Methods for knowledge graph (KG) completion need to capture semantic regularities and use these regularities to infer plausible knowledge that is not explicitly stated. Most embedding-based methods are opaque in the kinds of regularities they can capture, although region-based KG embedding models have emerged as a more transparent alternative. By modeling relations as geometric regions in high-dimensional vector spaces, such models can explicitly capture semantic regularities in terms of the spatial arrangement of these regions. Unfortunately, existing region-based approaches are severely limited in the kinds of rules they can capture. We argue that this limitation arises because the considered regions are defined as the Cartesian product of two-dimensional regions. As an alternative, in this paper, we propose RESHUFFLE, a simple model based on ordering constraints that can faithfully capture a much larger class of rule bases than existing approaches. Moreover, the embeddings in our framework can be learned by a monotonic Graph Neural Network (GNN), which effectively acts as a differentiable rule base. This approach has the important advantage that embeddings can be easily updated as new knowledge is added to the KG. At the same time, since the resulting representations can be used similarly to standard KG embeddings, our approach is significantly more efficient than existing approaches to differentiable reasoning.
Capturing molecular knowledge with representation learning approaches holds significant potential in vast scientific fields such as chemistry and life science. An effective and generalizable molecular representation is expected to capture the consensus and complementary molecular expertise from diverse views and perspectives. However, existing works fall short in learning multi-view molecular representations, due to challenges in explicitly incorporating view information and handling molecular knowledge from heterogeneous sources. To address these issues, we present MV-Mol, a molecular representation learning model that harvests multi-view molecular expertise from chemical structures, unstructured knowledge from biomedical texts, and structured knowledge from knowledge graphs. We utilize text prompts to model view information and design a fusion architecture to extract view-based molecular representations. We develop a two-stage pre-training procedure, exploiting heterogeneous data of varying quality and quantity. Through extensive experiments, we show that MV-Mol provides improved representations that substantially benefit molecular property prediction. Additionally, MV-Mol exhibits state-of-the-art performance in multi-modal comprehension of molecular structures and texts. Code and data are available at https://github.com/PharMolix/OpenBioMed.
Rule mining on knowledge graphs allows for explainable link prediction. Contrarily, embedding-based methods for link prediction are well known for their generalization capabilities, but their predictions are not interpretable. Several approaches combining the two families have been proposed in recent years. The majority of the resulting hybrid approaches are usually trained within a unified learning framework, which often leads to convergence issues due to the complexity of the learning task. In this work, we propose a new way to combine the two families of approaches. Specifically, we enrich a given knowledge graph by means of its pre-trained entity and relation embeddings before applying rule mining systems on the enriched knowledge graph. To validate our approach, we conduct extensive experiments on seven benchmark datasets. An analysis of the results generated by our approach suggests that we discover new valuable rules on the enriched graphs. We provide an open source implementation of our approach as well as pretrained models and datasets at https://github.com/Jean-KOUAGOU/EnhancedRuleLearning
Entity summarization aims to compute concise summaries for entities in knowledge graphs. Existing datasets and benchmarks are often limited to a few hundred entities and discard graph structure in source knowledge graphs. This limitation is particularly pronounced when it comes to ground-truth summaries, where there exist only a few labeled summaries for evaluation and training. We propose WikES, a comprehensive benchmark comprising of entities, their summaries, and their connections. Additionally, WikES features a dataset generator to test entity summarization algorithms in different areas of the knowledge graph. Importantly, our approach combines graph algorithms and NLP models as well as different data sources such that WikES does not require human annotation, rendering the approach cost-effective and generalizable to multiple domains. Finally, WikES is scalable and capable of capturing the complexities of knowledge graphs in terms of topology and semantics. WikES features existing datasets for comparison. Empirical studies of entity summarization methods confirm the usefulness of our benchmark. Data, code, and models are available at: https://github.com/msorkhpar/wiki-entity-summarization.
Multi-hop reasoning (MHR) is a process in artificial intelligence and natural language processing where a system needs to make multiple inferential steps to arrive at a conclusion or answer. In the context of knowledge graphs or databases, it involves traversing multiple linked entities and relationships to understand complex queries or perform tasks requiring a deeper understanding. Multi-hop reasoning is a critical function in various applications, including question answering, knowledge base completion, and link prediction. It has garnered significant interest in artificial intelligence, machine learning, and graph analytics. This paper focuses on optimizing MHR for time efficiency on large-scale graphs, diverging from the traditional emphasis on accuracy which is an orthogonal goal. We introduce a novel parallel algorithm that harnesses domain-specific learned embeddings to efficiently identify the top K paths between vertices in a knowledge graph to find the best answers to a three-hop query. Our contributions are: (1) We present a new parallel algorithm to enhance MHR performance, scalability and efficiency. (2) We demonstrate the algorithm's superior performance on leading-edge Intel and AMD architectures through empirical results. We showcase the algorithm's practicality through a case study on identifying academic affiliations of potential Turing Award laureates in Deep Learning, highlighting its capability to handle intricate entity relationships. This demonstrates the potential of our approach to enabling high-performance MHR, useful to navigate the growing complexity of modern knowledge graphs.
