Semi-supervised learning for disabilities detection on English and Spanish biomedical text

This paper describes the disability detection model approaches presented by UPC’s TALP 3 team for the DIANN 2018 shared task. The best of those approaches was ranked in 3rd place for exact-matching of disability detection. The models combine a semi-supervised learning model using CRFs and LSTM with word embedding features with a supervised CRF model for the detection of disabilities and negations respectively.Peer ReviewedPostprint (published version

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.This work was partially funded by the Spanish Ministry of Science and Innovation (MCI/AEI/FEDER, UE, DOTT-HEALTH/PAT-MED PID2019-106942RB-C31), the Basque Government (IXA IT1570-22), MCIN/AEI/ 10.13039/501100011033 and European Union NextGeneration EU/PRTR (DeepR3, TED2021-130295B-C31) and the EU ERA-Net CHIST-ERA and the Spanish Research Agency (ANTIDOTE PCI2020-120717-2)

Lexical simplification for the systematic support of cognitive accessibility guidelines

The Internet has come a long way in recent years, contributing to the proliferation of large volumes of digitally available information. Through user interfaces we can access these contents, however, they are not accessible to everyone. The main users affected are people with disabilities, who are already a considerable number, but accessibility barriers affect a wide range of user groups and contexts of use in accessing digital information. Some of these barriers are caused by language inaccessibility when texts contain long sentences, unusual words and complex linguistic structures. These accessibility barriers directly affect people with cognitive disabilities. For the purpose of making textual content more accessible, there are initiatives such as the Easy Reading guidelines, the Plain Language guidelines and some of the languagespecific Web Content Accessibility Guidelines (WCAG). These guidelines provide documentation, but do not specify methods for meeting the requirements implicit in these guidelines in a systematic way. To obtain a solution, methods from the Natural Language Processing (NLP) discipline can provide support for achieving compliance with the cognitive accessibility guidelines for the language. The task of text simplification aims at reducing the linguistic complexity of a text from a syntactic and lexical perspective, the latter being the main focus of this Thesis. In this sense, one solution space is to identify in a text which words are complex or uncommon, and in the case that there were, to provide a more usual and simpler synonym, together with a simple definition, all oriented to people with cognitive disabilities. With this goal in mind, this Thesis presents the study, analysis, design and development of an architecture, NLP methods, resources and tools for the lexical simplification of texts for the Spanish language in a generic domain in the field of cognitive accessibility. To achieve this, each of the steps present in the lexical simplification processes is studied, together with methods for word sense disambiguation. As a contribution, different types of word embedding are explored and created, supported by traditional and dynamic embedding methods, such as transfer learning methods. In addition, since most of the NLP methods require data for their operation, a resource in the framework of cognitive accessibility is presented as a contribution.Internet ha avanzado mucho en los últimos años contribuyendo a la proliferación de grandes volúmenes de información disponible digitalmente. A través de interfaces de usuario podemos acceder a estos contenidos, sin embargo, estos no son accesibles a todas las personas. Los usuarios afectados principalmente son las personas con discapacidad siendo ya un número considerable, pero las barreras de accesibilidad afectan a un gran rango de grupos de usuarios y contextos de uso en el acceso a la información digital. Algunas de estas barreras son causadas por la inaccesibilidad al lenguaje cuando los textos contienen oraciones largas, palabras inusuales y estructuras lingüísticas complejas. Estas barreras de accesibilidad afectan directamente a las personas con discapacidad cognitiva. Con el fin de hacer el contenido textual más accesible, existen iniciativas como las pautas de Lectura Fácil, las pautas de Lenguaje Claro y algunas de las pautas de Accesibilidad al Contenido en la Web (WCAG) específicas para el lenguaje. Estas pautas proporcionan documentación, pero no especifican métodos para cumplir con los requisitos implícitos en estas pautas de manera sistemática. Para obtener una solución, los métodos de la disciplina del Procesamiento del Lenguaje Natural (PLN) pueden dar un soporte para alcanzar la conformidad con las pautas de accesibilidad cognitiva relativas al lenguaje La tarea de la simplificación de textos del PLN tiene como objetivo reducir la complejidad lingüística de un texto desde una perspectiva sintáctica y léxica, siendo esta última el enfoque principal de esta Tesis. En este sentido, un espacio de solución es identificar en un texto qué palabras son complejas o poco comunes, y en el caso de que sí hubiera, proporcionar un sinónimo más usual y sencillo, junto con una definición sencilla, todo ello orientado a las personas con discapacidad cognitiva. Con tal meta, en esta Tesis, se presenta el estudio, análisis, diseño y desarrollo de una arquitectura, métodos PLN, recursos y herramientas para la simplificación léxica de textos para el idioma español en un dominio genérico en el ámbito de la accesibilidad cognitiva. Para lograr esto, se estudia cada uno de los pasos presentes en los procesos de simplificación léxica, junto con métodos para la desambiguación del sentido de las palabras. Como contribución, diferentes tipos de word embedding son explorados y creados, apoyados por métodos embedding tradicionales y dinámicos, como son los métodos de transfer learning. Además, debido a que gran parte de los métodos PLN requieren datos para su funcionamiento, se presenta como contribución un recurso en el marco de la accesibilidad cognitiva.Programa de Doctorado en Ciencia y Tecnología Informática por la Universidad Carlos III de MadridPresidente: José Antonio Macías Iglesias.- Secretario: Israel González Carrasco.- Vocal: Raquel Hervás Ballestero

