complex features flow, and find that simpler features tend to bypass the visual hierarchy via residual connections. Fourth, we explore the connection between features complexity and their importance in driving the networks decision. We find that complex features tend to be less important. Surprisingly, important features become accessible at earlier layers during training, like a sedimentation process, allowing the model to build upon these foundational elements.

Large Language Models (LLMs) have demonstrated promising capabilities in solving mathematical reasoning tasks, leveraging Chain-of-Thought (CoT) data as a vital component in guiding answer generation. Current paradigms typically generate CoT and answers directly for a given problem, diverging from human problem-solving strategies to some extent. Humans often solve problems by recalling analogous cases and leveraging their solutions to reason about the current task. Inspired by this cognitive process, we propose MetaLadder, a novel framework that explicitly prompts LLMs to recall and reflect on meta-problems, those structurally or semantically analogous problems, alongside their CoT solutions before addressing the target problem. Additionally, we introduce a problem-restating mechanism to enhance the model's comprehension of the target problem by regenerating the original question, which further improves reasoning accuracy. Therefore, the model can achieve reasoning transfer from analogical problems, mimicking human-like "learning from examples" and generalization abilities. Extensive experiments on mathematical benchmarks demonstrate that our MetaLadder significantly boosts LLMs' problem-solving accuracy, largely outperforming standard CoT-based methods (10.3\% accuracy gain) and other methods. Our code and data has been released at https://github.com/LHL3341/MetaLadder.

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of ``slow thinking" into multimodal large language models (MLLMs). Contrary to existing methods that rely on direct or fast thinking, our key idea is to construct long chains of thought (CoT) consisting of atomic actions in a step-by-step manner, guiding MLLMs to perform complex reasoning. To this end, we design a novel AtomThink framework composed of three key modules: (i) a CoT annotation engine that automatically generates high-quality CoT annotations to address the lack of high-quality visual mathematical data; (ii) an atomic step fine-tuning strategy that jointly optimizes an MLLM and a policy reward model (PRM) for step-wise reasoning; and (iii) four different search strategies that can be applied with the PRM to complete reasoning. Additionally, we propose AtomMATH, a large-scale multimodal dataset of long CoTs, and an atomic capability evaluation metric for mathematical tasks. Extensive experimental results show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving approximately 50\% relative accuracy gains on MathVista and 120\% on MathVerse. To support the advancement of multimodal slow-thinking models, we will make our code and dataset publicly available on https://github.com/Quinn777/AtomThink.

Large language models (LLMs) have shown remarkable improvements in reasoning and many existing benchmarks have been addressed by models such as o1 and o3 either fully or partially. However, a majority of these benchmarks emphasize deductive reasoning, including mathematical and coding tasks in which rules such as mathematical axioms or programming syntax are clearly defined, based on which LLMs can plan and apply these rules to arrive at a solution. In contrast, inductive reasoning, where one infers the underlying rules from observed data, remains less explored. Such inductive processes lie at the heart of scientific discovery, as they enable researchers to extract general principles from empirical observations. To assess whether LLMs possess this capacity, we introduce InductionBench, a new benchmark designed to evaluate the inductive reasoning ability of LLMs. Our experimental findings reveal that even the most advanced models available struggle to master the simplest complexity classes within the subregular hierarchy of functions, highlighting a notable deficiency in current LLMs' inductive reasoning capabilities. Coda and data are available https://github.com/Wenyueh/inductive_reasoning_benchmark.

