Entity linking (EL) aligns textual mentions with their corresponding entities in a knowledge base, facilitating various applications such as semantic search and question answering. Recent advances in multimodal entity linking (MEL) have shown that combining text and images can reduce ambiguity and improve alignment accuracy. However, most existing MEL methods overlook the rich structural information available in the form of knowledge-graph (KG) triples. In this paper, we propose KGMEL, a novel framework that leverages KG triples to enhance MEL. Specifically, it operates in three stages: (1) Generation: Produces high-quality triples for each mention by employing vision-language models based on its text and images. (2) Retrieval: Learns joint mention-entity representations, via contrastive learning, that integrate text, images, and (generated or KG) triples to retrieve candidate entities for each mention. (3) Reranking: Refines the KG triples of the candidate entities and employs large language models to identify the best-matching entity for the mention. Extensive experiments on benchmark datasets demonstrate that KGMEL outperforms existing methods. Our code and datasets are available at: https://github.com/juyeonnn/KGMEL.
With the rise of knowledge graph based retrieval-augmented generation (RAG) techniques such as GraphRAG and Pike-RAG, the role of knowledge graphs in enhancing the reasoning capabilities of large language models (LLMs) has become increasingly prominent. However, traditional Knowledge Graph Construction (KGC) methods face challenges like complex entity disambiguation, rigid schema definition, and insufficient cross-document knowledge integration. This paper focuses on the task of automatic document-level knowledge graph construction. It proposes the Document-level Retrieval Augmented Knowledge Graph Construction (RAKG) framework. RAKG extracts pre-entities from text chunks and utilizes these pre-entities as queries for RAG, effectively addressing the issue of long-context forgetting in LLMs and reducing the complexity of Coreference Resolution. In contrast to conventional KGC methods, RAKG more effectively captures global information and the interconnections among disparate nodes, thereby enhancing the overall performance of the model. Additionally, we transfer the RAG evaluation framework to the KGC field and filter and evaluate the generated knowledge graphs, thereby avoiding incorrectly generated entities and relationships caused by hallucinations in LLMs. We further developed the MINE dataset by constructing standard knowledge graphs for each article and experimentally validated the performance of RAKG. The results show that RAKG achieves an accuracy of 95.91 % on the MINE dataset, a 6.2 % point improvement over the current best baseline, GraphRAG (89.71 %). The code is available at https://github.com/LMMApplication/RAKG.
Large language models have shown remarkable language processing and reasoning ability but are prone to hallucinate when asked about private data. Retrieval-augmented generation (RAG) retrieves relevant data that fit into an LLM's context window and prompts the LLM for an answer. GraphRAG extends this approach to structured Knowledge Graphs (KGs) and questions regarding entities multiple hops away. The majority of recent GraphRAG methods either overlook the retrieval step or have ad hoc retrieval processes that are abstract or inefficient. This prevents them from being adopted when the KGs are stored in graph databases supporting graph query languages. In this work, we present GraphRAFT, a retrieve-and-reason framework that finetunes LLMs to generate provably correct Cypher queries to retrieve high-quality subgraph contexts and produce accurate answers. Our method is the first such solution that can be taken off-the-shelf and used on KGs stored in native graph DBs. Benchmarks suggest that our method is sample-efficient and scales with the availability of training data. Our method achieves significantly better results than all state-of-the-art models across all four standard metrics on two challenging Q\&As on large text-attributed KGs.
Recent advances in Large Language Models have demonstrated their capabilities across a variety of tasks. However, automatically extracting implicit knowledge from natural language remains a significant challenge, as machines lack active experience with the physical world. Given this scenario, semantic knowledge graphs can serve as conceptual spaces that guide the automated text generation reasoning process to achieve more efficient and explainable results. In this paper, we apply a logic-augmented generation (LAG) framework that leverages the explicit representation of a text through a semantic knowledge graph and applies it in combination with prompt heuristics to elicit implicit analogical connections. This method generates extended knowledge graph triples representing implicit meaning, enabling systems to reason on unlabeled multimodal data regardless of the domain. We validate our work through three metaphor detection and understanding tasks across four datasets, as they require deep analogical reasoning capabilities. The results show that this integrated approach surpasses current baselines, performs better than humans in understanding visual metaphors, and enables more explainable reasoning processes, though still has inherent limitations in metaphor understanding, especially for domain-specific metaphors. Furthermore, we propose a thorough error analysis, discussing issues with metaphorical annotations and current evaluation methods.
