Daily Papers

This work is devoted to unresolved problems of Artificial General Intelligence - the inefficiency of transfer learning. One of the mechanisms that are used to solve this problem in the area of reinforcement learning is a model-based approach. In the paper we are expanding the schema networks method which allows to extract the logical relationships between objects and actions from the environment data. We present algorithms for training a Delta Schema Network (DSN), predicting future states of the environment and planning actions that will lead to positive reward. DSN shows strong performance of transfer learning on the classic Atari game environment.

Graph retrieval-augmented generation (GraphRAG) has effectively enhanced large language models in complex reasoning by organizing fragmented knowledge into explicitly structured graphs. Prior efforts have been made to improve either graph construction or graph retrieval in isolation, yielding suboptimal performance, especially when domain shifts occur. In this paper, we propose a vertically unified agentic paradigm, Youtu-GraphRAG, to jointly connect the entire framework as an intricate integration. Specifically, (i) a seed graph schema is introduced to bound the automatic extraction agent with targeted entity types, relations and attribute types, also continuously expanded for scalability over unseen domains; (ii) To obtain higher-level knowledge upon the schema, we develop novel dually-perceived community detection, fusing structural topology with subgraph semantics for comprehensive knowledge organization. This naturally yields a hierarchical knowledge tree that supports both top-down filtering and bottom-up reasoning with community summaries; (iii) An agentic retriever is designed to interpret the same graph schema to transform complex queries into tractable and parallel sub-queries. It iteratively performs reflection for more advanced reasoning; (iv) To alleviate the knowledge leaking problem in pre-trained LLM, we propose a tailored anonymous dataset and a novel 'Anonymity Reversion' task that deeply measures the real performance of the GraphRAG frameworks. Extensive experiments across six challenging benchmarks demonstrate the robustness of Youtu-GraphRAG, remarkably moving the Pareto frontier with up to 90.71% saving of token costs and 16.62% higher accuracy over state-of-the-art baselines. The results indicate our adaptability, allowing seamless domain transfer with minimal intervention on schema.

Transferring latent structure from one environment or problem to another is a mechanism by which humans and animals generalize with very little data. Inspired by cognitive and neurobiological insights, we propose graph schemas as a mechanism of abstraction for transfer learning. Graph schemas start with latent graph learning where perceptually aliased observations are disambiguated in the latent space using contextual information. Latent graph learning is also emerging as a new computational model of the hippocampus to explain map learning and transitive inference. Our insight is that a latent graph can be treated as a flexible template -- a schema -- that models concepts and behaviors, with slots that bind groups of latent nodes to the specific observations or groundings. By treating learned latent graphs (schemas) as prior knowledge, new environments can be quickly learned as compositions of schemas and their newly learned bindings. We evaluate graph schemas on two previously published challenging tasks: the memory & planning game and one-shot StreetLearn, which are designed to test rapid task solving in novel environments. Graph schemas can be learned in far fewer episodes than previous baselines, and can model and plan in a few steps in novel variations of these tasks. We also demonstrate learning, matching, and reusing graph schemas in more challenging 2D and 3D environments with extensive perceptual aliasing and size variations, and show how different schemas can be composed to model larger and more complex environments. To summarize, our main contribution is a unified system, inspired and grounded in cognitive science, that facilitates rapid transfer learning of new environments using schemas via map-induction and composition that handles perceptual aliasing.

In-Context Learning (ICL) enables transformer-based language models to adapt to new tasks by conditioning on demonstration examples. However, traditional example-driven in-context learning lacks explicit modules for knowledge retrieval and transfer at the abstraction level. Inspired by cognitive science, specifically schema theory, which holds that humans interpret new information by activating pre-existing mental frameworks (schemas) to structure understanding, we introduce SCHEMA ACTIVATED IN CONTEXT LEARNING (SA-ICL). This framework extracts the representation of the building blocks of cognition for the reasoning process instilled from prior examples, creating an abstracted schema, a lightweight, structured template of key inferential steps and their relationships, which is then used to augment a model's reasoning process when presented with a novel question. We demonstrate that a broad range of large language models (LLMs) lack the capacity to form and utilize internal schema-based learning representations implicitly, but instead benefit significantly from explicit schema-based scaffolding. Across chemistry and physics questions from the GPQA dataset, our experiments show that SA-ICL consistently boosts performance, up to 36.19 percent, when the single demonstration example is of high quality, which simultaneously reduces reliance on the number of demonstrations and enhances interpretability. SCHEMA ACTIVATED IN CONTEXT LEARNING not only bridges disparate ICL strategies ranging from pattern priming to Chain-of-Thought prompting, but also paves a new path for enhancing human-like reasoning in LLMs.

We present AutoSchemaKG, a framework for fully autonomous knowledge graph construction that eliminates the need for predefined schemas. Our system leverages large language models to simultaneously extract knowledge triples and induce comprehensive schemas directly from text, modeling both entities and events while employing conceptualization to organize instances into semantic categories. Processing over 50 million documents, we construct ATLAS (Automated Triple Linking And Schema induction), a family of knowledge graphs with 900+ million nodes and 5.9 billion edges. This approach outperforms state-of-the-art baselines on multi-hop QA tasks and enhances LLM factuality. Notably, our schema induction achieves 92\% semantic alignment with human-crafted schemas with zero manual intervention, demonstrating that billion-scale knowledge graphs with dynamically induced schemas can effectively complement parametric knowledge in large language models.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

A widely used strategy to discover and understand language model mechanisms is circuit analysis. A circuit is a minimal subgraph of a model's computation graph that executes a specific task. We identify a gap in existing circuit discovery methods: they assume circuits are position-invariant, treating model components as equally relevant across input positions. This limits their ability to capture cross-positional interactions or mechanisms that vary across positions. To address this gap, we propose two improvements to incorporate positionality into circuits, even on tasks containing variable-length examples. First, we extend edge attribution patching, a gradient-based method for circuit discovery, to differentiate between token positions. Second, we introduce the concept of a dataset schema, which defines token spans with similar semantics across examples, enabling position-aware circuit discovery in datasets with variable length examples. We additionally develop an automated pipeline for schema generation and application using large language models. Our approach enables fully automated discovery of position-sensitive circuits, yielding better trade-offs between circuit size and faithfulness compared to prior work.

Research on parsing language to SQL has largely ignored the structure of the database (DB) schema, either because the DB was very simple, or because it was observed at both training and test time. In Spider, a recently-released text-to-SQL dataset, new and complex DBs are given at test time, and so the structure of the DB schema can inform the predicted SQL query. In this paper, we present an encoder-decoder semantic parser, where the structure of the DB schema is encoded with a graph neural network, and this representation is later used at both encoding and decoding time. Evaluation shows that encoding the schema structure improves our parser accuracy from 33.8% to 39.4%, dramatically above the current state of the art, which is at 19.7%.

Several approaches are proposed to deal with the problem of the Automatic Schema Matching (ASM). The challenges and difficulties caused by the complexity and uncertainty characterizing both the process and the outcome of Schema Matching motivated us to investigate how bio-inspired emerging paradigm can help with understanding, managing, and ultimately overcoming those challenges. In this paper, we explain how we approached Automatic Schema Matching as a systemic and Complex Adaptive System (CAS) and how we modeled it using the approach of Agent-Based Modeling and Simulation (ABMS). This effort gives birth to a tool (prototype) for schema matching called Reflex-SMAS. A set of experiments demonstrates the viability of our approach on two main aspects: (i) effectiveness (increasing the quality of the found matchings) and (ii) efficiency (reducing the effort required for this efficiency). Our approach represents a significant paradigm-shift, in the field of Automatic Schema Matching.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

Existing Text-to-SQL generators require the entire schema to be encoded with the user text. This is expensive or impractical for large databases with tens of thousands of columns. Standard dense retrieval techniques are inadequate for schema subsetting of a large structured database, where the correct semantics of retrieval demands that we rank sets of schema elements rather than individual elements. In response, we propose a two-stage process for effective coverage during retrieval. First, we instruct an LLM to hallucinate a minimal DB schema deemed adequate to answer the query. We use the hallucinated schema to retrieve a subset of the actual schema, by composing the results from multiple dense retrievals. Remarkably, hallucination x2013 generally considered a nuisance x2013 turns out to be actually useful as a bridging mechanism. Since no existing benchmarks exist for schema subsetting on large databases, we introduce three benchmarks. Two semi-synthetic datasets are derived from the union of schemas in two well-known datasets, SPIDER and BIRD, resulting in 4502 and 798 schema elements respectively. A real-life benchmark called SocialDB is sourced from an actual large data warehouse comprising 17844 schema elements. We show that our method1 leads to significantly higher recall than SOTA retrieval-based augmentation methods.

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

Schemata are structured representations of complex tasks that can aid artificial intelligence by allowing models to break down complex tasks into intermediate steps. We propose a novel system that induces schemata from web videos and generalizes them to capture unseen tasks with the goal of improving video retrieval performance. Our system proceeds in three major phases: (1) Given a task with related videos, we construct an initial schema for a task using a joint video-text model to match video segments with text representing steps from wikiHow; (2) We generalize schemata to unseen tasks by leveraging language models to edit the text within existing schemata. Through generalization, we can allow our schemata to cover a more extensive range of tasks with a small amount of learning data; (3) We conduct zero-shot instructional video retrieval with the unseen task names as the queries. Our schema-guided approach outperforms existing methods for video retrieval, and we demonstrate that the schemata induced by our system are better than those generated by other models.

