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Register a new userNeural Multi-Hop Reasoning With Logical Rules on Biomedical Knowledge Graphs
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Added by
Yushan Liu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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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 approach outperforms several baseline methods.
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 limitation of present methods is also that they cannot naturally model uncertainty. Here, we present BetaE, a probabilistic embedding framework for answering arbitrary FOL queries over KGs. BetaE is the first method that can handle a complete set of first-order logical operations: conjunction ($wedge$), disjunction ($vee$), and negation ($ eg$). A key insight of BetaE is to use probabilistic distributions with bounded support, specifically the Beta distribution, and embed queries/entities as distributions, which as a consequence allows us to also faithfully model uncertainty. Logical operations are performed in the embedding space by neural operators over the probabilistic embeddings. We demonstrate the performance of BetaE on answering arbitrary FOL queries on three large, incomplete KGs. While being more general, BetaE also increases relative performance by up to 25.4% over the current state-of-the-art KG reasoning methods that can only handle conjunctive queries without negation.
Despite the success of generative pre-trained language models on a series of text generation tasks, they still suffer in cases where reasoning over underlying commonsense knowledge is required during generation. Existing approaches that integrate commonsense knowledge into generative pre-trained language models simply transfer relational knowledge by post-training on individual knowledge triples while ignoring rich connections within the knowledge graph. We argue that exploiting both the structural and semantic information of the knowledge graph facilitates commonsense-aware text generation. In this paper, we propose Generation with Multi-Hop Reasoning Flow (GRF) that enables pre-trained models with dynamic multi-hop reasoning on multi-relational paths extracted from the external commonsense knowledge graph. We empirically show that our model outperforms existing baselines on three text generation tasks that require reasoning over commonsense knowledge. We also demonstrate the effectiveness of the dynamic multi-hop reasoning module with reasoning paths inferred by the model that provide rationale to the generation.
This paper studies learning logic rules for reasoning on knowledge graphs. Logic rules provide interpretable explanations when used for prediction as well as being able to generalize to other tasks, and hence are critical to learn. Existing methods either suffer from the problem of searching in a large search space (e.g., neural logic programming) or ineffective optimization due to sparse rewards (e.g., techniques based on reinforcement learning). To address these limitations, this paper proposes a probabilistic model called RNNLogic. RNNLogic treats logic rules as a latent variable, and simultaneously trains a rule generator as well as a reasoning predictor with logic rules. We develop an EM-based algorithm for optimization. In each iteration, the reasoning predictor is first updated to explore some generated logic rules for reasoning. Then in the E-step, we select a set of high-quality rules from all generated rules with both the rule generator and reasoning predictor via posterior inference; and in the M-step, the rule generator is updated with the rules selected in the E-step. Experiments on four datasets prove the effectiveness of RNNLogic.
Large scale knowledge graphs (KGs) such as Freebase are generally incomplete. Reasoning over multi-hop (mh) KG paths is thus an important capability that is needed for question answering or other NLP tasks that require knowledge about the world. mh-KG reasoning includes diverse scenarios, e.g., given a head entity and a relation path, predict the tail entity; or given two entities connected by some relation paths, predict the unknown relation between them. We present ROPs, recurrent one-hop predictors, that predict entities at each step of mh-KB paths by using recurrent neural networks and vector representations of entities and relations, with two benefits: (i) modeling mh-paths of arbitrary lengths while updating the entity and relation representations by the training signal at each step; (ii) handling different types of mh-KG reasoning in a unified framework. Our models show state-of-the-art for two important multi-hop KG reasoning tasks: Knowledge Base Completion and Path Query Answering.
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