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

Neural Methods for Effective, Efficient, and Exposure-Aware Information Retrieval

Neural networks with deep architectures have demonstrated significant performance improvements in computer vision, speech recognition, and natural language processing. The challenges in information retrieval (IR), however, are different from these other application areas. A common form of IR involves ranking of documents--or short passages--in response to keyword-based queries. Effective IR systems must deal with query-document vocabulary mismatch problem, by modeling relationships between different query and document terms and how they indicate relevance. Models should also consider lexical matches when the query contains rare terms--such as a person's name or a product model number--not seen during training, and to avoid retrieving semantically related but irrelevant results. In many real-life IR tasks, the retrieval involves extremely large collections--such as the document index of a commercial Web search engine--containing billions of documents. Efficient IR methods should take advantage of specialized IR data structures, such as inverted index, to efficiently retrieve from large collections. Given an information need, the IR system also mediates how much exposure an information artifact receives by deciding whether it should be displayed, and where it should be positioned, among other results. Exposure-aware IR systems may optimize for additional objectives, besides relevance, such as parity of exposure for retrieved items and content publishers. In this thesis, we present novel neural architectures and methods motivated by the specific needs and challenges of IR tasks.Comment: PhD thesis, Univ College London (2020

SEMANTIQUE DISTRIBUTIONNELLE

This special issue contains state-of-the-art papers on distributional semantic

Pretrained Transformers for Text Ranking: BERT and Beyond

The goal of text ranking is to generate an ordered list of texts retrieved from a corpus in response to a query. Although the most common formulation of text ranking is search, instances of the task can also be found in many natural language processing applications. This survey provides an overview of text ranking with neural network architectures known as transformers, of which BERT is the best-known example. The combination of transformers and self-supervised pretraining has been responsible for a paradigm shift in natural language processing (NLP), information retrieval (IR), and beyond. In this survey, we provide a synthesis of existing work as a single point of entry for practitioners who wish to gain a better understanding of how to apply transformers to text ranking problems and researchers who wish to pursue work in this area. We cover a wide range of modern techniques, grouped into two high-level categories: transformer models that perform reranking in multi-stage architectures and dense retrieval techniques that perform ranking directly. There are two themes that pervade our survey: techniques for handling long documents, beyond typical sentence-by-sentence processing in NLP, and techniques for addressing the tradeoff between effectiveness (i.e., result quality) and efficiency (e.g., query latency, model and index size). Although transformer architectures and pretraining techniques are recent innovations, many aspects of how they are applied to text ranking are relatively well understood and represent mature techniques. However, there remain many open research questions, and thus in addition to laying out the foundations of pretrained transformers for text ranking, this survey also attempts to prognosticate where the field is heading

Predicting Linguistic Structure with Incomplete and Cross-Lingual Supervision

Contemporary approaches to natural language processing are predominantly based on statistical machine learning from large amounts of text, which has been manually annotated with the linguistic structure of interest. However, such complete supervision is currently only available for the world's major languages, in a limited number of domains and for a limited range of tasks. As an alternative, this dissertation considers methods for linguistic structure prediction that can make use of incomplete and cross-lingual supervision, with the prospect of making linguistic processing tools more widely available at a lower cost. An overarching theme of this work is the use of structured discriminative latent variable models for learning with indirect and ambiguous supervision; as instantiated, these models admit rich model features while retaining efficient learning and inference properties. The first contribution to this end is a latent-variable model for fine-grained sentiment analysis with coarse-grained indirect supervision. The second is a model for cross-lingual word-cluster induction and the application thereof to cross-lingual model transfer. The third is a method for adapting multi-source discriminative cross-lingual transfer models to target languages, by means of typologically informed selective parameter sharing. The fourth is an ambiguity-aware self- and ensemble-training algorithm, which is applied to target language adaptation and relexicalization of delexicalized cross-lingual transfer parsers. The fifth is a set of sequence-labeling models that combine constraints at the level of tokens and types, and an instantiation of these models for part-of-speech tagging with incomplete cross-lingual and crowdsourced supervision. In addition to these contributions, comprehensive overviews are provided of structured prediction with no or incomplete supervision, as well as of learning in the multilingual and cross-lingual settings. Through careful empirical evaluation, it is established that the proposed methods can be used to create substantially more accurate tools for linguistic processing, compared to both unsupervised methods and to recently proposed cross-lingual methods. The empirical support for this claim is particularly strong in the latter case; our models for syntactic dependency parsing and part-of-speech tagging achieve the hitherto best published results for a wide number of target languages, in the setting where no annotated training data is available in the target language

