Biomedical knowledge graphs permit an integrative computational approach to reasoning about biological systems. The nature of biological data leads to a graph structure that differs from those typically encountered in benchmarking datasets. To understand the implications this may have on the performance of reasoning algorithms, we conduct an empirical study based on the real-world task of drug repurposing. We formulate this task as a link prediction problem where both compounds and diseases correspond to entities in a knowledge graph. To overcome apparent weaknesses of existing algorithms, we propose a new method, PoLo, that combines policy-guided walks based on reinforcement learning with logical rules. These rules are integrated into the algorithm by using a novel reward function. We apply our method to Hetionet, which integrates biomedical information from 29 prominent bioinformatics databases. Our experiments show that our approach outperforms several state-of-the-art methods for link prediction while providing interpretability.
Siemens AG（西门子股份公司）；Ludwig Maximilian University of Munich（慕尼黑大学）
The graph structure of biomedical data differs from those in typical knowledge graph benchmark tasks. A particular property of biomedical data is the presence of long-range dependencies, which can be captured by patterns described as logical rules. We propose a novel method that combines these rules with a neural multi-hop reasoning approach that uses reinforcement learning. We conduct an empirical study based on the real-world task of drug repurposing by formulating this task as a link prediction problem. We apply our method to the biomedical knowledge graph Hetionet and show that our approac…
For Artificial Intelligence to have a greater impact in biology and medicine, it is crucial that recommendations are both accurate and transparent. In other domains, a neurosymbolic approach of multi-hop reasoning on knowledge graphs has been shown to produce transparent explanations. However, there is a lack of research applying it to complex biomedical datasets and problems. In this paper, the approach is explored for drug discovery to draw solid conclusions on its applicability. For the first time, we systematically apply it to multiple biomedical datasets and recommendation tasks with fair…
Biomedical knowledge graphs (KG) are heterogenous networks consisting of biological entities as nodes and relations between them as edges. These entities and relations are extracted from millions of research papers and unified in a single resource. The goal of biomedical multi-hop question-answering over knowledge graph (KGQA) is to help biologist and scientist to get valuable insights by asking questions in natural language. Relevant answers can be found by first understanding the question and then querying the KG for right set of nodes and relationships to arrive at an answer. To model the q…
State-of-the-art approaches to reasoning and question answering over knowledge graphs (KGs) usually scale with the number of edges and can only be applied effectively on small instance-dependent subgraphs. In this paper, we address this issue by showing that multi-hop and more complex logical reasoning can be accomplished separately without losing expressive power. Motivated by this insight, we propose an approach to multi-hop reasoning that scales linearly with the number of relation types in the graph, which is usually significantly smaller than the number of edges or nodes. This produces a …
One of the fundamental problems in Artificial Intelligence is to perform complex multi-hop logical reasoning over the facts captured by a knowledge graph (KG). This problem is challenging, because KGs can be massive and incomplete. Recent approaches embed KG entities in a low dimensional space and then use these embeddings to find the answer entities. However, it has been an outstanding challenge of how to handle arbitrary first-order logic (FOL) queries as present methods are limited to only a subset of FOL operators. In particular, the negation operator is not supported. An additional limita…
Global Health Drug Discovery Institute（全球健康药物研发中心）
Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify hidden biological interactions and relationshipts between key entities such as compounds, targets, gene and diseases. We propose a Graph Neural Networks (GNN) method, namely Graph Pair based Link Prediction model (GPLP), for predicting biomedical network links simply based on their topological interaction information. In GPLP, 1-hop subgraphs extracted from kno…
DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge Graph Research
Keiji AI；Institute of Scientific and Industrial Research, Osaka University（大阪大学科学工业研究所）；Bioinformatics Center, Institute for Chemical Research, Kyoto University（京都大学化学研究所生物信息中心）；Division of Intramural Research, National Library of Medicine, National Institutes of Health（国家卫生研究院生物医学图书馆内部研究部）；Department of Population Health Sciences, Weill Cornell Medicine（韦尔·科恩医学中心流行病学与健康科学系）；School of Computing and Data Science, University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校计算机与数据科学学院）
Reasoning is a fundamental problem for computers and deeply studied in Artificial Intelligence. In this paper, we specifically focus on answering multi-hop logical queries on Knowledge Graphs (KGs). This is a complicated task because, in real-world scenarios, the graphs tend to be large and incomplete. Most previous works have been unable to create models that accept full First-Order Logical (FOL) queries, which include negative queries, and have only been able to process a limited set of query structures. Additionally, most methods present logic operators that can only perform the logical ope…
Stanford University（斯坦福大学）；Intel AI Lab（英特尔人工智能实验室）；Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）；Mila - Québec AI Institute（米拉-魁北克人工智能研究所）；Université de Montréal（蒙特利尔大学）
Complex logical query answering (CLQA) is a recently emerged task of graph machine learning that goes beyond simple one-hop link prediction and solves a far more complex task of multi-hop logical reasoning over massive, potentially incomplete graphs in a latent space. The task received a significant traction in the community; numerous works expanded the field along theoretical and practical axes to tackle different types of complex queries and graph modalities with efficient systems. In this paper, we provide a holistic survey of CLQA with a detailed taxonomy studying the field from multiple a…
Mila - Québec AI Institute（米拉-魁北克人工智能研究所）；Université de Montréal（蒙特利尔大学）；McGill University（麦吉尔大学）；HEC Montréal（蒙特利尔高等商学院）；CIFAR AI Chair（加拿大高等研究院人工智能讲席）
Answering complex first-order logic (FOL) queries on knowledge graphs is a fundamental task for multi-hop reasoning. Traditional symbolic methods traverse a complete knowledge graph to extract the answers, which provides good interpretation for each step. Recent neural methods learn geometric embeddings for complex queries. These methods can generalize to incomplete knowledge graphs, but their reasoning process is hard to interpret. In this paper, we propose Graph Neural Network Query Executor (GNN-QE), a neural-symbolic model that enjoys the advantages of both worlds. GNN-QE decomposes a comp…
Quebec Artificial Intelligence Institute (Mila)（魁北克人工智能研究所（Mila））；Polytechnique Montreal（蒙特利尔理工学院）；ServiceNow Research（ServiceNow研究院）；McGill University（麦吉尔大学）
We study the utility of incorporating entity type abstractions into pre-trained Transformers and test these methods on four NLP tasks requiring different forms of logical reasoning: (1) compositional language understanding with text-based relational reasoning (CLUTRR), (2) abductive reasoning (ProofWriter), (3) multi-hop question answering (HotpotQA), and (4) conversational question answering (CoQA). We propose and empirically explore three ways to add such abstraction: (i) as additional input embeddings, (ii) as a separate sequence to encode, and (iii) as an auxiliary prediction task for the …
Shanxi University（山西大学）；Cardiff University（卡迪夫大学）；A*STAR（新加坡科技研究局）；University of Edinburgh（爱丁堡大学）
Multi-hop reasoning over real-life knowledge graphs (KGs) is a highly challenging problem as traditional subgraph matching methods are not capable to deal with noise and missing information. To address this problem, it has been recently introduced a promising approach based on jointly embedding logical queries and KGs into a low-dimensional space to identify answer entities. However, existing proposals ignore critical semantic knowledge inherently available in KGs, such as type information. To leverage type information, we propose a novel TypE-aware Message Passing (TEMP) model, which enhances…
Pathformer: Recursive Path Query Encoding for Complex Logical Query Answering
School of Computer Science and Engineering, South China University of Technology（华南理工大学计算机科学与工程学院）；Guangdong University of Petrochemical Technology（广东石油化工学院）；Jiangmen Polytechnic（江门职业技术学院）
