Daily Papers

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.

Recently, Large Language Models (LLMs) have emerged as an alternative to training task-specific dialog agents, due to their broad reasoning capabilities and performance in zero-shot learning scenarios. However, many LLM-based dialog systems fall short in planning towards an overarching dialog goal and therefore cannot steer the conversation appropriately. Furthermore, these models struggle with hallucination, making them unsuitable for information access in sensitive domains, such as legal or medical domains, where correctness of information given to users is critical. The recently introduced task Conversational Tree Search (CTS) proposes the use of dialog graphs to avoid hallucination in sensitive domains, however, state-of-the-art agents are Reinforcement Learning (RL) based and require long training times, despite excelling at dialog strategy. This paper introduces a novel zero-shot method for controllable CTS agents, where LLMs guide the dialog planning through domain graphs by searching and pruning relevant graph nodes based on user interaction preferences. We show that these agents significantly outperform state-of-the-art CTS agents (p<0.0001; Barnard Exact test) in simulation. This generalizes to all available CTS domains. Finally, we perform user evaluation to test the agent's performance in the wild, showing that our policy significantly (p<0.05; Barnard Exact) improves task-success compared to the state-of-the-art RL-based CTS agent.

Existing frameworks for assessing robustness of large language models (LLMs) overly depend on specific benchmarks, increasing costs and failing to evaluate performance of LLMs in professional domains due to dataset limitations. This paper proposes a framework that systematically evaluates the robustness of LLMs under adversarial attack scenarios by leveraging knowledge graphs (KGs). Our framework generates original prompts from the triplets of knowledge graphs and creates adversarial prompts by poisoning, assessing the robustness of LLMs through the results of these adversarial attacks. We systematically evaluate the effectiveness of this framework and its modules. Experiments show that adversarial robustness of the ChatGPT family ranks as GPT-4-turbo > GPT-4o > GPT-3.5-turbo, and the robustness of large language models is influenced by the professional domains in which they operate.

Large Language Models (LLMs) have achieved exceptional capabilities in open generation across various domains, yet they encounter difficulties with tasks that require intensive knowledge. To address these challenges, methods for integrating knowledge have been developed, which augment LLMs with domain-specific knowledge graphs through external modules. These approaches, however, face data inefficiency issues as they necessitate the processing of both known and unknown knowledge for fine-tuning. Thus, our research focuses on a novel problem: efficiently integrating unknown knowledge into LLMs without unnecessary overlap of known knowledge. A risk of introducing new knowledge is the potential forgetting of existing knowledge. To mitigate this risk, we propose the innovative {\method} framework. This framework employs transformer internal states to determine when to enrich LLM outputs with additional information, effectively preventing knowledge forgetting. Performance evaluations using the UMLS-2.5k and MetaQA domain knowledge graphs reveal that {\method} not only successfully integrates new knowledge but also outperforms state-of-the-art baselines, reducing knowledge forgetting by 9\% and 6\%, respectively.

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.

Recently, the development of large language models (LLMs) has attracted wide attention in academia and industry. Deploying LLMs to real scenarios is one of the key directions in the current Internet industry. In this paper, we present a novel pipeline to apply LLMs for domain-specific question answering (QA) that incorporates domain knowledge graphs (KGs), addressing an important direction of LLM application. As a real-world application, the content generated by LLMs should be user-friendly to serve the customers. Additionally, the model needs to utilize domain knowledge properly to generate reliable answers. These two issues are the two major difficulties in the LLM application as vanilla fine-tuning can not adequately address them. We think both requirements can be unified as the model preference problem that needs to align with humans to achieve practical application. Thus, we introduce Knowledgeable Preference AlignmenT (KnowPAT), which constructs two kinds of preference set called style preference set and knowledge preference set respectively to tackle the two issues. Besides, we design a new alignment objective to align the LLM preference with human preference, aiming to train a better LLM for real-scenario domain-specific QA to generate reliable and user-friendly answers. Adequate experiments and comprehensive with 15 baseline methods demonstrate that our KnowPAT is an outperforming pipeline for real-scenario domain-specific QA with LLMs. Our code is open-source at https://github.com/zjukg/KnowPAT.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

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.

Dependency graph, as a heterogeneous graph representing the intrinsic relationships between different pairs of system entities, is essential to many data analysis applications, such as root cause diagnosis, intrusion detection, etc. Given a well-trained dependency graph from a source domain and an immature dependency graph from a target domain, how can we extract the entity and dependency knowledge from the source to enhance the target? One way is to directly apply a mature dependency graph learned from a source domain to the target domain. But due to the domain variety problem, directly using the source dependency graph often can not achieve good performance. Traditional transfer learning methods mainly focus on numerical data and are not applicable. In this paper, we propose ACRET, a knowledge transfer based model for accelerating dependency graph learning from heterogeneous categorical event streams. In particular, we first propose an entity estimation model to filter out irrelevant entities from the source domain based on entity embedding and manifold learning. Only the entities with statistically high correlations are transferred to the target domain. On the surviving entities, we propose a dependency construction model for constructing the unbiased dependency relationships by solving a two-constraint optimization problem. The experimental results on synthetic and real-world datasets demonstrate the effectiveness and efficiency of ACRET. We also apply ACRET to a real enterprise security system for intrusion detection. Our method is able to achieve superior detection performance at least 20 days lead lag time in advance with more than 70% accuracy.

Model editing aims to enhance the accuracy and reliability of large language models (LLMs) by efficiently adjusting their internal parameters. Currently, most LLM editing datasets are confined to narrow knowledge domains and cover a limited range of editing evaluation. They often overlook the broad scope of editing demands and the diversity of ripple effects resulting from edits. In this context, we introduce UniEdit, a unified benchmark for LLM editing grounded in open-domain knowledge. First, we construct editing samples by selecting entities from 25 common domains across five major categories, utilizing the extensive triple knowledge available in open-domain knowledge graphs to ensure comprehensive coverage of the knowledge domains. To address the issues of generality and locality in editing, we design an Neighborhood Multi-hop Chain Sampling (NMCS) algorithm to sample subgraphs based on a given knowledge piece to entail comprehensive ripple effects to evaluate. Finally, we employ proprietary LLMs to convert the sampled knowledge subgraphs into natural language text, guaranteeing grammatical accuracy and syntactical diversity. Extensive statistical analysis confirms the scale, comprehensiveness, and diversity of our UniEdit benchmark. We conduct comprehensive experiments across multiple LLMs and editors, analyzing their performance to highlight strengths and weaknesses in editing across open knowledge domains and various evaluation criteria, thereby offering valuable insights for future research endeavors.

The extraction of aspect terms is a critical step in fine-grained sentiment analysis of text. Existing approaches for this task have yielded impressive results when the training and testing data are from the same domain. However, these methods show a drastic decrease in performance when applied to cross-domain settings where the domain of the testing data differs from that of the training data. To address this lack of extensibility and robustness, we propose a novel approach for automatically constructing domain-specific knowledge graphs that contain information relevant to the identification of aspect terms. We introduce a methodology for injecting information from these knowledge graphs into Transformer models, including two alternative mechanisms for knowledge insertion: via query enrichment and via manipulation of attention patterns. We demonstrate state-of-the-art performance on benchmark datasets for cross-domain aspect term extraction using our approach and investigate how the amount of external knowledge available to the Transformer impacts model performance.

Current general-purpose large language models (LLMs) commonly exhibit knowledge hallucination and insufficient domain-specific adaptability in domain-specific tasks, limiting their effectiveness in specialized question answering scenarios. Retrieval-augmented generation (RAG) effectively tackles these challenges by integrating external knowledge to enhance accuracy and relevance. However, traditional RAG still faces limitations in domain knowledge accuracy and context modeling.To enhance domain-specific question answering performance, this work focuses on a graph-based RAG framework, emphasizing the critical role of knowledge graph quality during the generation process. We propose DSRAG (Domain-Specific RAG), a multimodal knowledge graph-driven retrieval-augmented generation framework designed for domain-specific applications. Our approach leverages domain-specific documents as the primary knowledge source, integrating heterogeneous information such as text, images, and tables to construct a multimodal knowledge graph covering both conceptual and instance layers. Building on this foundation, we introduce semantic pruning and structured subgraph retrieval mechanisms, combining knowledge graph context and vector retrieval results to guide the language model towards producing more reliable responses. Evaluations using the Langfuse multidimensional scoring mechanism show that our method excels in domain-specific question answering, validating the efficacy of integrating multimodal knowledge graphs with retrieval-augmented generation.

Graphs are able to model interconnected entities in many online services, supporting a wide range of applications on the Web. This raises an important question: How can we train a graph foundational model on multiple source domains and adapt to an unseen target domain? A major obstacle is that graphs from different domains often exhibit divergent characteristics. Some studies leverage large language models to align multiple domains based on textual descriptions associated with the graphs, limiting their applicability to text-attributed graphs. For text-free graphs, a few recent works attempt to align different feature distributions across domains, while generally neglecting structural differences. In this work, we propose a novel Structure Alignment framework for text-free Multi-domain Graph Pre-Training and cross-domain adaptation (SAMGPT). It is designed to learn multi-domain knowledge from graphs originating in multiple source domains, which can then be adapted to address applications in an unseen target domain. Specifically, we introduce a set of structure tokens to harmonize structure-based aggregation across source domains during the pre-training phase. Next, for cross-domain adaptation, we design dual prompts, namely, holistic prompts and specific prompts, which adapt unified multi-domain structural knowledge and fine-grained, domain-specific information, respectively, to a target domain. Finally, we conduct comprehensive experiments on seven public datasets to evaluate and analyze the effectiveness of SAMGPT.

