Dataset Information

Incorporating biological structure into machine learning models in biomedicine.

ABSTRACT: In biomedical applications of machine learning, relevant information often has a rich structure that is not easily encoded as real-valued predictors. Examples of such data include DNA or RNA sequences, gene sets or pathways, gene interaction or coexpression networks, ontologies, and phylogenetic trees. We highlight recent examples of machine learning models that use structure to constrain model architecture or incorporate structured data into model training. For machine learning in biomedicine, where sample size is limited and model interpretability is crucial, incorporating prior knowledge in the form of structured data can be particularly useful. The area of research would benefit from performant open source implementations and independent benchmarking efforts.

SUBMITTER: Crawford J

PROVIDER: S-EPMC7308204 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Incorporating biological structure into machine learning models in biomedicine.

Crawford Jake J Greene Casey S CS

Current opinion in biotechnology 20200118

In biomedical applications of machine learning, relevant information often has a rich structure that is not easily encoded as real-valued predictors. Examples of such data include DNA or RNA sequences, gene sets or pathways, gene interaction or coexpression networks, ontologies, and phylogenetic trees. We highlight recent examples of machine learning models that use structure to constrain model architecture or incorporate structured data into model training. For machine learning in biomedicine, ...[more]

PMID: 31962244

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Incorporating biological structure into machine learning models in biomedicine.

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Incorporating biological structure into machine learning models in biomedicine.

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