Identifying biomedical
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The field of biomedical informatics experienced a productive 2015 in terms of research. In order to highlight the accomplishments of that research, elicit trends, and identify shortcomings at a macro level, a 19-person team conducted an extensive review of the literature in clinical and consumer informatics.
6p visteverogers 24-06-2023 4 3 Download
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The repurposing of electronic health records (EHRs) can improve clinical and genetic research for rare diseases. This paper presents a method to detect family history and negation in narrative reports and evaluates its impact on selecting populations from a clinical data warehouse (CDW).
7p visteverogers 24-06-2023 2 2 Download
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Genetic ancestry is a critical co-factor to study phenotype-genotype associations using cohorts of human subjects. Most publicly available molecular datasets are, however, missing this information or only share self-reported race and ethnicity, representing a limitation to identify and repurpose datasets to investigate the contribution of ancestry to diseases and traits.
5p visteverogers 24-06-2023 3 2 Download
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In this study we explore the usability and reliability of such an approach by investigating whether different users identify the same privacy risks on applying the checklist to a sample of publications.
6p visteverogers 24-06-2023 6 2 Download
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Distributional semantics algorithms, which learn vector space representations of words and phrases from large corpora, identify related terms based on contextual usage patterns. We hypothesize that distributional semantics can speed up lexicon expansion in a clinical domain, radiology, by unearthing synonyms from the corpus.
7p visteverogers 24-06-2023 5 1 Download
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T Objective: Effective, scalable de-identification of personally identifying information (PII) for information-rich clinical text is critical to support secondary use, but no method is 100% effective. The hiding-in-plain-sight (HIPS) approach attempts to solve this “residual PII problem.”
9p vighostrider 25-05-2023 9 2 Download
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The Unified Medical Language System (UMLS) integrates various source terminologies to support interoperability between biomedical information systems. In this article, we introduce a novel transformationbased auditing method that leverages the UMLS knowledge to systematically identify missing hierarchical IS-A relations in the source terminologies.
8p vighostrider 25-05-2023 5 3 Download
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Re-identification risk methods for biomedical data often assume a worst case, in which attackers know all identifiable features (eg, age and race) about a subject. Yet, worst-case adversarial modeling can overestimate risk and induce heavy editing of shared data.
9p vighostrider 25-05-2023 10 2 Download
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Measurement and data entry of height and weight values are error prone. Aggregation of medical record data from multiple sites creates new challenges prompting the need to identify and correct errant values. We sought to characterize and correct issues with height and weight measurement values within the All of Us (AoU) Research Program.
5p vighostrider 25-05-2023 3 2 Download
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Triple-negative breast cancer (TNBC) is a molecular subtype of breast cancer, which is a major health burden of females worldwide. Thymoquinone (TQ), a natural compound, has been found to be effective against TNBC cells, and this study identified IL17RD as a novel target of TQ in TNBC cells.
11p visusanwojcicki 28-06-2022 8 3 Download
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Despite the success and fast adaptation of deep learning models in biomedical domains, their lack of interpretability remains an issue. Here, we introduce Enhanced Integrated Gradients (EIG), a method to identify significant features associated with a specific prediction task. Using RNA splicing prediction as well as digit classification as case studies, we demonstrate that EIG improves upon the original Integrated Gradients method and produces sets of informative features.
22p viarchimedes 26-01-2022 16 0 Download
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Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and Human Phenotype Ontology (HPO). Because of the advantage of identifying novel relationships between terms, calculating similarity between ontology terms is one of the major tasks in this research area.
10p vilarryellison 29-10-2021 6 0 Download
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Identifying potential associations between genes and diseases via biomedical experiments must be the time-consuming and expensive research works. The computational technologies based on machine learning models have been widely utilized to explore genetic information related to complex diseases.
16p vitzuyu2711 29-09-2021 9 1 Download
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Genome-wide association studies (GWAS) with metabolic traits and metabolome-wide association studies (MWAS) with traits of biomedical relevance are powerful tools to identify the contribution of genetic, environmental and lifestyle factors to the etiology of complex diseases.
7p viwyoming2711 16-12-2020 9 1 Download
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Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge.
10p viwyoming2711 16-12-2020 9 1 Download
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Biomedical semantic role labeling (BioSRL) is a natural language processing technique that identifies the semantic roles of the words or phrases in sentences describing biological processes and expresses them as predicate-argument structures (PAS’s). Currently, a major problem of BioSRL is that most systems label every node in a full parse tree independently; however, some nodes always exhibit dependency.
12p vikentucky2711 26-11-2020 14 0 Download
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Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is relation extraction, which aims to identify designated relations among biological entities reported in literature.
18p vikentucky2711 26-11-2020 5 1 Download
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Controlled vocabularies such as the Unified Medical Language System (UMLS®) and Medical Subject Headings (MeSH®) are widely used for biomedical natural language processing (NLP) tasks. However, the standard terminology in such collections suffers from low usage in biomedical literature, e.g. only 13% of UMLS terms appear in MEDLINE®.
10p vikentucky2711 26-11-2020 8 0 Download
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The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources.
21p vikentucky2711 24-11-2020 18 1 Download
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Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research in connectivity mapping mainly focused on two of the key components in the framework, namely, the reference gene expression profiles and the connectivity mapping algorithms.
11p vioklahoma2711 19-11-2020 14 1 Download