AI coding assistants like GitHub Copilot are rapidly transforming software development, but their safety remains deeply uncertain-especially in high-stakes domains like cybersecurity. Current red-teaming tools often rely on fixed benchmarks or unrealistic prompts, missing many real-world vulnerabilities. We present ASTRA, an automated agent system designed to systematically uncover safety flaws in AI-driven code generation and security guidance systems. ASTRA works in three stages: (1) it builds structured domain-specific knowledge graphs that model complex software tasks and known weaknesses; (2) it performs online vulnerability exploration of each target model by adaptively probing both its input space, i.e., the spatial exploration, and its reasoning processes, i.e., the temporal exploration, guided by the knowledge graphs; and (3) it generates high-quality violation-inducing cases to improve model alignment. Unlike prior methods, ASTRA focuses on realistic inputs-requests that developers might actually ask-and uses both offline abstraction guided domain modeling and online domain knowledge graph adaptation to surface corner-case vulnerabilities. Across two major evaluation domains, ASTRA finds 11-66% more issues than existing techniques and produces test cases that lead to 17% more effective alignment training, showing its practical value for building safer AI systems.

Adapting named entity recognition (NER) methods to new domains poses significant challenges. We introduce RapidNER, a framework designed for the rapid deployment of NER systems through efficient dataset construction. RapidNER operates through three key steps: (1) extracting domain-specific sub-graphs and triples from a general knowledge graph, (2) collecting and leveraging texts from various sources to build the NERsocial dataset, which focuses on entities typical in human-robot interaction, and (3) implementing an annotation scheme using Elasticsearch (ES) to enhance efficiency. NERsocial, validated by human annotators, includes six entity types, 153K tokens, and 99.4K sentences, demonstrating RapidNER's capability to expedite dataset creation.

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in https://github.com/ritaranx/ClinGen.

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.

Foundation models like ChatGPT and GPT-4 have revolutionized artificial intelligence, exhibiting remarkable abilities to generalize across a wide array of tasks and applications beyond their initial training objectives. However, graph learning has predominantly focused on single-graph models, tailored to specific tasks or datasets, lacking the ability to transfer learned knowledge to different domains. This limitation stems from the inherent complexity and diversity of graph structures, along with the different feature and label spaces specific to graph data. In this paper, we recognize text as an effective unifying medium and employ Text-Attributed Graphs (TAGs) to leverage this potential. We present our UniGraph framework, designed to learn a foundation model for TAGs, which is capable of generalizing to unseen graphs and tasks across diverse domains. Unlike single-graph models that use pre-computed node features of varying dimensions as input, our approach leverages textual features for unifying node representations, even for graphs such as molecular graphs that do not naturally have textual features. We propose a novel cascaded architecture of Language Models (LMs) and Graph Neural Networks (GNNs) as backbone networks. Additionally, we propose the first pre-training algorithm specifically designed for large-scale self-supervised learning on TAGs, based on Masked Graph Modeling. We introduce graph instruction tuning using Large Language Models (LLMs) to enable zero-shot prediction ability. Our comprehensive experiments across various graph learning tasks and domains demonstrate the model's effectiveness in self-supervised representation learning on unseen graphs, few-shot in-context transfer, and zero-shot transfer, even surpassing or matching the performance of GNNs that have undergone supervised training on target datasets.

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.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

This work proposes DyExpert, a dynamic graph model for cross-domain link prediction. It can explicitly model historical evolving processes to learn the evolution pattern of a specific downstream graph and subsequently make pattern-specific link predictions. DyExpert adopts a decode-only transformer and is capable of efficiently parallel training and inference by conditioned link generation that integrates both evolution modeling and link prediction. DyExpert is trained by extensive dynamic graphs across diverse domains, comprising 6M dynamic edges. Extensive experiments on eight untrained graphs demonstrate that DyExpert achieves state-of-the-art performance in cross-domain link prediction. Compared to the advanced baseline under the same setting, DyExpert achieves an average of 11.40% improvement Average Precision across eight graphs. More impressive, it surpasses the fully supervised performance of 8 advanced baselines on 6 untrained graphs.

Graph neural networks (GNNs) have achieved impressive performance in graph domain adaptation. However, extensive source graphs could be unavailable in real-world scenarios due to privacy and storage concerns. To this end, we investigate an underexplored yet practical problem of source-free graph domain adaptation, which transfers knowledge from source models instead of source graphs to a target domain. To solve this problem, we introduce a novel GNN-based approach called Rank and Align (RNA), which ranks graph similarities with spectral seriation for robust semantics learning, and aligns inharmonic graphs with harmonic graphs which close to the source domain for subgraph extraction. In particular, to overcome label scarcity, we employ the spectral seriation algorithm to infer the robust pairwise rankings, which can guide semantic learning using a similarity learning objective. To depict distribution shifts, we utilize spectral clustering and the silhouette coefficient to detect harmonic graphs, which the source model can easily classify. To reduce potential domain discrepancy, we extract domain-invariant subgraphs from inharmonic graphs by an adversarial edge sampling process, which guides the invariant learning of GNNs. Extensive experiments on several benchmark datasets demonstrate the effectiveness of our proposed RNA.

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.

Graph domain adaptation has emerged as a promising approach to facilitate knowledge transfer across different domains. Recently, numerous models have been proposed to enhance their generalization capabilities in this field. However, there is still no unified library that brings together existing techniques and simplifies their implementation. To fill this gap, we introduce PyGDA, an open-source Python library tailored for graph domain adaptation. As the first comprehensive library in this area, PyGDA covers more than 20 widely used graph domain adaptation methods together with different types of graph datasets. Specifically, PyGDA offers modular components, enabling users to seamlessly build custom models with a variety of commonly used utility functions. To handle large-scale graphs, PyGDA includes support for features such as sampling and mini-batch processing, ensuring efficient computation. In addition, PyGDA also includes comprehensive performance benchmarks and well-documented user-friendly API for both researchers and practitioners. To foster convenient accessibility, PyGDA is released under the MIT license at https://github.com/pygda-team/pygda, and the API documentation is https://pygda.readthedocs.io/en/stable/.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

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.

Distribution shift presents a significant challenge in machine learning, where models often underperform during the test stage when faced with a different distribution than the one they were trained on. This paper focuses on domain shifts, which occur when the model is applied to new domains that are different from the ones it was trained on, and propose a new approach called D^3G. Unlike previous methods that aim to learn a single model that is domain invariant, D^3G leverages domain similarities based on domain metadata to learn domain-specific models. Concretely, D^3G learns a set of training-domain-specific functions during the training stage and reweights them based on domain relations during the test stage. These domain relations can be directly obtained and learned from domain metadata. Under mild assumptions, we theoretically prove that using domain relations to reweight training-domain-specific functions achieves stronger out-of-domain generalization compared to the conventional averaging approach. Empirically, we evaluate the effectiveness of D^3G using real-world datasets for tasks such as temperature regression, land use classification, and molecule-protein binding affinity prediction. Our results show that D^3G consistently outperforms state-of-the-art methods.

The success of deep learning notoriously requires larger amounts of costly annotated data. This has led to the development of self-supervised learning (SSL) that aims to alleviate this limitation by creating domain specific pretext tasks on unlabeled data. Simultaneously, there are increasing interests in generalizing deep learning to the graph domain in the form of graph neural networks (GNNs). GNNs can naturally utilize unlabeled nodes through the simple neighborhood aggregation that is unable to thoroughly make use of unlabeled nodes. Thus, we seek to harness SSL for GNNs to fully exploit the unlabeled data. Different from data instances in the image and text domains, nodes in graphs present unique structure information and they are inherently linked indicating not independent and identically distributed (or i.i.d.). Such complexity is a double-edged sword for SSL on graphs. On the one hand, it determines that it is challenging to adopt solutions from the image and text domains to graphs and dedicated efforts are desired. On the other hand, it provides rich information that enables us to build SSL from a variety of perspectives. Thus, in this paper, we first deepen our understandings on when, why, and which strategies of SSL work with GNNs by empirically studying numerous basic SSL pretext tasks on graphs. Inspired by deep insights from the empirical studies, we propose a new direction SelfTask to build advanced pretext tasks that are able to achieve state-of-the-art performance on various real-world datasets. The specific experimental settings to reproduce our results can be found in https://github.com/ChandlerBang/SelfTask-GNN.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Knowledge Graphs (KG) provide us with a structured, flexible, transparent, cross-system, and collaborative way of organizing our knowledge and data across various domains in society and industrial as well as scientific disciplines. KGs surpass any other form of representation in terms of effectiveness. However, Knowledge Graph Engineering (KGE) requires in-depth experiences of graph structures, web technologies, existing models and vocabularies, rule sets, logic, as well as best practices. It also demands a significant amount of work. Considering the advancements in large language models (LLMs) and their interfaces and applications in recent years, we have conducted comprehensive experiments with ChatGPT to explore its potential in supporting KGE. In this paper, we present a selection of these experiments and their results to demonstrate how ChatGPT can assist us in the development and management of KGs.