Evaluation Methodologies for Visual Information Retrieval and Annotation

Die automatisierte Evaluation von Informations-Retrieval-Systemen erlaubt Performanz und Qualität der Informationsgewinnung zu bewerten. Bereits in den 60er Jahren wurden erste Methodologien für die system-basierte Evaluation aufgestellt und in den Cranfield Experimenten überprüft. Heutzutage gehören Evaluation, Test und Qualitätsbewertung zu einem aktiven Forschungsfeld mit erfolgreichen Evaluationskampagnen und etablierten Methoden. Evaluationsmethoden fanden zunächst in der Bewertung von Textanalyse-Systemen Anwendung. Mit dem rasanten Voranschreiten der Digitalisierung wurden diese Methoden sukzessive auf die Evaluation von Multimediaanalyse-Systeme übertragen. Dies geschah häufig, ohne die Evaluationsmethoden in Frage zu stellen oder sie an die veränderten Gegebenheiten der Multimediaanalyse anzupassen. Diese Arbeit beschäftigt sich mit der system-basierten Evaluation von Indizierungssystemen für Bildkollektionen. Sie adressiert drei Problemstellungen der Evaluation von Annotationen: Nutzeranforderungen für das Suchen und Verschlagworten von Bildern, Evaluationsmaße für die Qualitätsbewertung von Indizierungssystemen und Anforderungen an die Erstellung visueller Testkollektionen. Am Beispiel der Evaluation automatisierter Photo-Annotationsverfahren werden relevante Konzepte mit Bezug zu Nutzeranforderungen diskutiert, Möglichkeiten zur Erstellung einer zuverlässigen Ground Truth bei geringem Kosten- und Zeitaufwand vorgestellt und Evaluationsmaße zur Qualitätsbewertung eingeführt, analysiert und experimentell verglichen. Traditionelle Maße zur Ermittlung der Performanz werden in vier Dimensionen klassifiziert. Evaluationsmaße vergeben üblicherweise binäre Kosten für korrekte und falsche Annotationen. Diese Annahme steht im Widerspruch zu der Natur von Bildkonzepten. Das gemeinsame Auftreten von Bildkonzepten bestimmt ihren semantischen Zusammenhang und von daher sollten diese auch im Zusammenhang auf ihre Richtigkeit hin überprüft werden. In dieser Arbeit wird aufgezeigt, wie semantische Ähnlichkeiten visueller Konzepte automatisiert abgeschätzt und in den Evaluationsprozess eingebracht werden können. Die Ergebnisse der Arbeit inkludieren ein Nutzermodell für die konzeptbasierte Suche von Bildern, eine vollständig bewertete Testkollektion und neue Evaluationsmaße für die anforderungsgerechte Qualitätsbeurteilung von Bildanalysesystemen.Performance assessment plays a major role in the research on Information Retrieval (IR) systems. Starting with the Cranfield experiments in the early 60ies, methodologies for the system-based performance assessment emerged and established themselves, resulting in an active research field with a number of successful benchmarking activities. With the rise of the digital age, procedures of text retrieval evaluation were often transferred to multimedia retrieval evaluation without questioning their direct applicability. This thesis investigates the problem of system-based performance assessment of annotation approaches in generic image collections. It addresses three important parts of annotation evaluation, namely user requirements for the retrieval of annotated visual media, performance measures for multi-label evaluation, and visual test collections. Using the example of multi-label image annotation evaluation, I discuss which concepts to employ for indexing, how to obtain a reliable ground truth to moderate costs, and which evaluation measures are appropriate. This is accompanied by a thorough analysis of related work on system-based performance assessment in Visual Information Retrieval (VIR). Traditional performance measures are classified into four dimensions and investigated according to their appropriateness for visual annotation evaluation. One of the main ideas in this thesis adheres to the common assumption on the binary nature of the score prediction dimension in annotation evaluation. However, the predicted concepts and the set of true indexed concepts interrelate with each other. This work will show how to utilise these semantic relationships for a fine-grained evaluation scenario. Outcomes of this thesis result in a user model for concept-based image retrieval, a fully assessed image annotation test collection, and a number of novel performance measures for image annotation evaluation

