Multi-label text classification (MLTC) tasks in the medical domain often face the long-tail label distribution problem. Prior works have explored hierarchical label structures to find relevant information for few-shot classes, but mostly neglected to incorporate external knowledge from medical guidelines. This paper presents DKEC, Domain Knowledge Enhanced Classification for diagnosis prediction with two innovations: (1) automated construction of heterogeneous knowledge graphs from external sources to capture semantic relations among diverse medical entities, (2) incorporating the heterogeneous knowledge graphs in few-shot classification using a label-wise attention mechanism. We construct DKEC using three online medical knowledge sources and evaluate it on a real-world Emergency Medical Services (EMS) dataset and a public electronic health record (EHR) dataset. Results show that DKEC outperforms the state-of-the-art label-wise attention networks and transformer models of different sizes, particularly for the few-shot classes. More importantly, it helps the smaller language models achieve comparable performance to large language models.
Pre-trained Text-to-Text Language Models (LMs), such as T5 or BART yield promising results in the Knowledge Graph Question Answering (KGQA) task. However, the capacity of the models is limited and the quality decreases for questions with less popular entities. In this paper, we present a novel approach which works on top of the pre-trained Text-to-Text QA system to address this issue. Our simple yet effective method performs filtering and re-ranking of generated candidates based on their types derived from Wikidata "instance_of" property.
Multi-Modal Entity Alignment (MMEA) is a critical task that aims to identify equivalent entity pairs across multi-modal knowledge graphs (MMKGs). However, this task faces challenges due to the presence of different types of information, including neighboring entities, multi-modal attributes, and entity types. Directly incorporating the above information (e.g., concatenation or attention) can lead to an unaligned information space. To address these challenges, we propose a novel MMEA transformer, called MoAlign, that hierarchically introduces neighbor features, multi-modal attributes, and entity types to enhance the alignment task. Taking advantage of the transformer's ability to better integrate multiple information, we design a hierarchical modifiable self-attention block in a transformer encoder to preserve the unique semantics of different information. Furthermore, we design two entity-type prefix injection methods to integrate entity-type information using type prefixes, which help to restrict the global information of entities not present in the MMKGs. Our extensive experiments on benchmark datasets demonstrate that our approach outperforms strong competitors and achieves excellent entity alignment performance.
The challenge of answering graph queries over incomplete knowledge graphs is gaining significant attention in the machine learning community. Neuro-symbolic models have emerged as a promising approach, combining good performance with high interpretability. These models utilize trained architectures to execute atomic queries and integrate modules that mimic symbolic query operators. However, most neuro-symbolic query processors are constrained to tree-like graph pattern queries. These queries admit a bottom-up execution with constant values or anchors at the leaves and the target variable at the root. While expressive, tree-like queries fail to capture critical properties in knowledge graphs, such as the existence of multiple edges between entities or the presence of triangles. We introduce a framework for answering arbitrary graph pattern queries over incomplete knowledge graphs, encompassing both cyclic queries and tree-like queries with existentially quantified leaves. These classes of queries are vital for practical applications but are beyond the scope of most current neuro-symbolic models. Our approach employs an approximation scheme that facilitates acyclic traversals for cyclic patterns, thereby embedding additional symbolic bias into the query execution process. Our experimental evaluation demonstrates that our framework performs competitively on three datasets, effectively handling cyclic queries through our approximation strategy. Additionally, it maintains the performance of existing neuro-symbolic models on anchored tree-like queries and extends their capabilities to queries with existentially quantified variables.
Temporal knowledge graphs (TKGs) have shown promise for reasoning tasks by incorporating a temporal dimension to represent how facts evolve over time. However, existing TKG reasoning (TKGR) models lack explainability due to their black-box nature. Recent work has attempted to address this through customized model architectures that generate reasoning paths, but these recent approaches have limited generalizability and provide sparse explanatory output. To enable interpretability for most TKGR models, we propose GradXKG, a novel two-stage gradient-based approach for explaining Relational Graph Convolution Network (RGCN)-based TKGR models. First, a Grad-CAM-inspired RGCN explainer tracks gradients to quantify each node's contribution across timesteps in an efficient "explain-per-use" fashion. Second, an integrated gradients explainer consolidates importance scores for RGCN outputs, extending compatibility across diverse TKGR architectures based on RGCN. Together, the two explainers highlight the most critical nodes at each timestep for a given prediction. Our extensive experiments demonstrated that, by leveraging gradient information, GradXKG provides insightful explanations grounded in the model's logic in a timely manner for most RGCN-based TKGR models. This helps address the lack of interpretability in existing TKGR models and provides a universal explanation approach applicable across various models.
Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.