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

We present a neural approach called IRNet for complex and cross-domain Text-to-SQL. IRNet aims to address two challenges: 1) the mismatch between intents expressed in natural language (NL) and the implementation details in SQL; 2) the challenge in predicting columns caused by the large number of out-of-domain words. Instead of end-to-end synthesizing a SQL query, IRNet decomposes the synthesis process into three phases. In the first phase, IRNet performs a schema linking over a question and a database schema. Then, IRNet adopts a grammar-based neural model to synthesize a SemQL query which is an intermediate representation that we design to bridge NL and SQL. Finally, IRNet deterministically infers a SQL query from the synthesized SemQL query with domain knowledge. On the challenging Text-to-SQL benchmark Spider, IRNet achieves 46.7% accuracy, obtaining 19.5% absolute improvement over previous state-of-the-art approaches. At the time of writing, IRNet achieves the first position on the Spider leaderboard.

Text-to-SQL systems powered by Large Language Models have excelled on academic benchmarks but struggle in complex enterprise environments. The primary limitation lies in their reliance on static schema representations, which fails to resolve semantic ambiguity and scale effectively to large, complex databases. To address this, we propose APEX-SQL, an Agentic Text-to-SQL Framework that shifts the paradigm from passive translation to agentic exploration. Our framework employs a hypothesis-verification loop to ground model reasoning in real data. In the schema linking phase, we use logical planning to verbalize hypotheses, dual-pathway pruning to reduce the search space, and parallel data profiling to validate column roles against real data, followed by global synthesis to ensure topological connectivity. For SQL generation, we introduce a deterministic mechanism to retrieve exploration directives, allowing the agent to effectively explore data distributions, refine hypotheses, and generate semantically accurate SQLs. Experiments on BIRD (70.65% execution accuracy) and Spider 2.0-Snow (51.01% execution accuracy) demonstrate that APEX-SQL outperforms competitive baselines with reduced token consumption. Further analysis reveals that agentic exploration acts as a performance multiplier, unlocking the latent reasoning potential of foundation models in enterprise settings. Ablation studies confirm the critical contributions of each component in ensuring robust and accurate data analysis.

Schema linking is a critical bottleneck in applying existing Text-to-SQL models to real-world, large-scale, multi-database environments. Through error analysis, we identify two major challenges in schema linking: (1) Database Retrieval: accurately selecting the target database from a large schema pool, while effectively filtering out irrelevant ones; and (2) Schema Item Grounding: precisely identifying the relevant tables and columns within complex and often redundant schemas for SQL generation. Based on these, we introduce LinkAlign, a novel framework tailored for large-scale databases with thousands of fields. LinkAlign comprises three key steps: multi-round semantic enhanced retrieval and irrelevant information isolation for Challenge 1, and schema extraction enhancement for Challenge 2. Each stage supports both Agent and Pipeline execution modes, enabling balancing efficiency and performance via modular design. To enable more realistic evaluation, we construct AmbiDB, a synthetic dataset designed to reflect the ambiguity of real-world schema linking. Experiments on widely-used Text-to-SQL benchmarks demonstrate that LinkAlign consistently outperforms existing baselines on all schema linking metrics. Notably, it improves the overall Text-to-SQL pipeline and achieves a new state-of-the-art score of 33.09% on the Spider 2.0-Lite benchmark using only open-source LLMs, ranking first on the leaderboard at the time of submission. The codes are available at https://github.com/Satissss/LinkAlign

Schema matching -- the task of finding matches between attributes across disparate data sources with different tables and hierarchies -- is critical for creating interoperable machine learning (ML)-ready data. Addressing this fundamental data-centric problem has wide implications, especially in domains like healthcare, finance and e-commerce -- but also has the potential to benefit ML models more generally, by increasing the data available for ML model training. However, schema matching is a challenging ML task due to structural/hierarchical and semantic heterogeneity between different schemas. Previous ML approaches to automate schema matching have either required significant labeled data for model training, which is often unrealistic or suffer from poor zero-shot performance. To this end, we propose Matchmaker - a compositional language model program for schema matching, comprised of candidate generation, refinement and confidence scoring. Matchmaker also self-improves in a zero-shot manner without the need for labeled demonstrations via a novel optimization approach, which constructs synthetic in-context demonstrations to guide the language model's reasoning process. Empirically, we demonstrate on real-world medical schema matching benchmarks that Matchmaker outperforms previous ML-based approaches, highlighting its potential to accelerate data integration and interoperability of ML-ready data.

Text-to-SQL aims to map natural language questions to SQL queries. The sketch-based method combined with execution-guided (EG) decoding strategy has shown a strong performance on the WikiSQL benchmark. However, execution-guided decoding relies on database execution, which significantly slows down the inference process and is hence unsatisfactory for many real-world applications. In this paper, we present the Schema Dependency guided multi-task Text-to-SQL model (SDSQL) to guide the network to effectively capture the interactions between questions and schemas. The proposed model outperforms all existing methods in both the settings with or without EG. We show the schema dependency learning partially cover the benefit from EG and alleviates the need for it. SDSQL without EG significantly reduces time consumption during inference, sacrificing only a small amount of performance and provides more flexibility for downstream applications.

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.

Conventional Knowledge Graph Construction (KGC) approaches typically follow the static information extraction paradigm with a closed set of pre-defined schema. As a result, such approaches fall short when applied to dynamic scenarios or domains, whereas a new type of knowledge emerges. This necessitates a system that can handle evolving schema automatically to extract information for KGC. To address this need, we propose a new task called schema-adaptable KGC, which aims to continually extract entity, relation, and event based on a dynamically changing schema graph without re-training. We first split and convert existing datasets based on three principles to build a benchmark, i.e., horizontal schema expansion, vertical schema expansion, and hybrid schema expansion; then investigate the schema-adaptable performance of several well-known approaches such as Text2Event, TANL, UIE and GPT-3.5. We further propose a simple yet effective baseline dubbed AdaKGC, which contains schema-enriched prefix instructor and schema-conditioned dynamic decoding to better handle evolving schema. Comprehensive experimental results illustrate that AdaKGC can outperform baselines but still have room for improvement. We hope the proposed work can deliver benefits to the community. Code and datasets will be available in https://github.com/zjunlp/AdaKGC.

To tackle the challenges of large language model performance in natural language to SQL tasks, we introduce XiYan-SQL, an innovative framework that employs a multi-generator ensemble strategy to improve candidate generation. We introduce M-Schema, a semi-structured schema representation method designed to enhance the understanding of database structures. To enhance the quality and diversity of generated candidate SQL queries, XiYan-SQL integrates the significant potential of in-context learning (ICL) with the precise control of supervised fine-tuning. On one hand, we propose a series of training strategies to fine-tune models to generate high-quality candidates with diverse preferences. On the other hand, we implement the ICL approach with an example selection method based on named entity recognition to prevent overemphasis on entities. The refiner optimizes each candidate by correcting logical or syntactical errors. To address the challenge of identifying the best candidate, we fine-tune a selection model to distinguish nuances of candidate SQL queries. The experimental results on multiple dialect datasets demonstrate the robustness of XiYan-SQL in addressing challenges across different scenarios. Overall, our proposed XiYan-SQL achieves the state-of-the-art execution accuracy of 89.65% on the Spider test set, 69.86% on SQL-Eval, 41.20% on NL2GQL, and a competitive score of 72.23% on the Bird development benchmark. The proposed framework not only enhances the quality and diversity of SQL queries but also outperforms previous methods.

Most modern Text2SQL systems prompt large language models (LLMs) with entire schemas -- mostly column information -- alongside the user's question. While effective on small databases, this approach fails on real-world schemas that exceed LLM context limits, even for commercial models. The recent Spider 2.0 benchmark exemplifies this with hundreds of tables and tens of thousands of columns, where existing systems often break. Current mitigations either rely on costly multi-step prompting pipelines or filter columns by ranking them against user's question independently, ignoring inter-column structure. To scale existing systems, we introduce \toolname, an open-source, LLM-efficient schema filtering framework that compacts Text2SQL prompts by (i) ranking columns with a query-aware LLM encoder enriched with values and metadata, (ii) reranking inter-connected columns via a lightweight graph transformer over functional dependencies, and (iii) selecting a connectivity-preserving sub-schema with a Steiner-tree heuristic. Experiments on real datasets show that \toolname achieves near-perfect recall and higher precision than CodeS, SchemaExP, Qwen rerankers, and embedding retrievers, while maintaining sub-second median latency and scaling to schemas with 23,000+ columns. Our source code is available at https://github.com/thanhdath/grast-sql.

Extracting structured information from unstructured text is crucial for modeling real-world processes, but traditional schema mining relies on semi-structured data, limiting scalability. This paper introduces schema-miner, a novel tool that combines large language models with human feedback to automate and refine schema extraction. Through an iterative workflow, it organizes properties from text, incorporates expert input, and integrates domain-specific ontologies for semantic depth. Applied to materials science--specifically atomic layer deposition--schema-miner demonstrates that expert-guided LLMs generate semantically rich schemas suitable for diverse real-world applications.

Recent advances in language models opened new opportunities to address complex schema matching tasks. Schema matching approaches have been proposed that demonstrate the usefulness of language models, but they have also uncovered important limitations: Small language models (SLMs) require training data (which can be both expensive and challenging to obtain), and large language models (LLMs) often incur high computational costs and must deal with constraints imposed by context windows. We present Magneto, a cost-effective and accurate solution for schema matching that combines the advantages of SLMs and LLMs to address their limitations. By structuring the schema matching pipeline in two phases, retrieval and reranking, Magneto can use computationally efficient SLM-based strategies to derive candidate matches which can then be reranked by LLMs, thus making it possible to reduce runtime without compromising matching accuracy. We propose a self-supervised approach to fine-tune SLMs which uses LLMs to generate syntactically diverse training data, and prompting strategies that are effective for reranking. We also introduce a new benchmark, developed in collaboration with domain experts, which includes real biomedical datasets and presents new challenges to schema matching methods. Through a detailed experimental evaluation, using both our new and existing benchmarks, we show that Magneto is scalable and attains high accuracy for datasets from different domains.