Discovery gene-disease links is important in biology and medicine areas, enabling disease identification and drug repurposing. Machine learning approaches accelerate this process by leveraging biological knowledge represented in ontologies and the structure of knowledge graphs. Still, many existing works overlook ontologies explicitly representing diseases, missing causal and semantic relationships between them. The gene-disease association problem naturally frames itself as a link prediction task, where embedding algorithms directly predict associations by exploring the structure and properties of the knowledge graph. Some works frame it as a node-pair classification task, combining embedding algorithms with traditional machine learning algorithms. This strategy aligns with the logic of a machine learning pipeline. However, the use of negative examples and the lack of validated gene-disease associations to train embedding models may constrain its effectiveness. This work introduces a novel framework for comparing the performance of link prediction versus node-pair classification tasks, analyses the performance of state of the art gene-disease association approaches, and compares the different order-based formalizations of gene-disease association prediction. It also evaluates the impact of the semantic richness through a disease-specific ontology and additional links between ontologies. The framework involves five steps: data splitting, knowledge graph integration, embedding, modeling and prediction, and method evaluation. Results show that enriching the semantic representation of diseases slightly improves performance, while additional links generate a greater impact. Link prediction methods better explore the semantic richness encoded in knowledge graphs. Although node-pair classification methods identify all true positives, link prediction methods outperform overall.
Retrieval over knowledge graphs is usually performed using dedicated, complex query languages like SPARQL. We propose a novel system, Ontology and Semantic Exploration Toolkit (OnSET) that allows non-expert users to easily build queries with visual user guidance provided by topic modelling and semantic search throughout the application. OnSET allows users without any prior information about the ontology or networked knowledge to start exploring topics of interest over knowledge graphs, including the retrieval and detailed exploration of prototypical sub-graphs and their instances. Existing systems either focus on direct graph explorations or do not foster further exploration of the result set. We, however, provide a node-based editor that can extend on these missing properties of existing systems to support the search over big ontologies with sub-graph instances. Furthermore, OnSET combines efficient and open platforms to deploy the system on commodity hardware.
Knowledge graph embedding (KGE) models encode the structural information of knowledge graphs to predicting new links. Effective training of these models requires distinguishing between positive and negative samples with high precision. Although prior research has shown that improving the quality of negative samples can significantly enhance model accuracy, identifying high-quality negative samples remains a challenging problem. This paper theoretically investigates the condition under which negative samples lead to optimal KG embedding and identifies a sufficient condition for an effective negative sample distribution. Based on this theoretical foundation, we propose \textbf{E}mbedding \textbf{MU}tation (\textsc{EMU}), a novel framework that \emph{generates} negative samples satisfying this condition, in contrast to conventional methods that focus on \emph{identifying} challenging negative samples within the training data. Importantly, the simplicity of \textsc{EMU} ensures seamless integration with existing KGE models and negative sampling methods. To evaluate its efficacy, we conducted comprehensive experiments across multiple datasets. The results consistently demonstrate significant improvements in link prediction performance across various KGE models and negative sampling methods. Notably, \textsc{EMU} enables performance improvements comparable to those achieved by models with embedding dimension five times larger. An implementation of the method and experiments are available at https://github.com/nec-research/EMU-KG.
In this paper, we propose a new geometric approach for knowledge graph completion via low rank tensor approximation. We augment a pretrained and well-established Euclidean model based on a Tucker tensor decomposition with a novel hyperbolic interaction term. This correction enables more nuanced capturing of distributional properties in data better aligned with real-world knowledge graphs. By combining two geometries together, our approach improves expressivity of the resulting model achieving new state-of-the-art link prediction accuracy with a significantly lower number of parameters compared to the previous Euclidean and hyperbolic models.
