Patient-Centric Knowledge Graphs (PCKGs) represent an important shift in healthcare that focuses on individualized patient care by mapping the patient's health information in a holistic and multi-dimensional way. PCKGs integrate various types of health data to provide healthcare professionals with a comprehensive understanding of a patient's health, enabling more personalized and effective care. This literature review explores the methodologies, challenges, and opportunities associated with PCKGs, focusing on their role in integrating disparate healthcare data and enhancing patient care through a unified health perspective. In addition, this review also discusses the complexities of PCKG development, including ontology design, data integration techniques, knowledge extraction, and structured representation of knowledge. It highlights advanced techniques such as reasoning, semantic search, and inference mechanisms essential in constructing and evaluating PCKGs for actionable healthcare insights. We further explore the practical applications of PCKGs in personalized medicine, emphasizing their significance in improving disease prediction and formulating effective treatment plans. Overall, this review provides a foundational perspective on the current state-of-the-art and best practices of PCKGs, guiding future research and applications in this dynamic field.
Although large language models (LLMs) have demonstrated remarkable performance, the lack of transparency in their inference logic raises concerns about their trustworthiness. To gain a better understanding of LLMs, we conduct a detailed analysis of the operations of attention heads and aim to better understand the in-context learning of LLMs. Specifically, we investigate whether attention heads encode two types of relationships between tokens present in natural languages: the syntactic dependency parsed from sentences and the relation within knowledge graphs. We find that certain attention heads exhibit a pattern where, when attending to head tokens, they recall tail tokens and increase the output logits of those tail tokens. More crucially, the formulation of such semantic induction heads has a close correlation with the emergence of the in-context learning ability of language models. The study of semantic attention heads advances our understanding of the intricate operations of attention heads in transformers, and further provides new insights into the in-context learning of LLMs.
Large language models (LLMs) demonstrate strong reasoning abilities when prompted to generate chain-of-thought (CoT) explanations alongside answers. However, previous research on evaluating LLMs has solely focused on answer accuracy, neglecting the correctness of the generated CoT. In this paper, we delve deeper into the CoT reasoning capabilities of LLMs in multi-hop question answering by utilizing knowledge graphs (KGs). We propose a novel discriminative and generative CoT evaluation paradigm to assess LLMs' knowledge of reasoning and the accuracy of the generated CoT. Through experiments conducted on 5 different families of LLMs across 2 multi-hop question-answering datasets, we find that LLMs possess sufficient knowledge to perform reasoning. However, there exists a significant disparity between answer accuracy and faithfulness of the CoT reasoning generated by LLMs, indicating that they often arrive at correct answers through incorrect reasoning.
In this paper, we aim to improve the reasoning ability of large language models (LLMs) over knowledge graphs (KGs) to answer complex questions. Inspired by existing methods that design the interaction strategy between LLMs and KG, we propose an autonomous LLM-based agent framework, called KG-Agent, which enables a small LLM to actively make decisions until finishing the reasoning process over KGs. In KG-Agent, we integrate the LLM, multifunctional toolbox, KG-based executor, and knowledge memory, and develop an iteration mechanism that autonomously selects the tool then updates the memory for reasoning over KG. To guarantee the effectiveness, we leverage program language to formulate the multi-hop reasoning process over the KG, and synthesize a code-based instruction dataset to fine-tune the base LLM. Extensive experiments demonstrate that only using 10K samples for tuning LLaMA-7B can outperform state-of-the-art methods using larger LLMs or more data, on both in-domain and out-domain datasets. Our code and data will be publicly released.
Compared with static knowledge graphs, temporal knowledge graphs (tKG), which can capture the evolution and change of information over time, are more realistic and general. However, due to the complexity that the notion of time introduces to the learning of the rules, an accurate graph reasoning, e.g., predicting new links between entities, is still a difficult problem. In this paper, we propose TILP, a differentiable framework for temporal logical rules learning. By designing a constrained random walk mechanism and the introduction of temporal operators, we ensure the efficiency of our model. We present temporal features modeling in tKG, e.g., recurrence, temporal order, interval between pair of relations, and duration, and incorporate it into our learning process. We compare TILP with state-of-the-art methods on two benchmark datasets. We show that our proposed framework can improve upon the performance of baseline methods while providing interpretable results. In particular, we consider various scenarios in which training samples are limited, data is biased, and the time range between training and inference are different. In all these cases, TILP works much better than the state-of-the-art methods.