Multi-hop logical reasoning is an established problem in the field of representation learning on knowledge graphs (KGs). It subsumes both one-hop link prediction as well as other more complex types of logical queries. Existing algorithms operate only on classical, triple-based graphs, whereas modern KGs often employ a hyper-relational modeling paradigm. In this paradigm, typed edges may have several key-value pairs known as qualifiers that provide fine-grained context for facts. In queries, this context modifies the meaning of relations, and usually reduces the answer set. Hyper-relational que…
Fact or Guesswork? Evaluating Large Language Models' Medical Knowledge with Structured One-Hop Judgments
University of Georgia（佐治亚大学）；University of California, Merced（加州大学默塞德分校）；Lehigh University（莱特大学）；The University of Queensland（昆士兰大学）；National University of Singapore（新加坡国立大学）；University of California, Los Angeles（加州大学洛杉矶分校）
Multi-modal Representation Learning Enables Accurate Protein Function Prediction in Low-Data Setting
Karadeniz Technical University（卡拉德尼兹技术大学）；Middle East Technical University（中东技术大学）；Health Sciences University Trabzon Kanuni Training and Research Hospital（特拉布宗卡努尼健康科学大学培训与研究医院）；Hacettepe University（哈杰泰佩大学）
Language model (LM) pretraining can learn various knowledge from text corpora, helping downstream tasks. However, existing methods such as BERT model a single document, and do not capture dependencies or knowledge that span across documents. In this work, we propose LinkBERT, an LM pretraining method that leverages links between documents, e.g., hyperlinks. Given a text corpus, we view it as a graph of documents and create LM inputs by placing linked documents in the same context. We then pretrain the LM with two joint self-supervised objectives: masked language modeling and our new proposal, …
KAUST（阿卜杜拉国王科技大学）；University of Notre Dame（圣母大学）；Beihang University（北京航空航天大学）
Many ontologies, i.e., Description Logic (DL) knowledge bases, have been developed to provide rich knowledge about various domains. An ontology consists of an ABox, i.e., assertion axioms between two entities or between a concept and an entity, and a TBox, i.e., terminology axioms between two concepts. Neural logical reasoning (NLR) is a fundamental task to explore such knowledge bases, which aims at answering multi-hop queries with logical operations based on distributed representations of queries and answers. While previous NLR methods can give specific entity-level answers, i.e., ABox answe…
Knowledge graphs (KGs) capture knowledge in the form of head--relation--tail triples and are a crucial component in many AI systems. There are two important reasoning tasks on KGs: (1) single-hop knowledge graph completion, which involves predicting individual links in the KG; and (2), multi-hop reasoning, where the goal is to predict which KG entities satisfy a given logical query. Embedding-based methods solve both tasks by first computing an embedding for each entity and relation, then using them to form predictions. However, existing scalable KG embedding frameworks only support single-hop…
Knowledge Graphs (KGs) are ubiquitous structures for information storagein several real-world applications such as web search, e-commerce, social networks, and biology. Querying KGs remains a foundational and challenging problem due to their size and complexity. Promising approaches to tackle this problem include embedding the KG units (e.g., entities and relations) in a Euclidean space such that the query embedding contains the information relevant to its results. These approaches, however, fail to capture the hierarchical nature and semantic information of the entities present in the graph. …
University of Oxford（牛津大学）；University College London（伦敦大学学院）；Bloomsbury AI（布卢姆斯伯里人工智能公司）
We introduce neural networks for end-to-end differentiable proving of queries to knowledge bases by operating on dense vector representations of symbols. These neural networks are constructed recursively by taking inspiration from the backward chaining algorithm as used in Prolog. Specifically, we replace symbolic unification with a differentiable computation on vector representations of symbols using a radial basis function kernel, thereby combining symbolic reasoning with learning subsymbolic vector representations. By using gradient descent, the resulting neural network can be trained to in…
