Detección de la Negación y la Especulación en Textos Médicos y de Opinión

PhD Thesis written by Noa P. Cruz Díaz at the University of Huelva under the supervision of Dr. Manuel J. Maña López. The author was examined on 10th July 2014 by a committee formed by the doctors Manuel de Buenaga (European University of Madrid), Mariana Lara Neves (University of Berlin) and Jacinto Mata (University of Huelva). The PhD Thesis was awarded Summa cum laude (International Doctorate).Tesis doctoral realizada por Noa P. Cruz Díaz en la Universidad de Huelva bajo la dirección del Dr. Manuel J. Maña López. El acto de defensa tuvo lugar el jueves 10 de julio de 2014 ante el tribunal formado por los doctores Manuel de Buenaga (Universidad Europea de Madrid), Mariana Lara Neves (Universidad de Berlín) y Jacinto Mata (Universidad de Huelva). Obtuvo mención internacional y la calificación de Sobresaliente Cum Laude por unanimidad.This thesis has been funded by the University of Huelva (PP10-02 PhD Scholarship), the Spanish Ministry of Education and Science (TIN2009-14057-C03-03 Project) and the Andalusian Ministry of Economy, Innovation and Science (TIC 07629 Project)

The impact of pretrained language models on negation and speculation detection in cross-lingual medical text: Comparative study

Background: Negation and speculation are critical elements in natural language processing (NLP)-related tasks, such as information extraction, as these phenomena change the truth value of a proposition. In the clinical narrative that is informal, these linguistic facts are used extensively with the objective of indicating hypotheses, impressions, or negative findings. Previous state-of-the-art approaches addressed negation and speculation detection tasks using rule-based methods, but in the last few years, models based on machine learning and deep learning exploiting morphological, syntactic, and semantic features represented as spare and dense vectors have emerged. However, although such methods of named entity recognition (NER) employ a broad set of features, they are limited to existing pretrained models for a specific domain or language. Objective: As a fundamental subsystem of any information extraction pipeline, a system for cross-lingual and domain-independent negation and speculation detection was introduced with special focus on the biomedical scientific literature and clinical narrative. In this work, detection of negation and speculation was considered as a sequence-labeling task where cues and the scopes of both phenomena are recognized as a sequence of nested labels recognized in a single step. Methods: We proposed the following two approaches for negation and speculation detection: (1) bidirectional long short-term memory (Bi-LSTM) and conditional random field using character, word, and sense embeddings to deal with the extraction of semantic, syntactic, and contextual patterns and (2) bidirectional encoder representations for transformers (BERT) with fine tuning for NER. Results: The approach was evaluated for English and Spanish languages on biomedical and review text, particularly with the BioScope corpus, IULA corpus, and SFU Spanish Review corpus, with F-measures of 86.6%, 85.0%, and 88.1%, respectively, for NeuroNER and 86.4%, 80.8%, and 91.7%, respectively, for BERT. Conclusions: These results show that these architectures perform considerably better than the previous rule-based and conventional machine learning-based systems. Moreover, our analysis results show that pretrained word embedding and particularly contextualized embedding for biomedical corpora help to understand complexities inherent to biomedical text.This work was supported by the Research Program of the Ministry of Economy and Competitiveness, Government of Spain (DeepEMR Project TIN2017-87548-C2-1-R)

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

A machine-learning approach to negation and speculation detection for sentiment analysis

Recognizing negative and speculative information is highly relevant for sentiment analysis. This paper presents a machine-learning approach to automatically detect this kind of information in the review domain. The resulting system works in two steps: in the first pass, negation/speculation cues are identified, and in the second phase the full scope of these cues is determined. The system is trained and evaluated on the Simon Fraser University Review corpus, which is extensively used in opinion mining. The results show how the proposed method outstrips the baseline by as much as roughly 20% in the negation cue detection and around 13% in the scope recognition, both in terms of F1. In speculation, the performance obtained in the cue prediction phase is close to that obtained by a human rater carrying out the same task. In the scope detection, the results are also promising and represent a substantial improvement on the baseline (up by roughly 10%). A detailed error analysis is also provided. The extrinsic evaluation shows that the correct identification of cues and scopes is vital for the task of sentiment analysis.Maite Taboada from the Natural Sciences and Engineering Research Council of Canada (Discovery Grant 261104- 2008). This work was partly funded by the Spanish Ministry of Education and Science (TIN2009-14057-C03-03 Project) and the Andalusian Ministry of Economy, Innovation and Science (TIC 07629 and TIC 07684 Projects)

Contributions to information extraction for spanish written biomedical text

285 p.Healthcare practice and clinical research produce vast amounts of digitised, unstructured data in multiple languages that are currently underexploited, despite their potential applications in improving healthcare experiences, supporting trainee education, or enabling biomedical research, for example. To automatically transform those contents into relevant, structured information, advanced Natural Language Processing (NLP) mechanisms are required. In NLP, this task is known as Information Extraction. Our work takes place within this growing field of clinical NLP for the Spanish language, as we tackle three distinct problems. First, we compare several supervised machine learning approaches to the problem of sensitive data detection and classification. Specifically, we study the different approaches and their transferability in two corpora, one synthetic and the other authentic. Second, we present and evaluate UMLSmapper, a knowledge-intensive system for biomedical term identification based on the UMLS Metathesaurus. This system recognises and codifies terms without relying on annotated data nor external Named Entity Recognition tools. Although technically naive, it performs on par with more evolved systems, and does not exhibit a considerable deviation from other approaches that rely on oracle terms. Finally, we present and exploit a new corpus of real health records manually annotated with negation and uncertainty information: NUBes. This corpus is the basis for two sets of experiments, one on cue andscope detection, and the other on assertion classification. Throughout the thesis, we apply and compare techniques of varying levels of sophistication and novelty, which reflects the rapid advancement of the field