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

エンティティ・リンキングのための候補検索とランキング方法に関する研究

Tohoku University乾健太郎課

From Word to Sense Embeddings: A Survey on Vector Representations of Meaning

Over the past years, distributed semantic representations have proved to be effective and flexible keepers of prior knowledge to be integrated into downstream applications. This survey focuses on the representation of meaning. We start from the theoretical background behind word vector space models and highlight one of their major limitations: the meaning conflation deficiency, which arises from representing a word with all its possible meanings as a single vector. Then, we explain how this deficiency can be addressed through a transition from the word level to the more fine-grained level of word senses (in its broader acceptation) as a method for modelling unambiguous lexical meaning. We present a comprehensive overview of the wide range of techniques in the two main branches of sense representation, i.e., unsupervised and knowledge-based. Finally, this survey covers the main evaluation procedures and applications for this type of representation, and provides an analysis of four of its important aspects: interpretability, sense granularity, adaptability to different domains and compositionality.Comment: 46 pages, 8 figures. Published in Journal of Artificial Intelligence Researc

Web knowledge bases

Knowledge is key to natural language understanding. References to specific people, places and things in text are crucial to resolving ambiguity and extracting meaning. Knowledge Bases (KBs) codify this information for automated systems — enabling applications such as entity-based search and question answering. This thesis explores the idea that sites on the web may act as a KB, even if that is not their primary intent. Dedicated kbs like Wikipedia are a rich source of entity information, but are built and maintained at an ongoing cost in human effort. As a result, they are generally limited in terms of the breadth and depth of knowledge they index about entities. Web knowledge bases offer a distributed solution to the problem of aggregating entity knowledge. Social networks aggregate content about people, news sites describe events with tags for organizations and locations, and a diverse assortment of web directories aggregate statistics and summaries for long-tail entities notable within niche movie, musical and sporting domains. We aim to develop the potential of these resources for both web-centric entity Information Extraction (IE) and structured KB population. We first investigate the problem of Named Entity Linking (NEL), where systems must resolve ambiguous mentions of entities in text to their corresponding node in a structured KB. We demonstrate that entity disambiguation models derived from inbound web links to Wikipedia are able to complement and in some cases completely replace the role of resources typically derived from the KB. Building on this work, we observe that any page on the web which reliably disambiguates inbound web links may act as an aggregation point for entity knowledge. To uncover these resources, we formalize the task of Web Knowledge Base Discovery (KBD) and develop a system to automatically infer the existence of KB-like endpoints on the web. While extending our framework to multiple KBs increases the breadth of available entity knowledge, we must still consolidate references to the same entity across different web KBs. We investigate this task of Cross-KB Coreference Resolution (KB-Coref) and develop models for efficiently clustering coreferent endpoints across web-scale document collections. Finally, assessing the gap between unstructured web knowledge resources and those of a typical KB, we develop a neural machine translation approach which transforms entity knowledge between unstructured textual mentions and traditional KB structures. The web has great potential as a source of entity knowledge. In this thesis we aim to first discover, distill and finally transform this knowledge into forms which will ultimately be useful in downstream language understanding tasks