A unique aspect of human visual understanding is the ability to flexibly interpret abstract concepts: acquiring lifted rules explaining what they symbolize, grounding them across familiar and unfamiliar contexts, and making predictions or reasoning about them. While off-the-shelf vision-language models excel at making literal interpretations of images (e.g., recognizing object categories such as tree branches), they still struggle to make sense of such visual abstractions (e.g., how an arrangement of tree branches may form the walls of a maze). To address this challenge, we introduce Deep Schema Grounding (DSG), a framework that leverages explicit structured representations of visual abstractions for grounding and reasoning. At the core of DSG are schemas--dependency graph descriptions of abstract concepts that decompose them into more primitive-level symbols. DSG uses large language models to extract schemas, then hierarchically grounds concrete to abstract components of the schema onto images with vision-language models. The grounded schema is used to augment visual abstraction understanding. We systematically evaluate DSG and different methods in reasoning on our new Visual Abstractions Dataset, which consists of diverse, real-world images of abstract concepts and corresponding question-answer pairs labeled by humans. We show that DSG significantly improves the abstract visual reasoning performance of vision-language models, and is a step toward human-aligned understanding of visual abstractions.

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.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

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.

In this paper, we propose a new deep learning approach, called neural association model (NAM), for probabilistic reasoning in artificial intelligence. We propose to use neural networks to model association between any two events in a domain. Neural networks take one event as input and compute a conditional probability of the other event to model how likely these two events are to be associated. The actual meaning of the conditional probabilities varies between applications and depends on how the models are trained. In this work, as two case studies, we have investigated two NAM structures, namely deep neural networks (DNN) and relation-modulated neural nets (RMNN), on several probabilistic reasoning tasks in AI, including recognizing textual entailment, triple classification in multi-relational knowledge bases and commonsense reasoning. Experimental results on several popular datasets derived from WordNet, FreeBase and ConceptNet have all demonstrated that both DNNs and RMNNs perform equally well and they can significantly outperform the conventional methods available for these reasoning tasks. Moreover, compared with DNNs, RMNNs are superior in knowledge transfer, where a pre-trained model can be quickly extended to an unseen relation after observing only a few training samples. To further prove the effectiveness of the proposed models, in this work, we have applied NAMs to solving challenging Winograd Schema (WS) problems. Experiments conducted on a set of WS problems prove that the proposed models have the potential for commonsense reasoning.

Context-dependent text-to-SQL task has drawn much attention in recent years. Previous models on context-dependent text-to-SQL task only concentrate on utilizing historical user inputs. In this work, in addition to using encoders to capture historical information of user inputs, we propose a database schema interaction graph encoder to utilize historicalal information of database schema items. In decoding phase, we introduce a gate mechanism to weigh the importance of different vocabularies and then make the prediction of SQL tokens. We evaluate our model on the benchmark SParC and CoSQL datasets, which are two large complex context-dependent cross-domain text-to-SQL datasets. Our model outperforms previous state-of-the-art model by a large margin and achieves new state-of-the-art results on the two datasets. The comparison and ablation results demonstrate the efficacy of our model and the usefulness of the database schema interaction graph encoder.

Long-range tasks require reasoning over long inputs. Existing solutions either need large compute budgets, training data, access to model weights, or use complex, task-specific approaches. We present PRISM, which alleviates these concerns by processing information as a stream of chunks, maintaining a structured in-context memory specified by a typed hierarchy schema. This approach demonstrates superior performance to baselines on diverse tasks while using at least 4x smaller contexts than long-context models. Moreover, PRISM is token-efficient. By producing short outputs and efficiently leveraging key-value (KV) caches, it achieves up to 54% cost reduction when compared to alternative short-context approaches. The method also scales down to tiny information chunks (e.g., 500 tokens) without increasing the number of tokens encoded or sacrificing quality. Furthermore, we show that it is possible to generate schemas to generalize our approach to new tasks with minimal effort.

Schema linking -- the process of aligning natural language questions with database schema elements -- is a critical yet underexplored component of Text-to-SQL systems. While recent methods have focused primarily on improving SQL generation, they often neglect the retrieval of relevant schema elements, which can lead to hallucinations and execution failures. In this work, we propose a context-aware bidirectional schema retrieval framework that treats schema linking as a standalone problem. Our approach combines two complementary strategies: table-first retrieval followed by column selection, and column-first retrieval followed by table selection. It is further augmented with techniques such as question decomposition, keyword extraction, and keyphrase extraction. Through comprehensive evaluations on challenging benchmarks such as BIRD and Spider, we demonstrate that our method significantly improves schema recall while reducing false positives. Moreover, SQL generation using our retrieved schema consistently outperforms full-schema baselines and closely approaches oracle performance, all without requiring query refinement. Notably, our method narrows the performance gap between full and perfect schema settings by 50\%. Our findings highlight schema linking as a powerful lever for enhancing Text-to-SQL accuracy and efficiency.

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.

Tabular data, ubiquitous and rich in informational value, is an increasing focus for deep representation learning, yet progress is hindered by studies centered on single tables or isolated databases, which limits model capabilities due to data scale. While collaborative learning approaches such as federated learning, transfer learning, split learning, and tabular foundation models aim to learn from multiple correlated databases, they are challenged by a scarcity of real-world interconnected tabular resources. Current data lakes and corpora largely consist of isolated databases lacking defined inter-database correlations. To overcome this, we introduce WikiDBGraph, a large-scale graph of 100,000 real-world tabular databases from WikiData, interconnected by 17 million edges and characterized by 13 node and 12 edge properties derived from its database schema and data distribution. WikiDBGraph's weighted edges identify both instance- and feature-overlapped databases. Experiments on these newly identified databases confirm that collaborative learning yields superior performance, thereby offering considerable promise for structured foundation model training while also exposing key challenges and future directions for learning from interconnected tabular data.

Traditional similarity-based schema matching methods are incapable of resolving semantic ambiguities and conflicts in domain-specific complex mapping scenarios due to missing commonsense and domain-specific knowledge. The hallucination problem of large language models (LLMs) also makes it challenging for LLM-based schema matching to address the above issues. Therefore, we propose a Knowledge Graph-based Retrieval-Augmented Generation model for Schema Matching, referred to as the KG-RAG4SM. In particular, KG-RAG4SM introduces novel vector-based, graph traversal-based, and query-based graph retrievals, as well as a hybrid approach and ranking schemes that identify the most relevant subgraphs from external large knowledge graphs (KGs). We showcase that KG-based retrieval-augmented LLMs are capable of generating more accurate results for complex matching cases without any re-training. Our experimental results show that KG-RAG4SM outperforms the LLM-based state-of-the-art (SOTA) methods (e.g., Jellyfish-8B) by 35.89% and 30.50% in terms of precision and F1 score on the MIMIC dataset, respectively; KG-RAG4SM with GPT-4o-mini outperforms the pre-trained language model (PLM)-based SOTA methods (e.g., SMAT) by 69.20% and 21.97% in terms of precision and F1 score on the Synthea dataset, respectively. The results also demonstrate that our approach is more efficient in end-to-end schema matching, and scales to retrieve from large KGs. Our case studies on the dataset from the real-world schema matching scenario exhibit that the hallucination problem of LLMs for schema matching is well mitigated by our solution.

Schema linking is a crucial step in Text-to-SQL pipelines, which translate natural language queries into SQL. The goal of schema linking is to retrieve relevant tables and columns (signal) while disregarding irrelevant ones (noise). However, imperfect schema linking can often exclude essential columns needed for accurate query generation. In this work, we revisit the need for schema linking when using the latest generation of large language models (LLMs). We find empirically that newer models are adept at identifying relevant schema elements during generation, without the need for explicit schema linking. This allows Text-to-SQL pipelines to bypass schema linking entirely and instead pass the full database schema to the LLM, eliminating the risk of excluding necessary information. Furthermore, as alternatives to schema linking, we propose techniques that improve Text-to-SQL accuracy without compromising on essential schema information. Our approach achieves 71.83\% execution accuracy on the BIRD benchmark, ranking first at the time of submission.

Image Schemas are repetitive cognitive patterns that influence the way we conceptualize and reason about various concepts present in speech. These patterns are deeply embedded within our cognitive processes and are reflected in our bodily expressions including gestures. Particularly, metaphoric gestures possess essential characteristics and semantic meanings that align with Image Schemas, to visually represent abstract concepts. The shape and form of gestures can convey abstract concepts, such as extending the forearm and hand or tracing a line with hand movements to visually represent the image schema of PATH. Previous behavior generation models have primarily focused on utilizing speech (acoustic features and text) to drive the generation model of virtual agents. They have not considered key semantic information as those carried by Image Schemas to effectively generate metaphoric gestures. To address this limitation, we introduce META4, a deep learning approach that generates metaphoric gestures from both speech and Image Schemas. Our approach has two primary goals: computing Image Schemas from input text to capture the underlying semantic and metaphorical meaning, and generating metaphoric gestures driven by speech and the computed image schemas. Our approach is the first method for generating speech driven metaphoric gestures while leveraging the potential of Image Schemas. We demonstrate the effectiveness of our approach and highlight the importance of both speech and image schemas in modeling metaphoric gestures.