Inductive knowledge graph completion has been considered as the task of predicting missing triplets between new entities that are not observed during training. While most inductive knowledge graph completion methods assume that all entities can be new, they do not allow new relations to appear at inference time. This restriction prohibits the existing methods from appropriately handling real-world knowledge graphs where new entities accompany new relations. In this paper, we propose an INductive knowledge GRAph eMbedding method, InGram, that can generate embeddings of new relations as well as new entities at inference time. Given a knowledge graph, we define a relation graph as a weighted graph consisting of relations and the affinity weights between them. Based on the relation graph and the original knowledge graph, InGram learns how to aggregate neighboring embeddings to generate relation and entity embeddings using an attention mechanism. Experimental results show that InGram outperforms 14 different state-of-the-art methods on varied inductive learning scenarios.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Transforming a sentence into a two-dimensional (2D) representation (e.g., the table filling) has the ability to unfold a semantic plane, where an element of the plane is a word-pair representation of a sentence which may denote a possible relation representation composed of two named entities. The 2D representation is effective in resolving overlapped relation instances. However, in related works, the representation is directly transformed from a raw input. It is weak to utilize prior knowledge, which is important to support the relation extraction task. In this paper, we propose a two-dimensional feature engineering method in the 2D sentence representation for relation extraction. Our proposed method is evaluated on three public datasets (ACE05 Chinese, ACE05 English, and SanWen) and achieves the state-of-the-art performance. The results indicate that two-dimensional feature engineering can take advantage of a two-dimensional sentence representation and make full use of prior knowledge in traditional feature engineering. Our code is publicly available at https://github.com/Wang-ck123/A-Two-Dimensional-Feature-Engineering-Method-for-Entity-Relation-Extraction

Universal Information Extraction (UIE) has garnered significant attention due to its ability to address model explosion problems effectively. Extractive UIE can achieve strong performance using a relatively small model, making it widely adopted. Extractive UIEs generally rely on task instructions for different tasks, including single-target instructions and multiple-target instructions. Single-target instruction UIE enables the extraction of only one type of relation at a time, limiting its ability to model correlations between relations and thus restricting its capability to extract complex relations. While multiple-target instruction UIE allows for the extraction of multiple relations simultaneously, the inclusion of irrelevant relations introduces decision complexity and impacts extraction accuracy. Therefore, for multi-relation extraction, we propose LDNet, which incorporates multi-aspect relation modeling and a label drop mechanism. By assigning different relations to different levels for understanding and decision-making, we reduce decision confusion. Additionally, the label drop mechanism effectively mitigates the impact of irrelevant relations. Experiments show that LDNet outperforms or achieves competitive performance with state-of-the-art systems on 9 tasks, 33 datasets, in both single-modal and multi-modal, few-shot and zero-shot settings.https://github.com/Lu-Yang666/LDNet

Multi-agent interactions, such as communication, teaching, and bluffing, often rely on higher-order social inference, i.e., understanding how others infer oneself. Such intricate reasoning can be effectively modeled through nested multi-agent reasoning. Nonetheless, the computational complexity escalates exponentially with each level of reasoning, posing a significant challenge. However, humans effortlessly perform complex social inferences as part of their daily lives. To bridge the gap between human-like inference capabilities and computational limitations, we propose a novel approach: leveraging neural networks to amortize high-order social inference, thereby expediting nested multi-agent reasoning. We evaluate our method in two challenging multi-agent interaction domains. The experimental results demonstrate that our method is computationally efficient while exhibiting minimal degradation in accuracy.

Large reasoning models (LRMs) have demonstrated impressive capabilities in complex problem-solving, yet their internal reasoning mechanisms remain poorly understood. In this paper, we investigate the reasoning trajectories of LRMs from an information-theoretic perspective. By tracking how mutual information (MI) between intermediate representations and the correct answer evolves during LRM reasoning, we observe an interesting MI peaks phenomenon: the MI at specific generative steps exhibits a sudden and significant increase during LRM's reasoning process. We theoretically analyze such phenomenon and show that as MI increases, the probability of model's prediction error decreases. Furthermore, these MI peaks often correspond to tokens expressing reflection or transition, such as ``Hmm'', ``Wait'' and ``Therefore,'' which we term as the thinking tokens. We then demonstrate that these thinking tokens are crucial for LRM's reasoning performance, while other tokens has minimal impacts. Building on these analyses, we propose two simple yet effective methods to improve LRM's reasoning performance, by delicately leveraging these thinking tokens. Overall, our work provides novel insights into the reasoning mechanisms of LRMs and offers practical ways to improve their reasoning capabilities. The code is available at https://github.com/ChnQ/MI-Peaks.