This survey investigates the synergistic relationship between Large Language Models (LLMs) and Knowledge Graphs (KGs), which is crucial for advancing AI's capabilities in understanding, reasoning, and language processing. It aims to address gaps in current research by exploring areas such as KG Question Answering, ontology generation, KG validation, and the enhancement of KG accuracy and consistency through LLMs. The paper further examines the roles of LLMs in generating descriptive texts and natural language queries for KGs. Through a structured analysis that includes categorizing LLM-KG interactions, examining methodologies, and investigating collaborative uses and potential biases, this study seeks to provide new insights into the combined potential of LLMs and KGs. It highlights the importance of their interaction for improving AI applications and outlines future research directions.
The integration of multimodal Electronic Health Records (EHR) data has notably advanced clinical predictive capabilities. However, current models that utilize clinical notes and multivariate time-series EHR data often lack the necessary medical context for precise clinical tasks. Previous methods using knowledge graphs (KGs) primarily focus on structured knowledge extraction. To address this, we propose EMERGE, a Retrieval-Augmented Generation (RAG) driven framework aimed at enhancing multimodal EHR predictive modeling. Our approach extracts entities from both time-series data and clinical notes by prompting Large Language Models (LLMs) and aligns them with professional PrimeKG to ensure consistency. Beyond triplet relationships, we include entities' definitions and descriptions to provide richer semantics. The extracted knowledge is then used to generate task-relevant summaries of patients' health statuses. These summaries are fused with other modalities utilizing an adaptive multimodal fusion network with cross-attention. Extensive experiments on the MIMIC-III and MIMIC-IV datasets for in-hospital mortality and 30-day readmission tasks demonstrate the superior performance of the EMERGE framework compared to baseline models. Comprehensive ablation studies and analyses underscore the efficacy of each designed module and the framework's robustness to data sparsity. EMERGE significantly enhances the use of multimodal EHR data in healthcare, bridging the gap with nuanced medical contexts crucial for informed clinical predictions.
A Language Model is a term that encompasses various types of models designed to understand and generate human communication. Large Language Models (LLMs) have gained significant attention due to their ability to process text with human-like fluency and coherence, making them valuable for a wide range of data-related tasks fashioned as pipelines. The capabilities of LLMs in natural language understanding and generation, combined with their scalability, versatility, and state-of-the-art performance, enable innovative applications across various AI-related fields, including eXplainable Artificial Intelligence (XAI), Automated Machine Learning (AutoML), and Knowledge Graphs (KG). Furthermore, we believe these models can extract valuable insights and make data-driven decisions at scale, a practice commonly referred to as Big Data Analytics (BDA). In this position paper, we provide some discussions in the direction of unlocking synergies among these technologies, which can lead to more powerful and intelligent AI solutions, driving improvements in data pipelines across a wide range of applications and domains integrating humans, computers, and knowledge.
The cold start problem, where new users or items have no interaction history, remains a critical challenge in recommender systems (RS). A common solution involves using Knowledge Graphs (KG) to train entity embeddings or Graph Neural Networks (GNNs). Since KGs incorporate auxiliary data and not just user/item interactions, these methods can make relevant recommendations for cold users or items. Graph Reasoning (GR) methods, however, find paths from users to items to recommend using relations in the KG and, in the context of RS, have been used for interpretability. In this study, we propose GRECS: a framework for adapting GR to cold start recommendations. By utilizing explicit paths starting for users rather than relying only on entity embeddings, GRECS can find items corresponding to users' preferences by navigating the graph, even when limited information about users is available. Our experiments show that GRECS mitigates the cold start problem and outperforms competitive baselines across 5 standard datasets while being explainable. This study highlights the potential of GR for developing explainable recommender systems better suited for managing cold users and items.