We describe a new class of learning models called memory networks. Memory networks reason with inference components combined with a long-term memory component; they learn how to use these jointly. The long-term memory can be read and written to, with the goal of using it for prediction. We investigate these models in the context of question answering (QA) where the long-term memory effectively acts as a (dynamic) knowledge base, and the output is a textual response. We evaluate them on a large-scale QA task, and a smaller, but more complex, toy task generated from a simulated world. In the latter, we show the reasoning power of such models by chaining multiple supporting sentences to answer questions that require understanding the intension of verbs.

Neural networks have become an increasingly popular tool for solving many real-world problems. They are a general framework for differentiable optimization which includes many other machine learning approaches as special cases. In this thesis we build a category-theoretic formalism around a class of neural networks exemplified by CycleGAN. CycleGAN is a collection of neural networks, closed under composition, whose inductive bias is increased by enforcing composition invariants, i.e. cycle-consistencies. Inspired by Functorial Data Migration, we specify the interconnection of these networks using a categorical schema, and network instances as set-valued functors on this schema. We also frame neural network architectures, datasets, models, and a number of other concepts in a categorical setting and thus show a special class of functors, rather than functions, can be learned using gradient descent. We use the category-theoretic framework to conceive a novel neural network architecture whose goal is to learn the task of object insertion and object deletion in images with unpaired data. We test the architecture on three different datasets and obtain promising results.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

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.

JSON Schema is an important, evolving standard schema language for families of JSON documents. It is based on a complex combination of structural and Boolean assertions, and features negation and recursion. The static analysis of JSON Schema documents comprises practically relevant problems, including schema satisfiability, inclusion, and equivalence. These three problems can be reduced to witness generation: given a schema, generate an element of the schema, if it exists, and report failure otherwise. Schema satisfiability, inclusion, and equivalence have been shown to be decidable, by reduction to reachability in alternating tree automata. However, no witness generation algorithm has yet been formally described. We contribute a first, direct algorithm for JSON Schema witness generation. We study its effectiveness and efficiency, in experiments over several schema collections, including thousands of real-world schemas. Our focus is on the completeness of the language, where we only exclude the uniqueItems operator, and on the ability of the algorithm to run in a reasonable time on a large set of real-world examples, despite the exponential complexity of the underlying problem.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Graph neural architecture search has sparked much attention as Graph Neural Networks (GNNs) have shown powerful reasoning capability in many relational tasks. However, the currently used graph search space overemphasizes learning node features and neglects mining hierarchical relational information. Moreover, due to diverse mechanisms in the message passing, the graph search space is much larger than that of CNNs. This hinders the straightforward application of classical search strategies for exploring complicated graph search space. We propose Automatic Relation-aware Graph Network Proliferation (ARGNP) for efficiently searching GNNs with a relation-guided message passing mechanism. Specifically, we first devise a novel dual relation-aware graph search space that comprises both node and relation learning operations. These operations can extract hierarchical node/relational information and provide anisotropic guidance for message passing on a graph. Second, analogous to cell proliferation, we design a network proliferation search paradigm to progressively determine the GNN architectures by iteratively performing network division and differentiation. The experiments on six datasets for four graph learning tasks demonstrate that GNNs produced by our method are superior to the current state-of-the-art hand-crafted and search-based GNNs. Codes are available at https://github.com/phython96/ARGNP.

In this study, we propose a novel graph neural network called propagate-selector (PS), which propagates information over sentences to understand information that cannot be inferred when considering sentences in isolation. First, we design a graph structure in which each node represents an individual sentence, and some pairs of nodes are selectively connected based on the text structure. Then, we develop an iterative attentive aggregation and a skip-combine method in which a node interacts with its neighborhood nodes to accumulate the necessary information. To evaluate the performance of the proposed approaches, we conduct experiments with the standard HotpotQA dataset. The empirical results demonstrate the superiority of our proposed approach, which obtains the best performances, compared to the widely used answer-selection models that do not consider the intersentential relationship.

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.

Knowledge Graphs (KGs) have been used to support a wide range of applications, from web search to personal assistant. In this paper, we describe three generations of knowledge graphs: entity-based KGs, which have been supporting general search and question answering (e.g., at Google and Bing); text-rich KGs, which have been supporting search and recommendations for products, bio-informatics, etc. (e.g., at Amazon and Alibaba); and the emerging integration of KGs and LLMs, which we call dual neural KGs. We describe the characteristics of each generation of KGs, the crazy ideas behind the scenes in constructing such KGs, and the techniques developed over time to enable industry impact. In addition, we use KGs as examples to demonstrate a recipe to evolve research ideas from innovations to production practice, and then to the next level of innovations, to advance both science and business.

Knowledge Graph Foundation Models (KGFMs) are at the frontier for deep learning on knowledge graphs (KGs), as they can generalize to completely novel knowledge graphs with different relational vocabularies. Despite their empirical success, our theoretical understanding of KGFMs remains very limited. In this paper, we conduct a rigorous study of the expressive power of KGFMs. Specifically, we show that the expressive power of KGFMs directly depends on the motifs that are used to learn the relation representations. We then observe that the most typical motifs used in the existing literature are binary, as the representations are learned based on how pairs of relations interact, which limits the model's expressiveness. As part of our study, we design more expressive KGFMs using richer motifs, which necessitate learning relation representations based on, e.g., how triples of relations interact with each other. Finally, we empirically validate our theoretical findings, showing that the use of richer motifs results in better performance on a wide range of datasets drawn from different domains.

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.

Utilizing large language models (LLMs) for transforming natural language questions into SQL queries (text-to-SQL) is a promising yet challenging approach, particularly when applied to real-world databases with complex and extensive schemas. In particular, effectively incorporating data catalogs and database values for SQL generation remains an obstacle, leading to suboptimal solutions. We address this problem by proposing a new pipeline that effectively retrieves relevant data and context, selects an efficient schema, and synthesizes correct and efficient SQL queries. To increase retrieval precision, our pipeline introduces a hierarchical retrieval method leveraging model-generated keywords, locality-sensitive hashing indexing, and vector databases. Additionally, we have developed an adaptive schema pruning technique that adjusts based on the complexity of the problem and the model's context size. Our approach generalizes to both frontier proprietary models like GPT-4 and open-source models such as Llama-3-70B. Through a series of ablation studies, we demonstrate the effectiveness of each component of our pipeline and its impact on the end-to-end performance. Our method achieves new state-of-the-art performance on the cross-domain challenging BIRD dataset.

Universal information extraction (UIE) primarily employs an extractive generation approach with large language models (LLMs), typically outputting structured information based on predefined schemas such as JSON or tables. UIE suffers from a lack of adaptability when selecting between predefined schemas and on-the-fly schema generation within the in-context learning paradigm, especially when there are numerous schemas to choose from. In this paper, we propose a unified adaptive text-to-structure generation framework, called Schema as Parameterized Tools (SPT), which reimagines the tool-calling capability of LLMs by treating predefined schemas as parameterized tools for tool selection and parameter filling. Specifically, our SPT method can be applied to unify closed, open, and on-demand IE tasks by adopting Schema Retrieval by fetching the relevant schemas from a predefined pool, Schema Filling by extracting information and filling slots as with tool parameters, or Schema Generation by synthesizing new schemas with uncovered cases. Experiments show that the SPT method can handle four distinct IE tasks adaptively, delivering robust schema retrieval and selection performance. SPT also achieves comparable extraction performance to LoRA baselines and current leading UIE systems with significantly fewer trainable parameters.

We explore the ability of GPT-4 to perform ad-hoc schema based information extraction from scientific literature. We assess specifically whether it can, with a basic prompting approach, replicate two existing material science datasets, given the manuscripts from which they were originally manually extracted. We employ materials scientists to perform a detailed manual error analysis to assess where the model struggles to faithfully extract the desired information, and draw on their insights to suggest research directions to address this broadly important task.

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

Ontologies comprising of concepts, their attributes, and relationships are used in many knowledge based AI systems. While there have been efforts towards populating domain specific ontologies, we examine the role of document structure in learning ontological relationships between concepts in any document corpus. Inspired by ideas from hypernym discovery and explainability, our method performs about 15 points more accurate than a stand-alone R-GCN model for this task.

We present KNOW--the Knowledge Navigator Ontology for the World--the first ontology designed to capture everyday knowledge to augment large language models (LLMs) in real-world generative AI use cases such as personal AI assistants. Our domain is human life, both its everyday concerns and its major milestones. We have limited the initial scope of the modeled concepts to only established human universals: spacetime (places, events) plus social (people, groups, organizations). The inclusion criteria for modeled concepts are pragmatic, beginning with universality and utility. We compare and contrast previous work such as Schema.org and Cyc--as well as attempts at a synthesis of knowledge graphs and language models--noting how LLMs already encode internally much of the commonsense tacit knowledge that took decades to capture in the Cyc project. We also make available code-generated software libraries for the 12 most popular programming languages, enabling the direct use of ontology concepts in software engineering. We emphasize simplicity and developer experience in promoting AI interoperability.

Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of cellular sheaves: a knowledge graph embedding can be described as an approximate global section of an appropriate knowledge sheaf over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.

