Pseudo-data Generation For Improving Clinical Named Entity Recognition

One of the primary challenges for clinical Named Entity Recognition (NER) is the availability of annotated training data. Technical and legal hurdles prevent the creation and release of corpora related to electronic health records (EHRs). In this work, we look at the imapct of pseudo-data generation on clinical NER using gazetteering and thresholding utilizing a neural network model. We report that gazetteers can result in the inclusion of proper terms with the exclusion of determiners and pronouns in preceding and middle positions. Gazetteers that had higher numbers of terms inclusive to the original dataset had a higher impact. We also report that thresholding results in clear trend lines across the thresholds with some values oscillating around a fixed point at the most confidence points

Extraction and Classification of Drug-Drug Interaction from Biomedical Text Using a Two-Stage Classifier

One of the critical causes of medical errors is Drug-Drug interaction (DDI), which occurs when one drug increases or decreases the effect of another drug. We propose a machine learning system to extract and classify drug-drug interactions from the biomedical literature, using the annotated corpus from the DDIExtraction-2013 shared task challenge. Our approach applies a two-stage classifier to handle the highly unbalanced class distribution in the corpus. The first stage is designed for binary classification of drug pairs as interacting or non-interacting, and the second stage for further classification of interacting pairs into one of four interacting types: advise, effect, mechanism, and int. To find the set of best features for classification, we explored many features, including stemmed words, bigrams, part of speech tags, verb lists, parse tree information, mutual information, and similarity measures, among others. As the system faced two different classification tasks, binary and multi-class, we also explored various classifiers in each stage. Our results show that the best performing classifier in both stages was Support Vector Machines, and the best performing features were 1000 top informative words and part of speech tags between two main drugs. We obtained an F-Measure of 0.64, showing a 12% improvement over our submitted system to the DDIExtraction 2013 competition

A survey on recent advances in named entity recognition

Named Entity Recognition seeks to extract substrings within a text that name real-world objects and to determine their type (for example, whether they refer to persons or organizations). In this survey, we first present an overview of recent popular approaches, but we also look at graph- and transformer- based methods including Large Language Models (LLMs) that have not had much coverage in other surveys. Second, we focus on methods designed for datasets with scarce annotations. Third, we evaluate the performance of the main NER implementations on a variety of datasets with differing characteristics (as regards their domain, their size, and their number of classes). We thus provide a deep comparison of algorithms that are never considered together. Our experiments shed some light on how the characteristics of datasets affect the behavior of the methods that we compare.Comment: 30 page

Utility-Preserving Anonymization of Textual Documents

Cada dia els éssers humans afegim una gran quantitat de dades a Internet, tals com piulades, opinions, fotos i vídeos. Les organitzacions que recullen aquestes dades tan diverses n'extreuen informació per tal de millorar llurs serveis o bé per a propòsits comercials. Tanmateix, si les dades recollides contenen informació personal sensible, hom no les pot compartir amb tercers ni les pot publicar sense el consentiment o una protecció adequada dels subjectes de les dades. Els mecanismes de preservació de la privadesa forneixen maneres de sanejar les dades per tal que no revelin identitats o atributs confidencials. S'ha proposat una gran varietat de mecanismes per anonimitzar bases de dades estructurades amb atributs numèrics i categòrics; en canvi, la protecció automàtica de dades textuals no estructurades ha rebut molta menys atenció. En general, l'anonimització de dades textuals exigeix, primer, detectar trossos del text que poden revelar informació sensible i, després, emmascarar aquests trossos mitjançant supressió o generalització. En aquesta tesi fem servir diverses tecnologies per anonimitzar documents textuals. De primer, millorem les tècniques existents basades en etiquetatge de seqüències. Després, estenem aquestes tècniques per alinear-les millor amb el risc de revelació i amb les exigències de privadesa. Finalment, proposem un marc complet basat en models d'immersió de paraules que captura un concepte més ampli de protecció de dades i que forneix una protecció flexible guiada per les exigències de privadesa. També recorrem a les ontologies per preservar la utilitat del text emmascarat, és a dir, la seva semàntica i la seva llegibilitat. La nostra experimentació extensa i detallada mostra que els nostres mètodes superen els mètodes existents a l'hora de proporcionar anonimització robusta tot preservant raonablement la utilitat del text protegit.Cada día las personas añadimos una gran cantidad de datos a Internet, tales como tweets, opiniones, fotos y vídeos. Las organizaciones que recogen dichos datos los usan para extraer información para mejorar sus servicios o para propósitos comerciales. Sin embargo, si los datos recogidos contienen información personal sensible, no pueden compartirse ni publicarse sin el consentimiento o una protección adecuada de los sujetos de los datos. Los mecanismos de protección de la privacidad proporcionan maneras de sanear los datos de forma que no revelen identidades ni atributos confidenciales. Se ha propuesto una gran variedad de mecanismos para anonimizar bases de datos estructuradas con atributos numéricos y categóricos; en cambio, la protección automática de datos textuales no estructurados ha recibido mucha menos atención. En general, la anonimización de datos textuales requiere, primero, detectar trozos de texto que puedan revelar información sensible, para luego enmascarar dichos trozos mediante supresión o generalización. En este trabajo empleamos varias tecnologías para anonimizar documentos textuales. Primero mejoramos las técnicas existentes basadas en etiquetaje de secuencias. Posteriormente las extendmos para alinearlas mejor con la noción de riesgo de revelación y con los requisitos de privacidad. Finalmente, proponemos un marco completo basado en modelos de inmersión de palabras que captura una noción más amplia de protección de datos y ofrece protección flexible guiada por los requisitos de privacidad. También recurrimos a las ontologías para preservar la utilidad del texto enmascarado, es decir, su semantica y legibilidad. Nuestra experimentación extensa y detallada muestra que nuestros métodos superan a los existentes a la hora de proporcionar una anonimización más robusta al tiempo que se preserva razonablemente la utilidad del texto protegido.Every day, people post a significant amount of data on the Internet, such as tweets, reviews, photos, and videos. Organizations collecting these types of data use them to extract information in order to improve their services or for commercial purposes. Yet, if the collected data contain sensitive personal information, they cannot be shared with third parties or released publicly without consent or adequate protection of the data subjects. Privacy-preserving mechanisms provide ways to sanitize data so that identities and/or confidential attributes are not disclosed. A great variety of mechanisms have been proposed to anonymize structured databases with numerical and categorical attributes; however, automatically protecting unstructured textual data has received much less attention. In general, textual data anonymization requires, first, to detect pieces of text that may disclose sensitive information and, then, to mask those pieces via suppression or generalization. In this work, we leverage several technologies to anonymize textual documents. We first improve state-of-the-art techniques based on sequence labeling. After that, we extend them to make them more aligned with the notion of privacy risk and the privacy requirements. Finally, we propose a complete framework based on word embedding models that captures a broader notion of data protection and provides flexible protection driven by privacy requirements. We also leverage ontologies to preserve the utility of the masked text, that is, its semantics and readability. Extensive experimental results show that our methods outperform the state of the art by providing more robust anonymization while reasonably preserving the utility of the protected outcome

Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

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

Learning Data-Driven Models of Non-Verbal Behaviors for Building Rapport Using an Intelligent Virtual Agent

There is a growing societal need to address the increasing prevalence of behavioral health issues, such as obesity, alcohol or drug use, and general lack of treatment adherence for a variety of health problems. The statistics, worldwide and in the USA, are daunting. Excessive alcohol use is the third leading preventable cause of death in the United States (with 79,000 deaths annually), and is responsible for a wide range of health and social problems. On the positive side though, these behavioral health issues (and associated possible diseases) can often be prevented with relatively simple lifestyle changes, such as losing weight with a diet and/or physical exercise, or learning how to reduce alcohol consumption. Medicine has therefore started to move toward finding ways of preventively promoting wellness, rather than solely treating already established illness. Evidence-based patient-centered Brief Motivational Interviewing (BMI) interven- tions have been found particularly effective in helping people find intrinsic motivation to change problem behaviors after short counseling sessions, and to maintain healthy lifestyles over the long-term. Lack of locally available personnel well-trained in BMI, however, often limits access to successful interventions for people in need. To fill this accessibility gap, Computer-Based Interventions (CBIs) have started to emerge. Success of the CBIs, however, critically relies on insuring engagement and retention of CBI users so that they remain motivated to use these systems and come back to use them over the long term as necessary. Because of their text-only interfaces, current CBIs can therefore only express limited empathy and rapport, which are the most important factors of health interventions. Fortunately, in the last decade, computer science research has progressed in the design of simulated human characters with anthropomorphic communicative abilities. Virtual characters interact using humans’ innate communication modalities, such as facial expressions, body language, speech, and natural language understanding. By advancing research in Artificial Intelligence (AI), we can improve the ability of artificial agents to help us solve CBI problems. To facilitate successful communication and social interaction between artificial agents and human partners, it is essential that aspects of human social behavior, especially empathy and rapport, be considered when designing human-computer interfaces. Hence, the goal of the present dissertation is to provide a computational model of rapport to enhance an artificial agent’s social behavior, and to provide an experimental tool for the psychological theories shaping the model. Parts of this thesis were already published in [LYL+12, AYL12, AL13, ALYR13, LAYR13, YALR13, ALY14]

