A Biomedical Entity Extraction Pipeline for Oncology Health Records in Portuguese

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over $10$ years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved $F_1$ scores of $88.6$, $95.0$, and $55.8$ per cent in the mention extraction of procedures, drugs, and diseases, respectively

Transfer learning: bridging the gap between deep learning and domain-specific text mining

Inspired by the success of deep learning techniques in Natural Language Processing (NLP), this dissertation tackles the domain-specific text mining problems for which the generic deep learning approaches would fail. More specifically, the domain-specific problems are: (1) success prediction in crowdfunding, (2) variants identification in biomedical literature, and (3) text data augmentation for domains with low-resources. In the first part, transfer learning in a multimodal perspective is utilized to facilitate solving the project success prediction on the crowdfunding application. Even though the information in a project profile can be of different modalities such as text, images, and metadata, most existing prediction approaches leverage only the text modality. It is promising to utilize the visual images in project profiles to find out how images could contribute to the success prediction. An advanced neural network scheme is designed and evaluated combining information learned from different modalities for project success prediction. In the second part, transfer learning is combined with deep learning techniques to solve genomic variants Named Entity Recognition (NER) problems in biomedical literature. Most of the advanced generic NER algorithms can fail due to the restricted training corpus. However, those generic deep learning algorithms are capable of learning from a canonical corpus, without any effort on feature engineering. This work aims to build an end-to-end deep learning approach to transfer the domain-specific knowledge to those advanced generic NER algorithms, addressing the challenges in low-resource training and requiring neither hand-crafted features nor post-processing rules. For the last part, transfer learning with knowledge distillation and active learning are utilized to solve text augmentation for domains with low-resources. Most of the recent text augmentation methods heavily rely on large external resources. This work is dedicates to solving the text augmentation problem adaptively and consistently with minimal resources for token-level tasks like NER. The solution can also assure the reliability of machine labels for noisy data and can enhance training consistency with noisy labels. All the works are evaluated on different domain-specific benchmarks, respectively. Experimental results demonstrate the effectiveness of those proposed methods. The advantages also indicate promising potential for transfer learning in domain-specific applications

Leveraging distant supervision for improved named entity recognition

Les techniques d'apprentissage profond ont fait un bond au cours des dernières années, et ont considérablement changé la manière dont les tâches de traitement automatique du langage naturel (TALN) sont traitées. En quelques années, les réseaux de neurones et les plongements de mots sont rapidement devenus des composants centraux à adopter dans le domaine. La supervision distante (SD) est une technique connue en TALN qui consiste à générer automatiquement des données étiquetées à partir d'exemples partiellement annotés. Traditionnellement, ces données sont utilisées pour l'entraînement en l'absence d'annotations manuelles, ou comme données supplémentaires pour améliorer les performances de généralisation. Dans cette thèse, nous étudions comment la supervision distante peut être utilisée dans un cadre d'un TALN moderne basé sur l'apprentissage profond. Puisque les algorithmes d'apprentissage profond s'améliorent lorsqu'une quantité massive de données est fournie (en particulier pour l'apprentissage des représentations), nous revisitons la génération automatique des données avec la supervision distante à partir de Wikipédia. On applique des post-traitements sur Wikipédia pour augmenter la quantité d'exemples annotés, tout en introduisant une quantité raisonnable de bruit. Ensuite, nous explorons différentes méthodes d'utilisation de données obtenues par supervision distante pour l'apprentissage des représentations, principalement pour apprendre des représentations de mots classiques (statistiques) et contextuelles. À cause de sa position centrale pour de nombreuses applications du TALN, nous choisissons la reconnaissance d'entité nommée (NER) comme tâche principale. Nous expérimentons avec des bancs d’essai NER standards et nous observons des performances état de l’art. Ce faisant, nous étudions un cadre plus intéressant, à savoir l'amélioration des performances inter-domaines (généralisation).Recent years have seen a leap in deep learning techniques that greatly changed the way Natural Language Processing (NLP) tasks are tackled. In a couple of years, neural networks and word embeddings quickly became central components to be adopted in the domain. Distant supervision (DS) is a well-used technique in NLP to produce labeled data from partially annotated examples. Traditionally, it was mainly used as training data in the absence of manual annotations, or as additional training data to improve generalization performances. In this thesis, we study how distant supervision can be employed within a modern deep learning based NLP framework. As deep learning algorithms gets better when massive amount of data is provided (especially for representation learning), we revisit the task of generating distant supervision data from Wikipedia. We apply post-processing treatments on the original dump to further increase the quantity of labeled examples, while introducing a reasonable amount of noise. Then, we explore different methods for using distant supervision data for representation learning, mainly to learn classic and contextualized word representations. Due to its importance as a basic component in many NLP applications, we choose Named-Entity Recognition (NER) as our main task. We experiment on standard NER benchmarks showing state-of-the-art performances. By doing so, we investigate a more interesting setting, that is, improving the cross-domain (generalization) performances