When translating natural language questions into SQL queries to answer questions from a database, contemporary semantic parsing models struggle to generalize to unseen database schemas. The generalization challenge lies in (a) encoding the database relations in an accessible way for the semantic parser, and (b) modeling alignment between database columns and their mentions in a given query. We present a unified framework, based on the relation-aware self-attention mechanism, to address schema encoding, schema linking, and feature representation within a text-to-SQL encoder. On the challenging Spider dataset this framework boosts the exact match accuracy to 57.2%, surpassing its best counterparts by 8.7% absolute improvement. Further augmented with BERT, it achieves the new state-of-the-art performance of 65.6% on the Spider leaderboard. In addition, we observe qualitative improvements in the model's understanding of schema linking and alignment. Our implementation will be open-sourced at https://github.com/Microsoft/rat-sql.

Knowledge Bases (KBs) find applications in many knowledge-intensive tasks and, most notably, in information retrieval. Wikidata is one of the largest public general-purpose KBs. Yet, its collaborative nature has led to a convoluted schema and taxonomy. The YAGO 4 KB cleaned up the taxonomy by incorporating the ontology of Schema.org, resulting in a cleaner structure amenable to automated reasoning. However, it also cut away large parts of the Wikidata taxonomy, which is essential for information retrieval. In this paper, we extend YAGO 4 with a large part of the Wikidata taxonomy - while respecting logical constraints and the distinction between classes and instances. This yields YAGO 4.5, a new, logically consistent version of YAGO that adds a rich layer of informative classes. An intrinsic and an extrinsic evaluation show the value of the new resource.

The remarkable capabilities of modern large language models are rooted in their vast repositories of knowledge encoded within their parameters, enabling them to perceive the world and engage in reasoning. The inner workings of how these models store knowledge have long been a subject of intense interest and investigation among researchers. To date, most studies have concentrated on isolated components within these models, such as the Multilayer Perceptrons and attention head. In this paper, we delve into the computation graph of the language model to uncover the knowledge circuits that are instrumental in articulating specific knowledge. The experiments, conducted with GPT2 and TinyLLAMA, has allowed us to observe how certain information heads, relation heads, and Multilayer Perceptrons collaboratively encode knowledge within the model. Moreover, we evaluate the impact of current knowledge editing techniques on these knowledge circuits, providing deeper insights into the functioning and constraints of these editing methodologies. Finally, we utilize knowledge circuits to analyze and interpret language model behaviors such as hallucinations and in-context learning. We believe the knowledge circuit holds potential for advancing our understanding of Transformers and guiding the improved design of knowledge editing. Code and data are available in https://github.com/zjunlp/KnowledgeCircuits.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

When conducting literature reviews, scientists often create literature review tables - tables whose rows are publications and whose columns constitute a schema, a set of aspects used to compare and contrast the papers. Can we automatically generate these tables using language models (LMs)? In this work, we introduce a framework that leverages LMs to perform this task by decomposing it into separate schema and value generation steps. To enable experimentation, we address two main challenges: First, we overcome a lack of high-quality datasets to benchmark table generation by curating and releasing arxivDIGESTables, a new dataset of 2,228 literature review tables extracted from ArXiv papers that synthesize a total of 7,542 research papers. Second, to support scalable evaluation of model generations against human-authored reference tables, we develop DecontextEval, an automatic evaluation method that aligns elements of tables with the same underlying aspects despite differing surface forms. Given these tools, we evaluate LMs' abilities to reconstruct reference tables, finding this task benefits from additional context to ground the generation (e.g. table captions, in-text references). Finally, through a human evaluation study we find that even when LMs fail to fully reconstruct a reference table, their generated novel aspects can still be useful.

Despite exceptional capabilities in knowledge-intensive tasks, Large Language Models (LLMs) face a critical gap in understanding how they internalize new knowledge, particularly how to structurally embed acquired knowledge in their neural computations. We address this issue through the lens of knowledge circuit evolution, identifying computational subgraphs that facilitate knowledge storage and processing. Our systematic analysis of circuit evolution throughout continual pre-training reveals several key findings: (1) the acquisition of new knowledge is influenced by its relevance to pre-existing knowledge; (2) the evolution of knowledge circuits exhibits a distinct phase shift from formation to optimization; (3) the evolution of knowledge circuits follows a deep-to-shallow pattern. These insights not only advance our theoretical understanding of the mechanisms of new knowledge acquisition in LLMs, but also provide potential implications for improving continual pre-training strategies to enhance model performance. Code and data will be available at https://github.com/zjunlp/DynamicKnowledgeCircuits.

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.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.

Despite the impressive advancements of Large Language Models (LLMs) in generating text, they are often limited by the knowledge contained in the input and prone to producing inaccurate or hallucinated content. To tackle these issues, Retrieval-augmented Generation (RAG) is employed as an effective strategy to enhance the available knowledge base and anchor the responses in reality by pulling additional texts from external databases. In real-world applications, texts are often linked through entities within a graph, such as citations in academic papers or comments in social networks. This paper exploits these topological relationships to guide the retrieval process in RAG. Specifically, we explore two kinds of topological connections: proximity-based, focusing on closely connected nodes, and role-based, which looks at nodes sharing similar subgraph structures. Our empirical research confirms their relevance to text relationships, leading us to develop a Topology-aware Retrieval-augmented Generation framework. This framework includes a retrieval module that selects texts based on their topological relationships and an aggregation module that integrates these texts into prompts to stimulate LLMs for text generation. We have curated established text-attributed networks and conducted comprehensive experiments to validate the effectiveness of this framework, demonstrating its potential to enhance RAG with topological awareness.

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.

In this paper, we explore the question of whether large language models can support cost-efficient information extraction from tables. We introduce schema-driven information extraction, a new task that transforms tabular data into structured records following a human-authored schema. To assess various LLM's capabilities on this task, we present a benchmark comprised of tables from four diverse domains: machine learning papers, chemistry literature, material science journals, and webpages. We use this collection of annotated tables to evaluate the ability of open-source and API-based language models to extract information from tables covering diverse domains and data formats. Our experiments demonstrate that surprisingly competitive performance can be achieved without requiring task-specific pipelines or labels, achieving F1 scores ranging from 74.2 to 96.1, while maintaining cost efficiency. Moreover, through detailed ablation studies and analyses, we investigate the factors contributing to model success and validate the practicality of distilling compact models to reduce API reliance.

We introduce OneKE, a dockerized schema-guided knowledge extraction system, which can extract knowledge from the Web and raw PDF Books, and support various domains (science, news, etc.). Specifically, we design OneKE with multiple agents and a configure knowledge base. Different agents perform their respective roles, enabling support for various extraction scenarios. The configure knowledge base facilitates schema configuration, error case debugging and correction, further improving the performance. Empirical evaluations on benchmark datasets demonstrate OneKE's efficacy, while case studies further elucidate its adaptability to diverse tasks across multiple domains, highlighting its potential for broad applications. We have open-sourced the Code at https://github.com/zjunlp/OneKE and released a Video at http://oneke.openkg.cn/demo.mp4.

Universal Information Extraction (UIE) is an area of interest due to the challenges posed by varying targets, heterogeneous structures, and demand-specific schemas. However, previous works have only achieved limited success by unifying a few tasks, such as Named Entity Recognition (NER) and Relation Extraction (RE), which fall short of being authentic UIE models particularly when extracting other general schemas such as quadruples and quintuples. Additionally, these models used an implicit structural schema instructor, which could lead to incorrect links between types, hindering the model's generalization and performance in low-resource scenarios. In this paper, we redefine the authentic UIE with a formal formulation that encompasses almost all extraction schemas. To the best of our knowledge, we are the first to introduce UIE for any kind of schemas. In addition, we propose RexUIE, which is a Recursive Method with Explicit Schema Instructor for UIE. To avoid interference between different types, we reset the position ids and attention mask matrices. RexUIE shows strong performance under both full-shot and few-shot settings and achieves State-of-the-Art results on the tasks of extracting complex schemas.

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.

Knowledge editing techniques for large language models (LLMs) can inject knowledge that is later reproducible verbatim, but they fall short on propagating that knowledge: models cannot answer questions that require reasoning with the injected knowledge. We present a hypernetwork-based approach for knowledge propagation, named PropMEND, where we meta-learn how to modify gradients of a language modeling loss to encourage injected information to propagate. Our approach extends the meta-objective of MEND [29] so that gradient updates on knowledge are transformed to enable answering multi-hop questions involving that knowledge. We show improved performance on the RippleEdit dataset, showing almost 2x accuracy on challenging multi-hop questions whose answers are not explicitly stated in the injected fact. We further introduce a new dataset, Controlled RippleEdit, to evaluate the generalization of our hypernetwork, testing knowledge propagation along relations and entities unseen during hypernetwork training. PropMEND still outperforms existing approaches in unseen entity-relation pairs, yet the performance gap decreases substantially, suggesting future work in propagating knowledge to a wide range of relations.

Knowledge Graph Foundation Models (KGFMs) have shown promise in enabling zero-shot reasoning over unseen graphs by learning transferable patterns. However, most existing KGFMs rely solely on graph structure, overlooking the rich semantic signals encoded in textual attributes. We introduce SEMMA, a dual-module KGFM that systematically integrates transferable textual semantics alongside structure. SEMMA leverages Large Language Models (LLMs) to enrich relation identifiers, generating semantic embeddings that subsequently form a textual relation graph, which is fused with the structural component. Across 54 diverse KGs, SEMMA outperforms purely structural baselines like ULTRA in fully inductive link prediction. Crucially, we show that in more challenging generalization settings, where the test-time relation vocabulary is entirely unseen, structural methods collapse while SEMMA is 2x more effective. Our findings demonstrate that textual semantics are critical for generalization in settings where structure alone fails, highlighting the need for foundation models that unify structural and linguistic signals in knowledge reasoning.