Inductive reasoning is a core problem-solving capacity: humans can identify underlying principles from a few examples, which can then be robustly generalized to novel scenarios. Recent work has evaluated large language models (LLMs) on inductive reasoning tasks by directly prompting them yielding "in context learning." This can work well for straightforward inductive tasks, but performs very poorly on more complex tasks such as the Abstraction and Reasoning Corpus (ARC). In this work, we propose to improve the inductive reasoning ability of LLMs by generating explicit hypotheses at multiple levels of abstraction: we prompt the LLM to propose multiple abstract hypotheses about the problem, in natural language, then implement the natural language hypotheses as concrete Python programs. These programs can be directly verified by running on the observed examples and generalized to novel inputs. Because of the prohibitive cost of generation with state-of-the-art LLMs, we consider a middle step to filter the set of hypotheses that will be implemented into programs: we either ask the LLM to summarize into a smaller set of hypotheses, or ask human annotators to select a subset of the hypotheses. We verify our pipeline's effectiveness on the ARC visual inductive reasoning benchmark, its variant 1D-ARC, and string transformation dataset SyGuS. On a random 40-problem subset of ARC, our automated pipeline using LLM summaries achieves 27.5% accuracy, significantly outperforming the direct prompting baseline (accuracy of 12.5%). With the minimal human input of selecting from LLM-generated candidates, the performance is boosted to 37.5%. (And we argue this is a lower bound on the performance of our approach without filtering.) Our ablation studies show that abstract hypothesis generation and concrete program representations are both beneficial for LLMs to perform inductive reasoning tasks.

Entity Linking (EL) and Relation Extraction (RE) are fundamental tasks in Natural Language Processing, serving as critical components in a wide range of applications. In this paper, we propose ReLiK, a Retriever-Reader architecture for both EL and RE, where, given an input text, the Retriever module undertakes the identification of candidate entities or relations that could potentially appear within the text. Subsequently, the Reader module is tasked to discern the pertinent retrieved entities or relations and establish their alignment with the corresponding textual spans. Notably, we put forward an innovative input representation that incorporates the candidate entities or relations alongside the text, making it possible to link entities or extract relations in a single forward pass and to fully leverage pre-trained language models contextualization capabilities, in contrast with previous Retriever-Reader-based methods, which require a forward pass for each candidate. Our formulation of EL and RE achieves state-of-the-art performance in both in-domain and out-of-domain benchmarks while using academic budget training and with up to 40x inference speed compared to competitors. Finally, we show how our architecture can be used seamlessly for Information Extraction (cIE), i.e. EL + RE, and setting a new state of the art by employing a shared Reader that simultaneously extracts entities and relations.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Diffusion models gain increasing popularity for their generative capabilities. Recently, there have been surging needs to generate customized images by inverting diffusion models from exemplar images. However, existing inversion methods mainly focus on capturing object appearances. How to invert object relations, another important pillar in the visual world, remains unexplored. In this work, we propose ReVersion for the Relation Inversion task, which aims to learn a specific relation (represented as "relation prompt") from exemplar images. Specifically, we learn a relation prompt from a frozen pre-trained text-to-image diffusion model. The learned relation prompt can then be applied to generate relation-specific images with new objects, backgrounds, and styles. Our key insight is the "preposition prior" - real-world relation prompts can be sparsely activated upon a set of basis prepositional words. Specifically, we propose a novel relation-steering contrastive learning scheme to impose two critical properties of the relation prompt: 1) The relation prompt should capture the interaction between objects, enforced by the preposition prior. 2) The relation prompt should be disentangled away from object appearances. We further devise relation-focal importance sampling to emphasize high-level interactions over low-level appearances (e.g., texture, color). To comprehensively evaluate this new task, we contribute ReVersion Benchmark, which provides various exemplar images with diverse relations. Extensive experiments validate the superiority of our approach over existing methods across a wide range of visual relations.

The ability to derive underlying principles from a handful of observations and then generalize to novel situations -- known as inductive reasoning -- is central to human intelligence. Prior work suggests that language models (LMs) often fall short on inductive reasoning, despite achieving impressive success on research benchmarks. In this work, we conduct a systematic study of the inductive reasoning capabilities of LMs through iterative hypothesis refinement, a technique that more closely mirrors the human inductive process than standard input-output prompting. Iterative hypothesis refinement employs a three-step process: proposing, selecting, and refining hypotheses in the form of textual rules. By examining the intermediate rules, we observe that LMs are phenomenal hypothesis proposers (i.e., generating candidate rules), and when coupled with a (task-specific) symbolic interpreter that is able to systematically filter the proposed set of rules, this hybrid approach achieves strong results across inductive reasoning benchmarks that require inducing causal relations, language-like instructions, and symbolic concepts. However, they also behave as puzzling inductive reasoners, showing notable performance gaps between rule induction (i.e., identifying plausible rules) and rule application (i.e., applying proposed rules to instances), suggesting that LMs are proposing hypotheses without being able to actually apply the rules. Through empirical and human analyses, we further reveal several discrepancies between the inductive reasoning processes of LMs and humans, shedding light on both the potentials and limitations of using LMs in inductive reasoning tasks.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