Spatio-temporal knowledge graphs (STKGs) extend the concept of knowledge graphs (KGs) by incorporating time and location information. While the research community's focus on Knowledge Graph Question Answering (KGQA), the field of answering questions incorporating both spatio-temporal information based on STKGs remains largely unexplored. Furthermore, a lack of comprehensive datasets also has hindered progress in this area. To address this issue, we present STQAD, a dataset comprising 10,000 natural language questions for spatio-temporal knowledge graph question answering (STKGQA). Unfortunately, various state-of-the-art KGQA approaches fall far short of achieving satisfactory performance on our dataset. In response, we propose STCQA, a new spatio-temporal KGQA approach that utilizes a novel STKG embedding method named STComplEx. By extracting temporal and spatial information from a question, our QA model can better comprehend the question and retrieve accurate answers from the STKG. Through extensive experiments, we demonstrate the quality of our dataset and the effectiveness of our STKGQA method.
When we integrate factual knowledge from knowledge graphs (KGs) into large language models (LLMs) to enhance their performance, the cost of injection through training increases with the scale of the models. Consequently, there is significant interest in developing prompt strategies that effectively incorporate KG information into LLMs. However, the community has not yet comprehensively understood how LLMs process and interpret KG information in different input formats and organizations within prompts, and researchers often rely on trial and error. To address this gap, we design extensive experiments to empirically study LLMs' comprehension of different KG prompts. At the literal level, we reveal LLMs' preferences for various input formats (from linearized triples to fluent natural language text). At the attention distribution level, we discuss the underlying mechanisms driving these preferences. We then investigate how the organization of structured knowledge impacts LLMs and evaluate LLMs' robustness in processing and utilizing KG information in practical scenarios. Our experiments show that (1) linearized triples are more effective than fluent NL text in helping LLMs understand KG information and answer fact-intensive questions; (2) Different LLMs exhibit varying preferences for different organizational formats of triples; (3) LLMs with larger scales are more susceptible to noisy, incomplete subgraphs.
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.
Entity alignment (EA) aims to identify entities across different knowledge graphs that represent the same real-world objects. Recent embedding-based EA methods have achieved state-of-the-art performance in EA yet faced interpretability challenges as they purely rely on the embedding distance and neglect the logic rules behind a pair of aligned entities. In this paper, we propose the Align-Subgraph Entity Alignment (ASGEA) framework to exploit logic rules from Align-Subgraphs. ASGEA uses anchor links as bridges to construct Align-Subgraphs and spreads along the paths across KGs, which distinguishes it from the embedding-based methods. Furthermore, we design an interpretable Path-based Graph Neural Network, ASGNN, to effectively identify and integrate the logic rules across KGs. We also introduce a node-level multi-modal attention mechanism coupled with multi-modal enriched anchors to augment the Align-Subgraph. Our experimental results demonstrate the superior performance of ASGEA over the existing embedding-based methods in both EA and Multi-Modal EA (MMEA) tasks.
Knowledge graphs (KGs) have been increasingly employed for link prediction and recommendation using real-world datasets. However, the majority of current methods rely on static data, neglecting the dynamic nature and the hidden spatio-temporal attributes of real-world scenarios. This often results in suboptimal predictions and recommendations. Although there are effective spatio-temporal inference methods, they face challenges such as scalability with large datasets and inadequate semantic understanding, which impede their performance. To address these limitations, this paper introduces a novel framework - Simple Spatio-Temporal Knowledge Graph (SSTKG), for constructing and exploring spatio-temporal KGs. To integrate spatial and temporal data into KGs, our framework exploited through a new 3-step embedding method. Output embeddings can be used for future temporal sequence prediction and spatial information recommendation, providing valuable insights for various applications such as retail sales forecasting and traffic volume prediction. Our framework offers a simple but comprehensive way to understand the underlying patterns and trends in dynamic KG, thereby enhancing the accuracy of predictions and the relevance of recommendations. This work paves the way for more effective utilization of spatio-temporal data in KGs, with potential impacts across a wide range of sectors.
With the continuous growth of large Knowledge Graphs (KGs), extractive KG summarization becomes a trending task. Aiming at distilling a compact subgraph with condensed information, it facilitates various downstream KG-based tasks. In this survey paper, we are among the first to provide a systematic overview of its applications and define a taxonomy for existing methods from its interdisciplinary studies. Future directions are also laid out based on our extensive and comparative review.