Knowledge graphs (KGs) have been successfully applied to the analysis of complex scientific and technological domains, with automatic KG generation methods typically building upon relation extraction models capturing fine-grained relations between domain entities in text. While these relations are fully applicable across scientific areas, existing models are trained on few domain-specific datasets such as SciERC and do not perform well on new target domains. In this paper, we experiment with leveraging in-context learning capabilities of Large Language Models to perform schema-constrained data annotation, collecting in-domain training instances for a Transformer-based relation extraction model deployed on titles and abstracts of research papers in the Architecture, Construction, Engineering and Operations (AECO) domain. By assessing the performance gain with respect to a baseline Deep Learning architecture trained on off-domain data, we show that by using a few-shot learning strategy with structured prompts and only minimal expert annotation the presented approach can potentially support domain adaptation of a science KG generation model.

Graph neural networks (GNNs) have been successfully applied to learning representation on graphs in many relational tasks. Recently, researchers study neural architecture search (NAS) to reduce the dependence of human expertise and explore better GNN architectures, but they over-emphasize entity features and ignore latent relation information concealed in the edges. To solve this problem, we incorporate edge features into graph search space and propose Edge-featured Graph Neural Architecture Search to find the optimal GNN architecture. Specifically, we design rich entity and edge updating operations to learn high-order representations, which convey more generic message passing mechanisms. Moreover, the architecture topology in our search space allows to explore complex feature dependence of both entities and edges, which can be efficiently optimized by differentiable search strategy. Experiments at three graph tasks on six datasets show EGNAS can search better GNNs with higher performance than current state-of-the-art human-designed and searched-based GNNs.

Commonsense reasoning is a long-standing challenge for deep learning. For example, it is difficult to use neural networks to tackle the Winograd Schema dataset (Levesque et al., 2011). In this paper, we present a simple method for commonsense reasoning with neural networks, using unsupervised learning. Key to our method is the use of language models, trained on a massive amount of unlabled data, to score multiple choice questions posed by commonsense reasoning tests. On both Pronoun Disambiguation and Winograd Schema challenges, our models outperform previous state-of-the-art methods by a large margin, without using expensive annotated knowledge bases or hand-engineered features. We train an array of large RNN language models that operate at word or character level on LM-1-Billion, CommonCrawl, SQuAD, Gutenberg Books, and a customized corpus for this task and show that diversity of training data plays an important role in test performance. Further analysis also shows that our system successfully discovers important features of the context that decide the correct answer, indicating a good grasp of commonsense knowledge.

Machine learning about language can be improved by supplying it with specific knowledge and sources of external information. We present here a new version of the linked open data resource ConceptNet that is particularly well suited to be used with modern NLP techniques such as word embeddings. ConceptNet is a knowledge graph that connects words and phrases of natural language with labeled edges. Its knowledge is collected from many sources that include expert-created resources, crowd-sourcing, and games with a purpose. It is designed to represent the general knowledge involved in understanding language, improving natural language applications by allowing the application to better understand the meanings behind the words people use. When ConceptNet is combined with word embeddings acquired from distributional semantics (such as word2vec), it provides applications with understanding that they would not acquire from distributional semantics alone, nor from narrower resources such as WordNet or DBPedia. We demonstrate this with state-of-the-art results on intrinsic evaluations of word relatedness that translate into improvements on applications of word vectors, including solving SAT-style analogies.

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.

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.

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

Artificial intelligence (AI) has undergone a renaissance recently, making major progress in key domains such as vision, language, control, and decision-making. This has been due, in part, to cheap data and cheap compute resources, which have fit the natural strengths of deep learning. However, many defining characteristics of human intelligence, which developed under much different pressures, remain out of reach for current approaches. In particular, generalizing beyond one's experiences--a hallmark of human intelligence from infancy--remains a formidable challenge for modern AI. The following is part position paper, part review, and part unification. We argue that combinatorial generalization must be a top priority for AI to achieve human-like abilities, and that structured representations and computations are key to realizing this objective. Just as biology uses nature and nurture cooperatively, we reject the false choice between "hand-engineering" and "end-to-end" learning, and instead advocate for an approach which benefits from their complementary strengths. We explore how using relational inductive biases within deep learning architectures can facilitate learning about entities, relations, and rules for composing them. We present a new building block for the AI toolkit with a strong relational inductive bias--the graph network--which generalizes and extends various approaches for neural networks that operate on graphs, and provides a straightforward interface for manipulating structured knowledge and producing structured behaviors. We discuss how graph networks can support relational reasoning and combinatorial generalization, laying the foundation for more sophisticated, interpretable, and flexible patterns of reasoning. As a companion to this paper, we have released an open-source software library for building graph networks, with demonstrations of how to use them in practice.

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.

Recent work has demonstrated that semantics specified by pretraining data influence how representations of different concepts are organized in a large language model (LLM). However, given the open-ended nature of LLMs, e.g., their ability to in-context learn, we can ask whether models alter these pretraining semantics to adopt alternative, context-specified ones. Specifically, if we provide in-context exemplars wherein a concept plays a different role than what the pretraining data suggests, do models reorganize their representations in accordance with these novel semantics? To answer this question, we take inspiration from the theory of conceptual role semantics and define a toy "graph tracing" task wherein the nodes of the graph are referenced via concepts seen during training (e.g., apple, bird, etc.) and the connectivity of the graph is defined via some predefined structure (e.g., a square grid). Given exemplars that indicate traces of random walks on the graph, we analyze intermediate representations of the model and find that as the amount of context is scaled, there is a sudden re-organization from pretrained semantic representations to in-context representations aligned with the graph structure. Further, we find that when reference concepts have correlations in their semantics (e.g., Monday, Tuesday, etc.), the context-specified graph structure is still present in the representations, but is unable to dominate the pretrained structure. To explain these results, we analogize our task to energy minimization for a predefined graph topology, providing evidence towards an implicit optimization process to infer context-specified semantics. Overall, our findings indicate scaling context-size can flexibly re-organize model representations, possibly unlocking novel capabilities.

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.

While large language models (LLMs) have made significant progress in processing and reasoning over knowledge graphs, current methods suffer from a high non-retrieval rate. This limitation reduces the accuracy of answering questions based on these graphs. Our analysis reveals that the combination of greedy search and forward reasoning is a major contributor to this issue. To overcome these challenges, we introduce the concept of super-relations, which enables both forward and backward reasoning by summarizing and connecting various relational paths within the graph. This holistic approach not only expands the search space, but also significantly improves retrieval efficiency. In this paper, we propose the ReKnoS framework, which aims to Reason over Knowledge Graphs with Super-Relations. Our framework's key advantages include the inclusion of multiple relation paths through super-relations, enhanced forward and backward reasoning capabilities, and increased efficiency in querying LLMs. These enhancements collectively lead to a substantial improvement in the successful retrieval rate and overall reasoning performance. We conduct extensive experiments on nine real-world datasets to evaluate ReKnoS, and the results demonstrate the superior performance of ReKnoS over existing state-of-the-art baselines, with an average accuracy gain of 2.92%.

Graphs are ubiquitous structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. To model graph-structured data, graph neural networks (GNNs) have become a popular tool. However, existing GNN architectures encounter challenges in cross-graph learning where multiple graphs have different feature spaces. To address this, recent approaches introduce text-attributed graphs (TAGs), where each node is associated with a textual description, which can be projected into a unified feature space using textual encoders. While promising, this method relies heavily on the availability of text-attributed graph data, which is difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), leveraging large language models (LLMs) to convert existing graphs into text-attributed graphs. The key idea is to integrate topological information into LLMs to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating its applicability. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

Research community has witnessed substantial growth in the detection of mental health issues and their associated reasons from analysis of social media. We introduce a new dataset for Causal Analysis of Mental health issues in Social media posts (CAMS). Our contributions for causal analysis are two-fold: causal interpretation and causal categorization. We introduce an annotation schema for this task of causal analysis. We demonstrate the efficacy of our schema on two different datasets: (i) crawling and annotating 3155 Reddit posts and (ii) re-annotating the publicly available SDCNL dataset of 1896 instances for interpretable causal analysis. We further combine these into the CAMS dataset and make this resource publicly available along with associated source code: https://github.com/drmuskangarg/CAMS. We present experimental results of models learned from CAMS dataset and demonstrate that a classic Logistic Regression model outperforms the next best (CNN-LSTM) model by 4.9\% accuracy.

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.

Retrieval from graph data is crucial for augmenting large language models (LLM) with both open-domain knowledge and private enterprise data, and it is also a key component in the recent GraphRAG system (edge et al., 2024). Despite decades of research on knowledge graphs and knowledge base question answering, leading LLM frameworks (e.g. Langchain and LlamaIndex) have only minimal support for retrieval from modern encyclopedic knowledge graphs like Wikidata. In this paper, we analyze the root cause and suggest that modern RDF knowledge graphs (e.g. Wikidata, Freebase) are less efficient for LLMs due to overly large schemas that far exceed the typical LLM context window, use of resource identifiers, overlapping relation types and lack of normalization. As a solution, we propose property graph views on top of the underlying RDF graph that can be efficiently queried by LLMs using Cypher. We instantiated this idea on Wikidata and introduced CypherBench, the first benchmark with 11 large-scale, multi-domain property graphs with 7.8 million entities and over 10,000 questions. To achieve this, we tackled several key challenges, including developing an RDF-to-property graph conversion engine, creating a systematic pipeline for text-to-Cypher task generation, and designing new evaluation metrics.