The RareDis corpus: A corpus annotated with rare diseases, their signs and symptoms

Rare diseases affect a small number of people compared to the general population. However, more than 6,000 different rare diseases exist and, in total, they affect more than 300 million people worldwide. Rare diseases share as part of their main problem, the delay in diagnosis and the sparse information available for researchers, clinicians, and patients. Finding a diagnostic can be a very long and frustrating experience for patients and their families. The average diagnostic delay is between 6–8 years. Many of these diseases result in different manifestations among patients, which hampers even more their detection and the correct treatment choice. Therefore, there is an urgent need to increase the scientific and medical knowledge about rare diseases. Natural Language Processing (NLP) can help to extract relevant information about rare diseases to facilitate their diagnosis and treatments, but most NLP techniques require manually annotated corpora. Therefore, our goal is to create a gold standard corpus annotated with rare diseases and their clinical manifestations. It could be used to train and test NLP approaches and the information extracted through NLP could enrich the knowledge of rare diseases, and thereby, help to reduce the diagnostic delay and improve the treatment of rare diseases. The paper describes the selection of 1,041 texts to be included in the corpus, the annotation process and the annotation guidelines. The entities (disease, rare disease, symptom, sign and anaphor) and the relationships (produces, is a, is acron, is synon, increases risk of, anaphora) were annotated. The RareDis corpus contains more than 5,000 rare diseases and almost 6,000 clinical manifestations are annotated. Moreover, the Inter Annotator Agreement evaluation shows a relatively high agreement (F1-measure equal to 83.5% under exact match criteria for the entities and equal to 81.3% for the relations). Based on these results, this corpus is of high quality, supposing a significant step for the field since there is a scarcity of available corpus annotated with rare diseases. This could open the door to further NLP applications, which would facilitate the diagnosis and treatment of these rare diseases and, therefore, would improve dramatically the quality of life of these patients.This work was supported by the Madrid Government (Comunidad de Madrid) under the Multiannual Agreement with UC3M in the line of "Fostering Young Doctors Research" (NLP4RARE-CM-UC3M) and in the context of the V PRICIT (Regional Programme of Research and Technological Innovation; the Multiannual Agreement with UC3M in the line of "Excellence of University Professors (EPUC3M17)"; and a grant from Spanish Ministry of Economy and Competitiveness (SAF2017-86810-R)

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