Although graph neural networks (GNNs) have achieved impressive achievements in graph classification, they often need abundant task-specific labels, which could be extensively costly to acquire. A credible solution is to explore additional labeled graphs to enhance unsupervised learning on the target domain. However, how to apply GNNs to domain adaptation remains unsolved owing to the insufficient exploration of graph topology and the significant domain discrepancy. In this paper, we propose Coupled Contrastive Graph Representation Learning (CoCo), which extracts the topological information from coupled learning branches and reduces the domain discrepancy with coupled contrastive learning. CoCo contains a graph convolutional network branch and a hierarchical graph kernel network branch, which explore graph topology in implicit and explicit manners. Besides, we incorporate coupled branches into a holistic multi-view contrastive learning framework, which not only incorporates graph representations learned from complementary views for enhanced understanding, but also encourages the similarity between cross-domain example pairs with the same semantics for domain alignment. Extensive experiments on popular datasets show that our CoCo outperforms these competing baselines in different settings generally.

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

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

Open-domain question answering aims at solving the task of locating the answers to user-generated questions in massive collections of documents. There are two families of solutions available: retriever-readers, and knowledge-graph-based approaches. A retriever-reader usually first uses information retrieval methods like TF-IDF to locate some documents or paragraphs that are likely to be relevant to the question, and then feeds the retrieved text to a neural network reader to extract the answer. Alternatively, knowledge graphs can be constructed from the corpus and be queried against to answer user questions. We propose a novel algorithm with a reader-retriever structure that differs from both families. Our reader-retriever first uses an offline reader to read the corpus and generate collections of all answerable questions associated with their answers, and then uses an online retriever to respond to user queries by searching the pre-constructed question spaces for answers that are most likely to be asked in the given way. We further combine retriever-reader and reader-retriever results into one single answer by examining the consistency between the two components. We claim that our algorithm solves some bottlenecks in existing work, and demonstrate that it achieves superior accuracy on real-world datasets.

The computer vision domain has greatly benefited from an abundance of data across many modalities to improve on various visual tasks. Recently, there has been a lot of focus on self-supervised pre-training methods through Masked Autoencoders (MAE) he2022masked,bachmann2022multimae, usually used as a first step before optimizing for a downstream task, such as classification or regression. This is very useful as it doesn't require any manually labeled data. In this work, we introduce Probabilistic Hyper-Graphs using Masked Autoencoders (PHG-MAE): a novel model that unifies the classical work on neural graphs leordeanu2021semi with the modern approach of masked autoencoders under a common theoretical framework. Through random masking of entire modalities, not just patches, the model samples from the distribution of hyper-edges on each forward pass. Additionally, the model adapts the standard MAE algorithm by combining pre-training and fine-tuning into a single training loop. Moreover, our approach enables the creation of inference-time ensembles which, through aggregation, boost the final prediction performance and consistency. Lastly, we show that we can apply knowledge distillation on top of the ensembles with little loss in performance, even with models that have fewer than 1M parameters. While our work mostly focuses on outdoor UAV scenes that contain multiple world interpretations and modalities, the same steps can be followed in other similar domains, such as autonomous driving or indoor robotics. In order to streamline the process of integrating external pre-trained experts for computer vision multi-modal multi-task learning (MTL) scenarios, we developed a data-pipeline software. Using this tool, we have created and released a fully-automated extension of the Dronescapes dataset. All the technical details, code and reproduction steps are publicly released.

Cross-domain NER is a practical yet challenging problem since the data scarcity in the real-world scenario. A common practice is first to learn a NER model in a rich-resource general domain and then adapt the model to specific domains. Due to the mismatch problem between entity types across domains, the wide knowledge in the general domain can not effectively transfer to the target domain NER model. To this end, we model the label relationship as a probability distribution and construct label graphs in both source and target label spaces. To enhance the contextual representation with label structures, we fuse the label graph into the word embedding output by BERT. By representing label relationships as graphs, we formulate cross-domain NER as a graph matching problem. Furthermore, the proposed method has good applicability with pre-training methods and is potentially capable of other cross-domain prediction tasks. Empirical results on four datasets show that our method outperforms a series of transfer learning, multi-task learning, and few-shot learning methods.

In this work, we benchmark various graph-based retrieval-augmented generation (RAG) systems across a broad spectrum of query types, including OLTP-style (fact-based) and OLAP-style (thematic) queries, to address the complex demands of open-domain question answering (QA). Traditional RAG methods often fall short in handling nuanced, multi-document synthesis tasks. By structuring knowledge as graphs, we can facilitate the retrieval of context that captures greater semantic depth and enhances language model operations. We explore graph-based RAG methodologies and introduce TREX, a novel, cost-effective alternative that combines graph-based and vector-based retrieval techniques. Our benchmarking across four diverse datasets highlights the strengths of different RAG methodologies, demonstrates TREX's ability to handle multiple open-domain QA types, and reveals the limitations of current evaluation methods. In a real-world technical support case study, we demonstrate how TREX solutions can surpass conventional vector-based RAG in efficiently synthesizing data from heterogeneous sources. Our findings underscore the potential of augmenting large language models with advanced retrieval and orchestration capabilities, advancing scalable, graph-based AI solutions.

A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of downstream DL models for various NLP tasks. Many existing word embeddings techniques capture the context of words based on word co-occurrence in documents and text; however, they often cannot capture broader domain-specific relationships between concepts that may be crucial for the NLP task at hand. In this paper, we propose a method to integrate external knowledge from medical terminology ontologies into the context captured by word embeddings. Specifically, we use a medical knowledge graph, such as the unified medical language system (UMLS), to find connections between clinical terms in cancer pathology reports. This approach aims to minimize the distance between connected clinical concepts. We evaluate the proposed approach using a Multitask Convolutional Neural Network (MT-CNN) to extract six cancer characteristics -- site, subsite, laterality, behavior, histology, and grade -- from a dataset of ~900K cancer pathology reports. The results show that the MT-CNN model which uses our domain informed embeddings outperforms the same MT-CNN using standard word2vec embeddings across all tasks, with an improvement in the overall micro- and macro-F1 scores by 4.97\%and 22.5\%, respectively.

The financial domain poses unique challenges for knowledge graph (KG) construction at scale due to the complexity and regulatory nature of financial documents. Despite the critical importance of structured financial knowledge, the field lacks large-scale, open-source datasets capturing rich semantic relationships from corporate disclosures. We introduce an open-source, large-scale financial knowledge graph dataset built from the latest annual SEC 10-K filings of all S and P 100 companies - a comprehensive resource designed to catalyze research in financial AI. We propose a robust and generalizable knowledge graph (KG) construction framework that integrates intelligent document parsing, table-aware chunking, and schema-guided iterative extraction with a reflection-driven feedback loop. Our system incorporates a comprehensive evaluation pipeline, combining rule-based checks, statistical validation, and LLM-as-a-Judge assessments to holistically measure extraction quality. We support three extraction modes - single-pass, multi-pass, and reflection-agent-based - allowing flexible trade-offs between efficiency, accuracy, and reliability based on user requirements. Empirical evaluations demonstrate that the reflection-agent-based mode consistently achieves the best balance, attaining a 64.8 percent compliance score against all rule-based policies (CheckRules) and outperforming baseline methods (single-pass and multi-pass) across key metrics such as precision, comprehensiveness, and relevance in LLM-guided evaluations.

Despite significant popularity, Large-language Models (LLMs) require explicit, contextual facts to support domain-specific knowledge-intensive tasks in the design process. The applications built using LLMs should hence adopt Retrieval-Augmented Generation (RAG) to better suit the design process. In this article, we present a data-driven method to identify explicit facts from patent documents that provide standard descriptions of over 8 million artefacts. In our method, we train roBERTa Transformer-based sequence classification models using our dataset of 44,227 sentences and facts. Upon classifying tokens in a sentence as entities or relationships, our method uses another classifier to identify specific relationship tokens for a given pair of entities so that explicit facts of the form head entity :: relationship :: tail entity are identified. In the benchmark approaches for constructing facts, we use linear classifiers and Graph Neural Networks (GNNs) both incorporating BERT Transformer-based token embeddings to predict associations among the entities and relationships. We apply our method to 4,870 fan system related patents and populate a knowledge base of around 3 million facts. Upon retrieving the facts representing generalisable domain knowledge and the knowledge of specific subsystems and issues, we demonstrate how these facts contextualise LLMs for generating text that is more relevant to the design process.

