A two-stage deep learning approach for extracting entities and relationships from medical texts

This Work Presents A Two-Stage Deep Learning System For Named Entity Recognition (Ner) And Relation Extraction (Re) From Medical Texts. These Tasks Are A Crucial Step To Many Natural Language Understanding Applications In The Biomedical Domain. Automatic Medical Coding Of Electronic Medical Records, Automated Summarizing Of Patient Records, Automatic Cohort Identification For Clinical Studies, Text Simplification Of Health Documents For Patients, Early Detection Of Adverse Drug Reactions Or Automatic Identification Of Risk Factors Are Only A Few Examples Of The Many Possible Opportunities That The Text Analysis Can Offer In The Clinical Domain. In This Work, Our Efforts Are Primarily Directed Towards The Improvement Of The Pharmacovigilance Process By The Automatic Detection Of Drug-Drug Interactions (Ddi) From Texts. Moreover, We Deal With The Semantic Analysis Of Texts Containing Health Information For Patients. Our Two-Stage Approach Is Based On Deep Learning Architectures. Concretely, Ner Is Performed Combining A Bidirectional Long Short-Term Memory (Bi-Lstm) And A Conditional Random Field (Crf), While Re Applies A Convolutional Neural Network (Cnn). Since Our Approach Uses Very Few Language Resources, Only The Pre-Trained Word Embeddings, And Does Not Exploit Any Domain Resources (Such As Dictionaries Or Ontologies), This Can Be Easily Expandable To Support Other Languages And Clinical Applications That Require The Exploitation Of Semantic Information (Concepts And Relationships) From Texts...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)

Comparing Transformer-based NER approaches for analysing textual medical diagnoses

The automated analysis of medical documents has grown in research interest in recent years as a consequence of the social relevance of the thematic and the difficulties often encountered with short and very specific documents. In particular, this fervent area of research has stimulated the development of several techniques of automatic document classification, question answering, and name entity recognition (NER). Nevertheless, many open issues must be addressed to obtain results that are satisfactory for a field in which the effectiveness of predictions is a fundamental factor in order not to make mistakes that could compromise people’s lives. To this end, we focused on the name entity recognition task from medical documents and, in this work, we will discuss the results we obtained by our hybrid approach. In order to take advantage of the most relevant findings in the field of natural language processing, we decided to focus on deep neural network models. We compared several configurations of our model by varying the transformer architecture, such as BERT, RoBERTa and ELECTRA, until we obtained a configuration that we considered the best for our goals. The most promising model was used to participate in the SpRadIE task of the annual CLEF (Conference and Labs of the Evaluation Forum). The obtained results are encouraging and can be of reference for future studies on the topic

Overview of the eHealth Knowledge Discovery Challenge at IberLEF 2020

This paper summarises the results of the third edition of the eHealth Knowledge Discovery (KD) challenge, hosted at the Iberian Language Evaluation Forum 2020. The eHealth-KD challenge proposes two computational tasks involving the identification of semantic entities and relations in natural language text, focusing on Spanish language health documents. In this edition, besides text extracted from medical sources, Wikipedia content was introduced into the corpus, and a novel transfer-learning evaluation scenario was designed that challenges participants to create systems that provide cross-domain generalisation. A total of eight teams participated with a variety of approaches including deep learning end-to-end systems as well as rule-based and knowledge-driven techniques. This paper analyses the most successful approaches and highlights the most interesting challenges for future research in this field.This research has been partially supported by the University of Alicante and University of Havana, the Generalitat Valenciana (Conselleria d’Educació, Investigació, Cultura i Esport) and the Spanish Government through the projects SIIA (PROMETEO/2018/089, PROMETEU/2018/089) and LIVING-LANG (RTI2018-094653-B-C22)

Safeguarding Privacy Through Deep Learning Techniques

Over the last few years, there has been a growing need to meet minimum security and privacy requirements. Both public and private companies have had to comply with increasingly stringent standards, such as the ISO 27000 family of standards, or the various laws governing the management of personal data. The huge amount of data to be managed has required a huge effort from the employees who, in the absence of automatic techniques, have had to work tirelessly to achieve the certification objectives. Unfortunately, due to the delicate information contained in the documentation relating to these problems, it is difficult if not impossible to obtain material for research and study purposes on which to experiment new ideas and techniques aimed at automating processes, perhaps exploiting what is in ferment in the scientific community and linked to the fields of ontologies and artificial intelligence for data management. In order to bypass this problem, it was decided to examine data related to the medical world, which, especially for important reasons related to the health of individuals, have gradually become more and more freely accessible over time, without affecting the generality of the proposed methods, which can be reapplied to the most diverse fields in which there is a need to manage privacy-sensitive information

On the Use of Parsing for Named Entity Recognition

[Abstract] Parsing is a core natural language processing technique that can be used to obtain the structure underlying sentences in human languages. Named entity recognition (NER) is the task of identifying the entities that appear in a text. NER is a challenging natural language processing task that is essential to extract knowledge from texts in multiple domains, ranging from financial to medical. It is intuitive that the structure of a text can be helpful to determine whether or not a certain portion of it is an entity and if so, to establish its concrete limits. However, parsing has been a relatively little-used technique in NER systems, since most of them have chosen to consider shallow approaches to deal with text. In this work, we study the characteristics of NER, a task that is far from being solved despite its long history; we analyze the latest advances in parsing that make its use advisable in NER settings; we review the different approaches to NER that make use of syntactic information; and we propose a new way of using parsing in NER based on casting parsing itself as a sequence labeling task.Xunta de Galicia; ED431C 2020/11Xunta de Galicia; ED431G 2019/01This work has been funded by MINECO, AEI and FEDER of UE through the ANSWER-ASAP project (TIN2017-85160-C2-1-R); and by Xunta de Galicia through a Competitive Reference Group grant (ED431C 2020/11). CITIC, as Research Center of the Galician University System, is funded by the Consellería de Educación, Universidade e Formación Profesional of the Xunta de Galicia through the European Regional Development Fund (ERDF/FEDER) with 80%, the Galicia ERDF 2014-20 Operational Programme, and the remaining 20% from the Secretaría Xeral de Universidades (Ref. ED431G 2019/01). Carlos Gómez-Rodríguez has also received funding from the European Research Council (ERC), under the European Union’s Horizon 2020 research and innovation programme (FASTPARSE, Grant No. 714150)