The exploitation of syntactic graphs (SyGs) as a word's context has been shown to be beneficial for distributional semantic models (DSMs), both at the level of individual word representations and in deriving phrasal representations via composition. However, notwithstanding the potential performance benefit, the syntactically-aware DSMs proposed to date have huge numbers of parameters (compared to conventional DSMs) and suffer from data sparsity. Furthermore, the encoding of the SyG links (i.e., the syntactic relations) has been largely limited to linear maps. The knowledge graphs' literature, on the other hand, has proposed light-weight models employing different geometric transformations (GTs) to encode edges in a knowledge graph (KG). Our work explores the possibility of adopting this family of models to encode SyGs. Furthermore, we investigate which GT better encodes syntactic relations, so that these representations can be used to enhance phrase-level composition via syntactic contextualisation.

We design a new technique for the distributional semantic modeling with a neural network-based approach to learn distributed term representations (or term embeddings) - term vector space models as a result, inspired by the recent ontology-related approach (using different types of contextual knowledge such as syntactic knowledge, terminological knowledge, semantic knowledge, etc.) to the identification of terms (term extraction) and relations between them (relation extraction) called semantic pre-processing technology - SPT. Our method relies on automatic term extraction from the natural language texts and subsequent formation of the problem-oriented or application-oriented (also deeply annotated) text corpora where the fundamental entity is the term (includes non-compositional and compositional terms). This gives us an opportunity to changeover from distributed word representations (or word embeddings) to distributed term representations (or term embeddings). This transition will allow to generate more accurate semantic maps of different subject domains (also, of relations between input terms - it is useful to explore clusters and oppositions, or to test your hypotheses about them). The semantic map can be represented as a graph using Vec2graph - a Python library for visualizing word embeddings (term embeddings in our case) as dynamic and interactive graphs. The Vec2graph library coupled with term embeddings will not only improve accuracy in solving standard NLP tasks, but also update the conventional concept of automated ontology development. The main practical result of our work is the development kit (set of toolkits represented as web service APIs and web application), which provides all necessary routines for the basic linguistic pre-processing and the semantic pre-processing of the natural language texts in Ukrainian for future training of term vector space models.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

In this paper, we address the challenge of enforcing strict schema adherence in large language model (LLM) generation by leveraging LLM reasoning capabilities. Building on the DeepSeek R1 reinforcement learning framework, our approach trains structured reasoning skills of a 1.5B parameter model through a novel pipeline that combines synthetic reasoning dataset construction with custom reward functions under Group Relative Policy Optimization (GRPO). Specifically, we first perform R1 reinforcement learning on a 20K sample unstructured-to-structured dataset, mirroring the original DeepSeek R1 methods, to establish core reasoning abilities. Subsequently, we performed supervised fine-tuning on a separate 10K reasoning sample dataset, focusing on refining schema adherence for downstream tasks. Despite the relatively modest training scope, requiring approximately 20 hours on an 8xH100 GPU cluster for GRPO training and 3 hours on 1xA100 for SFT, our model demonstrates robust performance in enforcing schema consistency. We compare our ThinkJSON approach against the original DeepSeek R1 (671B), distilled versions of DeepSeek R1 (Qwen-1.5B and Qwen-7B), and Gemini 2.0 Flash (70B), showcasing its effectiveness in real-world applications. Our results underscore the practical utility of a resource-efficient framework for schema-constrained text generation.

Graph neural networks (GNNs) have shown promising performance for knowledge graph reasoning. A recent variant of GNN called progressive relational graph neural network (PRGNN), utilizes relational rules to infer missing knowledge in relational digraphs and achieves notable results. However, during reasoning with PRGNN, two important properties are often overlooked: (1) the sequentiality of relation composition, where the order of combining different relations affects the semantics of the relational rules, and (2) the lagged entity information propagation, where the transmission speed of required information lags behind the appearance speed of new entities. Ignoring these properties leads to incorrect relational rule learning and decreased reasoning accuracy. To address these issues, we propose a novel knowledge graph reasoning approach, the Relational rUle eNhanced Graph Neural Network (RUN-GNN). Specifically, RUN-GNN employs a query related fusion gate unit to model the sequentiality of relation composition and utilizes a buffering update mechanism to alleviate the negative effect of lagged entity information propagation, resulting in higher-quality relational rule learning. Experimental results on multiple datasets demonstrate the superiority of RUN-GNN is superior on both transductive and inductive link prediction tasks.

Network pruning, aimed at reducing network size while preserving accuracy, has attracted significant research interest. Numerous pruning techniques have been proposed over time. They are becoming increasingly effective, but more complex and harder to interpret as well. Given the inherent complexity of neural networks, we argue that manually designing pruning criteria has reached a bottleneck. To address this, we propose a novel approach in which we "use a neural network to prune neural networks". More specifically, we introduce the newly developed idea of metanetwork from meta-learning into pruning. A metanetwork is a network that takes another network as input and produces a modified network as output. In this paper, we first establish a bijective mapping between neural networks and graphs, and then employ a graph neural network as our metanetwork. We train a metanetwork that learns the pruning strategy automatically which can transform a network that is hard to prune into another network that is much easier to prune. Once the metanetwork is trained, our pruning needs nothing more than a feedforward through the metanetwork and the standard finetuning to prune at state-of-the-art. Our method achieved outstanding results on many popular and representative pruning tasks (including ResNet56 on CIFAR10, VGG19 on CIFAR100, ResNet50 on ImageNet). Our code is available at https://github.com/Yewei-Liu/MetaPruning

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

Recently, context-dependent text-to-SQL semantic parsing which translates natural language into SQL in an interaction process has attracted a lot of attention. Previous works leverage context-dependence information either from interaction history utterances or the previous predicted SQL queries but fail in taking advantage of both since of the mismatch between natural language and logic-form SQL. In this work, we propose a History Information Enhanced text-to-SQL model (HIE-SQL) to exploit context-dependence information from both history utterances and the last predicted SQL query. In view of the mismatch, we treat natural language and SQL as two modalities and propose a bimodal pre-trained model to bridge the gap between them. Besides, we design a schema-linking graph to enhance connections from utterances and the SQL query to the database schema. We show our history information enhanced methods improve the performance of HIE-SQL by a significant margin, which achieves new state-of-the-art results on the two context-dependent text-to-SQL benchmarks, the SparC and CoSQL datasets, at the writing time.

Many practical applications of dialogue technology require the generation of responses according to a particular developer-specified persona. While a variety of personas can be elicited from recent large language models, the opaqueness and unpredictability of these models make it desirable to be able to specify personas in an explicit form. In previous work, personas have typically been represented as sets of one-off pieces of self-knowledge that are retrieved by the dialogue system for use in generation. However, in realistic human conversations, personas are often revealed through story-like narratives that involve rich habitual knowledge -- knowledge about kinds of events that an agent often participates in (e.g., work activities, hobbies, sporting activities, favorite entertainments, etc.), including typical goals, sub-events, preconditions, and postconditions of those events. We capture such habitual knowledge using an explicit schema representation, and propose an approach to dialogue generation that retrieves relevant schemas to condition a large language model to generate persona-based responses. Furthermore, we demonstrate a method for bootstrapping the creation of such schemas by first generating generic passages from a set of simple facts, and then inducing schemas from the generated passages.

Structured knowledge bases (KBs) are the backbone of many know\-ledge-intensive applications, and their automated construction has received considerable attention. In particular, open information extraction (OpenIE) is often used to induce structure from a text. However, although it allows high recall, the extracted knowledge tends to inherit noise from the sources and the OpenIE algorithm. Besides, OpenIE tuples contain an open-ended, non-canonicalized set of relations, making the extracted knowledge's downstream exploitation harder. In this paper, we study the problem of mapping an open KB into the fixed schema of an existing KB, specifically for the case of commonsense knowledge. We propose approaching the problem by generative translation, i.e., by training a language model to generate fixed-schema assertions from open ones. Experiments show that this approach occupies a sweet spot between traditional manual, rule-based, or classification-based canonicalization and purely generative KB construction like COMET. Moreover, it produces higher mapping accuracy than the former while avoiding the association-based noise of the latter.

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.

Zero/few-shot transfer to unseen services is a critical challenge in task-oriented dialogue research. The Schema-Guided Dialogue (SGD) dataset introduced a paradigm for enabling models to support any service in zero-shot through schemas, which describe service APIs to models in natural language. We explore the robustness of dialogue systems to linguistic variations in schemas by designing SGD-X - a benchmark extending SGD with semantically similar yet stylistically diverse variants for every schema. We observe that two top state tracking models fail to generalize well across schema variants, measured by joint goal accuracy and a novel metric for measuring schema sensitivity. Additionally, we present a simple model-agnostic data augmentation method to improve schema robustness.

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.

In this work, we present X-SQL, a new network architecture for the problem of parsing natural language to SQL query. X-SQL proposes to enhance the structural schema representation with the contextual output from BERT-style pre-training model, and together with type information to learn a new schema representation for down-stream tasks. We evaluated X-SQL on the WikiSQL dataset and show its new state-of-the-art performance.

Metadata plays a critical role in indexing, documenting, and analyzing scientific literature, yet extracting it accurately and efficiently remains a challenging task. Traditional approaches often rely on rule-based or task-specific models, which struggle to generalize across domains and schema variations. In this paper, we present MeXtract, a family of lightweight language models designed for metadata extraction from scientific papers. The models, ranging from 0.5B to 3B parameters, are built by fine-tuning Qwen 2.5 counterparts. In their size family, MeXtract achieves state-of-the-art performance on metadata extraction on the MOLE benchmark. To further support evaluation, we extend the MOLE benchmark to incorporate model-specific metadata, providing an out-of-domain challenging subset. Our experiments show that fine-tuning on a given schema not only yields high accuracy but also transfers effectively to unseen schemas, demonstrating the robustness and adaptability of our approach. We release all the code, datasets, and models openly for the research community.

