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One Algorithm May Not Fit All: How Selection Bias Affects Machine Learning Performance.

Radiographics : a review publication of the Radiological Society of North America, Inc
Machine learning (ML) algorithms have demonstrated high diagnostic accuracy in identifying and categorizing disease on radiologic images. Despite the results of initial research studies that report ML algorithm diagnostic accuracy similar to or excee...

Use of word and graph embedding to measure semantic relatedness between Unified Medical Language System concepts.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: The study sought to explore the use of deep learning techniques to measure the semantic relatedness between Unified Medical Language System (UMLS) concepts.

LncLocation: Efficient Subcellular Location Prediction of Long Non-Coding RNA-Based Multi-Source Heterogeneous Feature Fusion.

International journal of molecular sciences
Recent studies uncover that subcellular location of long non-coding RNAs (lncRNAs) can provide significant information on its function. Due to the lack of experimental data, the number of lncRNAs is very limited, experimentally verified subcellular l...

Assessing the enrichment of dietary supplement coverage in the Unified Medical Language System.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: We sought to assess the need for additional coverage of dietary supplements (DS) in the Unified Medical Language System (UMLS) by investigating (1) the overlap between the integrated DIetary Supplements Knowledge base (iDISK) DS ingredient...

Learning and interpreting the gene regulatory grammar in a deep learning framework.

PLoS computational biology
Deep neural networks (DNNs) have achieved state-of-the-art performance in identifying gene regulatory sequences, but they have provided limited insight into the biology of regulatory elements due to the difficulty of interpreting the complex features...

PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: Developing algorithms to extract phenotypes from electronic health records (EHRs) can be challenging and time-consuming. We developed PheMap, a high-throughput phenotyping approach that leverages multiple independent, online resources to s...

A pre-training and self-training approach for biomedical named entity recognition.

PloS one
Named entity recognition (NER) is a key component of many scientific literature mining tasks, such as information retrieval, information extraction, and question answering; however, many modern approaches require large amounts of labeled training dat...

The Human Phenotype Ontology in 2021.

Nucleic acids research
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for ...