12 research outputs found
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
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Domain adaptation for neural machine translation
The development of deep learning techniques has allowed Neural Machine Translation (NMT) models to become extremely powerful, given sufficient training data and training time. However, such translation models struggle when translating text of a specific domain. A domain may consist of text on a well-defined topic, or text of unknown provenance with an identifiable vocabulary distribution, or language with some other stylometric feature. While NMT models can achieve good translation performance on domain-specific data via simple tuning on a representative training corpus, such data-centric approaches have negative side-effects. These include over-fitting, brittleness, and `catastrophic forgetting' of previous training examples.
In this thesis we instead explore more robust approaches to domain adaptation for NMT. We consider the case where a system is adapted to a specified domain of interest, but may also need to accommodate new language, or domain-mismatched sentences. We explore techniques relating to data selection and curriculum, model parameter adaptation procedure, and inference procedure. We show that iterative fine-tuning can achieve strong performance over multiple related domains, and that Elastic Weight Consolidation can be used to mitigate catastrophic forgetting in NMT domain adaptation across multiple sequential domains. We develop a robust variant of Minimum Risk Training which allows more beneficial use of small, highly domain-specific tuning sets than simple cross-entropy fine-tuning, and can mitigate exposure bias resulting from domain over-fitting. We extend Bayesian Interpolation inference schemes to Neural Machine Translation, allowing adaptive weighting of NMT ensembles to translate text from an unknown domain.
Finally we demonstrate the benefit of multi-domain adaptation approaches for other lines of NMT research. We show that NMT systems using multiple forms of data representation can benefit from multi-domain inference approaches. We also demonstrate a series of domain adaptation approaches to mitigating the effects of gender bias in machine translation