Language models traditionally used for cross-domain generalization have recently demonstrated task-specific reasoning. However, their top-down training approach on general corpora is insufficient for acquiring abstractions needed for deep domain expertise. This may require a bottom-up approach that acquires expertise by learning to compose simple domain concepts into more complex ones. A knowledge graph (KG) provides this compositional structure, where domain primitives are represented as head-relation-tail edges and their paths encode higher-level concepts. We present a task generation pipeline that synthesizes tasks directly from KG primitives, enabling models to acquire and compose them for reasoning. We fine-tune language models on the resultant KG-grounded curriculum to demonstrate domain-specific superintelligence. While broadly applicable, we validate our approach in medicine, where reliable KGs exist. Using a medical KG, we curate 24,000 reasoning tasks paired with thinking traces derived from diverse medical primitives. We fine-tune the QwQ-32B model on this curriculum to obtain QwQ-Med-3 that takes a step towards medical superintelligence. We also introduce ICD-Bench, an evaluation suite to quantify reasoning abilities across 15 medical domains. Our experiments demonstrate that QwQ-Med-3 significantly outperforms state-of-the-art reasoning models on ICD-Bench categories. Further analysis reveals that QwQ-Med-3 utilizes acquired primitives to widen the performance gap on the hardest tasks of ICD-Bench. Finally, evaluation on medical question-answer benchmarks shows that QwQ-Med-3 transfers acquired expertise to enhance the base model's performance. While the industry's approach to artificial general intelligence (AGI) emphasizes broad expertise, we envision a future in which AGI emerges from the composable interaction of efficient domain-specific superintelligent agents.

In real-world scenarios, most of the data obtained from information retrieval (IR) system is unstructured. Converting natural language sentences into structured Knowledge Graphs (KGs) remains a critical challenge. The quality of constructed KGs may also impact the performance of some KG-dependent domains like GraphRAG systems and recommendation systems. Recently, Large Language Models (LLMs) have demonstrated impressive capabilities in addressing a wide range of natural language processing tasks. However, there are still challenges when utilizing LLMs to address the task of generating structured KGs. And we have identified three limitations with respect to existing KG construction methods. (1)There is a large amount of information and excessive noise in real-world documents, which could result in extracting messy information. (2)Native LLMs struggle to effectively extract accuracy knowledge from some domain-specific documents. (3)Hallucinations phenomenon cannot be overlooked when utilizing LLMs directly as an unsupervised method for constructing KGs. In this paper, we propose GraphJudger, a knowledge graph construction framework to address the aforementioned challenges. We introduce three innovative modules in our method, which are entity-centric iterative text denoising, knowledge aware instruction tuning and graph judgement, respectively. We seek to utilize the capacity of LLMs to function as a graph judger, a capability superior to their role only as a predictor for KG construction problems. Experiments conducted on two general text-graph pair datasets and one domain-specific text-graph pair dataset show superior performances compared to baseline methods. The code of our proposed method is available at https://github.com/hhy-huang/GraphJudger.

Extraction and interpretation of intricate information from unstructured text data arising in financial applications, such as earnings call transcripts, present substantial challenges to large language models (LLMs) even using the current best practices to use Retrieval Augmented Generation (RAG) (referred to as VectorRAG techniques which utilize vector databases for information retrieval) due to challenges such as domain specific terminology and complex formats of the documents. We introduce a novel approach based on a combination, called HybridRAG, of the Knowledge Graphs (KGs) based RAG techniques (called GraphRAG) and VectorRAG techniques to enhance question-answer (Q&A) systems for information extraction from financial documents that is shown to be capable of generating accurate and contextually relevant answers. Using experiments on a set of financial earning call transcripts documents which come in the form of Q&A format, and hence provide a natural set of pairs of ground-truth Q&As, we show that HybridRAG which retrieves context from both vector database and KG outperforms both traditional VectorRAG and GraphRAG individually when evaluated at both the retrieval and generation stages in terms of retrieval accuracy and answer generation. The proposed technique has applications beyond the financial domain

The synergy between symbolic knowledge, often represented by Knowledge Graphs (KGs), and the generative capabilities of neural networks is central to advancing neurosymbolic AI. A primary bottleneck in realizing this potential is the difficulty of automating KG construction, which faces challenges related to output reliability, consistency, and verifiability. These issues can manifest as structural inconsistencies within the generated graphs, such as the formation of disconnected isolated islands of data or the inaccurate conflation of abstract classes with specific instances. To address these challenges, we propose HyDRA, a Hybrid-Driven Reasoning Architecture designed for verifiable KG automation. Given a domain or an initial set of documents, HyDRA first constructs an ontology via a panel of collaborative neurosymbolic agents. These agents collaboratively agree on a set of competency questions (CQs) that define the scope and requirements the ontology must be able to answer. Given these CQs, we build an ontology graph that subsequently guides the automated extraction of triplets for KG generation from arbitrary documents. Inspired by design-by-contracts (DbC) principles, our method leverages verifiable contracts as the primary control mechanism to steer the generative process of Large Language Models (LLMs). To verify the output of our approach, we extend beyond standard benchmarks and propose an evaluation framework that assesses the functional correctness of the resulting KG by leveraging symbolic verifications as described by the neurosymbolic AI framework, SymbolicAI. This work contributes a hybrid-driven architecture for improving the reliability of automated KG construction and the exploration of evaluation methods for measuring the functional integrity of its output. The code is publicly available.

Existing foundation models, such as CLIP, aim to learn a unified embedding space for multimodal data, enabling a wide range of downstream web-based applications like search, recommendation, and content classification. However, these models often overlook the inherent graph structures in multimodal datasets, where entities and their relationships are crucial. Multimodal graphs (MMGs) represent such graphs where each node is associated with features from different modalities, while the edges capture the relationships between these entities. On the other hand, existing graph foundation models primarily focus on text-attributed graphs (TAGs) and are not designed to handle the complexities of MMGs. To address these limitations, we propose UniGraph2, a novel cross-domain graph foundation model that enables general representation learning on MMGs, providing a unified embedding space. UniGraph2 employs modality-specific encoders alongside a graph neural network (GNN) to learn a unified low-dimensional embedding space that captures both the multimodal information and the underlying graph structure. We propose a new cross-domain multi-graph pre-training algorithm at scale to ensure effective transfer learning across diverse graph domains and modalities. Additionally, we adopt a Mixture of Experts (MoE) component to align features from different domains and modalities, ensuring coherent and robust embeddings that unify the information across modalities. Extensive experiments on a variety of multimodal graph tasks demonstrate that UniGraph2 significantly outperforms state-of-the-art models in tasks such as representation learning, transfer learning, and multimodal generative tasks, offering a scalable and flexible solution for learning on MMGs.

Dialogue benchmarks are crucial in training and evaluating chatbots engaging in domain-specific conversations. Knowledge graphs (KGs) represent semantically rich and well-organized data spanning various domains, such as DBLP, DBpedia, and YAGO. Traditionally, dialogue benchmarks have been manually created from documents, neglecting the potential of KGs in automating this process. Some question-answering benchmarks are automatically generated using extensive preprocessing from KGs, but they do not support dialogue generation. This paper introduces Chatty-Gen, a novel multi-stage retrieval-augmented generation platform for automatically generating high-quality dialogue benchmarks tailored to a specific domain using a KG. Chatty-Gen decomposes the generation process into manageable stages and uses assertion rules for automatic validation between stages. Our approach enables control over intermediate results to prevent time-consuming restarts due to hallucinations. It also reduces reliance on costly and more powerful commercial LLMs. Chatty-Gen eliminates upfront processing of the entire KG using efficient query-based retrieval to find representative subgraphs based on the dialogue context. Our experiments with several real and large KGs demonstrate that Chatty-Gen significantly outperforms state-of-the-art systems and ensures consistent model and system performance across multiple LLMs of diverse capabilities, such as GPT-4o, Gemini 1.5, Llama 3, and Mistral.

Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.

Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs.

In current youth-care programs, children with needs (mental health, family issues, learning disabilities, and autism) receive support from youth and family experts as one-to-one assistance at schools or hospitals. Occasionally, social robots have featured in such settings as support roles in a one-to-one interaction with the child. In this paper, we suggest the development of a symbiotic framework for real-time Emotional Support (ES) with social robots Knowledge Graphs (KG). By augmenting a domain-specific corpus from the literature on ES for children (between the age of 8 and 12) and providing scenario-driven context including the history of events, we suggest developing an experimental knowledge-aware ES framework. The framework both guides the social robot in providing ES statements to the child and assists the expert in tracking and interpreting the child's emotional state and related events over time.

Domain-specific QA systems require not just generative fluency but high factual accuracy grounded in structured expert knowledge. While recent Retrieval-Augmented Generation (RAG) frameworks improve context recall, they struggle with integrating heterogeneous data and maintaining reasoning consistency. To address these challenges, we propose DO-RAG, a scalable and customizable hybrid QA framework that integrates multi-level knowledge graph construction with semantic vector retrieval. Our system employs a novel agentic chain-of-thought architecture to extract structured relationships from unstructured, multimodal documents, constructing dynamic knowledge graphs that enhance retrieval precision. At query time, DO-RAG fuses graph and vector retrieval results to generate context-aware responses, followed by hallucination mitigation via grounded refinement. Experimental evaluations in the database and electrical domains show near-perfect recall and over 94% answer relevancy, with DO-RAG outperforming baseline frameworks by up to 33.38%. By combining traceability, adaptability, and performance efficiency, DO-RAG offers a reliable foundation for multi-domain, high-precision QA at scale.