Exploratory search is an open-ended information retrieval process that aims at discovering knowledge about a topic or domain rather than searching for a specific answer or piece of information. Conversational interfaces are particularly suitable for supporting exploratory search, allowing users to refine queries and examine search results through interactive dialogues. In addition to conversational search interfaces, knowledge graphs are also useful in supporting information exploration due to their rich semantic representation of data items. In this study, we demonstrate the synergistic effects of combining knowledge graphs and conversational interfaces for exploratory search, bridging the gap between structured and unstructured information retrieval. To this end, we propose a knowledge-driven dialogue system for exploring news articles by asking natural language questions and using the graph structure to navigate between related topics. Based on a user study with 54 participants, we empirically evaluate the effectiveness of the graph-based exploratory search and discuss design implications for developing such systems.
The automated generation of radiology diagnostic reports helps radiologists make timely and accurate diagnostic decisions while also enhancing clinical diagnostic efficiency. However, the significant imbalance in the distribution of data between normal and abnormal samples (including visual and textual biases) poses significant challenges for a data-driven task like automatically generating diagnostic radiology reports. Therefore, we propose a Dynamic Multi-Domain Knowledge(DMDK) network for radiology diagnostic report generation. The DMDK network consists of four modules: Chest Feature Extractor(CFE), Dynamic Knowledge Extractor(DKE), Specific Knowledge Extractor(SKE), and Multi-knowledge Integrator(MKI) module. Specifically, the CFE module is primarily responsible for extracting the unprocessed visual medical features of the images. The DKE module is responsible for extracting dynamic disease topic labels from the retrieved radiology diagnostic reports. We then fuse the dynamic disease topic labels with the original visual features of the images to highlight the abnormal regions in the original visual features to alleviate the visual data bias problem. The SKE module expands upon the conventional static knowledge graph to mitigate textual data biases and amplify the interpretability capabilities of the model via domain-specific dynamic knowledge graphs. The MKI distills all the knowledge and generates the final diagnostic radiology report. We performed extensive experiments on two widely used datasets, IU X-Ray and MIMIC-CXR. The experimental results demonstrate the effectiveness of our method, with all evaluation metrics outperforming previous state-of-the-art models.
The fusion of language models (LMs) and knowledge graphs (KGs) is widely used in commonsense question answering, but generating faithful explanations remains challenging. Current methods often overlook path decoding faithfulness, leading to divergence between graph encoder outputs and model predictions. We identify confounding effects and LM-KG misalignment as key factors causing spurious explanations. To address this, we introduce the LM-KG Fidelity metric to assess KG representation reliability and propose the LM-KG Distribution-aware Alignment (\textit{LKDA}) algorithm to improve explanation faithfulness. Without ground truth, we evaluate KG explanations using the proposed Fidelity-Sparsity Trade-off Curve. Experiments on CommonsenseQA and OpenBookQA show that LKDA significantly enhances explanation fidelity and model performance, highlighting the need to address distributional misalignment for reliable commonsense reasoning.
Knowledge graphs (KGs) are structured representations of diversified knowledge. They are widely used in various intelligent applications. In this article, we provide a comprehensive survey on the evolution of various types of knowledge graphs (i.e., static KGs, dynamic KGs, temporal KGs, and event KGs) and techniques for knowledge extraction and reasoning. Furthermore, we introduce the practical applications of different types of KGs, including a case study in financial analysis. Finally, we propose our perspective on the future directions of knowledge engineering, including the potential of combining the power of knowledge graphs and large language models (LLMs), and the evolution of knowledge extraction, reasoning, and representation.
The objective of Entity Alignment (EA) is to identify equivalent entity pairs from multiple Knowledge Graphs (KGs) and create a more comprehensive and unified KG. The majority of EA methods have primarily focused on the structural modality of KGs, lacking exploration of multi-modal information. A few multi-modal EA methods have made good attempts in this field. Still, they have two shortcomings: (1) inconsistent and inefficient modality modeling that designs complex and distinct models for each modality; (2) ineffective modality fusion due to the heterogeneous nature of modalities in EA. To tackle these challenges, we propose PathFusion, consisting of two main components: (1) MSP, a unified modeling approach that simplifies the alignment process by constructing paths connecting entities and modality nodes to represent multiple modalities; (2) IRF, an iterative fusion method that effectively combines information from different modalities using the path as an information carrier. Experimental results on real-world datasets demonstrate the superiority of PathFusion over state-of-the-art methods, with 22.4%-28.9% absolute improvement on Hits@1, and 0.194-0.245 absolute improvement on MRR.
Efficiently finding doctors and locations is an important search problem for patients in the healthcare domain, for which traditional information retrieval methods tend not to work optimally. In the last ten years, knowledge graphs (KGs) have emerged as a powerful way to combine the benefits of gleaning insights from semi-structured data using semantic modeling, natural language processing techniques like information extraction, and robust querying using structured query languages like SPARQL and Cypher. In this short paper, we present a KG-based search engine architecture for robustly finding doctors and locations in the healthcare domain. Early results demonstrate that our approach can lead to significantly higher coverage for complex queries without degrading quality.
