The effective analysis of high-dimensional Electronic Health Record (EHR) data, with substantial potential for healthcare research, presents notable methodological challenges. Employing predictive modeling guided by a knowledge graph (KG), which enables efficient feature selection, can enhance both statistical efficiency and interpretability. While various methods have emerged for constructing KGs, existing techniques often lack statistical certainty concerning the presence of links between entities, especially in scenarios where the utilization of patient-level EHR data is limited due to privacy concerns. In this paper, we propose the first inferential framework for deriving a sparse KG with statistical guarantee based on the dynamic log-linear topic model proposed by \cite{arora2016latent}. Within this model, the KG embeddings are estimated by performing singular value decomposition on the empirical pointwise mutual information matrix, offering a scalable solution. We then establish entrywise asymptotic normality for the KG low-rank estimator, enabling the recovery of sparse graph edges with controlled type I error. Our work uniquely addresses the under-explored domain of statistical inference about non-linear statistics under the low-rank temporal dependent models, a critical gap in existing research. We validate our approach through extensive simulation studies and then apply the method to real-world EHR data in constructing clinical KGs and generating clinical feature embeddings.

Recent advances in natural language processing (NLP) owe their success to pre-training language models on large amounts of unstructured data. Still, there is an increasing effort to combine the unstructured nature of LMs with structured knowledge and reasoning. Particularly in the rapidly evolving field of biomedical NLP, knowledge-enhanced language models (KELMs) have emerged as promising tools to bridge the gap between large language models and domain-specific knowledge, considering the available biomedical knowledge graphs (KGs) curated by experts over the decades. In this paper, we develop an approach that uses lightweight adapter modules to inject structured biomedical knowledge into pre-trained language models (PLMs). We use two large KGs, the biomedical knowledge system UMLS and the novel biochemical ontology OntoChem, with two prominent biomedical PLMs, PubMedBERT and BioLinkBERT. The approach includes partitioning knowledge graphs into smaller subgraphs, fine-tuning adapter modules for each subgraph, and combining the knowledge in a fusion layer. We test the performance on three downstream tasks: document classification,question answering, and natural language inference. We show that our methodology leads to performance improvements in several instances while keeping requirements in computing power low. Finally, we provide a detailed interpretation of the results and report valuable insights for future work.

Aiming to accurately predict missing edges representing relations between entities, which are pervasive in real-world Knowledge Graphs (KGs), relation prediction plays a critical role in enhancing the comprehensiveness and utility of KGs. Recent research focuses on path-based methods due to their inductive and explainable properties. However, these methods face a great challenge when lots of reasoning paths do not form Closed Paths (CPs) in the KG. To address this challenge, we propose Anchoring Path Sentence Transformer (APST) by introducing Anchoring Paths (APs) to alleviate the reliance of CPs. Specifically, we develop a search-based description retrieval method to enrich entity descriptions and an assessment mechanism to evaluate the rationality of APs. APST takes both APs and CPs as the inputs of a unified Sentence Transformer architecture, enabling comprehensive predictions and high-quality explanations. We evaluate APST on three public datasets and achieve state-of-the-art (SOTA) performance in 30 of 36 transductive, inductive, and few-shot experimental settings.

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.

Recently decades have witnessed the empirical success of framing Knowledge Graph (KG) embeddings via language models. However, language model-based KG embeddings are usually deployed as static artifacts, making them difficult to modify post-deployment without re-training after deployment. To address this issue, we propose a new task of editing language model-based KG embeddings in this paper. This task is designed to facilitate rapid, data-efficient updates to KG embeddings without compromising the performance of other aspects. We build four new datasets: E-FB15k237, A-FB15k237, E-WN18RR, and A-WN18RR, and evaluate several knowledge editing baselines demonstrating the limited ability of previous models to handle the proposed challenging task. We further propose a simple yet strong baseline dubbed KGEditor, which utilizes additional parametric layers of the hypernetwork to edit/add facts. Our comprehensive experimental results reveal that KGEditor excels in updating specific facts without impacting the overall performance, even when faced with limited training resources. Code and datasets are available in https://github.com/zjunlp/PromptKG/tree/main/deltaKG.

