Clinicians are increasingly looking towards machine learning to gain insights about patient evolutions. We propose a novel approach named Multi-Modal UMLS Graph Learning (MMUGL) for learning meaningful representations of medical concepts using graph neural networks over knowledge graphs based on the unified medical language system. These representations are aggregated to represent entire patient visits and then fed into a sequence model to perform predictions at the granularity of multiple hospital visits of a patient. We improve performance by incorporating prior medical knowledge and considering multiple modalities. We compare our method to existing architectures proposed to learn representations at different granularities on the MIMIC-III dataset and show that our approach outperforms these methods. The results demonstrate the significance of multi-modal medical concept representations based on prior medical knowledge.
Recent work within the Argument Mining community has shown the applicability of Natural Language Processing systems for solving problems found within competitive debate. One of the most important tasks within competitive debate is for debaters to create high quality debate cases. We show that effective debate cases can be constructed using constrained shortest path traversals on Argumentative Semantic Knowledge Graphs. We study this potential in the context of a type of American Competitive Debate, called Policy Debate, which already has a large scale dataset targeting it called DebateSum. We significantly improve upon DebateSum by introducing 53180 new examples, as well as further useful metadata for every example, to the dataset. We leverage the txtai semantic search and knowledge graph toolchain to produce and contribute 9 semantic knowledge graphs built on this dataset. We create a unique method for evaluating which knowledge graphs are better in the context of producing policy debate cases. A demo which automatically generates debate cases, along with all other code and the Knowledge Graphs, are open-sourced and made available to the public here: https://huggingface.co/spaces/Hellisotherpeople/DebateKG
Few-shot inductive link prediction on knowledge graphs (KGs) aims to predict missing links for unseen entities with few-shot links observed. Previous methods are limited to transductive scenarios, where entities exist in the knowledge graphs, so they are unable to handle unseen entities. Therefore, recent inductive methods utilize the sub-graphs around unseen entities to obtain the semantics and predict links inductively. However, in the few-shot setting, the sub-graphs are often sparse and cannot provide meaningful inductive patterns. In this paper, we propose a novel relational anonymous walk-guided neural process for few-shot inductive link prediction on knowledge graphs, denoted as RawNP. Specifically, we develop a neural process-based method to model a flexible distribution over link prediction functions. This enables the model to quickly adapt to new entities and estimate the uncertainty when making predictions. To capture general inductive patterns, we present a relational anonymous walk to extract a series of relational motifs from few-shot observations. These motifs reveal the distinctive semantic patterns on KGs that support inductive predictions. Extensive experiments on typical benchmark datasets demonstrate that our model derives new state-of-the-art performance.
In order to construct or extend entity-centric and event-centric knowledge graphs (KG and EKG), the information extraction (IE) annotation toolkit is essential. However, existing IE toolkits have several non-trivial problems, such as not supporting multi-tasks, not supporting automatic updates. In this work, we present CollabKG, a learnable human-machine-cooperative IE toolkit for KG and EKG construction. Specifically, for the multi-task issue, CollabKG unifies different IE subtasks, including named entity recognition (NER), entity-relation triple extraction (RE), and event extraction (EE), and supports both KG and EKG. Then, combining advanced prompting-based IE technology, the human-machine-cooperation mechanism with LLMs as the assistant machine is presented which can provide a lower cost as well as a higher performance. Lastly, owing to the two-way interaction between the human and machine, CollabKG with learning ability allows self-renewal. Besides, CollabKG has several appealing features (e.g., customization, training-free, propagation, etc.) that make the system powerful, easy-to-use, and high-productivity. We holistically compare our toolkit with other existing tools on these features. Human evaluation quantitatively illustrates that CollabKG significantly improves annotation quality, efficiency, and stability simultaneously.
AI legal assistants based on Large Language Models (LLMs) can provide accessible legal consulting services, but the hallucination problem poses potential legal risks. This paper presents Chatlaw, an innovative legal assistant utilizing a Mixture-of-Experts (MoE) model and a multi-agent system to enhance the reliability and accuracy of AI-driven legal services. By integrating knowledge graphs with artificial screening, we construct a high-quality legal dataset to train the MoE model. This model utilizes different experts to address various legal issues, optimizing the accuracy of legal responses. Additionally, Standardized Operating Procedures (SOP), modeled after real law firm workflows, significantly reduce errors and hallucinations in legal services. Our MoE model outperforms GPT-4 in the Lawbench and Unified Qualification Exam for Legal Professionals by 7.73% in accuracy and 11 points, respectively, and also surpasses other models in multiple dimensions during real-case consultations, demonstrating our robust capability for legal consultation.