Knowledge Graph (KG) inductive reasoning, which aims to infer missing facts from new KGs that are not seen during training, has been widely adopted in various applications. One critical challenge of KG inductive reasoning is handling low-resource scenarios with scarcity in both textual and structural aspects. In this paper, we attempt to address this challenge with Large Language Models (LLMs). Particularly, we utilize the state-of-the-art LLMs to generate a graph-structural prompt to enhance the pre-trained Graph Neural Networks (GNNs), which brings us new methodological insights into the KG inductive reasoning methods, as well as high generalizability in practice. On the methodological side, we introduce a novel pretraining and prompting framework ProLINK, designed for low-resource inductive reasoning across arbitrary KGs without requiring additional training. On the practical side, we experimentally evaluate our approach on 36 low-resource KG datasets and find that ProLINK outperforms previous methods in three-shot, one-shot, and zero-shot reasoning tasks, exhibiting average performance improvements by 20%, 45%, and 147%, respectively. Furthermore, ProLINK demonstrates strong robustness for various LLM promptings as well as full-shot scenarios.
Zero-shot link prediction (ZSLP) on knowledge graphs aims at automatically identifying relations between given entities. Existing methods primarily employ auxiliary information to predict tail entity given head entity and its relation, yet face challenges due to the occasional unavailability of such detailed information and the inherent simplicity of predicting tail entities based on semantic similarities. Even though Large Language Models (LLMs) offer a promising solution to predict unobserved relations between the head and tail entity in a zero-shot manner, their performance is still restricted due to the inability to leverage all the (exponentially many) paths' information between two entities, which are critical in collectively indicating their relation types. To address this, in this work, we introduce a Condensed Transition Graph Framework for Zero-Shot Link Prediction (CTLP), which encodes all the paths' information in linear time complexity to predict unseen relations between entities, attaining both efficiency and information preservation. Specifically, we design a condensed transition graph encoder with theoretical guarantees on its coverage, expressiveness, and efficiency. It is learned by a transition graph contrastive learning strategy. Subsequently, we design a soft instruction tuning to learn and map the all-path embedding to the input of LLMs. Experimental results show that our proposed CTLP method achieves state-of-the-art performance on three standard ZSLP datasets
Commonsense knowledge graph completion is a new challenge for commonsense knowledge graph construction and application. In contrast to factual knowledge graphs such as Freebase and YAGO, commonsense knowledge graphs (CSKGs; e.g., ConceptNet) utilize free-form text to represent named entities, short phrases, and events as their nodes. Such a loose structure results in large and sparse CSKGs, which makes the semantic understanding of these nodes more critical for learning rich commonsense knowledge graph embedding. While current methods leverage semantic similarities to increase the graph density, the semantic plausibility of the nodes and their relations are under-explored. Previous works adopt conceptual abstraction to improve the consistency of modeling (event) plausibility, but they are not scalable enough and still suffer from data sparsity. In this paper, we propose to adopt textual entailment to find implicit entailment relations between CSKG nodes, to effectively densify the subgraph connecting nodes within the same conceptual class, which indicates a similar level of plausibility. Each node in CSKG finds its top entailed nodes using a finetuned transformer over natural language inference (NLI) tasks, which sufficiently capture textual entailment signals. The entailment relation between these nodes are further utilized to: 1) build new connections between source triplets and entailed nodes to densify the sparse CSKGs; 2) enrich the generalization ability of node representations by comparing the node embeddings with a contrastive loss. Experiments on two standard CSKGs demonstrate that our proposed framework EntailE can improve the performance of CSKG completion tasks under both transductive and inductive settings.
Mitigating the hallucinations of Large Language Models (LLMs) and enhancing them is a crucial task. Although some existing methods employ model self-enhancement techniques, they fall short of effectively addressing unknown factual hallucinations. Using Knowledge Graph (KG) enhancement approaches fails to address the generalization across different KG sources and the enhancement of open-ended answer questions simultaneously. To tackle these limitations, there is a framework that combines Pseudo-Graph Generation and Atomic Knowledge Verification proposed. The enhancement of LLM using KG in an open-ended question-answering setting is implemented by leveraging the Pseudo-Graph Generation. Atomic Knowledge Verification utilizes atomic-level knowledge querying and verification to achieve generalizability under different KG sources. Compared to the baseline, this approach yields a minimum improvement of 11.5 in the ROUGE-L score for open-ended questions. For precise questions, we observe a minimum accuracy improvement of 7.5. Moreover, there is also demonstration that this framework exhibits generalizability across different KG sources. In summary, our results pave the way for enhancing LLMs by incorporating Pseudo- and Multisource-KGs, particularly in the context of open-ended questions.
