Clinical concept normalization on medical records using word embeddings and heuristics

Electronic health records contain valuable information on patients' clinical history in the form of free text. Manually analyzing millions of these documents is unfeasible and automatic natural language processing methods are essential for efficiently exploiting these data. Within this, normalization of clinical entities, where the aim is to link entity mentions to reference vocabularies, is of utmost importance to successfully extract knowledge from clinical narratives. In this paper we present sieve-based models combined with heuristics and word embeddings and present results of our participation in the 2019 n2c2 (National NLP Clinical Challenges) shared-task on clinical concept normalization.publishe

Deep Neural Models for Medical Concept Normalization in User-Generated Texts

In this work, we consider the medical concept normalization problem, i.e., the problem of mapping a health-related entity mention in a free-form text to a concept in a controlled vocabulary, usually to the standard thesaurus in the Unified Medical Language System (UMLS). This is a challenging task since medical terminology is very different when coming from health care professionals or from the general public in the form of social media texts. We approach it as a sequence learning problem with powerful neural networks such as recurrent neural networks and contextualized word representation models trained to obtain semantic representations of social media expressions. Our experimental evaluation over three different benchmarks shows that neural architectures leverage the semantic meaning of the entity mention and significantly outperform an existing state of the art models.Comment: This is preprint of the paper "Deep Neural Models for Medical Concept Normalization in User-Generated Texts" to be published at ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Student Research Worksho

Biomedical Information Extraction Pipelines for Public Health in the Age of Deep Learning

abstract: Unstructured texts containing biomedical information from sources such as electronic health records, scientific literature, discussion forums, and social media offer an opportunity to extract information for a wide range of applications in biomedical informatics. Building scalable and efficient pipelines for natural language processing and extraction of biomedical information plays an important role in the implementation and adoption of applications in areas such as public health. Advancements in machine learning and deep learning techniques have enabled rapid development of such pipelines. This dissertation presents entity extraction pipelines for two public health applications: virus phylogeography and pharmacovigilance. For virus phylogeography, geographical locations are extracted from biomedical scientific texts for metadata enrichment in the GenBank database containing 2.9 million virus nucleotide sequences. For pharmacovigilance, tools are developed to extract adverse drug reactions from social media posts to open avenues for post-market drug surveillance from non-traditional sources. Across these pipelines, high variance is observed in extraction performance among the entities of interest while using state-of-the-art neural network architectures. To explain the variation, linguistic measures are proposed to serve as indicators for entity extraction performance and to provide deeper insight into the domain complexity and the challenges associated with entity extraction. For both the phylogeography and pharmacovigilance pipelines presented in this work the annotated datasets and applications are open source and freely available to the public to foster further research in public health.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Integrating speculation detection and deep learning to extract lung cancer diagnosis from clinical notes

Despite efforts to develop models for extracting medical concepts from clinical notes, there are still some challenges in particular to be able to relate concepts to dates. The high number of clinical notes written for each single patient, the use of negation, speculation, and different date formats cause ambiguity that has to be solved to reconstruct the patient’s natural history. In this paper, we concentrate on extracting from clinical narratives the cancer diagnosis and relating it to the diagnosis date. To address this challenge, a hybrid approach that combines deep learning-based and rule-based methods is proposed. The approach integrates three steps: (i) lung cancer named entity recognition, (ii) negation and speculation detection, and (iii) relating the cancer diagnosis to a valid date. In particular, we apply the proposed approach to extract the lung cancer diagnosis and its diagnosis date from clinical narratives written in Spanish. Results obtained show an F-score of 90% in the named entity recognition task, and a 89% F-score in the task of relating the cancer diagnosis to the diagnosis date. Our findings suggest that speculation detection is together with negation detection a key component to properly extract cancer diagnosis from clinical notesThis work is supported by the EU Horizon 2020 innovation program under grant agreement No. 780495, project BigMedilytics (Big Data for Medical Analytics). It has been also supported by Fundación AECC and Instituto de Salud Carlos III (grant AC19/00034), under the frame of ERA-NET PerMe