Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Automatic Synonym Discovery with Knowledge Bases

Recognizing entity synonyms from text has become a crucial task in many entity-leveraging applications. However, discovering entity synonyms from domain-specific text corpora (e.g., news articles, scientific papers) is rather challenging. Current systems take an entity name string as input to find out other names that are synonymous, ignoring the fact that often times a name string can refer to multiple entities (e.g., "apple" could refer to both Apple Inc and the fruit apple). Moreover, most existing methods require training data manually created by domain experts to construct supervised-learning systems. In this paper, we study the problem of automatic synonym discovery with knowledge bases, that is, identifying synonyms for knowledge base entities in a given domain-specific corpus. The manually-curated synonyms for each entity stored in a knowledge base not only form a set of name strings to disambiguate the meaning for each other, but also can serve as "distant" supervision to help determine important features for the task. We propose a novel framework, called DPE, to integrate two kinds of mutually-complementing signals for synonym discovery, i.e., distributional features based on corpus-level statistics and textual patterns based on local contexts. In particular, DPE jointly optimizes the two kinds of signals in conjunction with distant supervision, so that they can mutually enhance each other in the training stage. At the inference stage, both signals will be utilized to discover synonyms for the given entities. Experimental results prove the effectiveness of the proposed framework

Learning Relation Prototype from Unlabeled Texts for Long-tail Relation Extraction

Relation Extraction (RE) is a vital step to complete Knowledge Graph (KG) by extracting entity relations from texts.However, it usually suffers from the long-tail issue. The training data mainly concentrates on a few types of relations, leading to the lackof sufficient annotations for the remaining types of relations. In this paper, we propose a general approach to learn relation prototypesfrom unlabeled texts, to facilitate the long-tail relation extraction by transferring knowledge from the relation types with sufficient trainingdata. We learn relation prototypes as an implicit factor between entities, which reflects the meanings of relations as well as theirproximities for transfer learning. Specifically, we construct a co-occurrence graph from texts, and capture both first-order andsecond-order entity proximities for embedding learning. Based on this, we further optimize the distance from entity pairs tocorresponding prototypes, which can be easily adapted to almost arbitrary RE frameworks. Thus, the learning of infrequent or evenunseen relation types will benefit from semantically proximate relations through pairs of entities and large-scale textual information.We have conducted extensive experiments on two publicly available datasets: New York Times and Google Distant Supervision.Compared with eight state-of-the-art baselines, our proposed model achieves significant improvements (4.1% F1 on average). Furtherresults on long-tail relations demonstrate the effectiveness of the learned relation prototypes. We further conduct an ablation study toinvestigate the impacts of varying components, and apply it to four basic relation extraction models to verify the generalization ability.Finally, we analyze several example cases to give intuitive impressions as qualitative analysis. Our codes will be released later

Improving Neural Relation Extraction with Implicit Mutual Relations

Relation extraction (RE) aims at extracting the relation between two entities from the text corpora. It is a crucial task for Knowledge Graph (KG) construction. Most existing methods predict the relation between an entity pair by learning the relation from the training sentences, which contain the targeted entity pair. In contrast to existing distant supervision approaches that suffer from insufficient training corpora to extract relations, our proposal of mining implicit mutual relation from the massive unlabeled corpora transfers the semantic information of entity pairs into the RE model, which is more expressive and semantically plausible. After constructing an entity proximity graph based on the implicit mutual relations, we preserve the semantic relations of entity pairs via embedding each vertex of the graph into a low-dimensional space. As a result, we can easily and flexibly integrate the implicit mutual relations and other entity information, such as entity types, into the existing RE methods. Our experimental results on a New York Times and another Google Distant Supervision datasets suggest that our proposed neural RE framework provides a promising improvement for the RE task, and significantly outperforms the state-of-the-art methods. Moreover, the component for mining implicit mutual relations is so flexible that can help to improve the performance of both CNN-based and RNN-based RE models significant.Comment: 12 page