This paper presents a translation-based knowledge geraph embedding method via efficient relation rotation (TransERR), a straightforward yet effective alternative to traditional translation-based knowledge graph embedding models. Different from the previous translation-based models, TransERR encodes knowledge graphs in the hypercomplex-valued space, thus enabling it to possess a higher degree of translation freedom in mining latent information between the head and tail entities. To further minimize the translation distance, TransERR adaptively rotates the head entity and the tail entity with their corresponding unit quaternions, which are learnable in model training. We also provide mathematical proofs to demonstrate the ability of TransERR in modeling various relation patterns, including symmetry, antisymmetry, inversion, composition, and subrelation patterns. The experiments on 10 benchmark datasets validate the effectiveness and the generalization of TransERR. The results also indicate that TransERR can better encode large-scale datasets with fewer parameters than the previous translation-based models. Our code and datasets are available at~\url{https://github.com/dellixx/TransERR}.
Knowledge graphs (KGs), as structured representations of real world facts, are intelligent databases incorporating human knowledge that can help machine imitate the way of human problem solving. However, KGs are usually huge and there are inevitably missing facts in KGs, thus undermining applications such as question answering and recommender systems that are based on knowledge graph reasoning. Link prediction for knowledge graphs is the task aiming to complete missing facts by reasoning based on the existing knowledge. Two main streams of research are widely studied: one learns low-dimensional embeddings for entities and relations that can explore latent patterns, and the other gains good interpretability by mining logical rules. Unfortunately, the heterogeneity of modern KGs that involve entities and relations of various types is not well considered in the previous studies. In this paper, we propose DegreEmbed, a model that combines embedding-based learning and logic rule mining for inferring on KGs. Specifically, we study the problem of predicting missing links in heterogeneous KGs from the perspective of the degree of nodes. Experimentally, we demonstrate that our DegreEmbed model outperforms the state-of-the-art methods on real world datasets and the rules mined by our model are of high quality and interpretability.
The proliferation of open knowledge graphs has led to a surge in scholarly research on the topic over the past decade. This paper presents a bibliometric analysis of the scholarly literature on open knowledge graphs published between 2013 and 2023. The study aims to identify the trends, patterns, and impact of research in this field, as well as the key topics and research questions that have emerged. The work uses bibliometric techniques to analyze a sample of 4445 scholarly articles retrieved from Scopus. The findings reveal an ever-increasing number of publications on open knowledge graphs published every year, particularly in developed countries (+50 per year). These outputs are published in highly-referred scholarly journals and conferences. The study identifies three main research themes: (1) knowledge graph construction and enrichment, (2) evaluation and reuse, and (3) fusion of knowledge graphs into NLP systems. Within these themes, the study identifies specific tasks that have received considerable attention, including entity linking, knowledge graph embedding, and graph neural networks.
Knowledge graphs (KGs), containing many entity-relation-entity triples, provide rich information for downstream applications. Although extracting triples from unstructured texts has been widely explored, most of them require a large number of labeled instances. The performance will drop dramatically when only few labeled data are available. To tackle this problem, we propose the Mutually Guided Few-shot learning framework for Relational Triple Extraction (MG-FTE). Specifically, our method consists of an entity-guided relation proto-decoder to classify the relations firstly and a relation-guided entity proto-decoder to extract entities based on the classified relations. To draw the connection between entity and relation, we design a proto-level fusion module to boost the performance of both entity extraction and relation classification. Moreover, a new cross-domain few-shot triple extraction task is introduced. Extensive experiments show that our method outperforms many state-of-the-art methods by 12.6 F1 score on FewRel 1.0 (single-domain) and 20.5 F1 score on FewRel 2.0 (cross-domain).
Recent research on predicting the binding affinity between drug molecules and proteins use representations learned, through unsupervised learning techniques, from large databases of molecule SMILES and protein sequences. While these representations have significantly enhanced the predictions, they are usually based on a limited set of modalities, and they do not exploit available knowledge about existing relations among molecules and proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results for drug-target binding affinity prediction in the established Therapeutic Data Commons (TDC) benchmarks. We release a set of multimodal knowledge graphs, integrating data from seven public data sources, and containing over 30 million triples. Our intention is to foster additional research to explore how multimodal knowledge enhanced protein/molecule embeddings can improve prediction tasks, including prediction of binding affinity. We also release some pretrained models learned from our multimodal knowledge graphs, along with source code for running standard benchmark tasks for prediction of biding affinity.