Medical tasks such as diagnosis and treatment planning require precise and complex reasoning, particularly in life-critical domains. Unlike mathematical reasoning, medical reasoning demands meticulous, verifiable thought processes to ensure reliability and accuracy. However, there is a notable lack of datasets that provide transparent, step-by-step reasoning to validate and enhance the medical reasoning ability of AI models. To bridge this gap, we introduce MedReason, a large-scale high-quality medical reasoning dataset designed to enable faithful and explainable medical problem-solving in large language models (LLMs). We utilize a structured medical knowledge graph (KG) to convert clinical QA pairs into logical chains of reasoning, or ``thinking paths'', which trace connections from question elements to answers via relevant KG entities. Each path is validated for consistency with clinical logic and evidence-based medicine. Our pipeline generates detailed reasoning for various medical questions from 7 medical datasets, resulting in a dataset of 32,682 question-answer pairs, each with detailed, step-by-step explanations. Experiments demonstrate that fine-tuning with our dataset consistently boosts medical problem-solving capabilities, achieving significant gains of up to 7.7% for DeepSeek-Ditill-8B. Our top-performing model, MedReason-8B, outperforms the Huatuo-o1-8B, a state-of-the-art medical reasoning model, by up to 4.2% on the clinical benchmark MedBullets. We also engage medical professionals from diverse specialties to assess our dataset's quality, ensuring MedReason offers accurate and coherent medical reasoning. Our data, models, and code will be publicly available.
Large Language Models (LLMs) often struggle with tasks requiring external knowledge, such as knowledge-intensive Multiple Choice Question Answering (MCQA). Integrating Knowledge Graphs (KGs) can enhance reasoning; however, existing methods typically demand costly fine-tuning or retrieve noisy KG information. Recent approaches leverage Graph Neural Networks (GNNs) to generate KG-based input embedding prefixes as soft prompts for LLMs but fail to account for question relevance, resulting in noisy prompts. Moreover, in MCQA tasks, the absence of relevant KG knowledge for certain answer options remains a significant challenge. To address these issues, we propose Question-Aware Knowledge Graph Prompting (QAP), which incorporates question embeddings into GNN aggregation to dynamically assess KG relevance. QAP employs global attention to capture inter-option relationships, enriching soft prompts with inferred knowledge. Experimental results demonstrate that QAP outperforms state-of-the-art methods across multiple datasets, highlighting its effectiveness.
While large language models (LLMs) have made significant progress in processing and reasoning over knowledge graphs, current methods suffer from a high non-retrieval rate. This limitation reduces the accuracy of answering questions based on these graphs. Our analysis reveals that the combination of greedy search and forward reasoning is a major contributor to this issue. To overcome these challenges, we introduce the concept of super-relations, which enables both forward and backward reasoning by summarizing and connecting various relational paths within the graph. This holistic approach not only expands the search space, but also significantly improves retrieval efficiency. In this paper, we propose the ReKnoS framework, which aims to Reason over Knowledge Graphs with Super-Relations. Our framework's key advantages include the inclusion of multiple relation paths through super-relations, enhanced forward and backward reasoning capabilities, and increased efficiency in querying LLMs. These enhancements collectively lead to a substantial improvement in the successful retrieval rate and overall reasoning performance. We conduct extensive experiments on nine real-world datasets to evaluate ReKnoS, and the results demonstrate the superior performance of ReKnoS over existing state-of-the-art baselines, with an average accuracy gain of 2.92%.
Biomedical ontologies, which comprehensively define concepts and relations for biomedical entities, are crucial for structuring and formalizing domain-specific information representations. Biomedical code mapping identifies similarity or equivalence between concepts from different ontologies. Obtaining high-quality mapping usually relies on automatic generation of unrefined mapping with ontology domain fine-tuned language models (LMs), followed by manual selections or corrections by coding experts who have extensive domain expertise and familiarity with ontology schemas. The LMs usually provide unrefined code mapping suggestions as a list of candidates without reasoning or supporting evidence, hence coding experts still need to verify each suggested candidate against ontology sources to pick the best matches. This is also a recurring task as ontology sources are updated regularly to incorporate new research findings. Consequently, the need of regular LM retraining and manual refinement make code mapping time-consuming and labour intensive. In this work, we created OntologyRAG, an ontology-enhanced retrieval-augmented generation (RAG) method that leverages the inductive biases from ontological knowledge graphs for in-context-learning (ICL) in large language models (LLMs). Our solution grounds LLMs to knowledge graphs with unrefined mappings between ontologies and processes questions by generating an interpretable set of results that include prediction rational with mapping proximity assessment. Our solution doesn't require re-training LMs, as all ontology updates could be reflected by updating the knowledge graphs with a standard process. Evaluation results on a self-curated gold dataset show promises of using our method to enable coding experts to achieve better and faster code mapping. The code is available at https://github.com/iqvianlp/ontologyRAG.