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

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

While the capabilities of generative models heavily improved in different domains (images, text, graphs, molecules, etc.), their evaluation metrics largely remain based on simplified quantities or manual inspection with limited practicality. To this end, we propose a framework for Multi-level Performance Evaluation of Generative mOdels (MPEGO), which could be employed across different domains. MPEGO aims to quantify generation performance hierarchically, starting from a sub-feature-based low-level evaluation to a global features-based high-level evaluation. MPEGO offers great customizability as the employed features are entirely user-driven and can thus be highly domain/problem-specific while being arbitrarily complex (e.g., outcomes of experimental procedures). We validate MPEGO using multiple generative models across several datasets from the material discovery domain. An ablation study is conducted to study the plausibility of intermediate steps in MPEGO. Results demonstrate that MPEGO provides a flexible, user-driven, and multi-level evaluation framework, with practical insights on the generation quality. The framework, source code, and experiments will be available at https://github.com/GT4SD/mpego.

Replicating AI research is a crucial yet challenging task for large language model (LLM) agents. Existing approaches often struggle to generate executable code, primarily due to insufficient background knowledge and the limitations of retrieval-augmented generation (RAG) methods, which fail to capture latent technical details hidden in referenced papers. Furthermore, previous approaches tend to overlook valuable implementation-level code signals and lack structured knowledge representations that support multi-granular retrieval and reuse. To overcome these challenges, we propose Executable Knowledge Graphs (xKG), a modular and pluggable knowledge base that automatically integrates technical insights, code snippets, and domain-specific knowledge extracted from scientific literature. When integrated into three agent frameworks with two different LLMs, xKG shows substantial performance gains (10.9% with o3-mini) on PaperBench, demonstrating its effectiveness as a general and extensible solution for automated AI research replication. Code will released at https://github.com/zjunlp/xKG.

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: https://github.com/XiaoxinHe/Graph-ViT-MLPMixer.

In many real-world applications, graph-structured data used for training and testing have differences in distribution, such as in high energy physics (HEP) where simulation data used for training may not match real experiments. Graph domain adaptation (GDA) is a method used to address these differences. However, current GDA primarily works by aligning the distributions of node representations output by a single graph neural network encoder shared across the training and testing domains, which may often yield sub-optimal solutions. This work examines different impacts of distribution shifts caused by either graph structure or node attributes and identifies a new type of shift, named conditional structure shift (CSS), which current GDA approaches are provably sub-optimal to deal with. A novel approach, called structural reweighting (StruRW), is proposed to address this issue and is tested on synthetic graphs, four benchmark datasets, and a new application in HEP. StruRW has shown significant performance improvement over the baselines in the settings with large graph structure shifts, and reasonable performance improvement when node attribute shift dominates.

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

Enterprise applications of Large Language Models (LLMs) hold promise for question answering on enterprise SQL databases. However, the extent to which LLMs can accurately respond to enterprise questions in such databases remains unclear, given the absence of suitable Text-to-SQL benchmarks tailored to enterprise settings. Additionally, the potential of Knowledge Graphs (KGs) to enhance LLM-based question answering by providing business context is not well understood. This study aims to evaluate the accuracy of LLM-powered question answering systems in the context of enterprise questions and SQL databases, while also exploring the role of knowledge graphs in improving accuracy. To achieve this, we introduce a benchmark comprising an enterprise SQL schema in the insurance domain, a range of enterprise queries encompassing reporting to metrics, and a contextual layer incorporating an ontology and mappings that define a knowledge graph. Our primary finding reveals that question answering using GPT-4, with zero-shot prompts directly on SQL databases, achieves an accuracy of 16%. Notably, this accuracy increases to 54% when questions are posed over a Knowledge Graph representation of the enterprise SQL database. Therefore, investing in Knowledge Graph provides higher accuracy for LLM powered question answering systems.

The advancement of Large Language Models (LLMs) has led to significant improvements in various service domains, including search, recommendation, and chatbot applications. However, applying state-of-the-art (SOTA) research to industrial settings presents challenges, as it requires maintaining flexible conversational abilities while also strictly complying with service-specific constraints. This can be seen as two conflicting requirements due to the probabilistic nature of LLMs. In this paper, we propose our approach to addressing this challenge and detail the strategies we employed to overcome their inherent limitations in real-world applications. We conduct a practical case study of a conversational agent designed for the e-commerce domain, detailing our implementation workflow and optimizations. Our findings provide insights into bridging the gap between academic research and real-world application, introducing a framework for developing scalable, controllable, and reliable AI-driven agents.

Collections of probability distributions arise in a variety of applications ranging from user activity pattern analysis to brain connectomics. In practice these distributions can be defined over diverse domain types including finite intervals, circles, cylinders, spheres, other manifolds, and graphs. This paper introduces an approach for detecting differences between two collections of distributions over such general domains. To this end, we propose the intrinsic slicing construction that yields a novel class of Wasserstein distances on manifolds and graphs. These distances are Hilbert embeddable, allowing us to reduce the distribution collection comparison problem to a more familiar mean testing problem in a Hilbert space. We provide two testing procedures one based on resampling and another on combining p-values from coordinate-wise tests. Our experiments in various synthetic and real data settings show that the resulting tests are powerful and the p-values are well-calibrated.

The latest Deep Learning (DL) models for detection and classification have achieved an unprecedented performance over classical machine learning algorithms. However, DL models are black-box methods hard to debug, interpret, and certify. DL alone cannot provide explanations that can be validated by a non technical audience. In contrast, symbolic AI systems that convert concepts into rules or symbols -- such as knowledge graphs -- are easier to explain. However, they present lower generalisation and scaling capabilities. A very important challenge is to fuse DL representations with expert knowledge. One way to address this challenge, as well as the performance-explainability trade-off is by leveraging the best of both streams without obviating domain expert knowledge. We tackle such problem by considering the symbolic knowledge is expressed in form of a domain expert knowledge graph. We present the eXplainable Neural-symbolic learning (X-NeSyL) methodology, designed to learn both symbolic and deep representations, together with an explainability metric to assess the level of alignment of machine and human expert explanations. The ultimate objective is to fuse DL representations with expert domain knowledge during the learning process to serve as a sound basis for explainability. X-NeSyL methodology involves the concrete use of two notions of explanation at inference and training time respectively: 1) EXPLANet: Expert-aligned eXplainable Part-based cLAssifier NETwork Architecture, a compositional CNN that makes use of symbolic representations, and 2) SHAP-Backprop, an explainable AI-informed training procedure that guides the DL process to align with such symbolic representations in form of knowledge graphs. We showcase X-NeSyL methodology using MonuMAI dataset for monument facade image classification, and demonstrate that our approach improves explainability and performance.

There is growing interest in utilizing large language models (LLMs) as co-pilots for combinatorial optimization and constraint programming tasks across various problems. This paper aims to advance this line of research by introducing Text2Zinc}, a cross-domain dataset for capturing optimization and satisfaction problems specified in natural language text. Our work is distinguished from previous attempts by integrating both satisfaction and optimization problems within a unified dataset using a solver-agnostic modeling language. To achieve this, we leverage MiniZinc's solver-and-paradigm-agnostic modeling capabilities to formulate these problems. Using the Text2Zinc dataset, we conduct comprehensive baseline experiments to compare execution and solution accuracy across several methods, including off-the-shelf prompting strategies, chain-of-thought reasoning, and a compositional approach. Additionally, we explore the effectiveness of intermediary representations, specifically knowledge graphs. Our findings indicate that LLMs are not yet a push-button technology to model combinatorial problems from text. We hope that Text2Zinc serves as a valuable resource for researchers and practitioners to advance the field further.

The research of knowledge-driven conversational systems is largely limited due to the lack of dialog data which consist of multi-turn conversations on multiple topics and with knowledge annotations. In this paper, we propose a Chinese multi-domain knowledge-driven conversation dataset, KdConv, which grounds the topics in multi-turn conversations to knowledge graphs. Our corpus contains 4.5K conversations from three domains (film, music, and travel), and 86K utterances with an average turn number of 19.0. These conversations contain in-depth discussions on related topics and natural transition between multiple topics. To facilitate the following research on this corpus, we provide several benchmark models. Comparative results show that the models can be enhanced by introducing background knowledge, yet there is still a large space for leveraging knowledge to model multi-turn conversations for further research. Results also show that there are obvious performance differences between different domains, indicating that it is worth to further explore transfer learning and domain adaptation. The corpus and benchmark models are publicly available.

High-quality data plays a critical role in the pretraining and fine-tuning of large language models (LLMs), even determining their performance ceiling to some degree. Consequently, numerous data selection methods have been proposed to identify subsets of data that can effectively and efficiently enhance model performance. However, most of these methods focus on general data selection and tend to overlook the specific nuances of domain-related data. In this paper, we introduce MASS, a MAthematical data Selection framework using the Skill graph for pretraining LLMs in the mathematical reasoning domain. By taking into account the unique characteristics of mathematics and reasoning, we construct a skill graph that captures the mathematical skills and their interrelations from a reference dataset. This skill graph guides us in assigning quality scores to the target dataset, enabling us to select the top-ranked subset which is further used to pretrain LLMs. Experimental results demonstrate the efficiency and effectiveness of MASS across different model sizes (1B and 7B) and pretraining datasets (web data and synthetic data). Specifically, in terms of efficiency, models trained on subsets selected by MASS can achieve similar performance to models trained on the original datasets, with a significant reduction in the number of trained tokens - ranging from 50\% to 70\% fewer tokens. In terms of effectiveness, when trained on the same amount of tokens, models trained on the data selected by MASS outperform those trained on the original datasets by 3.3\% to 5.9\%. These results underscore the potential of MASS to improve both the efficiency and effectiveness of pretraining LLMs.

