482 research outputs found

    An Evaluation Methodology of Named Entities Recognition in Spanish Language: ECU 911 Case Study

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    The importance of the gathered information in Integrated Security Services as ECU911 in Ecuador is evidenced in terms of its quality and availability in order to perform decision-making tasks. It is a priority to avoid the loss of relevant information such as event address, places references, names, etc. In this context it is present Named Entity Recognition (NER) analysis for discovering information into informal texts. Unlike structured corpus and labeled for NER analysis like CONLL2002 or ANCORA, informal texts generated from emergency call dialogues have a very wide linguistic variety; in addition, there is a strong tending to lose important information in their processing. A relevant aspect to considerate is the identification of texts that denotes entities such as the physical address where emergency events occurred. This study aims to extract the locations in which an emergency event has been issued. A set of experiments was performed with NER models based on Convolutional Neural Network (CNN). The performance of models was evaluated according to parameters such as training dataset size, dropout rate, location dictionary, and denoting location. An experimentation methodology was proposed, with it follows the next steps: i) Data preprocessing, ii) Dataset labeling, iii) Model structuring, and iv) Model evaluating. Results revealed that the performance of a model improves when having more training data, an adequate dropout rate to control overfitting problems, and a combination of a dictionary of locations and replacing words denoting entities

    De-Identification of French Unstructured Clinical Notes for Machine Learning Tasks

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    Unstructured textual data are at the heart of health systems: liaison letters between doctors, operating reports, coding of procedures according to the ICD-10 standard, etc. The details included in these documents make it possible to get to know the patient better, to better manage him or her, to better study the pathologies, to accurately remunerate the associated medical acts\ldots All this seems to be (at least partially) within reach of today by artificial intelligence techniques. However, for obvious reasons of privacy protection, the designers of these AIs do not have the legal right to access these documents as long as they contain identifying data. De-identifying these documents, i.e. detecting and deleting all identifying information present in them, is a legally necessary step for sharing this data between two complementary worlds. Over the last decade, several proposals have been made to de-identify documents, mainly in English. While the detection scores are often high, the substitution methods are often not very robust to attack. In French, very few methods are based on arbitrary detection and/or substitution rules. In this paper, we propose a new comprehensive de-identification method dedicated to French-language medical documents. Both the approach for the detection of identifying elements (based on deep learning) and their substitution (based on differential privacy) are based on the most proven existing approaches. The result is an approach that effectively protects the privacy of the patients at the heart of these medical documents. The whole approach has been evaluated on a French language medical dataset of a French public hospital and the results are very encouraging

