Author

Aaron M. Smith

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Approach:machine learning (classical)· 2 Approach:statistical model· 2 Research Focus:batch correction / integration· 1 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Charles K. FisheriD· 3 shared Jonathan R. WalshiD· 3 shared Anton D. LoukianoviD· 1 shared Craig B. DavisiD· 1 shared Daniel Ziemek· 1 shared David Li‐Bland· 1 shared John Long· 1 shared Martin R. Hodge· 1 shared

Activity by Year

2018-2020 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersBioinformatics

Charles K. FisherORCID

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Author profile →

3 papers

Recent·Most cited

Generating Digital Twins with Multiple Sclerosis Using Probabilistic Neural Networks

Jonathan R. Walsh, Aaron M. Smith, Yannick Pouliot, David Li‐Bland, Anton D. Loukianov, Charles K. Fisher

The paper uses a Conditional Restricted Boltzmann Machine to generate digital twins of MS patients, enabling subject-level analysis of disease progression.

bioRxiv · Feb 4, 2020 · PreprintBioinformatics

Deep Learning of Representations for Transcriptomics-based Phenotype Prediction

Aaron M. Smith, Jonathan R. Walsh, John Long, Craig B. Davis, Peter V. Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek, Charles K. Fisher

The paper evaluates representation learning techniques for transcriptomics-based phenotype prediction using public data and finds that l2-regularized regression on centered log-ratio transformed abundances performs best.

bioRxiv · Mar 15, 2019 · PreprintBioinformatics

Who is this gene and what does it do? A toolkit for munging transcriptomics data in python

Charles K. Fisher, Aaron M. Smith, Jonathan R. Walsh

The paper introduces a Python library, genemunge, to simplify handling transcriptomics data by managing gene identifiers, GO information, expression levels, batch correction, and gene set selection.

bioRxiv · Apr 10, 2018 · PreprintBioinformatics