Multi-hop Knowledge Base Question Answering(KBQA) aims to find the answer entity in a knowledge graph (KG), which requires multiple steps of reasoning. Existing retrieval-based approaches solve this task by concentrating on the specific relation at different hops and predicting the intermediate entity within the reasoning path. During the reasoning process of these methods, the representation of relations are fixed but the initial relation representation may not be optimal. We claim they fail to utilize information from head-tail entities and the semantic connection between relations to enhance the current relation representation, which undermines the ability to capture information of relations in KGs. To address this issue, we construct a \textbf{dual relation graph} where each node denotes a relation in the original KG (\textbf{primal entity graph}) and edges are constructed between relations sharing same head or tail entities. Then we iteratively do primal entity graph reasoning, dual relation graph information propagation, and interaction between these two graphs. In this way, the interaction between entity and relation is enhanced, and we derive better entity and relation representations. Experiments on two public datasets, WebQSP and CWQ, show that our approach achieves a significant performance gain over the prior state-of-the-art. Our code is available on \url{https://github.com/yanmenxue/RAH-KBQA}.

Knowledge graph completion (KGC) aims to predict missing facts in knowledge graphs (KGs), which is crucial as modern KGs remain largely incomplete. While training KGC models on multiple aligned KGs can improve performance, previous methods that rely on transferring raw data among KGs raise privacy concerns. To address this challenge, we propose a new federated learning framework that implicitly aggregates knowledge from multiple KGs without demanding raw data exchange and entity alignment. We treat each KG as a client that trains a local language model through textbased knowledge representation learning. A central server then aggregates the model weights from clients. As natural language provides a universal representation, the same knowledge thus has similar semantic representations across KGs. As such, the aggregated language model can leverage complementary knowledge from multilingual KGs without demanding raw user data sharing. Extensive experiments on a benchmark dataset demonstrate that our method substantially improves KGC on multilingual KGs, achieving comparable performance to state-of-the-art alignment-based models without requiring any labeled alignments or raw user data sharing. Our codes will be publicly available.

Knowledge graphs (KGs) have become valuable knowledge resources in various applications, and knowledge graph embedding (KGE) methods have garnered increasing attention in recent years. However, conventional KGE methods still face challenges when it comes to handling unseen entities or relations during model testing. To address this issue, much effort has been devoted to various fields of KGs. In this paper, we use a set of general terminologies to unify these methods and refer to them collectively as Knowledge Extrapolation. We comprehensively summarize these methods, classified by our proposed taxonomy, and describe their interrelationships. Additionally, we introduce benchmarks and provide comparisons of these methods based on aspects that are not captured by the taxonomy. Finally, we suggest potential directions for future research.

Trajectory prediction in traffic scenes involves accurately forecasting the behaviour of surrounding vehicles. To achieve this objective it is crucial to consider contextual information, including the driving path of vehicles, road topology, lane dividers, and traffic rules. Although studies demonstrated the potential of leveraging heterogeneous context for improving trajectory prediction, state-of-the-art deep learning approaches still rely on a limited subset of this information. This is mainly due to the limited availability of comprehensive representations. This paper presents an approach that utilizes knowledge graphs to model the diverse entities and their semantic connections within traffic scenes. Further, we present nuScenes Knowledge Graph (nSKG), a knowledge graph for the nuScenes dataset, that models explicitly all scene participants and road elements, as well as their semantic and spatial relationships. To facilitate the usage of the nSKG via graph neural networks for trajectory prediction, we provide the data in a format, ready-to-use by the PyG library. All artefacts can be found here: https://github.com/boschresearch/nuScenes_Knowledge_Graph

Reasoning with knowledge graphs (KGs) has primarily focused on triple-shaped facts. Recent advancements have been explored to enhance the semantics of these facts by incorporating more potent representations, such as hyper-relational facts. However, these approaches are limited to \emph{atomic facts}, which describe a single piece of information. This paper extends beyond \emph{atomic facts} and delves into \emph{nested facts}, represented by quoted triples where subjects and objects are triples themselves (e.g., ((\emph{BarackObama}, \emph{holds\_position}, \emph{President}), \emph{succeed\_by}, (\emph{DonaldTrump}, \emph{holds\_position}, \emph{President}))). These nested facts enable the expression of complex semantics like \emph{situations} over time and \emph{logical patterns} over entities and relations. In response, we introduce NestE, a novel KG embedding approach that captures the semantics of both atomic and nested factual knowledge. NestE represents each atomic fact as a $1\times3$ matrix, and each nested relation is modeled as a $3\times3$ matrix that rotates the $1\times3$ atomic fact matrix through matrix multiplication. Each element of the matrix is represented as a complex number in the generalized 4D hypercomplex space, including (spherical) quaternions, hyperbolic quaternions, and split-quaternions. Through thorough analysis, we demonstrate the embedding's efficacy in capturing diverse logical patterns over nested facts, surpassing the confines of first-order logic-like expressions. Our experimental results showcase NestE's significant performance gains over current baselines in triple prediction and conditional link prediction. The code and pre-trained models are open available at https://github.com/xiongbo010/NestE.