Recent research in tabular data synthesis has focused on single tables, whereas real-world applications often involve complex data with tens or hundreds of interconnected tables. Previous approaches to synthesizing multi-relational (multi-table) data fall short in two key aspects: scalability for larger datasets and capturing long-range dependencies, such as correlations between attributes spread across different tables. Inspired by the success of diffusion models in tabular data modeling, we introduce Cluster Latent Variable guided Denoising Diffusion Probabilistic Models (ClavaDDPM). This novel approach leverages clustering labels as intermediaries to model relationships between tables, specifically focusing on foreign key constraints. ClavaDDPM leverages the robust generation capabilities of diffusion models while incorporating efficient algorithms to propagate the learned latent variables across tables. This enables ClavaDDPM to capture long-range dependencies effectively. Extensive evaluations on multi-table datasets of varying sizes show that ClavaDDPM significantly outperforms existing methods for these long-range dependencies while remaining competitive on utility metrics for single-table data.

How humans and machines make sense of current inputs for relation reasoning and question-answering while putting the perceived information into context of our past memories, has been a challenging conundrum in cognitive science and artificial intelligence. Inspired by human brain's memory system and cognitive architectures, we propose a PMI framework that consists of perception, memory and inference components. Notably, the memory module comprises working and long-term memory, with the latter endowed with a higher-order structure to retain more accumulated knowledge and experiences. Through a differentiable competitive write access, current perceptions update working memory, which is later merged with long-term memory via outer product associations, averting memory overflow and minimizing information conflicts. In the inference module, relevant information is retrieved from two separate memory origins and associatively integrated to attain a more comprehensive and precise interpretation of current perceptions. We exploratively apply our PMI to improve prevailing Transformers and CNN models on question-answering tasks like bAbI-20k and Sort-of-CLEVR datasets, as well as relation calculation and image classification tasks, and in each case, our PMI enhancements consistently outshine their original counterparts significantly. Visualization analyses reveal that memory consolidation, along with the interaction and integration of information from diverse memory sources, substantially contributes to the model effectiveness on inference tasks.

Knowledge graphs enable a wide variety of applications, including question answering and information retrieval. Despite the great effort invested in their creation and maintenance, even the largest (e.g., Yago, DBPedia or Wikidata) remain incomplete. We introduce Relational Graph Convolutional Networks (R-GCNs) and apply them to two standard knowledge base completion tasks: Link prediction (recovery of missing facts, i.e. subject-predicate-object triples) and entity classification (recovery of missing entity attributes). R-GCNs are related to a recent class of neural networks operating on graphs, and are developed specifically to deal with the highly multi-relational data characteristic of realistic knowledge bases. We demonstrate the effectiveness of R-GCNs as a stand-alone model for entity classification. We further show that factorization models for link prediction such as DistMult can be significantly improved by enriching them with an encoder model to accumulate evidence over multiple inference steps in the relational graph, demonstrating a large improvement of 29.8% on FB15k-237 over a decoder-only baseline.

Despite the success of deep learning for text and image data, tree-based ensemble models are still state-of-the-art for machine learning with heterogeneous tabular data. However, there is a significant need for tabular-specific gradient-based methods due to their high flexibility. In this paper, we propose GRANDE, GRAdieNt-Based Decision Tree Ensembles, a novel approach for learning hard, axis-aligned decision tree ensembles using end-to-end gradient descent. GRANDE is based on a dense representation of tree ensembles, which affords to use backpropagation with a straight-through operator to jointly optimize all model parameters. Our method combines axis-aligned splits, which is a useful inductive bias for tabular data, with the flexibility of gradient-based optimization. Furthermore, we introduce an advanced instance-wise weighting that facilitates learning representations for both, simple and complex relations, within a single model. We conducted an extensive evaluation on a predefined benchmark with 19 classification datasets and demonstrate that our method outperforms existing gradient-boosting and deep learning frameworks on most datasets. The method is available under: https://github.com/s-marton/GRANDE