Answering Questions over Knowledge Graphs (KGQA) is key to well-functioning autonomous language agents in various real-life applications. To improve the neural-symbolic reasoning capabilities of language agents powered by Large Language Models (LLMs) in KGQA, we propose the DecompositionAlignment-Reasoning Agent (DARA) framework. DARA effectively parses questions into formal queries through a dual mechanism: high-level iterative task decomposition and low-level task grounding. Importantly, DARA can be efficiently trained with a small number of high-quality reasoning trajectories. Our experimental results demonstrate that DARA fine-tuned on LLMs (e.g. Llama-2-7B, Mistral) outperforms both in-context learning-based agents with GPT-4 and alternative fine-tuned agents, across different benchmarks in zero-shot evaluation, making such models more accessible for real-life applications. We also show that DARA attains performance comparable to state-of-the-art enumerating-and-ranking-based methods for KGQA.
Machine learning, deep learning, and NLP methods on knowledge graphs are present in different fields and have important roles in various domains from self-driving cars to friend recommendations on social media platforms. However, to apply these methods to knowledge graphs, the data usually needs to be in an acceptable size and format. In fact, knowledge graphs normally have high dimensions and therefore we need to transform them to a low-dimensional vector space. An embedding is a low-dimensional space into which you can translate high dimensional vectors in a way that intrinsic features of the input data are preserved. In this review, we first explain knowledge graphs and their embedding and then review some of the random walk-based embedding methods that have been developed recently.
Multi-hop logical reasoning on knowledge graphs is a pivotal task in natural language processing, with numerous approaches aiming to answer First-Order Logic (FOL) queries. Recent geometry (e.g., box, cone) and probability (e.g., beta distribution)-based methodologies have effectively addressed complex FOL queries. However, a common challenge across these methods lies in determining accurate geometric bounds or probability parameters for these queries. The challenge arises because existing methods rely on linear sequential operations within their computation graphs, overlooking the logical structure of the query and the relation-induced information that can be gleaned from the relations of the query, which we call the context of the query. To address the problem, we propose a model-agnostic methodology that enhances the effectiveness of existing multi-hop logical reasoning approaches by fully integrating the context of the FOL query graph. Our approach distinctively discerns (1) the structural context inherent to the query structure and (2) the relation-induced context unique to each node in the query graph as delineated in the corresponding knowledge graph. This dual-context paradigm helps nodes within a query graph attain refined internal representations throughout the multi-hop reasoning steps. Through experiments on two datasets, our method consistently enhances the three multi-hop reasoning foundation models, achieving performance improvements of up to 19.5%. Our code is available at https://github.com/kjh9503/caqr.
Language models (LMs) encode world knowledge in their internal parameters through training. However, LMs may learn personal and confidential information from the training data, leading to privacy concerns such as data leakage. Therefore, research on knowledge deletion from LMs is essential. This study focuses on the knowledge stored in LMs and analyzes the relationship between the side effects of knowledge deletion and the entities related to the knowledge. Our findings reveal that deleting knowledge related to popular entities can have catastrophic side effects. Furthermore, this research is the first to analyze knowledge deletion in models trained on synthetic knowledge graphs, indicating a new direction for controlled experiments.
Given unstructured text, Large Language Models (LLMs) are adept at answering simple (single-hop) questions. However, as the complexity of the questions increase, the performance of LLMs degrade. We believe this is due to the overhead associated with understanding the complex question followed by filtering and aggregating unstructured information in the raw text. Recent methods try to reduce this burden by integrating structured knowledge triples into the raw text, aiming to provide a structured overview that simplifies information processing. However, this simplistic approach is query-agnostic and the extracted facts are ambiguous as they lack context. To address these drawbacks and to enable LLMs to answer complex (multi-hop) questions with ease, we propose to use a knowledge graph (KG) that is context-aware and is distilled to contain query-relevant information. The use of our compressed distilled KG as input to the LLM results in our method utilizing up to $67\%$ fewer tokens to represent the query relevant information present in the supporting documents, compared to the state-of-the-art (SoTA) method. Our experiments show consistent improvements over the SoTA across several metrics (EM, F1, BERTScore, and Human Eval) on two popular benchmark datasets (HotpotQA and MuSiQue).
Grounded language models use external sources of information, such as knowledge graphs, to meet some of the general challenges associated with pre-training. By extending previous work on compositional generalization in semantic parsing, we allow for a controlled evaluation of the degree to which these models learn and generalize from patterns in knowledge graphs. We develop a procedure for generating natural language questions paired with knowledge graphs that targets different aspects of compositionality and further avoids grounding the language models in information already encoded implicitly in their weights. We evaluate existing methods for combining language models with knowledge graphs and find them to struggle with generalization to sequences of unseen lengths and to novel combinations of seen base components. While our experimental results provide some insight into the expressive power of these models, we hope our work and released datasets motivate future research on how to better combine language models with structured knowledge representations.
