Predicting controlled vocabulary based on text and citations: Case studies in medical subject headings in MEDLINE and patents

This dissertation makes three contributions in the area of controlled vocabulary prediction of Medical Subject Headings. The first contribution is a new partial matching measure based on distributional semantics. The second contribution is a probabilistic model based on text similarity and citations. The third contribution is a case study of cross-domain vocabulary prediction in US Patents. Medical subject headings (MeSH) are an important life sciences controlled vocabulary. They are an ideal ground to study controlled vocabulary prediction due to their complexity, hierarchical nature, and practical significance. The dissertation begins with an updated analysis of human indexing consistency in MEDLINE. This study demonstrates the need for partial matching measures to account for indexing variability. Here, I develop four measures combining the MeSH hierarchy and contextual similarity. These measures provide several new tools for evaluating and diagnosing controlled vocabulary models. Next, a generalized predictive model is introduced. This model uses citations and abstract similarity as inputs to a hybrid KNN classifier. Citations and abstracts are found to be complimentary in that they reliably produce unique and relevant candidate terms. Finally, the predictive model is applied to a corpus of approximately 65,000 biomedical US patents. This case study explores differences in the vocabulary of MEDLINE and patents, as well as the prospect for MeSH prediction to open new scholarly opportunities in economics and health policy research

Embedding Probabilities in Predication Space with Hermitian Holographic Reduced Representations

Abstract. Predication-based Semantic Indexing (PSI) is an approach to generating high-dimensional vector representations of concept-relation-concept triplets. In this paper, we develop a variant of PSI that accommodates estimation of the probability of encountering a particular predication (such as fluoxetine TREATS major depressive disorder) in a collection of predications concerning a concept of interest (such as major depressive disorder). PSI leverages reversible vector transformations provided by representational approaches known as Vector Symbolic Architectures (VSA). To embed probabilities we develop a novel VSA variant, Hermitian Holographic Reduced Representations, with improvements in predictive modeling experiments. The probabilistic interpretation this facilitates reveals previously unrecognized connections between PSI and quantum theory -perhaps most notably that PSI's estimation of relatedness across multiple reasoning pathways corresponds to the estimation of the probability of traversing indistinguishable pathways in accordance with the rules of quantum probability

Characterizing the Information Needs of Rural Healthcare Practitioners with Language Agnostic Automated Text Analysis

Objectives – Previous research has characterized urban healthcare providers\u27 information needs, using various qualitative methods. However, little is known about the needs of rural primary care practitioners in Brazil. Communication exchanged during tele-consultations presents a unique data source for the study of these information needs. In this study, I characterize rural healthcare providers\u27 information needs expressed electronically, using automated methods. Methods – I applied automated methods to categorize messages obtained from the telehealth system from two regions in Brazil. A subset of these messages, annotated with top-level categories in the DeCS terminology (the regional equivalent of MeSH), was used to train text categorization models, which were then applied to a larger, unannotated data set. On account of their more granular nature, I focused on answers provided to the queries sent by rural healthcare providers. I studied these answers, as surrogates for the information needs they met. Message representations were generated using methods of distributional semantics, permitting the application of k-Nearest Neighbor classification for category assignment. The resulting category assignments were analyzed to determine differences across regions, and healthcare providers. Results – Analysis of the assigned categories revealed differences in information needs across regions, corresponding to known differences in the distributions of diseases and tele-consultant expertise across these regions. Furthermore, information needs of rural nurses were observed to be different from those documented in qualitative studies of their urban counterparts, and the distribution of expressed information needs categories differed across types of providers (e.g. nurses vs. physicians). Discussion – The automated analysis of large amounts of digitally-captured tele-consultation data suggests that rural healthcare providers\u27 information needs in Brazil are different than those of their urban counterparts in developed countries. The observed disparities in information needs correspond to known differences in the distribution of illness and expertise in these regions, supporting the applicability of my methods in this context. In addition, these methods have the potential to mediate near real-time monitoring of information needs, without imposing a direct burden upon healthcare providers. Potential applications include automated delivery of needed information at the point of care, needs-based deployment of tele-consultation resources and syndromic surveillance. Conclusion – I used automated text categorization methods to assess the information needs expressed at the point of care in rural Brazil. My findings reveal differences in information needs across regions, and across practitioner types, demonstrating the utility of these methods and data as a means to characterize information needs

