BIOMEDICAL WORD SENSE DISAMBIGUATION WITH NEURAL WORD AND CONCEPT EMBEDDINGS

Addressing ambiguity issues is an important step in natural language processing (NLP) pipelines designed for information extraction and knowledge discovery. This problem is also common in biomedicine where NLP applications have become indispensable to exploit latent information from biomedical literature and clinical narratives from electronic medical records. In this thesis, we propose an ensemble model that employs recent advances in neural word embeddings along with knowledge based approaches to build a biomedical word sense disambiguation (WSD) system. Specifically, our system identities the correct sense from a given set of candidates for each ambiguous word when presented in its context (surrounding words). We use the MSH WSD dataset, a well known public dataset consisting of 203 ambiguous terms each with nearly 200 different instances and an average of two candidate senses represented by concepts in the unified medical language system (UMLS). We employ a popular biomedical concept, Our linear time (in terms of number of senses and context length) unsupervised and knowledge based approach improves over the state-of-the-art methods by over 3% in accuracy. A more expensive approach based on the k-nearest neighbor framework improves over prior best results by 5% in accuracy. Our results demonstrate that recent advances in neural dense word vector representations offer excellent potential for solving biomedical WSD

Jointly Embedding Entities and Text with Distant Supervision

Learning representations for knowledge base entities and concepts is becoming increasingly important for NLP applications. However, recent entity embedding methods have relied on structured resources that are expensive to create for new domains and corpora. We present a distantly-supervised method for jointly learning embeddings of entities and text from an unnanotated corpus, using only a list of mappings between entities and surface forms. We learn embeddings from open-domain and biomedical corpora, and compare against prior methods that rely on human-annotated text or large knowledge graph structure. Our embeddings capture entity similarity and relatedness better than prior work, both in existing biomedical datasets and a new Wikipedia-based dataset that we release to the community. Results on analogy completion and entity sense disambiguation indicate that entities and words capture complementary information that can be effectively combined for downstream use.Comment: 12 pages; Accepted to 3rd Workshop on Representation Learning for NLP (Repl4NLP 2018). Code at https://github.com/OSU-slatelab/JE

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Biomedical word sense disambiguation with word embeddings

There is a growing need for automatic extraction of information and knowledge from the increasing amount of biomedical and clinical data produced, namely in textual form. Natural language processing comes in this direction, helping in tasks such as information extraction and information retrieval. Word sense disambiguation is an important part of this process, being responsible for assigning the proper concept to an ambiguous term. In this paper, we present results from machine learning and knowledge-based algorithms applied to biomedical word sense disambiguation. For the supervised machine learning algorithms we used word embeddings, calculated from the full MEDLINE literature database, as global features and compare the results to the use of local unigram and bigram features. For the knowledge-based method we represented the textual definitions of biomedical concepts from the UMLS database as word embedding vectors, and combined this with concept associations derived from the MeSH term co-occurrences. Both the machine learning and the knowledge-based results indicate that word embeddings are informative and improve the biomedical word disambiguation accuracy. Applied to the reference MSH WSD data set, our knowledge-based approach achieves 85.1% disambiguation accuracy, which is higher than some previously proposed approaches that do not use machine-learning strategies.publishe

Evaluation of word embedding vector averaging functions for biomedical word sense disambiguation

The biomedical lexicon contains a large amount of term ambiguity, which hinders correct identification of concepts and reduces the accuracy of semantic indexing and information retrieval tools. Previous work on biomedical word sense disambiguation has shown that supervised machine learning leads to better results than knowledge-based approaches. However, machine learning approaches require the availability of sufficient training data, and generalization performance behind the test data is not known. Knowledge-based methods on the other hand make use of existing knowledge-bases and are therefore mostly limited to the quality of such sources of information about concepts. In this work, we used word embedding vectors to complement the knowledge-base information. We represent the context of an ambiguous term by the average of the embedding vectors of words around the term, and evaluate the impact of using word distance for weighting this average. We show how this weighting improves the disambiguation accuracy of the knowledge-based approach in a subset of the reference MSH WSD data set from 86% to 88%.publishe

Improving Broad-Coverage Medical Entity Linking with Semantic Type Prediction and Large-Scale Datasets