This paper introduces a new in-context learning (ICL) mechanism called In-Image Learning (I^2L) that combines demonstration examples, visual cues, and chain-of-thought reasoning into an aggregated image to enhance the capabilities of Large Multimodal Models (e.g., GPT-4V) in multimodal reasoning tasks. Unlike previous approaches that rely on converting images to text or incorporating visual input into language models, I^2L consolidates all information into an aggregated image and leverages image processing, understanding, and reasoning abilities. This has several advantages: it reduces inaccurate textual descriptions of complex images, provides flexibility in positioning demonstration examples, and avoids multiple input images and lengthy prompts. We also introduce I^2L-Hybrid, a method that combines the strengths of I^2L with other ICL methods. Specifically, it uses an automatic strategy to select the most suitable method (I^2L or another certain ICL method) for a specific task instance. We conduct extensive experiments to assess the effectiveness of I^2L and I^2L-Hybrid on MathVista, which covers a variety of complex multimodal reasoning tasks. Additionally, we investigate the influence of image resolution, the number of demonstration examples in a single image, and the positions of these demonstrations in the aggregated image on the effectiveness of I^2L. Our code is publicly available at https://github.com/AGI-Edgerunners/IIL.

Pretrained Vision-Language Models (VLMs) have achieved remarkable performance in image retrieval from text. However, their performance drops drastically when confronted with linguistically complex texts that they struggle to comprehend. Inspired by the Divide-and-Conquer algorithm and dual-process theory, in this paper, we regard linguistically complex texts as compound proposition texts composed of multiple simple proposition sentences and propose an end-to-end Neural Divide-and-Conquer Reasoning framework, dubbed NDCR. It contains three main components: 1) Divide: a proposition generator divides the compound proposition text into simple proposition sentences and produces their corresponding representations, 2) Conquer: a pretrained VLMs-based visual-linguistic interactor achieves the interaction between decomposed proposition sentences and images, 3) Combine: a neural-symbolic reasoner combines the above reasoning states to obtain the final solution via a neural logic reasoning approach. According to the dual-process theory, the visual-linguistic interactor and neural-symbolic reasoner could be regarded as analogical reasoning System 1 and logical reasoning System 2. We conduct extensive experiments on a challenging image retrieval from contextual descriptions data set. Experimental results and analyses indicate NDCR significantly improves performance in the complex image-text reasoning problem. Code link: https://github.com/YunxinLi/NDCR.

To achieve faithful reasoning that aligns with human expectations, large language models (LLMs) need to ground their reasoning to real-world knowledge (e.g., web facts, math and physical rules). Tools help LLMs access this external knowledge, but there remains challenges for fine-tuning LLM agents (e.g., Toolformer) to invoke tools in multi-step reasoning problems, where inter-connected tool calls require holistic and efficient tool usage planning. In this work, we propose a new method for LLMs to better leverage tools in multi-step reasoning. Our method, Chain-of-Abstraction (CoA), trains LLMs to first decode reasoning chains with abstract placeholders, and then call domain tools to reify each reasoning chain by filling in specific knowledge. This planning with abstract chains enables LLMs to learn more general reasoning strategies, which are robust to shifts of domain knowledge (e.g., math results) relevant to different reasoning questions. It also allows LLMs to perform decoding and calling of external tools in parallel, which avoids the inference delay caused by waiting for tool responses. In mathematical reasoning and Wiki QA domains, we show that our method consistently outperforms previous chain-of-thought and tool-augmented baselines on both in-distribution and out-of-distribution test sets, with an average ~6% absolute QA accuracy improvement. LLM agents trained with our method also show more efficient tool use, with inference speed being on average ~1.4x faster than baseline tool-augmented LLMs.

Rule-based reasoning, a fundamental type of legal reasoning, enables us to draw conclusions by accurately applying a rule to a set of facts. We explore causal language models as rule-based reasoners, specifically with respect to compositional rules - rules consisting of multiple elements which form a complex logical expression. Reasoning about compositional rules is challenging because it requires multiple reasoning steps, and attending to the logical relationships between elements. We introduce a new prompting method, Chain of Logic, which elicits rule-based reasoning through decomposition (solving elements as independent threads of logic), and recomposition (recombining these sub-answers to resolve the underlying logical expression). This method was inspired by the IRAC (Issue, Rule, Application, Conclusion) framework, a sequential reasoning approach used by lawyers. We evaluate chain of logic across eight rule-based reasoning tasks involving three distinct compositional rules from the LegalBench benchmark and demonstrate it consistently outperforms other prompting methods, including chain of thought and self-ask, using open-source and commercial language models.

