Advances in monolingual and crosslingual automatic disability annotation in Spanish.

BACKGROUND: Unlike diseases, automatic recognition of disabilities has not received the same attention in the area of medical NLP. Progress in this direction is hampered by obstacles like the lack of annotated corpus. Neural architectures learn to translate sequences from spontaneous representations into their corresponding standard representations given a set of samples. The aim of this paper is to present the last advances in monolingual (Spanish) and crosslingual (from English to Spanish and vice versa) automatic disability annotation. The task consists of identifying disability mentions in medical texts written in Spanish within a collection of abstracts from journal papers related to the biomedical domain. RESULTS: In order to carry out the task, we have combined deep learning models that use different embedding granularities for sequence to sequence tagging with a simple acronym and abbreviation detection module to boost the coverage. CONCLUSIONS: Our monolingual experiments demonstrate that a good combination of different word embedding representations provide better results than single representations, significantly outperforming the state of the art in disability annotation in Spanish. Additionally, we have experimented crosslingual transfer (zero-shot) for disability annotation between English and Spanish with interesting results that might help overcoming the data scarcity bottleneck, specially significant for the disabilities.

A section identification tool: Towards HL7 CDA/CCR standardization in Spanish discharge summaries.

BACKGROUND: Nowadays, with the digitalization of healthcare systems, huge amounts of clinical narratives are available. However, despite the wealth of information contained in them, interoperability and extraction of relevant information from documents remains a challenge. OBJECTIVE: This work presents an approach towards automatically standardizing Spanish Electronic Discharge Summaries (EDS) following the HL7 Clinical Document Architecture. We address the task of section annotation in EDSs written in Spanish, experimenting with three different approaches, with the aim of boosting interoperability across healthcare systems and hospitals. METHODS: The paper presents three different methods, ranging from a knowledge-based solution by means of manually constructed rules to supervised Machine Learning approaches, using state of the art algorithms like the Perceptron and transfer learning-based Neural Networks. RESULTS: The paper presents a detailed evaluation of the three approaches on two different hospitals. Overall, the best system obtains a 93.03% F-score for section identification. It is worth mentioning that this result is not completely homogeneous over all section types and hospitals, showing that cross-hospital variability in certain sections is bigger than in others. CONCLUSIONS: As a main result, this work proves the feasibility of accurate automatic detection and standardization of section blocks in clinical narratives, opening the way to interoperability and secondary use of clinical data.

Measuring the effect of different types of unsupervised word representations on Medical Named Entity Recognition.

BACKGROUND: This work deals with Natural Language Processing applied to the clinical domain. Specifically, the work deals with a Medical Entity Recognition (MER) on Electronic Health Records (EHRs). Developing a MER system entailed heavy data preprocessing and feature engineering until Deep Neural Networks (DNNs) emerged. However, the quality of the word representations in terms of embedded layers is still an important issue for the inference of the DNNs. GOAL: The main goal of this work is to develop a robust MER system adapting general-purpose DNNs to cope with the high lexical variability shown in EHRs. In addition, given that EHRs tend to be scarce when there are out-domain corpora available, the aim is to assess the impact of the word representations on the performance of the MER as we move to other domains. In this line, exhaustive experimentation varying information generation methods and network parameters are crucial. METHODS: We adapted a general purpose sequential tagger based on Bidirectional Long-Short Term Memory cells and Conditional Random Fields (CRFs) in order to make it tolerant to high lexical variability and a limited amount of corpora. To this end, we incorporated part of speech (POS) and semantic-tag embedding layers to the word representations. RESULTS: One of the strengths of this work is the exhaustive evaluation of dense word representations obtained varying not only the domain and genre but also the learning algorithms and their parameter settings. With the proposed method, we attained an error reduction of 1.71 (5.7%) compared to the state-of-the-art even that no preprocessing or feature engineering was used. CONCLUSIONS: Our results indicate that dense representations built taking word order into account leverage the entity extraction system. Besides, we found that using a medical corpus (not necessarily EHRs) to infer the representations improves the performance, even if it does not correspond to the same genre.