Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results

Automatic information search for countering covid-19 misinformation through semantic similarity

Trabajo Fin de Máster en Bioinformática y Biología ComputacionalInformation quality in social media is an increasingly important issue and misinformation problem has become even more critical in the current COVID-19 pandemic, leading people exposed to false and potentially harmful claims and rumours. Civil society organizations, such as the World Health Organization, have demanded a global call for action to promote access to health information and mitigate harm from health misinformation. Consequently, this project pursues countering the spread of COVID-19 infodemic and its potential health hazards. In this work, we give an overall view of models and methods that have been employed in the NLP field from its foundations to the latest state-of-the-art approaches. Focusing on deep learning methods, we propose applying multilingual Transformer models based on siamese networks, also called bi-encoders, combined with ensemble and PCA dimensionality reduction techniques. The goal is to counter COVID-19 misinformation by analyzing the semantic similarity between a claim and tweets from a collection gathered from official fact-checkers verified by the International Fact-Checking Network of the Poynter Institute. It is factual that the number of Internet users increases every year and the language spoken determines access to information online. For this reason, we give a special effort in the application of multilingual models to tackle misinformation across the globe. Regarding semantic similarity, we firstly evaluate these multilingual ensemble models and improve the result in the STS-Benchmark compared to monolingual and single models. Secondly, we enhance the interpretability of the models’ performance through the SentEval toolkit. Lastly, we compare these models’ performance against biomedical models in TREC-COVID task round 1 using the BM25 Okapi ranking method as the baseline. Moreover, we are interested in understanding the ins and outs of misinformation. For that purpose, we extend interpretability using machine learning and deep learning approaches for sentiment analysis and topic modelling. Finally, we developed a dashboard to ease visualization of the results. In our view, the results obtained in this project constitute an excellent initial step toward incorporating multilingualism and will assist researchers and people in countering COVID-19 misinformation

Natural Language Processing and Graph Representation Learning for Clinical Data

The past decade has witnessed remarkable progress in biomedical informatics and its related fields: the development of high-throughput technologies in genomics, the mass adoption of electronic health records systems, and the AI renaissance largely catalyzed by deep learning. Deep learning has played an undeniably important role in our attempts to reduce the gap between the exponentially growing amount of biomedical data and our ability to make sense of them. In particular, the two main pillars of this dissertation---natural language processing and graph representation learning---have improved our capacity to learn useful representations of language and structured data to an extent previously considered unattainable in such a short time frame. In the context of clinical data, characterized by its notorious heterogeneity and complexity, natural language processing and graph representation learning have begun to enrich our toolkits for making sense and making use of the wealth of biomedical data beyond rule-based systems or traditional regression techniques. This dissertation comes at the cusp of such a paradigm shift, detailing my journey across the fields of biomedical and clinical informatics through the lens of natural language processing and graph representation learning. The takeaway is quite optimistic: despite the many layers of inefficiencies and challenges in the healthcare ecosystem, AI for healthcare is gearing up to transform the world in new and exciting ways

Neural Representations of Concepts and Texts for Biomedical Information Retrieval

Information retrieval (IR) methods are an indispensable tool in the current landscape of exponentially increasing textual data, especially on the Web. A typical IR task involves fetching and ranking a set of documents (from a large corpus) in terms of relevance to a user\u27s query, which is often expressed as a short phrase. IR methods are the backbone of modern search engines where additional system-level aspects including fault tolerance, scale, user interfaces, and session maintenance are also addressed. In addition to fetching documents, modern search systems may also identify snippets within the documents that are potentially most relevant to the input query. Furthermore, current systems may also maintain preprocessed structured knowledge derived from textual data as so called knowledge graphs, so certain types of queries that are posed as questions can be parsed as such; a response can be an output of one or more named entities instead of a ranked list of documents (e.g., what diseases are associated with EGFR mutations? ). This refined setup is often termed as question answering (QA) in the IR and natural language processing (NLP) communities. In biomedicine and healthcare, specialized corpora are often at play including research articles by scientists, clinical notes generated by healthcare professionals, consumer forums for specific conditions (e.g., cancer survivors network), and clinical trial protocols (e.g., www.clinicaltrials.gov). Biomedical IR is specialized given the types of queries and the variations in the texts are different from that of general Web documents. For example, scientific articles are more formal with longer sentences but clinical notes tend to have less grammatical conformity and are rife with abbreviations. There is also a mismatch between the vocabulary of consumers and the lingo of domain experts and professionals. Queries are also different and can range from simple phrases (e.g., COVID-19 symptoms ) to more complex implicitly fielded queries (e.g., chemotherapy regimens for stage IV lung cancer patients with ALK mutations ). Hence, developing methods for different configurations (corpus, query type, user type) needs more deliberate attention in biomedical IR. Representations of documents and queries are at the core of IR methods and retrieval methodology involves coming up with these representations and matching queries with documents based on them. Traditional IR systems follow the approach of keyword based indexing of documents (the so called inverted index) and matching query phrases against the document index. It is not difficult to see that this keyword based matching ignores the semantics of texts (synonymy at the lexeme level and entailment at phrase/clause/sentence levels) and this has lead to dimensionality reduction methods such as latent semantic indexing that generally have scale-related concerns; such methods also do not address similarity at the sentence level. Since the resurgence of neural network methods in NLP, the IR field has also moved to incorporate advances in neural networks into current IR methods. This dissertation presents four specific methodological efforts toward improving biomedical IR. Neural methods always begin with dense embeddings for words and concepts to overcome the limitations of one-hot encoding in traditional NLP/IR. In the first effort, we present a new neural pre-training approach to jointly learn word and concept embeddings for downstream use in applications. In the second study, we present a joint neural model for two essential subtasks of information extraction (IE): named entity recognition (NER) and entity normalization (EN). Our method detects biomedical concept phrases in texts and links them to the corresponding semantic types and entity codes. These first two studies provide essential tools to model textual representations as compositions of both surface forms (lexical units) and high level concepts with potential downstream use in QA. In the third effort, we present a document reranking model that can help surface documents that are likely to contain answers (e.g, factoids, lists) to a question in a QA task. The model is essentially a sentence matching neural network that learns the relevance of a candidate answer sentence to the given question parametrized with a bilinear map. In the fourth effort, we present another document reranking approach that is tailored for precision medicine use-cases. It combines neural query-document matching and faceted text summarization. The main distinction of this effort from previous efforts is to pivot from a query manipulation setup to transforming candidate documents into pseudo-queries via neural text summarization. Overall, our contributions constitute nontrivial advances in biomedical IR using neural representations of concepts and texts