Knowledge Graph (KG)-augmented Large Language Models (LLMs) have recently propelled significant advances in complex reasoning tasks, thanks to their broad domain knowledge and contextual awareness. Unfortunately, current methods often assume KGs to be complete, which is impractical given the inherent limitations of KG construction and the potential loss of contextual cues when converting unstructured text into entity-relation triples. In response, this paper proposes the Triple Context Restoration and Query-driven Feedback (TCR-QF) framework, which reconstructs the textual context underlying each triple to mitigate information loss, while dynamically refining the KG structure by iteratively incorporating query-relevant missing knowledge. Experiments on five benchmark question-answering datasets substantiate the effectiveness of TCR-QF in KG and LLM integration, where itachieves a 29.1% improvement in Exact Match and a 15.5% improvement in F1 over its state-of-the-art GraphRAG competitors.

Multimodal Attributed Graphs (MAGs) are ubiquitous in real-world applications, encompassing extensive knowledge through multimodal attributes attached to nodes (e.g., texts and images) and topological structure representing node interactions. Despite its potential to advance diverse research fields like social networks and e-commerce, MAG representation learning (MAGRL) remains underexplored due to the lack of standardized datasets and evaluation frameworks. In this paper, we first propose MAGB, a comprehensive MAG benchmark dataset, featuring curated graphs from various domains with both textual and visual attributes. Based on MAGB dataset, we further systematically evaluate two mainstream MAGRL paradigms: GNN-as-Predictor, which integrates multimodal attributes via Graph Neural Networks (GNNs), and VLM-as-Predictor, which harnesses Vision Language Models (VLMs) for zero-shot reasoning. Extensive experiments on MAGB reveal following critical insights: (i) Modality significances fluctuate drastically with specific domain characteristics. (ii) Multimodal embeddings can elevate the performance ceiling of GNNs. However, intrinsic biases among modalities may impede effective training, particularly in low-data scenarios. (iii) VLMs are highly effective at generating multimodal embeddings that alleviate the imbalance between textual and visual attributes. These discoveries, which illuminate the synergy between multimodal attributes and graph topologies, contribute to reliable benchmarks, paving the way for future MAG research. The MAGB dataset and evaluation pipeline are publicly available at https://github.com/sktsherlock/MAGB.

Fair machine learning aims to prevent discrimination against individuals or sub-populations based on sensitive attributes such as gender and race. In recent years, causal inference methods have been increasingly used in fair machine learning to measure unfairness by causal effects. However, current methods assume that the true causal graph is given, which is often not true in real-world applications. To address this limitation, this paper proposes a framework for achieving causal fairness based on the notion of interventions when the true causal graph is partially known. The proposed approach involves modeling fair prediction using a Partially Directed Acyclic Graph (PDAG), specifically, a class of causal DAGs that can be learned from observational data combined with domain knowledge. The PDAG is used to measure causal fairness, and a constrained optimization problem is formulated to balance between fairness and accuracy. Results on both simulated and real-world datasets demonstrate the effectiveness of this method.

Pretrained language models (PLMs) for data-to-text (D2T) generation can use human-readable data labels such as column headings, keys, or relation names to generalize to out-of-domain examples. However, the models are well-known in producing semantically inaccurate outputs if these labels are ambiguous or incomplete, which is often the case in D2T datasets. In this paper, we expose this issue on the task of descibing a relation between two entities. For our experiments, we collect a novel dataset for verbalizing a diverse set of 1,522 unique relations from three large-scale knowledge graphs (Wikidata, DBPedia, YAGO). We find that although PLMs for D2T generation expectedly fail on unclear cases, models trained with a large variety of relation labels are surprisingly robust in verbalizing novel, unseen relations. We argue that using data with a diverse set of clear and meaningful labels is key to training D2T generation systems capable of generalizing to novel domains.

Cross-domain sentiment classification (CDSC) aims to use the transferable semantics learned from the source domain to predict the sentiment of reviews in the unlabeled target domain. Existing studies in this task attach more attention to the sequence modeling of sentences while largely ignoring the rich domain-invariant semantics embedded in graph structures (i.e., the part-of-speech tags and dependency relations). As an important aspect of exploring characteristics of language comprehension, adaptive graph representations have played an essential role in recent years. To this end, in the paper, we aim to explore the possibility of learning invariant semantic features from graph-like structures in CDSC. Specifically, we present Graph Adaptive Semantic Transfer (GAST) model, an adaptive syntactic graph embedding method that is able to learn domain-invariant semantics from both word sequences and syntactic graphs. More specifically, we first raise a POS-Transformer module to extract sequential semantic features from the word sequences as well as the part-of-speech tags. Then, we design a Hybrid Graph Attention (HGAT) module to generate syntax-based semantic features by considering the transferable dependency relations. Finally, we devise an Integrated aDaptive Strategy (IDS) to guide the joint learning process of both modules. Extensive experiments on four public datasets indicate that GAST achieves comparable effectiveness to a range of state-of-the-art models.

Knowledge graphs (KGs) provide structured, verifiable grounding for large language models (LLMs), but current LLM-based systems commonly use KGs as auxiliary structures for text retrieval, leaving their intrinsic quality underexplored. In this work, we propose Wikontic, a multi-stage pipeline that constructs KGs from open-domain text by extracting candidate triplets with qualifiers, enforcing Wikidata-based type and relation constraints, and normalizing entities to reduce duplication. The resulting KGs are compact, ontology-consistent, and well-connected; on MuSiQue, the correct answer entity appears in 96% of generated triplets. On HotpotQA, our triplets-only setup achieves 76.0 F1, and on MuSiQue 59.8 F1, matching or surpassing several retrieval-augmented generation baselines that still require textual context. In addition, Wikontic attains state-of-the-art information-retention performance on the MINE-1 benchmark (86%), outperforming prior KG construction methods. Wikontic is also efficient at build time: KG construction uses less than 1,000 output tokens, about 3times fewer than AriGraph and <1/20 of GraphRAG. The proposed pipeline enhances the quality of the generated KG and offers a scalable solution for leveraging structured knowledge in LLMs.

Camera traps are valuable tools in animal ecology for biodiversity monitoring and conservation. However, challenges like poor generalization to deployment at new unseen locations limit their practical application. Images are naturally associated with heterogeneous forms of context possibly in different modalities. In this work, we leverage the structured context associated with the camera trap images to improve out-of-distribution generalization for the task of species identification in camera traps. For example, a photo of a wild animal may be associated with information about where and when it was taken, as well as structured biology knowledge about the animal species. While typically overlooked by existing work, bringing back such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively integrating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that reformulates species classification as link prediction in a multimodal knowledge graph (KG). This framework seamlessly integrates various forms of multimodal context for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework successfully incorporates biological taxonomy for improved generalization and enhances sample efficiency for recognizing under-represented species.

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP

Domain generalization (DG) seeks robust Vision Transformer (ViT) performance on unseen domains. Efficiently adapting pretrained ViTs for DG is challenging; standard fine-tuning is costly and can impair generalization. We propose GNN-MoE, enhancing Parameter-Efficient Fine-Tuning (PEFT) for DG with a Mixture-of-Experts (MoE) framework using efficient Kronecker adapters. Instead of token-based routing, a novel Graph Neural Network (GNN) router (GCN, GAT, SAGE) operates on inter-patch graphs to dynamically assign patches to specialized experts. This context-aware GNN routing leverages inter-patch relationships for better adaptation to domain shifts. GNN-MoE achieves state-of-the-art or competitive DG benchmark performance with high parameter efficiency, highlighting the utility of graph-based contextual routing for robust, lightweight DG.

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.

The ability to summarize and organize knowledge into abstract concepts is key to learning and reasoning. Many industrial applications rely on the consistent and systematic use of concepts, especially when dealing with decision-critical knowledge. However, we demonstrate that, when methodically questioned, large language models (LLMs) often display and demonstrate significant inconsistencies in their knowledge. Computationally, the basic aspects of the conceptualization of a given domain can be represented as Is-A hierarchies in a knowledge graph (KG) or ontology, together with a few properties or axioms that enable straightforward reasoning. We show that even simple ontologies can be used to reveal conceptual inconsistencies across several LLMs. We also propose strategies that domain experts can use to evaluate and improve the coverage of key domain concepts in LLMs of various sizes. In particular, we have been able to significantly enhance the performance of LLMs of various sizes with openly available weights using simple knowledge-graph (KG) based prompting strategies.