Analyzing transfer learning impact in biomedical cross lingual named entity recognition and normalization

Background The volume of biomedical literature and clinical data is growing at an exponential rate. Therefore, efficient access to data described in unstructured biomedical texts is a crucial task for the biomedical industry and research. Named Entity Recognition (NER) is the first step for information and knowledge acquisition when we deal with unstructured texts. Recent NER approaches use contextualized word representations as input for a downstream classification task. However, distributed word vectors (embeddings) are very limited in Spanish and even more for the biomedical domain. Methods In this work, we develop several biomedical Spanish word representations, and we introduce two Deep Learning approaches for pharmaceutical, chemical, and other biomedical entities recognition in Spanish clinical case texts and biomedical texts, one based on a Bi-STM-CRF model and the other on a BERT-based architecture. Results Several Spanish biomedical embeddigns together with the two deep learning models were evaluated on the PharmaCoNER and CORD-19 datasets. The PharmaCoNER dataset is composed of a set of Spanish clinical cases annotated with drugs, chemical compounds and pharmacological substances; our extended Bi-LSTM-CRF model obtains an F-score of 85.24% on entity identification and classification and the BERT model obtains an F-score of 88.80% . For the entity normalization task, the extended Bi-LSTM-CRF model achieves an F-score of 72.85% and the BERT model achieves 79.97%. The CORD-19 dataset consists of scholarly articles written in English annotated with biomedical concepts such as disorder, species, chemical or drugs, gene and protein, enzyme and anatomy. Bi-LSTM-CRF model and BERT model obtain an F-measure of 78.23% and 78.86% on entity identification and classification, respectively on the CORD-19 dataset. Conclusion These results prove that deep learning models with in-domain knowledge learned from large-scale datasets highly improve named entity recognition performance. Moreover, contextualized representations help to understand complexities and ambiguity inherent to biomedical texts. Embeddings based on word, concepts, senses, etc. other than those for English are required to improve NER tasks in other languages.This work was partially supported by the Research Program of the Ministry of Economy and Competitiveness - Government of Spain, (DeepEMR project TIN2017-87548-C2-1-R)

Linking social media, medical literature, and clinical notes using deep learning.

Researchers analyze data, information, and knowledge through many sources, formats, and methods. The dominant data format includes text and images. In the healthcare industry, professionals generate a large quantity of unstructured data. The complexity of this data and the lack of computational power causes delays in analysis. However, with emerging deep learning algorithms and access to computational powers such as graphics processing unit (GPU) and tensor processing units (TPUs), processing text and images is becoming more accessible. Deep learning algorithms achieve remarkable results in natural language processing (NLP) and computer vision. In this study, we focus on NLP in the healthcare industry and collect data not only from electronic medical records (EMRs) but also medical literature and social media. We propose a framework for linking social media, medical literature, and EMRs clinical notes using deep learning algorithms. Connecting data sources requires defining a link between them, and our key is finding concepts in the medical text. The National Library of Medicine (NLM) introduces a Unified Medical Language System (UMLS) and we use this system as the foundation of our own system. We recognize social media’s dynamic nature and apply supervised and semi-supervised methodologies to generate concepts. Named entity recognition (NER) allows efficient extraction of information, or entities, from medical literature, and we extend the model to process the EMRs’ clinical notes via transfer learning. The results include an integrated, end-to-end, web-based system solution that unifies social media, literature, and clinical notes, and improves access to medical knowledge for the public and experts

A computational ecosystem to support eHealth Knowledge Discovery technologies in Spanish

The massive amount of biomedical information published online requires the development of automatic knowledge discovery technologies to effectively make use of this available content. To foster and support this, the research community creates linguistic resources, such as annotated corpora, and designs shared evaluation campaigns and academic competitive challenges. This work describes an ecosystem that facilitates research and development in knowledge discovery in the biomedical domain, specifically in Spanish language. To this end, several resources are developed and shared with the research community, including a novel semantic annotation model, an annotated corpus of 1045 sentences, and computational resources to build and evaluate automatic knowledge discovery techniques. Furthermore, a research task is defined with objective evaluation criteria, and an online evaluation environment is setup and maintained, enabling researchers interested in this task to obtain immediate feedback and compare their results with the state-of-the-art. As a case study, we analyze the results of a competitive challenge based on these resources and provide guidelines for future research. The constructed ecosystem provides an effective learning and evaluation environment to encourage research in knowledge discovery in Spanish biomedical documents.This research has been partially supported by the University of Alicante and University of Havana, the Generalitat Valenciana (Conselleria d’Educació, Investigació, Cultura i Esport) and the Spanish Government through the projects SIIA (PROMETEO/2018/089, PROMETEU/2018/089) and LIVING-LANG (RTI2018-094653-B-C22)

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