N-ary relational facts represent semantic correlations among more than two entities. While recent studies have developed link prediction (LP) methods to infer missing relations for knowledge graphs (KGs) containing n-ary relational facts, they are generally limited to transductive settings. Fully inductive settings, where predictions are made on previously unseen entities, remain a significant challenge. As existing methods are mainly entity embedding-based, they struggle to capture entity-independent logical rules. To fill in this gap, we propose an n-ary subgraph reasoning framework for fully inductive link prediction (ILP) on n-ary relational facts. This framework reasons over local subgraphs and has a strong inductive inference ability to capture n-ary patterns. Specifically, we introduce a novel graph structure, the n-ary semantic hypergraph, to facilitate subgraph extraction. Moreover, we develop a subgraph aggregating network, NS-HART, to effectively mine complex semantic correlations within subgraphs. Theoretically, we provide a thorough analysis from the score function optimization perspective to shed light on NS-HART's effectiveness for n-ary ILP tasks. Empirically, we conduct extensive experiments on a series of inductive benchmarks, including transfer reasoning (with and without entity features) and pairwise subgraph reasoning. The results highlight the superiority of the n-ary subgraph reasoning framework and the exceptional inductive ability of NS-HART. The source code of this paper has been made publicly available at https://github.com/yin-gz/Nary-Inductive-SubGraph.
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of disease pathology. Therefore, machine learning has been used to process gene expression data, with patient diagnosis emerging as one of the most popular applications. Although gene expression data can provide valuable insights, challenges arise because the number of patients in expression datasets is usually limited, and the data from different datasets with different gene expressions cannot be easily combined. This work proposes a novel methodology to address these challenges by integrating multiple gene expression datasets and domain-specific knowledge using knowledge graphs, a unique tool for biomedical data integration. Then, vector representations are produced using knowledge graph embedding techniques, which are used as inputs for a graph neural network and a multi-layer perceptron. We evaluate the efficacy of our methodology in three settings: single-dataset learning, multi-dataset learning, and transfer learning. The experimental results show that combining gene expression datasets and domain-specific knowledge improves patient diagnosis in all three settings.
The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.
Knowledge graphs serve as critical resources supporting intelligent systems, but they can be noisy due to imperfect automatic generation processes. Existing approaches to noise detection often rely on external facts, logical rule constraints, or structural embeddings. These methods are often challenged by imperfect entity alignment, flexible knowledge graph construction, and overfitting on structures. In this paper, we propose to exploit the consistency between entity and relation type information for noise detection, resulting a novel self-supervised knowledge graph denoising method that avoids those problems. We formalize type inconsistency noise as triples that deviate from the majority with respect to type-dependent reasoning along the topological structure. Specifically, we first extract a compact representation of a given knowledge graph via an encoder that models the type dependencies of triples. Then, the decoder reconstructs the original input knowledge graph based on the compact representation. It is worth noting that, our proposal has the potential to address the problems of knowledge graph compression and completion, although this is not our focus. For the specific task of noise detection, the discrepancy between the reconstruction results and the input knowledge graph provides an opportunity for denoising, which is facilitated by the type consistency embedded in our method. Experimental validation demonstrates the effectiveness of our approach in detecting potential noise in real-world data.