In this paper, we aim to develop a large language model (LLM) with the reasoning ability on complex graph data. Currently, LLMs have achieved very impressive performance on various natural language learning tasks, extensions of which have also been applied to study the vision tasks with multi-modal data. However, when it comes to the graph learning tasks, existing LLMs present very serious flaws due to their several inherited weaknesses in performing {multi-step logic reasoning}, {precise mathematical calculation} and {perception about the spatial and temporal factors}. To address such challenges, in this paper, we will investigate the principles, methodologies and algorithms to empower existing LLMs with graph reasoning ability, which will have tremendous impacts on the current research of both LLMs and graph learning. Inspired by the latest ChatGPT and Toolformer models, we propose the Graph-ToolFormer (Graph Reasoning oriented Toolformer) framework to teach LLMs themselves with prompts augmented by ChatGPT to use external graph reasoning API tools. Specifically, we will investigate to teach Graph-ToolFormer to handle various graph data reasoning tasks in this paper, including both (1) very basic graph data loading and graph property reasoning tasks, ranging from simple graph order and size to the graph diameter and periphery, and (2) more advanced reasoning tasks on real-world graph data, such as bibliographic networks, protein molecules, sequential recommender systems, social networks and knowledge graphs.

Large language models (LLMs) have demonstrated impressive performance on reasoning tasks, including mathematical reasoning. However, the current evaluation mostly focuses on carefully constructed benchmarks and neglects the consideration of real-world reasoning problems that present missing or contradictory conditions, known as ill-defined problems. To further study this problem, we develop a largescale benchmark called Problems with Missing and Contradictory conditions ( PMC) containing over 5,000 validated ill-defined mathematical problems. Our preliminary experiments through PMC reveal two challenges about existing methods: (1) traditional methods exhibit a trade-off between solving accuracy and rejection capabilities, and (2) formal methods struggle with modeling complex problems. To address these challenges, We develop Variable-Constraint Search (VCSEARCH), a trainingfree framework that leverages formal language to detect ill-defined problems, where a variableconstraint pair search strategy is incorporated to improve the modeling capability of formal language. Extensive experiments demonstrate that VCSEARCH improves the accuracy of identifying unsolvable problems by at least 12% across different LLMs, thus achieving stronger robust mathematical reasoning ability.

Relation triple extraction, which outputs a set of triples from long sentences, plays a vital role in knowledge acquisition. Large language models can accurately extract triples from simple sentences through few-shot learning or fine-tuning when given appropriate instructions. However, they often miss out when extracting from complex sentences. In this paper, we design an evaluation-filtering framework that integrates large language models with small models for relational triple extraction tasks. The framework includes an evaluation model that can extract related entity pairs with high precision. We propose a simple labeling principle and a deep neural network to build the model, embedding the outputs as prompts into the extraction process of the large model. We conduct extensive experiments to demonstrate that the proposed method can assist large language models in obtaining more accurate extraction results, especially from complex sentences containing multiple relational triples. Our evaluation model can also be embedded into traditional extraction models to enhance their extraction precision from complex sentences.

Within this study, we propose a new approach for natural language processing using Bayesian networks to predict and analyze the context and how this approach can be applied to the Community Question Answering domain. We discuss how Bayesian networks can detect semantic relationships and dependencies between entities, and this is connected to different score-based approaches of structure-learning. We compared the Bayesian networks with different score metrics, such as the BIC, BDeu, K2 and Chow-Liu trees. Our proposed approach out-performs the baseline model at the precision metric. We also discuss the influence of penalty terms on the structure of Bayesian networks and how they can be used to analyze the relationships between entities. In addition, we examine the visualization of directed acyclic graphs to analyze semantic relationships. The article further identifies issues with detecting certain semantic classes that are separated in the structure of directed acyclic graphs. Finally, we evaluate potential improvements for the Bayesian network approach.