Recent advancements in generative models have established state-of-the-art benchmarks in the generation of molecules and novel drug candidates. Despite these successes, a significant gap persists between generative models and the utilization of extensive biomedical knowledge, often systematized within knowledge graphs, whose potential to inform and enhance generative processes has not been realized. In this paper, we present a novel approach that bridges this divide by developing a framework for knowledge-enhanced generative models called KARL. We develop a scalable methodology to extend the functionality of knowledge graphs while preserving semantic integrity, and incorporate this contextual information into a generative framework to guide a diffusion-based model. The integration of knowledge graph embeddings with our generative model furnishes a robust mechanism for producing novel drug candidates possessing specific characteristics while ensuring validity and synthesizability. KARL outperforms state-of-the-art generative models on both unconditional and targeted generation tasks.
The exponential growth in scientific publications poses a severe challenge for human researchers. It forces attention to more narrow sub-fields, which makes it challenging to discover new impactful research ideas and collaborations outside one's own field. While there are ways to predict a scientific paper's future citation counts, they need the research to be finished and the paper written, usually assessing impact long after the idea was conceived. Here we show how to predict the impact of onsets of ideas that have never been published by researchers. For that, we developed a large evolving knowledge graph built from more than 21 million scientific papers. It combines a semantic network created from the content of the papers and an impact network created from the historic citations of papers. Using machine learning, we can predict the dynamic of the evolving network into the future with high accuracy (AUC values beyond 0.9 for most experiments), and thereby the impact of new research directions. We envision that the ability to predict the impact of new ideas will be a crucial component of future artificial muses that can inspire new impactful and interesting scientific ideas.
In this paper, we address the challenge of learning with limited fault data for power transformers. Traditional operation and maintenance tools lack effective predictive capabilities for potential faults. The scarcity of extensive fault data makes it difficult to apply machine learning techniques effectively. To solve this problem, we propose a novel approach that leverages the knowledge graph (KG) technology in combination with gradient boosting decision trees (GBDT). This method is designed to efficiently learn from a small set of high-dimensional data, integrating various factors influencing transformer faults and historical operational data. Our approach enables accurate safe state assessments and fault analyses of power transformers despite the limited fault characteristic data. Experimental results demonstrate that this method outperforms other learning approaches in prediction accuracy, such as artificial neural networks (ANN) and logistic regression (LR). Furthermore, it offers significant improvements in progressiveness, practicality, and potential for widespread application.
Integrating large language models (LLMs) with knowledge graphs derived from domain-specific data represents an important advancement towards more powerful and factual reasoning. As these models grow more capable, it is crucial to enable them to perform multi-step inferences over real-world knowledge graphs while minimizing hallucination. While large language models excel at conversation and text generation, their ability to reason over domain-specialized graphs of interconnected entities remains limited. For example, can we query a LLM to identify the optimal contact in a professional network for a specific goal, based on relationships and attributes in a private database? The answer is no--such capabilities lie beyond current methods. However, this question underscores a critical technical gap that must be addressed. Many high-value applications in areas such as science, security, and e-commerce rely on proprietary knowledge graphs encoding unique structures, relationships, and logical constraints. We introduce a fine-tuning framework for developing Graph-aligned LAnguage Models (GLaM) that transforms a knowledge graph into an alternate text representation with labeled question-answer pairs. We demonstrate that grounding the models in specific graph-based knowledge expands the models' capacity for structure-based reasoning. Our methodology leverages the large-language model's generative capabilities to create the dataset and proposes an efficient alternate to retrieval-augmented generation styled methods.
Aspect-based Sentiment Analysis (ABSA) evaluates sentiment expressions within a text to comprehend sentiment information. Previous studies integrated external knowledge, such as knowledge graphs, to enhance the semantic features in ABSA models. Recent research has examined the use of Graph Neural Networks (GNNs) on dependency and constituent trees for syntactic analysis. With the ongoing development of ABSA, more innovative linguistic and structural features are being incorporated (e.g. latent graph), but this also introduces complexity and confusion. As of now, a scalable framework for integrating diverse linguistic and structural features into ABSA does not exist. This paper presents the Extensible Multi-Granularity Fusion (EMGF) network, which integrates information from dependency and constituent syntactic, attention semantic , and external knowledge graphs. EMGF, equipped with multi-anchor triplet learning and orthogonal projection, efficiently harnesses the combined potential of each granularity feature and their synergistic interactions, resulting in a cumulative effect without additional computational expenses. Experimental findings on SemEval 2014 and Twitter datasets confirm EMGF's superiority over existing ABSA methods.