SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations

Background Blood cancers (BCs) are responsible for over 720 K yearly deaths worldwide. Their prevalence and mortality-rate uphold the relevance of research related to BCs. Despite the availability of different resources establishing Disease-Disease Associations (DDAs), the knowledge is scattered and not accessible in a straightforward way to the scientific community. Here, we propose SicknessMiner, a biomedical Text-Mining (TM) approach towards the centralization of DDAs. Our methodology encompasses Named Entity Recognition (NER) and Named Entity Normalization (NEN) steps, and the DDAs retrieved were compared to the DisGeNET resource for qualitative and quantitative comparison. Results We obtained the DDAs via co-mention using our SicknessMiner or gene- or variant-disease similarity on DisGeNET. SicknessMiner was able to retrieve around 92% of the DisGeNET results and nearly 15% of the SicknessMiner results were specific to our pipeline. Conclusions SicknessMiner is a valuable tool to extract disease-disease relationship from RAW input corpus.

Context-aware multi-token concept recognition of biological entities

Background Concept recognition is a term that corresponds to the two sequential steps of named entity recognition and named entity normalization, and plays an essential role in the field of bioinformatics. However, the conventional dictionary-based methods did not sufficiently addressed the variation of the concepts in actual use in literature, resulting in the particularly degraded performances in recognition of multi-token concepts. Results In this paper, we propose a concept recognition method of multi-token biological entities using neural models combined with literature contexts. The key aspect of our method is utilizing the contextual information from the biological knowledge-bases for concept normalization, which is followed by named entity recognition procedure. The model showed improved performances over conventional methods, particularly for multi-token concepts with higher variations. Conclusions We expect that our model can be utilized for effective concept recognition and variety of natural language processing tasks on bioinformatics.

Large-Scale Occupational Skills Normalization for Online Recruitment

Job openings often go unfulfilled despite a surfeit of unemployed or underemployed workers. One of the main reasons for this is a mismatch between the skills required by employers and the skills that workers possess. This mismatch, also known as the skills gap, can pose socioeconomic challenges for an economy. A first step in alleviating the skills gap is to accurately detect skills in human capital data such as resumes and job ads. Comprehensive and accurate detection of skills facilitates analysis of labor market dynamics. It also helps bridge the divide between supply and demand of labor by facilitating reskilling and workforce training programs. In this paper, we describe SKILL, a Named Entity Normalization (NEN) system for occupational skills. SKILL is composed of 1) A skills tagger which uses properties of semantic word vectors to recognize and normalize relevant skills, and 2) A skill entity sense disambiguation component which infers the correct meaning of an identified skill. We discuss the technical design and the synergy between data science and engineering that was required to transform the system from a research prototype to a production service that serves customers from across the organization. We also discuss establishing customer feedback loops, and it led to improvements to the system over time. SKILL is currently used by various internal teams at CareerBuilder for big data workforce analytics, semantic search, job matching, and recommendations.