To tackle the problem of domain-specific knowledge scarcity within large language models (LLMs), knowledge graph-retrievalaugmented method has been proven to be an effective and efficient technique for knowledge infusion. However, existing approaches face two primary challenges: knowledge mismatch between public available knowledge graphs and the specific domain of the task at hand, and poor information compliance of LLMs with knowledge graphs. In this paper, we leverage a small set of labeled samples and a large-scale corpus to efficiently construct domain-specific knowledge graphs by an LLM, addressing the issue of knowledge mismatch. Additionally, we propose a three-stage KG-LLM alignment strategyto enhance the LLM's capability to utilize information from knowledge graphs. We conduct experiments with a limited-sample setting on two biomedical question-answering datasets, and the results demonstrate that our approach outperforms existing baselines.
While there are a plethora of methods for link prediction in knowledge graphs, state-of-the-art approaches are often black box, obfuscating model reasoning and thereby limiting the ability of users to make informed decisions about model predictions. Recently, methods have emerged to generate prediction explanations for Knowledge Graph Embedding models, a widely-used class of methods for link prediction. The question then becomes, how well do these explanation systems work? To date this has generally been addressed anecdotally, or through time-consuming user research. In this work, we present an in-depth exploration of a simple link prediction explanation method we call LinkLogic, that surfaces and ranks explanatory information used for the prediction. Importantly, we construct the first-ever link prediction explanation benchmark, based on family structures present in the FB13 dataset. We demonstrate the use of this benchmark as a rich evaluation sandbox, probing LinkLogic quantitatively and qualitatively to assess the fidelity, selectivity and relevance of the generated explanations. We hope our work paves the way for more holistic and empirical assessment of knowledge graph prediction explanation methods in the future.
Even for a conservative estimate, 80% of enterprise data reside in unstructured files, stored in data lakes that accommodate heterogeneous formats. Classical search engines can no longer meet information seeking needs, especially when the task is to browse and explore for insight formulation. In other words, there are no obvious search keywords to use. Knowledge graphs, due to their natural visual appeals that reduce the human cognitive load, become the winning candidate for heterogeneous data integration and knowledge representation. In this paper, we introduce Docs2KG, a novel framework designed to extract multimodal information from diverse and heterogeneous unstructured documents, including emails, web pages, PDF files, and Excel files. Dynamically generates a unified knowledge graph that represents the extracted key information, Docs2KG enables efficient querying and exploration of document data lakes. Unlike existing approaches that focus on domain-specific data sources or pre-designed schemas, Docs2KG offers a flexible and extensible solution that can adapt to various document structures and content types. The proposed framework unifies data processing supporting a multitude of downstream tasks with improved domain interpretability. Docs2KG is publicly accessible at https://docs2kg.ai4wa.com, and a demonstration video is available at https://docs2kg.ai4wa.com/Video.
Fact-checking is a crucial natural language processing (NLP) task that verifies the truthfulness of claims by considering reliable evidence. Traditional methods are often limited by labour-intensive data curation and rule-based approaches. In this paper, we present FactGenius, a novel method that enhances fact-checking by combining zero-shot prompting of large language models (LLMs) with fuzzy text matching on knowledge graphs (KGs). Leveraging DBpedia, a structured linked data dataset derived from Wikipedia, FactGenius refines LLM-generated connections using similarity measures to ensure accuracy. The evaluation of FactGenius on the FactKG, a benchmark dataset for fact verification, demonstrates that it significantly outperforms existing baselines, particularly when fine-tuning RoBERTa as a classifier. The two-stage approach of filtering and validating connections proves crucial, achieving superior performance across various reasoning types and establishing FactGenius as a promising tool for robust fact-checking. The code and materials are available at https://github.com/SushantGautam/FactGenius.
While large language models (LLMs) have shown remarkable capabilities in natural language processing, they struggle with complex, multi-step reasoning tasks involving knowledge graphs (KGs). Existing approaches that integrate LLMs and KGs either underutilize the reasoning abilities of LLMs or suffer from prohibitive computational costs due to tight coupling. To address these limitations, we propose a novel collaborative framework named EffiQA that can strike a balance between performance and efficiency via an iterative paradigm. EffiQA consists of three stages: global planning, efficient KG exploration, and self-reflection. Specifically, EffiQA leverages the commonsense capability of LLMs to explore potential reasoning pathways through global planning. Then, it offloads semantic pruning to a small plug-in model for efficient KG exploration. Finally, the exploration results are fed to LLMs for self-reflection to further improve the global planning and efficient KG exploration. Empirical evidence on multiple KBQA benchmarks shows EffiQA's effectiveness, achieving an optimal balance between reasoning accuracy and computational costs. We hope the proposed new framework will pave the way for efficient, knowledge-intensive querying by redefining the integration of LLMs and KGs, fostering future research on knowledge-based question answering.