Representation learning for dialogue systems

Cette thèse présente une série de mesures prises pour étudier l’apprentissage de représentations (par exemple, l’apprentissage profond) afin de mettre en place des systèmes de dialogue et des agents de conversation virtuels. La thèse est divisée en deux parties générales. La première partie de la thèse examine l’apprentissage des représentations pour les modèles de dialogue génératifs. Conditionnés sur une séquence de tours à partir d’un dialogue textuel, ces modèles ont la tâche de générer la prochaine réponse appropriée dans le dialogue. Cette partie de la thèse porte sur les modèles séquence-à-séquence, qui est une classe de réseaux de neurones profonds génératifs. Premièrement, nous proposons un modèle d’encodeur-décodeur récurrent hiérarchique ("Hierarchical Recurrent Encoder-Decoder"), qui est une extension du modèle séquence-à-séquence traditionnel incorporant la structure des tours de dialogue. Deuxièmement, nous proposons un modèle de réseau de neurones récurrents multi-résolution ("Multiresolution Recurrent Neural Network"), qui est un modèle empilé séquence-à-séquence avec une représentation stochastique intermédiaire (une "représentation grossière") capturant le contenu sémantique abstrait communiqué entre les locuteurs. Troisièmement, nous proposons le modèle d’encodeur-décodeur récurrent avec variables latentes ("Latent Variable Recurrent Encoder-Decoder"), qui suivent une distribution normale. Les variables latentes sont destinées à la modélisation de l’ambiguïté et l’incertitude qui apparaissent naturellement dans la communication humaine. Les trois modèles sont évalués et comparés sur deux tâches de génération de réponse de dialogue: une tâche de génération de réponses sur la plateforme Twitter et une tâche de génération de réponses de l’assistance technique ("Ubuntu technical response generation task"). La deuxième partie de la thèse étudie l’apprentissage de représentations pour un système de dialogue utilisant l’apprentissage par renforcement dans un contexte réel. Cette partie porte plus particulièrement sur le système "Milabot" construit par l’Institut québécois d’intelligence artificielle (Mila) pour le concours "Amazon Alexa Prize 2017". Le Milabot est un système capable de bavarder avec des humains sur des sujets populaires à la fois par la parole et par le texte. Le système consiste d’un ensemble de modèles de récupération et de génération en langage naturel, comprenant des modèles basés sur des références, des modèles de sac de mots et des variantes des modèles décrits ci-dessus. Cette partie de la thèse se concentre sur la tâche de sélection de réponse. À partir d’une séquence de tours de dialogues et d’un ensemble des réponses possibles, le système doit sélectionner une réponse appropriée à fournir à l’utilisateur. Une approche d’apprentissage par renforcement basée sur un modèle appelée "Bottleneck Simulator" est proposée pour sélectionner le candidat approprié pour la réponse. Le "Bottleneck Simulator" apprend un modèle approximatif de l’environnement en se basant sur les trajectoires de dialogue observées et le "crowdsourcing", tout en utilisant un état abstrait représentant la sémantique du discours. Le modèle d’environnement est ensuite utilisé pour apprendre une stratégie d’apprentissage du renforcement par le biais de simulations. La stratégie apprise a été évaluée et comparée à des approches concurrentes via des tests A / B avec des utilisateurs réel, où elle démontre d’excellente performance.This thesis presents a series of steps taken towards investigating representation learning (e.g. deep learning) for building dialogue systems and conversational agents. The thesis is split into two general parts. The first part of the thesis investigates representation learning for generative dialogue models. Conditioned on a sequence of turns from a text-based dialogue, these models are tasked with generating the next, appropriate response in the dialogue. This part of the thesis focuses on sequence-to-sequence models, a class of generative deep neural networks. First, we propose the Hierarchical Recurrent Encoder-Decoder model, which is an extension of the vanilla sequence-to sequence model incorporating the turn-taking structure of dialogues. Second, we propose the Multiresolution Recurrent Neural Network model, which is a stacked sequence-to-sequence model with an intermediate, stochastic representation (a "coarse representation") capturing the abstract semantic content communicated between the dialogue speakers. Third, we propose the Latent Variable Recurrent Encoder-Decoder model, which is a variant of the Hierarchical Recurrent Encoder-Decoder model with latent, stochastic normally-distributed variables. The latent, stochastic variables are intended for modelling the ambiguity and uncertainty occurring naturally in human language communication. The three models are evaluated and compared on two dialogue response generation tasks: a Twitter response generation task and the Ubuntu technical response generation task. The second part of the thesis investigates representation learning for a real-world reinforcement learning dialogue system. Specifically, this part focuses on the Milabot system built by the Quebec Artificial Intelligence Institute (Mila) for the Amazon Alexa Prize 2017 competition. Milabot is a system capable of conversing with humans on popular small talk topics through both speech and text. The system consists of an ensemble of natural language retrieval and generation models, including template-based models, bag-of-words models, and variants of the models discussed in the first part of the thesis. This part of the thesis focuses on the response selection task. Given a sequence of turns from a dialogue and a set of candidate responses, the system must select an appropriate response to give the user. A model-based reinforcement learning approach, called the Bottleneck Simulator, is proposed for selecting the appropriate candidate response. The Bottleneck Simulator learns an approximate model of the environment based on observed dialogue trajectories and human crowdsourcing, while utilizing an abstract (bottleneck) state representing high-level discourse semantics. The learned environment model is then employed to learn a reinforcement learning policy through rollout simulations. The learned policy has been evaluated and compared to competing approaches through A/B testing with real-world users, where it was found to yield excellent performance

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio