Statistical Inference Relief (STIR) feature selection
Happy to be a collaborator on this paper to add inference to the ReliefF method for feature selection. We have done a lot of work on this algorithm that is capable of detecting epistasis. Le TT,...
View ArticleGeneralized multifactor dimensionality reduction approaches to identification...
I love seeing new extensions and modifications to our MDR method. Here is a new from Dr. Lou.Hou TT, Lin F, Bai S, Cleves MA, Xu HM, Lou XY. Generalized multifactor dimensionality reduction approaches...
View ArticleAnalysis validation has been neglected in the Age of Reproducibility
Our paper on the use of simulation to help improve analysis validation and results reproducibility. Lotterhos KE, Moore JH, Stapleton AE. Analysis validation has been neglected in the Age of...
View ArticlePreparing next-generation scientists for biomedical big data: artificial...
Our paper on how to prepare next-gen scientists for big data is out. We outline here a curriculum focused on precision medicine, data science, and artificial intelligence.Moore JH, Boland MR, Camara...
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Testing the assumptions of parametric linear models: the need for biological...
This editorial is in response to some claims that an observed linear relationship between relative pair trait correlation and IBD genetic sharing is indicative of a simple additive genetic architecture...
View ArticleHow to increase our belief in discovered statistical interactions via...
Our new paper with Dr. Kristel van Steen on approaches for improving evidence for statistical interactions.Van Steen K, Moore JH. How to increase our belief in discovered statistical interactions via...
View ArticleAutomated discovery of test statistics
This was a fun proof-of-principle paper we did on using genetic programming to discover test statistics. We showed that with general principles that we could re-discover the two-sample t-test. This...
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Accessible AI for Automated Machine Learning
We released our open-source PennAI software for automated machine learning this week. Here is the Penn Medicine press release. Here is the Github link to the source code. More info can be found at the...
View ArticleWorkflows for regulome and transcriptome-based prioritization of genetic...
Manduchi E, Hemerich D, van Setten J, Tragante V, Harakalova M, Pei J, Williams SM, van der Harst P, Asselbergs FW, Moore JH. A comparison of two workflows for regulome and transcriptome-based...
View ArticleScaling tree-based automated machine learning
Le TT, Fu W, Moore JH. Scaling tree-based automated machine learning to biomedical big data with a feature set selector. Bioinformatics, in press (2019). [PubMed] [Bioinformatics]MOTIVATION: Automated...
View ArticleAlternative measures of association for GWAS
Manduchi E, Orzechowski PR, Ritchie MD, Moore JH. Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies. BioData Min. 2019 Jul 9;12:14....
View ArticleEmbracing study heterogeneity for finding genetic interactions in large-scale...
New collaborative paper in Genetic Epidemiology with Dr. Yong ChenLiu Y, Huang J, Urbanowicz RJ, Chen K, Manduchi E, Greene CS, Moore JH, Scheet P, Chen Y. Embracing study heterogeneity for finding...
View ArticleAutomated machine learning analysis of metabolomics data
We have expanded our TPOT automated machine learning method (AutoML) to metabolomics data.Orlenko A, Kofink D, Lyytikäinen LP, Nikus K, Mishra P, Kuukasjärvi P, Karhunen PJ, Kähönen M, Laurikka JO,...
View ArticleThe Human Pancreas Analysis Program (HPAP)
We are assisting with the bioinformatics support for The Human Pancreas Analysis Program (HPAP) which consists of two interlocking, collaborative projects at three institutions that seek to provide...
View ArticleGetting started with TPOT for automated machine learning
A great post from Dr. Trang Le on how to get started with automated machine learning (AutoML) with our Tree-Based Pipeline Optimization Tool (TPOT) in Python.
View ArticleUsing simulations to understand the relationship between epistasis and...
Moore JH, Olson RS, Schmitt P, Chen Y, Manduchi E. How Computational Experiments Can Improve Our Understanding of the Genetic Architecture of Common Human Diseases. Artif Life. 2020 Winter;26(1):23-37....
View ArticleIdeas for how informaticians can get involved with COVID-19 research
Moore JH, Barnett I, Boland MR, Chen Y, Demiris G, Gonzalez-Hernandez G, Herman DS, Himes BE, Hubbard RA, Kim D, Morris JS, Mowery DL, Ritchie MD, Shen L, Urbanowicz R, Holmes JH. Ideas for how...
View Articletreeheatr: an R package for interpretable decision tree visualizations
Le TT, Moore JH. treeheatr: an R package for interpretable decision tree visualizations. Bioinformatics. 2020 Jul 23:btaa662. doi: 10.1093/bioinformatics/btaa662. Epub ahead of print. PMID: 32702108....
View ArticleA brief introduction to my artificial intelligence and machine learning...
A 12-minute overview of my artificial intelligence and machine learning research program [YouTube]
View ArticleElectronic health records and polygenic risk scores for predicting disease risk
Li R, Chen Y, Ritchie MD, Moore JH. Electronic health records and polygenic risk scores for predicting disease risk. Nat Rev Genet. 2020 Aug;21(8):493-502. doi: 10.1038/s41576-020-0224-1. Epub 2020 Mar...
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