Clinical decision-making is a fundamental stage in delivering appropriate care to patients. In recent years several decision-making systems designed to aid the clinician in this process have been developed. However, technical solutions currently in use are based on simple regression models and are only able to take into account simple pre-defined multiple-choice features, such as patient age, pre-existing conditions, smoker status, etc. One particular source of patient data, that available decision-making systems are incapable of processing is the collection of patient consultation GP notes. These contain crucial signs and symptoms - the information used by clinicians in order to make a final decision and direct the patient to the appropriate care. Extracting information from GP notes is a technically challenging problem, as they tend to include abbreviations, typos, and incomplete sentences. This paper addresses this open challenge. We present a framework that performs knowledge graph construction from raw GP medical notes written during or after patient consultations. By relying on support phrases mined from the SNOMED ontology, as well as predefined supported facts from values used in the RECAP (REmote COVID-19 Assessment in Primary Care) patient risk prediction tool, our graph generative framework is able to extract structured knowledge graphs from the highly unstructured and inconsistent format that consultation notes are written in. Our knowledge graphs include information about existing patient symptoms, their duration, and their severity. We apply our framework to consultation notes of COVID-19 patients in the UK COVID-19 Clinical Assesment Servcie (CCAS) patient dataset. We provide a quantitative evaluation of the performance of our framework, demonstrating that our approach has better accuracy than traditional NLP methods when answering questions about patients.
Ontology matching (OM) entails the identification of semantic relationships between concepts within two or more knowledge graphs (KGs) and serves as a critical step in integrating KGs from various sources. Recent advancements in deep OM models have harnessed the power of transformer-based language models and the advantages of knowledge graph embedding. Nevertheless, these OM models still face persistent challenges, such as a lack of reference alignments, runtime latency, and unexplored different graph structures within an end-to-end framework. In this study, we introduce a novel self-supervised learning OM framework with input ontologies, called LaKERMap. This framework capitalizes on the contextual and structural information of concepts by integrating implicit knowledge into transformers. Specifically, we aim to capture multiple structural contexts, encompassing both local and global interactions, by employing distinct training objectives. To assess our methods, we utilize the Bio-ML datasets and tasks. The findings from our innovative approach reveal that LaKERMap surpasses state-of-the-art systems in terms of alignment quality and inference time. Our models and codes are available here: https://github.com/ellenzhuwang/lakermap.
Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.
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.
Knowledge graphs (KGs) have emerged as a powerful framework for representing and integrating complex biomedical information. However, assembling KGs from diverse sources remains a significant challenge in several aspects, including entity alignment, scalability, and the need for continuous updates to keep pace with scientific advancements. Moreover, the representative power of KGs is often limited by the scarcity of multi-modal data integration. To overcome these challenges, we propose Know2BIO, a general-purpose heterogeneous KG benchmark for the biomedical domain. Know2BIO integrates data from 30 diverse sources, capturing intricate relationships across 11 biomedical categories. It currently consists of ~219,000 nodes and ~6,200,000 edges. Know2BIO is capable of user-directed automated updating to reflect the latest knowledge in biomedical science. Furthermore, Know2BIO is accompanied by multi-modal data: node features including text descriptions, protein and compound sequences and structures, enabling the utilization of emerging natural language processing methods and multi-modal data integration strategies. We evaluate KG representation models on Know2BIO, demonstrating its effectiveness as a benchmark for KG representation learning in the biomedical field. Data and source code of Know2BIO are available at https://github.com/Yijia-Xiao/Know2BIO/.
Recently, it has been shown that the incorporation of structured knowledge into Large Language Models significantly improves the results for a variety of NLP tasks. In this paper, we propose a method for exploring pre-trained Text-to-Text Language Models enriched with additional information from Knowledge Graphs for answering factoid questions. More specifically, we propose an algorithm for subgraphs extraction from a Knowledge Graph based on question entities and answer candidates. Then, we procure easily interpreted information with Transformer-based models through the linearization of the extracted subgraphs. Final re-ranking of the answer candidates with the extracted information boosts Hits@1 scores of the pre-trained text-to-text language models by 4-6%.
Temporal heterogeneous networks (THNs) are evolving networks that characterize many real-world applications such as citation and events networks, recommender systems, and knowledge graphs. Although different Graph Neural Networks (GNNs) have been successfully applied to dynamic graphs, most of them only support homogeneous graphs or suffer from model design heavily influenced by specific THNs prediction tasks. Furthermore, there is a lack of temporal heterogeneous networked data in current standard graph benchmark datasets. Hence, in this work, we propose DURENDAL, a graph deep learning framework for THNs. DURENDAL can help to easily repurpose any heterogeneous graph learning model to evolving networks by combining design principles from snapshot-based and multirelational message-passing graph learning models. We introduce two different schemes to update embedding representations for THNs, discussing the strengths and weaknesses of both strategies. We also extend the set of benchmarks for TNHs by introducing two novel high-resolution temporal heterogeneous graph datasets derived from an emerging Web3 platform and a well-established e-commerce website. Overall, we conducted the experimental evaluation of the framework over four temporal heterogeneous network datasets on future link prediction tasks in an evaluation setting that takes into account the evolving nature of the data. Experiments show the prediction power of DURENDAL compared to current solutions for evolving and dynamic graphs, and the effectiveness of its model design.
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 \textbf{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.