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

An attentive neural architecture for joint segmentation and parsing and its application to real estate ads

In processing human produced text using natural language processing (NLP) techniques, two fundamental subtasks that arise are (i) segmentation of the plain text into meaningful subunits (e.g., entities), and (ii) dependency parsing, to establish relations between subunits. In this paper, we develop a relatively simple and effective neural joint model that performs both segmentation and dependency parsing together, instead of one after the other as in most state-of-the-art works. We will focus in particular on the real estate ad setting, aiming to convert an ad to a structured description, which we name property tree, comprising the tasks of (1) identifying important entities of a property (e.g., rooms) from classifieds and (2) structuring them into a tree format. In this work, we propose a new joint model that is able to tackle the two tasks simultaneously and construct the property tree by (i) avoiding the error propagation that would arise from the subtasks one after the other in a pipelined fashion, and (ii) exploiting the interactions between the subtasks. For this purpose, we perform an extensive comparative study of the pipeline methods and the new proposed joint model, reporting an improvement of over three percentage points in the overall edge F1 score of the property tree. Also, we propose attention methods, to encourage our model to focus on salient tokens during the construction of the property tree. Thus we experimentally demonstrate the usefulness of attentive neural architectures for the proposed joint model, showcasing a further improvement of two percentage points in edge F1 score for our application.Comment: Preprint - Accepted for publication in Expert Systems with Application