Knowledge graphs represent real-world entities and their relations in a semantically-rich structure supported by ontologies. Exploring this data with machine learning methods often relies on knowledge graph embeddings, which produce latent representations of entities that preserve structural and local graph neighbourhood properties, but sacrifice explainability. However, in tasks such as link or relation prediction, understanding which specific features better explain a relation is crucial to support complex or critical applications. We propose SEEK, a novel approach for explainable representations to support relation prediction in knowledge graphs. It is based on identifying relevant shared semantic aspects (i.e., subgraphs) between entities and learning representations for each subgraph, producing a multi-faceted and explainable representation. We evaluate SEEK on two real-world highly complex relation prediction tasks: protein-protein interaction prediction and gene-disease association prediction. Our extensive analysis using established benchmarks demonstrates that SEEK achieves significantly better performance than standard learning representation methods while identifying both sufficient and necessary explanations based on shared semantic aspects.
Entity Linking (EL) is a fundamental task for Information Extraction and Knowledge Graphs. The general form of EL (i.e., end-to-end EL) aims to first find mentions in the given input document and then link the mentions to corresponding entities in a specific knowledge base. Recently, the paradigm of retriever-reader promotes the progress of end-to-end EL, benefiting from the advantages of dense entity retrieval and machine reading comprehension. However, the existing study only trains the retriever and the reader separately in a pipeline manner, which ignores the benefit that the interaction between the retriever and the reader can bring to the task. To advance the retriever-reader paradigm to perform more perfectly on end-to-end EL, we propose BEER$^2$, a Bidirectional End-to-End training framework for Retriever and Reader. Through our designed bidirectional end-to-end training, BEER$^2$ guides the retriever and the reader to learn from each other, make progress together, and ultimately improve EL performance. Extensive experiments on benchmarks of multiple domains demonstrate the effectiveness of our proposed BEER$^2$.
Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical domain. Several methods have been proposed for learning embeddings that can be used to predict new links in such graphs. Some methods ignore valuable attribute data associated with entities in biomedical KGs, such as protein sequences, or molecular graphs. Other works incorporate such data, but assume that entities can be represented with the same data modality. This is not always the case for biomedical KGs, where entities exhibit heterogeneous modalities that are central to their representation in the subject domain. We propose a modular framework for learning embeddings in KGs with entity attributes, that allows encoding attribute data of different modalities while also supporting entities with missing attributes. We additionally propose an efficient pretraining strategy for reducing the required training runtime. We train models using a biomedical KG containing approximately 2 million triples, and evaluate the performance of the resulting entity embeddings on the tasks of link prediction, and drug-protein interaction prediction, comparing against methods that do not take attribute data into account. In the standard link prediction evaluation, the proposed method results in competitive, yet lower performance than baselines that do not use attribute data. When evaluated in the task of drug-protein interaction prediction, the method compares favorably with the baselines. We find settings involving low degree entities, which make up for a substantial amount of the set of entities in the KG, where our method outperforms the baselines. Our proposed pretraining strategy yields significantly higher performance while reducing the required training runtime. Our implementation is available at https://github.com/elsevier-AI-Lab/BioBLP .
In this paper, we present the ``joint pre-training and local re-training'' framework for learning and applying multi-source knowledge graph (KG) embeddings. We are motivated by the fact that different KGs contain complementary information to improve KG embeddings and downstream tasks. We pre-train a large teacher KG embedding model over linked multi-source KGs and distill knowledge to train a student model for a task-specific KG. To enable knowledge transfer across different KGs, we use entity alignment to build a linked subgraph for connecting the pre-trained KGs and the target KG. The linked subgraph is re-trained for three-level knowledge distillation from the teacher to the student, i.e., feature knowledge distillation, network knowledge distillation, and prediction knowledge distillation, to generate more expressive embeddings. The teacher model can be reused for different target KGs and tasks without having to train from scratch. We conduct extensive experiments to demonstrate the effectiveness and efficiency of our framework.
Intelligent Traffic Monitoring (ITMo) technologies hold the potential for improving road safety/security and for enabling smart city infrastructure. Understanding traffic situations requires a complex fusion of perceptual information with domain-specific and causal commonsense knowledge. Whereas prior work has provided benchmarks and methods for traffic monitoring, it remains unclear whether models can effectively align these information sources and reason in novel scenarios. To address this assessment gap, we devise three novel text-based tasks for situational reasoning in the traffic domain: i) BDD-QA, which evaluates the ability of Language Models (LMs) to perform situational decision-making, ii) TV-QA, which assesses LMs' abilities to reason about complex event causality, and iii) HDT-QA, which evaluates the ability of models to solve human driving exams. We adopt four knowledge-enhanced methods that have shown generalization capability across language reasoning tasks in prior work, based on natural language inference, commonsense knowledge-graph self-supervision, multi-QA joint training, and dense retrieval of domain information. We associate each method with a relevant knowledge source, including knowledge graphs, relevant benchmarks, and driving manuals. In extensive experiments, we benchmark various knowledge-aware methods against the three datasets, under zero-shot evaluation; we provide in-depth analyses of model performance on data partitions and examine model predictions categorically, to yield useful insights on traffic understanding, given different background knowledge and reasoning strategies.
