Knowledge-Base Enriched Word Embeddings for Biomedical Domain

Word embeddings have been shown adept at capturing the semantic and syntactic regularities of the natural language text, as a result of which these representations have found their utility in a wide variety of downstream content analysis tasks. Commonly, these word embedding techniques derive the distributed representation of words based on the local context information. However, such approaches ignore the rich amount of explicit information present in knowledge-bases. This is problematic, as it might lead to poor representation for words with insufficient local context such as domain specific words. Furthermore, the problem becomes pronounced in domain such as bio-medicine where the presence of these domain specific words are relatively high. Towards this end, in this project, we propose a new word embedding based model for biomedical domain that jointly leverages the information from available corpora and domain knowledge in order to generate knowledge-base powered embeddings. Unlike existing approaches, the proposed methodology is simple but adept at capturing the precise knowledge available in domain resources in an accurate way. Experimental results on biomedical concept similarity and relatedness task validates the effectiveness of the proposed approach.Comment: Work in progres

AGATHA: Automatic Graph-mining And Transformer based Hypothesis generation Approach

Medical research is risky and expensive. Drug discovery, as an example, requires that researchers efficiently winnow thousands of potential targets to a small candidate set for more thorough evaluation. However, research groups spend significant time and money to perform the experiments necessary to determine this candidate set long before seeing intermediate results. Hypothesis generation systems address this challenge by mining the wealth of publicly available scientific information to predict plausible research directions. We present AGATHA, a deep-learning hypothesis generation system that can introduce data-driven insights earlier in the discovery process. Through a learned ranking criteria, this system quickly prioritizes plausible term-pairs among entity sets, allowing us to recommend new research directions. We massively validate our system with a temporal holdout wherein we predict connections first introduced after 2015 using data published beforehand. We additionally explore biomedical sub-domains, and demonstrate AGATHA's predictive capacity across the twenty most popular relationship types. This system achieves best-in-class performance on an established benchmark, and demonstrates high recommendation scores across subdomains. Reproducibility: All code, experimental data, and pre-trained models are available online: sybrandt.com/2020/agath