Graph representation learning has emerged as a powerful technique for addressing real-world problems. Various downstream graph learning tasks have benefited from its recent developments, such as node classification, similarity search, and graph classification. However, prior arts on graph representation learning focus on domain specific problems and train a dedicated model for each graph dataset, which is usually non-transferable to out-of-domain data. Inspired by the recent advances in pre-training from natural language processing and computer vision, we design Graph Contrastive Coding (GCC) -- a self-supervised graph neural network pre-training framework -- to capture the universal network topological properties across multiple networks. We design GCC's pre-training task as subgraph instance discrimination in and across networks and leverage contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations. We conduct extensive experiments on three graph learning tasks and ten graph datasets. The results show that GCC pre-trained on a collection of diverse datasets can achieve competitive or better performance to its task-specific and trained-from-scratch counterparts. This suggests that the pre-training and fine-tuning paradigm presents great potential for graph representation learning.

Large-scale commercial platforms usually involve numerous business domains for diverse business strategies and expect their recommendation systems to provide click-through rate (CTR) predictions for multiple domains simultaneously. Existing promising and widely-used multi-domain models discover domain relationships by explicitly constructing domain-specific networks, but the computation and memory boost significantly with the increase of domains. To reduce computational complexity, manually grouping domains with particular business strategies is common in industrial applications. However, this pre-defined data partitioning way heavily relies on prior knowledge, and it may neglect the underlying data distribution of each domain, hence limiting the model's representation capability. Regarding the above issues, we propose an elegant and flexible multi-distribution modeling paradigm, named Adaptive Distribution Hierarchical Model (AdaptDHM), which is an end-to-end optimization hierarchical structure consisting of a clustering process and classification process. Specifically, we design a distribution adaptation module with a customized dynamic routing mechanism. Instead of introducing prior knowledge for pre-defined data allocation, this routing algorithm adaptively provides a distribution coefficient for each sample to determine which cluster it belongs to. Each cluster corresponds to a particular distribution so that the model can sufficiently capture the commonalities and distinctions between these distinct clusters. Extensive experiments on both public and large-scale Alibaba industrial datasets verify the effectiveness and efficiency of AdaptDHM: Our model achieves impressive prediction accuracy and its time cost during the training stage is more than 50% less than that of other models.

Knowledge graphs are useful tools to organize, recommend and sort data. Hierarchies in knowledge graphs provide significant benefit in improving understanding and compartmentalization of the data within a knowledge graph. This work leverages large language models to generate and augment hierarchies in an existing knowledge graph. For small (<100,000 node) domain-specific KGs, we find that a combination of few-shot prompting with one-shot generation works well, while larger KG may require cyclical generation. We present techniques for augmenting hierarchies, which led to coverage increase by 98% for intents and 99% for colors in our knowledge graph.

Large Language Models~(LLMs) have demonstrated capabilities across various applications but face challenges such as hallucination, limited reasoning abilities, and factual inconsistencies, especially when tackling complex, domain-specific tasks like question answering~(QA). While Knowledge Graphs~(KGs) have been shown to help mitigate these issues, research on the integration of LLMs with background KGs remains limited. In particular, user accessibility and the flexibility of the underlying KG have not been thoroughly explored. We introduce AGENTiGraph (Adaptive Generative ENgine for Task-based Interaction and Graphical Representation), a platform for knowledge management through natural language interaction. It integrates knowledge extraction, integration, and real-time visualization. AGENTiGraph employs a multi-agent architecture to dynamically interpret user intents, manage tasks, and integrate new knowledge, ensuring adaptability to evolving user requirements and data contexts. Our approach demonstrates superior performance in knowledge graph interactions, particularly for complex domain-specific tasks. Experimental results on a dataset of 3,500 test cases show AGENTiGraph significantly outperforms state-of-the-art zero-shot baselines, achieving 95.12\% accuracy in task classification and 90.45\% success rate in task execution. User studies corroborate its effectiveness in real-world scenarios. To showcase versatility, we extended AGENTiGraph to legislation and healthcare domains, constructing specialized KGs capable of answering complex queries in legal and medical contexts.

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

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.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

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

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.

A backbone of knowledge graphs are their class membership relations, which assign entities to a given class. As part of the knowledge engineering process, we propose a new method for evaluating the quality of these relations by processing descriptions of a given entity and class using a zero-shot chain-of-thought classifier that uses a natural language intensional definition of a class. We evaluate the method using two publicly available knowledge graphs, Wikidata and CaLiGraph, and 7 large language models. Using the gpt-4-0125-preview large language model, the method's classification performance achieves a macro-averaged F1-score of 0.830 on data from Wikidata and 0.893 on data from CaLiGraph. Moreover, a manual analysis of the classification errors shows that 40.9% of errors were due to the knowledge graphs, with 16.0% due to missing relations and 24.9% due to incorrectly asserted relations. These results show how large language models can assist knowledge engineers in the process of knowledge graph refinement. The code and data are available on Github.

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.

We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Large language models (LLMs) have demonstrated remarkable capabilities in a wide range of tasks, yet their application to specialized domains remains challenging due to the need for deep expertise. Retrieval-augmented generation (RAG) has emerged as a promising solution to customize LLMs for professional fields by seamlessly integrating external knowledge bases, enabling real-time access to domain-specific expertise during inference. Despite its potential, traditional RAG systems, based on flat text retrieval, face three critical challenges: (i) complex query understanding in professional contexts, (ii) difficulties in knowledge integration across distributed sources, and (iii) system efficiency bottlenecks at scale. This survey presents a systematic analysis of Graph-based Retrieval-Augmented Generation (GraphRAG), a new paradigm that revolutionizes domain-specific LLM applications. GraphRAG addresses traditional RAG limitations through three key innovations: (i) graph-structured knowledge representation that explicitly captures entity relationships and domain hierarchies, (ii) efficient graph-based retrieval techniques that enable context-preserving knowledge retrieval with multihop reasoning ability, and (iii) structure-aware knowledge integration algorithms that leverage retrieved knowledge for accurate and logical coherent generation of LLMs. In this survey, we systematically analyze the technical foundations of GraphRAG and examine current implementations across various professional domains, identifying key technical challenges and promising research directions. All the related resources of GraphRAG, including research papers, open-source data, and projects, are collected for the community in blue{https://github.com/DEEP-PolyU/Awesome-GraphRAG}.

The construction of Generalized Knowledge Graph (GKG), including knowledge graph, event knowledge graph and commonsense knowledge graph, is fundamental for various natural language processing tasks. Current studies typically construct these types of graph separately, overlooking holistic insights and potential unification that could be beneficial in computing resources and usage perspectives. However, a key challenge in developing a unified framework for GKG is obstacles arising from task-specific differences. In this study, we propose a unified framework for constructing generalized knowledge graphs to address this challenge. First, we collect data from 15 sub-tasks in 29 datasets across the three types of graphs, categorizing them into in-sample, counter-task, and out-of-distribution (OOD) data. Then, we propose a three-stage curriculum learning fine-tuning framework, by iteratively injecting knowledge from the three types of graphs into the Large Language Models. Extensive experiments show that our proposed model improves the construction of all three graph types across in-domain, OOD and counter-task data.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

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

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

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

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.

Domain Generalization (DG) is a fundamental challenge for machine learning models, which aims to improve model generalization on various domains. Previous methods focus on generating domain invariant features from various source domains. However, we argue that the domain variantions also contain useful information, ie, classification-aware information, for downstream tasks, which has been largely ignored. Different from learning domain invariant features from source domains, we decouple the input images into Domain Expert Features and noise. The proposed domain expert features lie in a learned latent space where the images in each domain can be classified independently, enabling the implicit use of classification-aware domain variations. Based on the analysis, we proposed a novel paradigm called Domain Disentanglement Network (DDN) to disentangle the domain expert features from the source domain images and aggregate the source domain expert features for representing the target test domain. We also propound a new contrastive learning method to guide the domain expert features to form a more balanced and separable feature space. Experiments on the widely-used benchmarks of PACS, VLCS, OfficeHome, DomainNet, and TerraIncognita demonstrate the competitive performance of our method compared to the recently proposed alternatives.

This work aims to tackle the challenging heterogeneous graph encoding problem in the text-to-SQL task. Previous methods are typically node-centric and merely utilize different weight matrices to parameterize edge types, which 1) ignore the rich semantics embedded in the topological structure of edges, and 2) fail to distinguish local and non-local relations for each node. To this end, we propose a Line Graph Enhanced Text-to-SQL (LGESQL) model to mine the underlying relational features without constructing meta-paths. By virtue of the line graph, messages propagate more efficiently through not only connections between nodes, but also the topology of directed edges. Furthermore, both local and non-local relations are integrated distinctively during the graph iteration. We also design an auxiliary task called graph pruning to improve the discriminative capability of the encoder. Our framework achieves state-of-the-art results (62.8% with Glove, 72.0% with Electra) on the cross-domain text-to-SQL benchmark Spider at the time of writing.