    Neural information extraction from natural language text

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    Natural language processing (NLP) deals with building computational techniques that allow computers to automatically analyze and meaningfully represent human language. With an exponential growth of data in this digital era, the advent of NLP-based systems has enabled us to easily access relevant information via a wide range of applications, such as web search engines, voice assistants, etc. To achieve it, a long-standing research for decades has been focusing on techniques at the intersection of NLP and machine learning. In recent years, deep learning techniques have exploited the expressive power of Artificial Neural Networks (ANNs) and achieved state-of-the-art performance in a wide range of NLP tasks. Being one of the vital properties, Deep Neural Networks (DNNs) can automatically extract complex features from the input data and thus, provide an alternative to the manual process of handcrafted feature engineering. Besides ANNs, Probabilistic Graphical Models (PGMs), a coupling of graph theory and probabilistic methods have the ability to describe causal structure between random variables of the system and capture a principled notion of uncertainty. Given the characteristics of DNNs and PGMs, they are advantageously combined to build powerful neural models in order to understand the underlying complexity of data. Traditional machine learning based NLP systems employed shallow computational methods (e.g., SVM or logistic regression) and relied on handcrafting features which is time-consuming, complex and often incomplete. However, deep learning and neural network based methods have recently shown superior results on various NLP tasks, such as machine translation, text classification, namedentity recognition, relation extraction, textual similarity, etc. These neural models can automatically extract an effective feature representation from training data. This dissertation focuses on two NLP tasks: relation extraction and topic modeling. The former aims at identifying semantic relationships between entities or nominals within a sentence or document. Successfully extracting the semantic relationships greatly contributes in building structured knowledge bases, useful in downstream NLP application areas of web search, question-answering, recommendation engines, etc. On other hand, the task of topic modeling aims at understanding the thematic structures underlying in a collection of documents. Topic modeling is a popular text-mining tool to automatically analyze a large collection of documents and understand topical semantics without actually reading them. In doing so, it generates word clusters (i.e., topics) and document representations useful in document understanding and information retrieval, respectively. Essentially, the tasks of relation extraction and topic modeling are built upon the quality of representations learned from text. In this dissertation, we have developed task-specific neural models for learning representations, coupled with relation extraction and topic modeling tasks in the realms of supervised and unsupervised machine learning paradigms, respectively. More specifically, we make the following contributions in developing neural models for NLP tasks: 1. Neural Relation Extraction: Firstly, we have proposed a novel recurrent neural network based architecture for table-filling in order to jointly perform entity and relation extraction within sentences. Then, we have further extended our scope of extracting relationships between entities across sentence boundaries, and presented a novel dependency-based neural network architecture. The two contributions lie in the supervised paradigm of machine learning. Moreover, we have contributed in building a robust relation extractor constrained by the lack of labeled data, where we have proposed a novel weakly-supervised bootstrapping technique. Given the contributions, we have further explored interpretability of the recurrent neural networks to explain their predictions for the relation extraction task. 2. Neural Topic Modeling: Besides the supervised neural architectures, we have also developed unsupervised neural models to learn meaningful document representations within topic modeling frameworks. Firstly, we have proposed a novel dynamic topic model that captures topics over time. Next, we have contributed in building static topic models without considering temporal dependencies, where we have presented neural topic modeling architectures that also exploit external knowledge, i.e., word embeddings to address data sparsity. Moreover, we have developed neural topic models that incorporate knowledge transfers using both the word embeddings and latent topics from many sources. Finally, we have shown improving neural topic modeling by introducing language structures (e.g., word ordering, local syntactic and semantic information, etc.) that deals with bag-of-words issues in traditional topic models. The class of proposed neural NLP models in this section are based on techniques at the intersection of PGMs, deep learning and ANNs. Here, the task of neural relation extraction employs neural networks to learn representations typically at the sentence level, without access to the broader document context. However, topic models have access to statistical information across documents. Therefore, we advantageously combine the two complementary learning paradigms in a neural composite model, consisting of a neural topic and a neural language model that enables us to jointly learn thematic structures in a document collection via the topic model, and word relations within a sentence via the language model. Overall, our research contributions in this dissertation extend NLP-based systems for relation extraction and topic modeling tasks with state-of-the-art performances

    Contributions to information extraction for spanish written biomedical text

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    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

    Deep Learning Models For Biomedical Data Analysis

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    The field of biomedical data analysis is a vibrant area of research dedicated to extracting valuable insights from a wide range of biomedical data sources, including biomedical images and genomics data. The emergence of deep learning, an artificial intelligence approach, presents significant prospects for enhancing biomedical data analysis and knowledge discovery. This dissertation focused on exploring innovative deep-learning methods for biomedical image processing and gene data analysis. During the COVID-19 pandemic, biomedical imaging data, including CT scans and chest x-rays, played a pivotal role in identifying COVID-19 cases by categorizing patient chest x-ray outcomes as COVID-19-positive or negative. While supervised deep learning methods have effectively recognized COVID-19 patterns in chest x-ray datasets, the availability of annotated training data remains limited. To address this challenge, the thesis introduced a semi-supervised deep learning model named ssResNet, built upon the Residual Neural Network (ResNet) architecture. The model combines supervised and unsupervised paths, incorporating a weighted supervised loss function to manage data imbalance. The strategies to diminish prediction uncertainty in deep learning models for critical applications like medical image processing is explore. It achieves this through an ensemble deep learning model, integrating bagging deep learning and model calibration techniques. This ensemble model not only boosts biomedical image segmentation accuracy but also reduces prediction uncertainty, as validated on a comprehensive chest x-ray image segmentation dataset. Furthermore, the thesis introduced an ensemble model integrating Proformer and ensemble learning methodologies. This model constructs multiple independent Proformers for predicting gene expression, their predictions are combined through weighted averaging to generate final predictions. Experimental outcomes underscore the efficacy of this ensemble model in enhancing prediction performance across various metrics. In conclusion, this dissertation advances biomedical data analysis by harnessing the potential of deep learning techniques. It devises innovative approaches for processing biomedical images and gene data. By leveraging deep learning\u27s capabilities, this work paves the way for further progress in biomedical data analytics and its applications within clinical contexts. Index Terms- biomedical data analysis, COVID-19, deep learning, ensemble learning, gene data analytics, medical image segmentation, prediction uncertainty, Proformer, Residual Neural Network (ResNet), semi-supervised learning
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