Text Mining Biomedical Literature for Genomic Knowledge Discovery

The last decade has been marked by unprecedented growth in both the production of biomedical data and the amount of published literature discussing it. Almost every known or postulated piece of information pertaining to genes, proteins, and their role in biological processes is reported somewhere in the vast amount of published biomedical literature. We believe the ability to rapidly survey and analyze this literature and extract pertinent information constitutes a necessary step toward both the design and the interpretation of any large-scale experiment. Moreover, automated literature mining offers a yet untapped opportunity to integrate many fragments of information gathered by researchers from multiple fields of expertise into a complete picture exposing the interrelated roles of various genes, proteins, and chemical reactions in cells and organisms. In this thesis, we show that functional keywords in biomedical literature, particularly Medline, represent very valuable information and can be used to discover new genomic knowledge. To validate our claim we present an investigation into text mining biomedical literature to assist microarray data analysis, yeast gene function classification, and biomedical literature categorization. We conduct following studies: 1. We test sets of genes to discover common functional keywords among them and use these keywords to cluster them into groups; 2. We show that it is possible to link genes to diseases by an expert human interpretation of the functional keywords for the genes- none of these diseases are as yet mentioned in public databases; 3. By clustering genes based on commonality of functional keywords it is possible to group genes into meaningful clusters that reveal more information about their functions, link to diseases and roles in metabolism pathways; 4. Using extracted functional keywords, we are able to demonstrate that for yeast genes, we can make a better functional grouping of genes in comparison to available public microarray and phylogenetic databases; 5. We show an application of our approach to literature classification. Using functional keywords as features, we are able to extract epidemiological abstracts automatically from Medline with higher sensitivity and accuracy than a human expert.Ph.D.Committee Chair: Shamkant B. Navathe; Committee Co-Chair: Brian J. Ciliax; Committee Member: Ashwin Ram; Committee Member: Edward Omiecinski; Committee Member: Ray Dingledine; Committee Member: Venu Dasig

Text Classification

There is an abundance of text data in this world but most of it is raw. We need to extract information from this data to make use of it. One way to extract this information from raw text is to apply informative labels drawn from a pre-defined fixed set i.e. Text Classification. In this thesis, we focus on the general problem of text classification, and work towards solving challenges associated to binary/multi-class/multi-label classification. More specifically, we deal with the problem of (i) Zero-shot labels during testing; (ii) Active learning for text screening; (iii) Multi-label classification under low supervision; (iv) Structured label space; (v) Classifying pairs of words in raw text i.e. Relation Extraction. For (i), we use a zero-shot classification model that utilizes independently learned semantic embeddings. Regarding (ii), we propose a novel active learning algorithm that reduces problem of bias in naive active learning algorithms. For (iii), we propose neural candidate-selector architecture that starts from a set of high-recall candidate labels to obtain high-precision predictions. In the case of (iv), we proposed an attention based neural tree decoder that recursively decodes an abstract into the ontology tree. For (v), we propose using second-order relations that are derived by explicitly connecting pairs of words via context token(s) for improved relation extraction. We use a wide variety of both traditional and deep machine learning tools. More specifically, we used traditional machine learning models like multi-valued linear regression and logistic regression for (i, ii), deep convolutional neural networks for (iii), recurrent neural networks for (iv) and transformer networks for (v)

Generating High Precision Classification Rules for Screening of Irrelevant Studies in Systematic Review Literature Searches