Medical entity linking is the task of identifying and standardizing medical concepts referred to in an unstructured text. Most of the existing methods adopt a three-step approach of (1) detecting mentions, (2) generating a list of candidate concepts, and finally (3) picking the best concept among them. In this paper, we probe into alleviating the problem of overgeneration of candidate concepts in the candidate generation module, the most under-studied component of medical entity linking. For this, we present MedType, a fully modular system that prunes out irrelevant candidate concepts based on the predicted semantic type of an entity mention. We incorporate MedType into five off-the-shelf toolkits for medical entity linking and demonstrate that it consistently improves entity linking performance across several benchmark datasets. To address the dearth of annotated training data for medical entity linking, we present WikiMed and PubMedDS, two large-scale medical entity linking datasets, and demonstrate that pre-training MedType on these datasets further improves entity linking performance. We make our source code and datasets publicly available for medical entity linking research.Comment: 35 page

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

Data-efficient methods for information extraction

Strukturierte Wissensrepräsentationssysteme wie Wissensdatenbanken oder Wissensgraphen bieten Einblicke in Entitäten und Beziehungen zwischen diesen Entitäten in der realen Welt. Solche Wissensrepräsentationssysteme können in verschiedenen Anwendungen der natürlichen Sprachverarbeitung eingesetzt werden, z. B. bei der semantischen Suche, der Beantwortung von Fragen und der Textzusammenfassung. Es ist nicht praktikabel und ineffizient, diese Wissensrepräsentationssysteme manuell zu befüllen. In dieser Arbeit entwickeln wir Methoden, um automatisch benannte Entitäten und Beziehungen zwischen den Entitäten aus Klartext zu extrahieren. Unsere Methoden können daher verwendet werden, um entweder die bestehenden unvollständigen Wissensrepräsentationssysteme zu vervollständigen oder ein neues strukturiertes Wissensrepräsentationssystem von Grund auf zu erstellen. Im Gegensatz zu den gängigen überwachten Methoden zur Informationsextraktion konzentrieren sich unsere Methoden auf das Szenario mit wenigen Daten und erfordern keine große Menge an kommentierten Daten. Im ersten Teil der Arbeit haben wir uns auf das Problem der Erkennung von benannten Entitäten konzentriert. Wir haben an der gemeinsamen Aufgabe von Bacteria Biotope 2019 teilgenommen. Die gemeinsame Aufgabe besteht darin, biomedizinische Entitätserwähnungen zu erkennen und zu normalisieren. Unser linguistically informed Named-Entity-Recognition-System besteht aus einem Deep-Learning-basierten Modell, das sowohl verschachtelte als auch flache Entitäten extrahieren kann; unser Modell verwendet mehrere linguistische Merkmale und zusätzliche Trainingsziele, um effizientes Lernen in datenarmen Szenarien zu ermöglichen. Unser System zur Entitätsnormalisierung verwendet String-Match, Fuzzy-Suche und semantische Suche, um die extrahierten benannten Entitäten mit den biomedizinischen Datenbanken zu verknüpfen. Unser System zur Erkennung von benannten Entitäten und zur Entitätsnormalisierung erreichte die niedrigste Slot-Fehlerrate von 0,715 und belegte den ersten Platz in der gemeinsamen Aufgabe. Wir haben auch an zwei gemeinsamen Aufgaben teilgenommen: Adverse Drug Effect Span Detection (Englisch) und Profession Span Detection (Spanisch); beide Aufgaben sammeln Daten von der Social Media Plattform Twitter. Wir haben ein Named-Entity-Recognition-Modell entwickelt, das die Eingabedarstellung des Modells durch das Stapeln heterogener Einbettungen aus verschiedenen Domänen verbessern kann; unsere empirischen Ergebnisse zeigen komplementäres Lernen aus diesen heterogenen Einbettungen. Unser Beitrag belegte den 3. Platz in den beiden gemeinsamen Aufgaben. Im zweiten Teil der Arbeit untersuchten wir Strategien zur Erweiterung synthetischer Daten, um ressourcenarme Informationsextraktion in spezialisierten Domänen zu ermöglichen. Insbesondere haben wir backtranslation an die Aufgabe der Erkennung von benannten Entitäten auf Token-Ebene und der Extraktion von Beziehungen auf Satzebene angepasst. Wir zeigen, dass die Rückübersetzung sprachlich vielfältige und grammatikalisch kohärente synthetische Sätze erzeugen kann und als wettbewerbsfähige Erweiterungsstrategie für die Aufgaben der Erkennung von benannten Entitäten und der Extraktion von Beziehungen dient. Bei den meisten realen Aufgaben zur Extraktion von Beziehungen stehen keine kommentierten Daten zur Verfügung, jedoch ist häufig ein großer unkommentierter Textkorpus vorhanden. Bootstrapping-Methoden zur Beziehungsextraktion können mit diesem großen Korpus arbeiten, da sie nur eine Handvoll Startinstanzen benötigen. Bootstrapping-Methoden