Link prediction on knowledge graphs (KGs) has been extensively studied on binary relational KGs, wherein each fact is represented by a triple. A significant amount of important knowledge, however, is represented by hyper-relational facts where each fact is composed of a primal triple and a set of qualifiers comprising a key-value pair that allows for expressing more complicated semantics. Although some recent works have proposed to embed hyper-relational KGs, these methods fail to capture essential inference patterns of hyper-relational facts such as qualifier monotonicity, qualifier implication, and qualifier mutual exclusion, limiting their generalization capability. To unlock this, we present \emph{ShrinkE}, a geometric hyper-relational KG embedding method aiming to explicitly model these patterns. ShrinkE models the primal triple as a spatial-functional transformation from the head into a relation-specific box. Each qualifier ``shrinks'' the box to narrow down the possible answer set and, thus, realizes qualifier monotonicity. The spatial relationships between the qualifier boxes allow for modeling core inference patterns of qualifiers such as implication and mutual exclusion. Experimental results demonstrate ShrinkE's superiority on three benchmarks of hyper-relational KGs.
Joint representation learning over multi-sourced knowledge graphs (KGs) yields transferable and expressive embeddings that improve downstream tasks. Entity alignment (EA) is a critical step in this process. Despite recent considerable research progress in embedding-based EA, how it works remains to be explored. In this paper, we provide a similarity flooding perspective to explain existing translation-based and aggregation-based EA models. We prove that the embedding learning process of these models actually seeks a fixpoint of pairwise similarities between entities. We also provide experimental evidence to support our theoretical analysis. We propose two simple but effective methods inspired by the fixpoint computation in similarity flooding, and demonstrate their effectiveness on benchmark datasets. Our work bridges the gap between recent embedding-based models and the conventional similarity flooding algorithm. It would improve our understanding of and increase our faith in embedding-based EA.
A complex logic query in a knowledge graph refers to a query expressed in logic form that conveys a complex meaning, such as where did the Canadian Turing award winner graduate from? Knowledge graph reasoning-based applications, such as dialogue systems and interactive search engines, rely on the ability to answer complex logic queries as a fundamental task. In most knowledge graphs, edges are typically used to either describe the relationships between entities or their associated attribute values. An attribute value can be in categorical or numerical format, such as dates, years, sizes, etc. However, existing complex query answering (CQA) methods simply treat numerical values in the same way as they treat entities. This can lead to difficulties in answering certain queries, such as which Australian Pulitzer award winner is born before 1927, and which drug is a pain reliever and has fewer side effects than Paracetamol. In this work, inspired by the recent advances in numerical encoding and knowledge graph reasoning, we propose numerical complex query answering. In this task, we introduce new numerical variables and operations to describe queries involving numerical attribute values. To address the difference between entities and numerical values, we also propose the framework of Number Reasoning Network (NRN) for alternatively encoding entities and numerical values into separate encoding structures. During the numerical encoding process, NRN employs a parameterized density function to encode the distribution of numerical values. During the entity encoding process, NRN uses established query encoding methods for the original CQA problem. Experimental results show that NRN consistently improves various query encoding methods on three different knowledge graphs and achieves state-of-the-art results.
Inductive knowledge graph completion has been considered as the task of predicting missing triplets between new entities that are not observed during training. While most inductive knowledge graph completion methods assume that all entities can be new, they do not allow new relations to appear at inference time. This restriction prohibits the existing methods from appropriately handling real-world knowledge graphs where new entities accompany new relations. In this paper, we propose an INductive knowledge GRAph eMbedding method, InGram, that can generate embeddings of new relations as well as new entities at inference time. Given a knowledge graph, we define a relation graph as a weighted graph consisting of relations and the affinity weights between them. Based on the relation graph and the original knowledge graph, InGram learns how to aggregate neighboring embeddings to generate relation and entity embeddings using an attention mechanism. Experimental results show that InGram outperforms 14 different state-of-the-art methods on varied inductive learning scenarios.
Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates the limited efficacy of these embedding algorithms when applied to biomedical knowledge graphs, raising the question of whether knowledge graph embeddings have limitations in biomedical settings. This study aims to apply state-of-the-art knowledge graph embedding models in the context of a recent biomedical knowledge graph, BioKG, and evaluate their performance and potential downstream uses. We achieve a three-fold improvement in terms of performance based on the HITS@10 score over previous work on the same biomedical knowledge graph. Additionally, we provide interpretable predictions through a rule-based method. We demonstrate that knowledge graph embedding models are applicable in practice by evaluating the best-performing model on four tasks that represent real-life polypharmacy situations. Results suggest that knowledge learnt from large biomedical knowledge graphs can be transferred to such downstream use cases. Our code is available at https://github.com/aryopg/biokge.