Evaluation Methodologies for Visual Information Retrieval and Annotation

Die automatisierte Evaluation von Informations-Retrieval-Systemen erlaubt Performanz und Qualität der Informationsgewinnung zu bewerten. Bereits in den 60er Jahren wurden erste Methodologien für die system-basierte Evaluation aufgestellt und in den Cranfield Experimenten überprüft. Heutzutage gehören Evaluation, Test und Qualitätsbewertung zu einem aktiven Forschungsfeld mit erfolgreichen Evaluationskampagnen und etablierten Methoden. Evaluationsmethoden fanden zunächst in der Bewertung von Textanalyse-Systemen Anwendung. Mit dem rasanten Voranschreiten der Digitalisierung wurden diese Methoden sukzessive auf die Evaluation von Multimediaanalyse-Systeme übertragen. Dies geschah häufig, ohne die Evaluationsmethoden in Frage zu stellen oder sie an die veränderten Gegebenheiten der Multimediaanalyse anzupassen. Diese Arbeit beschäftigt sich mit der system-basierten Evaluation von Indizierungssystemen für Bildkollektionen. Sie adressiert drei Problemstellungen der Evaluation von Annotationen: Nutzeranforderungen für das Suchen und Verschlagworten von Bildern, Evaluationsmaße für die Qualitätsbewertung von Indizierungssystemen und Anforderungen an die Erstellung visueller Testkollektionen. Am Beispiel der Evaluation automatisierter Photo-Annotationsverfahren werden relevante Konzepte mit Bezug zu Nutzeranforderungen diskutiert, Möglichkeiten zur Erstellung einer zuverlässigen Ground Truth bei geringem Kosten- und Zeitaufwand vorgestellt und Evaluationsmaße zur Qualitätsbewertung eingeführt, analysiert und experimentell verglichen. Traditionelle Maße zur Ermittlung der Performanz werden in vier Dimensionen klassifiziert. Evaluationsmaße vergeben üblicherweise binäre Kosten für korrekte und falsche Annotationen. Diese Annahme steht im Widerspruch zu der Natur von Bildkonzepten. Das gemeinsame Auftreten von Bildkonzepten bestimmt ihren semantischen Zusammenhang und von daher sollten diese auch im Zusammenhang auf ihre Richtigkeit hin überprüft werden. In dieser Arbeit wird aufgezeigt, wie semantische Ähnlichkeiten visueller Konzepte automatisiert abgeschätzt und in den Evaluationsprozess eingebracht werden können. Die Ergebnisse der Arbeit inkludieren ein Nutzermodell für die konzeptbasierte Suche von Bildern, eine vollständig bewertete Testkollektion und neue Evaluationsmaße für die anforderungsgerechte Qualitätsbeurteilung von Bildanalysesystemen.Performance assessment plays a major role in the research on Information Retrieval (IR) systems. Starting with the Cranfield experiments in the early 60ies, methodologies for the system-based performance assessment emerged and established themselves, resulting in an active research field with a number of successful benchmarking activities. With the rise of the digital age, procedures of text retrieval evaluation were often transferred to multimedia retrieval evaluation without questioning their direct applicability. This thesis investigates the problem of system-based performance assessment of annotation approaches in generic image collections. It addresses three important parts of annotation evaluation, namely user requirements for the retrieval of annotated visual media, performance measures for multi-label evaluation, and visual test collections. Using the example of multi-label image annotation evaluation, I discuss which concepts to employ for indexing, how to obtain a reliable ground truth to moderate costs, and which evaluation measures are appropriate. This is accompanied by a thorough analysis of related work on system-based performance assessment in Visual Information Retrieval (VIR). Traditional performance measures are classified into four dimensions and investigated according to their appropriateness for visual annotation evaluation. One of the main ideas in this thesis adheres to the common assumption on the binary nature of the score prediction dimension in annotation evaluation. However, the predicted concepts and the set of true indexed concepts interrelate with each other. This work will show how to utilise these semantic relationships for a fine-grained evaluation scenario. Outcomes of this thesis result in a user model for concept-based image retrieval, a fully assessed image annotation test collection, and a number of novel performance measures for image annotation evaluation

Can humain association norm evaluate latent semantic analysis?

This paper presents the comparison of word association norm created by a psycholinguistic experiment to association lists generated by algorithms operating on text corpora. We compare lists generated by Church and Hanks algorithm and lists generated by LSA algorithm. An argument is presented on how those automatically generated lists reflect real semantic relations