Text-to-image (T2I) generation has seen significant growth over the past few years. Despite this, there has been little work on generating diagrams with T2I models. A diagram is a symbolic/schematic representation that explains information using structurally rich and spatially complex visualizations (e.g., a dense combination of related objects, text labels, directional arrows, connection lines, etc.). Existing state-of-the-art T2I models often fail at diagram generation because they lack fine-grained object layout control when many objects are densely connected via complex relations such as arrows/lines and also often fail to render comprehensible text labels. To address this gap, we present DiagrammerGPT, a novel two-stage text-to-diagram generation framework that leverages the layout guidance capabilities of LLMs (e.g., GPT-4) to generate more accurate open-domain, open-platform diagrams. In the first stage, we use LLMs to generate and iteratively refine 'diagram plans' (in a planner-auditor feedback loop) which describe all the entities (objects and text labels), their relationships (arrows or lines), and their bounding box layouts. In the second stage, we use a diagram generator, DiagramGLIGEN, and a text label rendering module to generate diagrams following the diagram plans. To benchmark the text-to-diagram generation task, we introduce AI2D-Caption, a densely annotated diagram dataset built on top of the AI2D dataset. We show quantitatively and qualitatively that our DiagrammerGPT framework produces more accurate diagrams, outperforming existing T2I models. We also provide comprehensive analysis including open-domain diagram generation, vector graphic diagram generation in different platforms, human-in-the-loop diagram plan editing, and multimodal planner/auditor LLMs (e.g., GPT-4Vision). We hope our work can inspire further research on diagram generation via T2I models and LLMs.

Can one inject new concepts into an already trained generative model, while respecting its existing structure and knowledge? We propose a new task - domain expansion - to address this. Given a pretrained generator and novel (but related) domains, we expand the generator to jointly model all domains, old and new, harmoniously. First, we note the generator contains a meaningful, pretrained latent space. Is it possible to minimally perturb this hard-earned representation, while maximally representing the new domains? Interestingly, we find that the latent space offers unused, "dormant" directions, which do not affect the output. This provides an opportunity: By "repurposing" these directions, we can represent new domains without perturbing the original representation. In fact, we find that pretrained generators have the capacity to add several - even hundreds - of new domains! Using our expansion method, one "expanded" model can supersede numerous domain-specific models, without expanding the model size. Additionally, a single expanded generator natively supports smooth transitions between domains, as well as composition of domains. Code and project page available at https://yotamnitzan.github.io/domain-expansion/.

Developing domain models is one of the few remaining places that require manual human labor in AI planning. Thus, in order to make planning more accessible, it is desirable to automate the process of domain model generation. To this end, we investigate if large language models (LLMs) can be used to generate planning domain models from simple textual descriptions. Specifically, we introduce a framework for automated evaluation of LLM-generated domains by comparing the sets of plans for domain instances. Finally, we perform an empirical analysis of 7 large language models, including coding and chat models across 9 different planning domains, and under three classes of natural language domain descriptions. Our results indicate that LLMs, particularly those with high parameter counts, exhibit a moderate level of proficiency in generating correct planning domains from natural language descriptions. Our code is available at https://github.com/IBM/NL2PDDL.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

There has been an influx of biomedical domain-specific language models, showing language models pre-trained on biomedical text perform better on biomedical domain benchmarks than those trained on general domain text corpora such as Wikipedia and Books. Yet, most works do not study the factors affecting each domain language application deeply. Additionally, the study of model size on domain-specific models has been mostly missing. We empirically study and evaluate several factors that can affect performance on domain language applications, such as the sub-word vocabulary set, model size, pre-training corpus, and domain transfer. We show consistent improvements on benchmarks with our larger BioMegatron model trained on a larger domain corpus, contributing to our understanding of domain language model applications. We demonstrate noticeable improvements over the previous state-of-the-art (SOTA) on standard biomedical NLP benchmarks of named entity recognition, relation extraction, and question answering. Model checkpoints and code are available at [https://ngc.nvidia.com] and [https://github.com/NVIDIA/NeMo].

Inferring objects and their relationships from an image in the form of a scene graph is useful in many applications at the intersection of vision and language. We consider a challenging problem of compositional generalization that emerges in this task due to a long tail data distribution. Current scene graph generation models are trained on a tiny fraction of the distribution corresponding to the most frequent compositions, e.g. <cup, on, table>. However, test images might contain zero- and few-shot compositions of objects and relationships, e.g. <cup, on, surfboard>. Despite each of the object categories and the predicate (e.g. 'on') being frequent in the training data, the models often fail to properly understand such unseen or rare compositions. To improve generalization, it is natural to attempt increasing the diversity of the training distribution. However, in the graph domain this is non-trivial. To that end, we propose a method to synthesize rare yet plausible scene graphs by perturbing real ones. We then propose and empirically study a model based on conditional generative adversarial networks (GANs) that allows us to generate visual features of perturbed scene graphs and learn from them in a joint fashion. When evaluated on the Visual Genome dataset, our approach yields marginal, but consistent improvements in zero- and few-shot metrics. We analyze the limitations of our approach indicating promising directions for future research.

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

Domain Generalization (DG) is a challenging task in machine learning that requires a coherent ability to comprehend shifts across various domains through extraction of domain-invariant features. DG performance is typically evaluated by performing image classification in domains of various image styles. However, current methodology lacks quantitative understanding about shifts in stylistic domain, and relies on a vast amount of pre-training data, such as ImageNet1K, which are predominantly in photo-realistic style with weakly supervised class labels. Such a data-driven practice could potentially result in spurious correlation and inflated performance on DG benchmarks. In this paper, we introduce a new DG paradigm to address these risks. We first introduce two new quantitative measures ICV and IDD to describe domain shifts in terms of consistency of classes within one domain and similarity between two stylistic domains. We then present SuperMarioDomains (SMD), a novel synthetic multi-domain dataset sampled from video game scenes with more consistent classes and sufficient dissimilarity compared to ImageNet1K. We demonstrate our DG method SMOS. SMOS first uses SMD to train a precursor model, which is then used to ground the training on a DG benchmark. We observe that SMOS contributes to state-of-the-art performance across five DG benchmarks, gaining large improvements to performances on abstract domains along with on-par or slight improvements to those on photo-realistic domains. Our qualitative analysis suggests that these improvements can be attributed to reduced distributional divergence between originally distant domains. Our data are available at https://github.com/fpsluozi/SMD-SMOS .

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.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

Convolutional Neural Networks have revolutionized vision applications. There are image domains and representations, however, that cannot be handled by standard CNNs (e.g., spherical images, superpixels). Such data are usually processed using networks and algorithms specialized for each type. In this work, we show that it may not always be necessary to use specialized neural networks to operate on such spaces. Instead, we introduce a new structured graph convolution operator that can copy 2D convolution weights, transferring the capabilities of already trained traditional CNNs to our new graph network. This network can then operate on any data that can be represented as a positional graph. By converting non-rectilinear data to a graph, we can apply these convolutions on these irregular image domains without requiring training on large domain-specific datasets. Results of transferring pre-trained image networks for segmentation, stylization, and depth prediction are demonstrated for a variety of such data forms.

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.

Knowledge Graphs (KG) are of vital importance for multiple applications on the web, including information retrieval, recommender systems, and metadata annotation. Regardless of whether they are built manually by domain experts or with automatic pipelines, KGs are often incomplete. Recent work has begun to explore the use of textual descriptions available in knowledge graphs to learn vector representations of entities in order to preform link prediction. However, the extent to which these representations learned for link prediction generalize to other tasks is unclear. This is important given the cost of learning such representations. Ideally, we would prefer representations that do not need to be trained again when transferring to a different task, while retaining reasonable performance. In this work, we propose a holistic evaluation protocol for entity representations learned via a link prediction objective. We consider the inductive link prediction and entity classification tasks, which involve entities not seen during training. We also consider an information retrieval task for entity-oriented search. We evaluate an architecture based on a pretrained language model, that exhibits strong generalization to entities not observed during training, and outperforms related state-of-the-art methods (22% MRR improvement in link prediction on average). We further provide evidence that the learned representations transfer well to other tasks without fine-tuning. In the entity classification task we obtain an average improvement of 16% in accuracy compared with baselines that also employ pre-trained models. In the information retrieval task, we obtain significant improvements of up to 8.8% in NDCG@10 for natural language queries. We thus show that the learned representations are not limited KG-specific tasks, and have greater generalization properties than evaluated in previous work.

Large Language Models (LLMs) have made remarkable strides in reasoning tasks, yet their performance often falters on novel and complex problems. Domain-specific continued pretraining (CPT) methods, such as those tailored for mathematical reasoning, have shown promise but lack transferability to broader reasoning tasks. In this work, we pioneer the use of Graph Problem Reasoning (GPR) to enhance the general reasoning capabilities of LLMs. GPR tasks, spanning pathfinding, network analysis, numerical computation, and topological reasoning, require sophisticated logical and relational reasoning, making them ideal for teaching diverse reasoning patterns. To achieve this, we introduce GraphPile, the first large-scale corpus specifically designed for CPT using GPR data. Spanning 10.9 billion tokens across 23 graph tasks, the dataset includes chain-of-thought, program-of-thought, trace of execution, and real-world graph data. Using GraphPile, we train GraphMind on popular base models Llama 3 and 3.1, as well as Gemma 2, achieving up to 4.9 percent higher accuracy in mathematical reasoning and up to 21.2 percent improvement in non-mathematical reasoning tasks such as logical and commonsense reasoning. By being the first to harness GPR for enhancing reasoning patterns and introducing the first dataset of its kind, our work bridges the gap between domain-specific pretraining and universal reasoning capabilities, advancing the adaptability and robustness of LLMs.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.