Graph Neural Networks (GNNs) have been popularly used for analyzing non-Euclidean data such as social network data and biological data. Despite their success, the design of graph neural networks requires a lot of manual work and domain knowledge. In this paper, we propose a Graph Neural Architecture Search method (GraphNAS for short) that enables automatic search of the best graph neural architecture based on reinforcement learning. Specifically, GraphNAS first uses a recurrent network to generate variable-length strings that describe the architectures of graph neural networks, and then trains the recurrent network with reinforcement learning to maximize the expected accuracy of the generated architectures on a validation data set. Extensive experimental results on node classification tasks in both transductive and inductive learning settings demonstrate that GraphNAS can achieve consistently better performance on the Cora, Citeseer, Pubmed citation network, and protein-protein interaction network. On node classification tasks, GraphNAS can design a novel network architecture that rivals the best human-invented architecture in terms of test set accuracy.

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.

In this paper, we propose KnowCoder, a Large Language Model (LLM) to conduct Universal Information Extraction (UIE) via code generation. KnowCoder aims to develop a kind of unified schema representation that LLMs can easily understand and an effective learning framework that encourages LLMs to follow schemas and extract structured knowledge accurately. To achieve these, KnowCoder introduces a code-style schema representation method to uniformly transform different schemas into Python classes, with which complex schema information, such as constraints among tasks in UIE, can be captured in an LLM-friendly manner. We further construct a code-style schema library covering over 30,000 types of knowledge, which is the largest one for UIE, to the best of our knowledge. To ease the learning process of LLMs, KnowCoder contains a two-phase learning framework that enhances its schema understanding ability via code pretraining and its schema following ability via instruction tuning. After code pretraining on around 1.5B automatically constructed data, KnowCoder already attains remarkable generalization ability and achieves relative improvements by 49.8% F1, compared to LLaMA2, under the few-shot setting. After instruction tuning, KnowCoder further exhibits strong generalization ability on unseen schemas and achieves up to 12.5% and 21.9%, compared to sota baselines, under the zero-shot setting and the low resource setting, respectively. Additionally, based on our unified schema representations, various human-annotated datasets can simultaneously be utilized to refine KnowCoder, which achieves significant improvements up to 7.5% under the supervised setting.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

Pretrained language models (LMs) encode implicit representations of knowledge in their parameters. However, localizing these representations and disentangling them from each other remains an open problem. In this work, we investigate whether pretrained language models contain various knowledge-critical subnetworks: particular sparse computational subgraphs responsible for encoding specific knowledge the model has memorized. We propose a multi-objective differentiable weight masking scheme to discover these subnetworks and show that we can use them to precisely remove specific knowledge from models while minimizing adverse effects on the behavior of the original language model. We demonstrate our method on multiple GPT2 variants, uncovering highly sparse subnetworks (98%+) that are solely responsible for specific collections of relational knowledge. When these subnetworks are removed, the remaining network maintains most of its initial capacity (modeling language and other memorized relational knowledge) but struggles to express the removed knowledge, and suffers performance drops on examples needing this removed knowledge on downstream tasks after finetuning.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

Knowledge graph embedding (KGE) is an increasingly popular technique that aims to represent entities and relations of knowledge graphs into low-dimensional semantic spaces for a wide spectrum of applications such as link prediction, knowledge reasoning and knowledge completion. In this paper, we provide a systematic review of existing KGE techniques based on representation spaces. Particularly, we build a fine-grained classification to categorise the models based on three mathematical perspectives of the representation spaces: (1) Algebraic perspective, (2) Geometric perspective, and (3) Analytical perspective. We introduce the rigorous definitions of fundamental mathematical spaces before diving into KGE models and their mathematical properties. We further discuss different KGE methods over the three categories, as well as summarise how spatial advantages work over different embedding needs. By collating the experimental results from downstream tasks, we also explore the advantages of mathematical space in different scenarios and the reasons behind them. We further state some promising research directions from a representation space perspective, with which we hope to inspire researchers to design their KGE models as well as their related applications with more consideration of their mathematical space properties.

Modeling dynamic graphs, such as those found in social networks, recommendation systems, and e-commerce platforms, is crucial for capturing evolving relationships and delivering relevant insights over time. Traditional approaches primarily rely on graph neural networks with temporal components or sequence generation models, which often focus narrowly on the historical context of target nodes. This limitation restricts the ability to adapt to new and emerging patterns in dynamic graphs. To address this challenge, we propose a novel framework, Retrieval-Augmented Generation for Dynamic Graph modeling (RAG4DyG), which enhances dynamic graph predictions by incorporating contextually and temporally relevant examples from broader graph structures. Our approach includes a time- and context-aware contrastive learning module to identify high-quality demonstrations and a graph fusion strategy to effectively integrate these examples with historical contexts. The proposed framework is designed to be effective in both transductive and inductive scenarios, ensuring adaptability to previously unseen nodes and evolving graph structures. Extensive experiments across multiple real-world datasets demonstrate the effectiveness of RAG4DyG in improving predictive accuracy and adaptability for dynamic graph modeling. The code and datasets are publicly available at https://github.com/YuxiaWu/RAG4DyG.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

Text-to-SQL simplifies database interactions by enabling non-experts to convert their natural language (NL) questions into Structured Query Language (SQL) queries. While recent advances in large language models (LLMs) have improved the zero-shot text-to-SQL paradigm, existing methods face scalability challenges when dealing with massive, dynamically changing databases. This paper introduces DBCopilot, a framework that addresses these challenges by employing a compact and flexible copilot model for routing across massive databases. Specifically, DBCopilot decouples the text-to-SQL process into schema routing and SQL generation, leveraging a lightweight sequence-to-sequence neural network-based router to formulate database connections and navigate natural language questions through databases and tables. The routed schemas and questions are then fed into LLMs for efficient SQL generation. Furthermore, DBCopilot also introduced a reverse schema-to-question generation paradigm, which can learn and adapt the router over massive databases automatically without requiring manual intervention. Experimental results demonstrate that DBCopilot is a scalable and effective solution for real-world text-to-SQL tasks, providing a significant advancement in handling large-scale schemas.

Knowledge Graphs (KGs) are valuable tools for representing relationships between entities in a structured format. Traditionally, these knowledge bases are queried to extract specific information. However, question-answering (QA) over such KGs poses a challenge due to the intrinsic complexity of natural language compared to the structured format and the size of these graphs. Despite these challenges, the structured nature of KGs can provide a solid foundation for grounding the outputs of Large Language Models (LLMs), offering organizations increased reliability and control. Recent advancements in LLMs have introduced reasoning methods at inference time to improve their performance and maximize their capabilities. In this work, we propose integrating these reasoning strategies with KGs to anchor every step or "thought" of the reasoning chains in KG data. Specifically, we evaluate both agentic and automated search methods across several reasoning strategies, including Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT), using GRBench, a benchmark dataset for graph reasoning with domain-specific graphs. Our experiments demonstrate that this approach consistently outperforms baseline models, highlighting the benefits of grounding LLM reasoning processes in structured KG data.

Procedural text describes dynamic state changes during a step-by-step natural process (e.g., photosynthesis). In this work, we focus on the task of procedural text understanding, which aims to comprehend such documents and track entities' states and locations during a process. Although recent approaches have achieved substantial progress, their results are far behind human performance. Two challenges, the difficulty of commonsense reasoning and data insufficiency, still remain unsolved, which require the incorporation of external knowledge bases. Previous works on external knowledge injection usually rely on noisy web mining tools and heuristic rules with limited applicable scenarios. In this paper, we propose a novel KnOwledge-Aware proceduraL text understAnding (KOALA) model, which effectively leverages multiple forms of external knowledge in this task. Specifically, we retrieve informative knowledge triples from ConceptNet and perform knowledge-aware reasoning while tracking the entities. Besides, we employ a multi-stage training schema which fine-tunes the BERT model over unlabeled data collected from Wikipedia before further fine-tuning it on the final model. Experimental results on two procedural text datasets, ProPara and Recipes, verify the effectiveness of the proposed methods, in which our model achieves state-of-the-art performance in comparison to various baselines.

Large language models (LLMs), such as ChatGPT and GPT-4, are versatile and can solve different tasks due to their emergent ability and generalizability. However, LLMs sometimes lack domain-specific knowledge to perform tasks, which would also cause hallucination during inference. In some previous works, additional modules like graph neural networks (GNNs) are trained on retrieved knowledge from external knowledge bases, aiming to mitigate the problem of lacking domain-specific knowledge. However, incorporating additional modules: 1) would need retraining additional modules when encountering novel domains; 2) would become a bottleneck since LLMs' strong abilities are not fully utilized for retrieval. In this paper, we propose a paradigm, termed Knowledge Solver (KSL), to teach LLMs to search for essential knowledge from external knowledge bases by harnessing their own strong generalizability. Specifically, we design a simple yet effective prompt to transform retrieval into a multi-hop decision sequence, which empowers LLMs with searching knowledge ability in zero-shot manner. Additionally, KSL is able to provide complete retrieval paths and therefore increase explainability of LLMs' reasoning processes. We conduct experiments on three datasets: CommonsenseQA, OpenbookQA, and MedQA-USMLE, and found that our approach improves LLM baseline performance by a relatively large margin.