neigen jedoch dazu, im Laufe der Zeit Rauschen zu akkumulieren (bekannt als semantische Drift), und dieses Phänomen hat einen drastischen negativen Einfluss auf die endgültige Genauigkeit der Extraktionen. Wir entwickeln zwei Methoden zur Einschränkung des Bootstrapping-Prozesses, um die semantische Drift bei der Extraktion von Beziehungen zu minimieren. Unsere Methoden nutzen die Graphentheorie und vortrainierte Sprachmodelle, um verrauschte Extraktionsmuster explizit zu identifizieren und zu entfernen. Wir berichten über die experimentellen Ergebnisse auf dem TACRED-Datensatz für vier Relationen. Im letzten Teil der Arbeit demonstrieren wir die Anwendung der Domänenanpassung auf die anspruchsvolle Aufgabe der mehrsprachigen Akronymextraktion. Unsere Experimente zeigen, dass die Domänenanpassung die Akronymextraktion in wissenschaftlichen und juristischen Bereichen in sechs Sprachen verbessern kann, darunter auch Sprachen mit geringen Ressourcen wie Persisch und Vietnamesisch.The structured knowledge representation systems such as knowledge base or knowledge graph can provide insights regarding entities and relationship(s) among these entities in the real-world, such knowledge representation systems can be employed in various natural language processing applications such as semantic search, question answering and text summarization. It is infeasible and inefficient to manually populate these knowledge representation systems. In this work, we develop methods to automatically extract named entities and relationships among the entities from plain text and hence our methods can be used to either complete the existing incomplete knowledge representation systems to create a new structured knowledge representation system from scratch. Unlike mainstream supervised methods for information extraction, our methods focus on the low-data scenario and do not require a large amount of annotated data. In the first part of the thesis, we focused on the problem of named entity recognition. We participated in the shared task of Bacteria Biotope 2019, the shared task consists of recognizing and normalizing the biomedical entity mentions. Our linguistically informed named entity recognition system consists of a deep learning based model which can extract both nested and flat entities; our model employed several linguistic features and auxiliary training objectives to enable efficient learning in data-scarce scenarios. Our entity normalization system employed string match, fuzzy search and semantic search to link the extracted named entities to the biomedical databases. Our named entity recognition and entity normalization system achieved the lowest slot error rate of 0.715 and ranked first in the shared task. We also participated in two shared tasks of Adverse Drug Effect Span detection (English) and Profession Span Detection (Spanish); both of these tasks collect data from the social media platform Twitter. We developed a named entity recognition model which can improve the input representation of the model by stacking heterogeneous embeddings from a diverse domain(s); our empirical results demonstrate complementary learning from these heterogeneous embeddings. Our submission ranked 3rd in both of the shared tasks. In the second part of the thesis, we explored synthetic data augmentation strategies to address low-resource information extraction in specialized domains. Specifically, we adapted backtranslation to the token-level task of named entity recognition and sentence-level task of relation extraction. We demonstrate that backtranslation can generate linguistically diverse and grammatically coherent synthetic sentences and serve as a competitive augmentation strategy for the task of named entity recognition and relation extraction. In most of the real-world relation extraction tasks, the annotated data is not available, however, quite often a large unannotated text corpus is available. Bootstrapping methods for relation extraction can operate on this large corpus as they only require a handful of seed instances. However, bootstrapping methods tend to accumulate noise over time (known as semantic drift) and this phenomenon has a drastic negative impact on the final precision of the extractions. We develop two methods to constrain the bootstrapping process to minimise semantic drift for relation extraction; our methods leverage graph theory and pre-trained language models to explicitly identify and remove noisy extraction patterns. We report the experimental results on the TACRED dataset for four relations. In the last part of the thesis, we demonstrate the application of domain adaptation to the challenging task of multi-lingual acronym extraction. Our experiments demonstrate that domain adaptation can improve acronym extraction within scientific and legal domains in 6 languages including low-resource languages such as Persian and Vietnamese