Systematic reviews aim to produce repeatable, unbiased, and comprehensive answers to clinical questions. Systematic reviews are an essential component of modern evidence based medicine, however due to the risks of omitting relevant research they are highly time consuming to create and are largely conducted manually. This thesis presents a novel framework for partial automation of systematic review literature searches. We exploit the ubiquitous multi-stage screening process by training the classifier using annotations made by reviewers in previous screening stages. Our approach has the benefit of integrating seamlessly with the existing screening process, minimising disruption to users. Ideally, classification models for systematic reviews should be easily interpretable by users. We propose a novel, rule based algorithm for use with our framework. A new approach for identifying redundant associations when generating rules is also presented. The proposed approach to redundancy seeks to both exclude redundant specialisations of existing rules (those with additional terms in their antecedent), as well as redundant generalisations (those with fewer terms in their antecedent). We demonstrate the ability of the proposed approach to improve the usability of the generated rules. The proposed rule based algorithm is evaluated by simulated application to several existing systematic reviews. Workload savings of up to 10% are demonstrated. There is an increasing demand for systematic reviews related to a variety of clinical disciplines, such as diagnosis. We examine reviews of diagnosis and contrast them against more traditional systematic reviews of treatment. We demonstrate existing challenges such as target class heterogeneity and high data imbalance are even more pronounced for this class of reviews. The described algorithm accounts for this by seeking to label subsets of non-relevant studies with high precision, avoiding the need to generate a high recall model of the minority class

Sec-Lib: Protecting Scholarly Digital Libraries From Infected Papers Using Active Machine Learning Framework

Researchers from academia and the corporate-sector rely on scholarly digital libraries to access articles. Attackers take advantage of innocent users who consider the articles' files safe and thus open PDF-files with little concern. In addition, researchers consider scholarly libraries a reliable, trusted, and untainted corpus of papers. For these reasons, scholarly digital libraries are an attractive-target and inadvertently support the proliferation of cyber-attacks launched via malicious PDF-files. In this study, we present related vulnerabilities and malware distribution approaches that exploit the vulnerabilities of scholarly digital libraries. We evaluated over two-million scholarly papers in the CiteSeerX library and found the library to be contaminated with a surprisingly large number (0.3-2%) of malicious PDF documents (over 55% were crawled from the IPs of US-universities). We developed a two layered detection framework aimed at enhancing the detection of malicious PDF documents, Sec-Lib, which offers a security solution for large digital libraries. Sec-Lib includes a deterministic layer for detecting known malware, and a machine learning based layer for detecting unknown malware. Our evaluation showed that scholarly digital libraries can detect 96.9% of malware with Sec-Lib, while minimizing the number of PDF-files requiring labeling, and thus reducing the manual inspection efforts of security-experts by 98%

Sec-Lib: Protecting Scholarly Digital Libraries From Infected Papers Using Active Machine Learning Framework

Researchers from academia and the corporate-sector rely on scholarly digital libraries to access articles. Attackers take advantage of innocent users who consider the articles\u27 files safe and thus open PDF-files with little concern. In addition, researchers consider scholarly libraries a reliable, trusted, and untainted corpus of papers. For these reasons, scholarly digital libraries are an attractive-target and inadvertently support the proliferation of cyber-attacks launched via malicious PDF-files. In this study, we present related vulnerabilities and malware distribution approaches that exploit the vulnerabilities of scholarly digital libraries. We evaluated over two-million scholarly papers in the CiteSeerX library and found the library to be contaminated with a surprisingly large number (0.3-2%) of malicious PDF documents (over 55% were crawled from the IPs of US-universities). We developed a two layered detection framework aimed at enhancing the detection of malicious PDF documents, Sec-Lib, which offers a security solution for large digital libraries. Sec-Lib includes a deterministic layer for detecting known malware, and a machine learning based layer for detecting unknown malware. Our evaluation showed that scholarly digital libraries can detect 96.9% of malware with Sec-Lib, while minimizing the number of PDF-files requiring labeling, and thus reducing the manual inspection efforts of security-experts by 98%