Recent studies have combined Large Language Models (LLMs) with Knowledge Graphs (KGs) to enhance reasoning, improving inference accuracy without additional training while mitigating hallucination. However, existing frameworks still suffer two practical drawbacks: they must be re-tuned whenever the KG or reasoning task changes, and they depend on a single, high-capacity LLM for reliable (i.e., trustworthy) reasoning. To address this, we introduce R2-KG, a plug-and-play, dual-agent framework that separates reasoning into two roles: an Operator (a low-capacity LLM) that gathers evidence and a Supervisor (a high-capacity LLM) that makes final judgments. This design is cost-efficient for LLM inference while still maintaining strong reasoning accuracy. Additionally, R2-KG employs an Abstention mechanism, generating answers only when sufficient evidence is collected from KG, which significantly enhances reliability. Experiments across five diverse benchmarks show that R2-KG consistently outperforms baselines in both accuracy and reliability, regardless of the inherent capability of LLMs used as the Operator. Further experiments reveal that the single-agent version of R2-KG, equipped with a strict self-consistency strategy, achieves significantly higher-than-baseline reliability with reduced inference cost but increased abstention rate in complex KGs. Our findings establish R2-KG as a flexible and cost-effective solution for KG-based reasoning, reducing reliance on high-capacity LLMs while ensuring trustworthy inference. The code is available at https://github.com/ekrxjwh2009/R2-KG/.
Complex Logical Query Answering (CLQA) involves intricate multi-hop logical reasoning over large-scale and potentially incomplete Knowledge Graphs (KGs). Although existing CLQA algorithms achieve high accuracy in answering such queries, their reasoning time and memory usage scale significantly with the number of First-Order Logic (FOL) operators involved, creating serious challenges for practical deployment. In addition, current research primarily focuses on algorithm-level optimizations for CLQA tasks, often overlooking compiler-level optimizations, which can offer greater generality and scalability. To address these limitations, we introduce a Knowledge Graph Compiler, namely KGCompiler, the first deep learning compiler specifically designed for CLQA tasks. By incorporating KG-specific optimizations proposed in this paper, KGCompiler enhances the reasoning performance of CLQA algorithms without requiring additional manual modifications to their implementations. At the same time, it significantly reduces memory usage. Extensive experiments demonstrate that KGCompiler accelerates CLQA algorithms by factors ranging from 1.04x to 8.26x, with an average speedup of 3.71x. We also provide an interface to enable hands-on experience with KGCompiler.
Agentic Generative AI, powered by Large Language Models (LLMs) with Retrieval-Augmented Generation (RAG), Knowledge Graphs (KGs), and Vector Stores (VSs), represents a transformative technology applicable to specialized domains such as legal systems, research, recommender systems, cybersecurity, and global security, including proliferation research. This technology excels at inferring relationships within vast unstructured or semi-structured datasets. The legal domain here comprises complex data characterized by extensive, interrelated, and semi-structured knowledge systems with complex relations. It comprises constitutions, statutes, regulations, and case law. Extracting insights and navigating the intricate networks of legal documents and their relations is crucial for effective legal research. Here, we introduce a generative AI system that integrates RAG, VS, and KG, constructed via Non-Negative Matrix Factorization (NMF), to enhance legal information retrieval and AI reasoning and minimize hallucinations. In the legal system, these technologies empower AI agents to identify and analyze complex connections among cases, statutes, and legal precedents, uncovering hidden relationships and predicting legal trends-challenging tasks that are essential for ensuring justice and improving operational efficiency. Our system employs web scraping techniques to systematically collect legal texts, such as statutes, constitutional provisions, and case law, from publicly accessible platforms like Justia. It bridges the gap between traditional keyword-based searches and contextual understanding by leveraging advanced semantic representations, hierarchical relationships, and latent topic discovery. This framework supports legal document clustering, summarization, and cross-referencing, for scalable, interpretable, and accurate retrieval for semi-structured data while advancing computational law and AI.
Fully inductive knowledge graph models can be trained on multiple domains and subsequently perform zero-shot knowledge graph completion (KGC) in new unseen domains. This is an important capability towards the goal of having foundation models for knowledge graphs. In this work, we introduce a more expressive and capable fully inductive model, dubbed TRIX, which not only yields strictly more expressive triplet embeddings (head entity, relation, tail entity) compared to state-of-the-art methods, but also introduces a new capability: directly handling both entity and relation prediction tasks in inductive settings. Empirically, we show that TRIX outperforms the state-of-the-art fully inductive models in zero-shot entity and relation predictions in new domains, and outperforms large-context LLMs in out-of-domain predictions. The source code is available at https://github.com/yuchengz99/TRIX.