J
Joshua J. Levy
Researcher at Dartmouth College
Publications - 62
Citations - 386
Joshua J. Levy is an academic researcher from Dartmouth College. The author has contributed to research in topics: Medicine & Computer science. The author has an hindex of 6, co-authored 44 publications receiving 150 citations. Previous affiliations of Joshua J. Levy include Dartmouth–Hitchcock Medical Center & Joint Genome Institute.
Papers
More filters
Journal ArticleDOI
MethylNet: an automated and modular deep learning approach for DNA methylation analysis
Joshua J. Levy,Alexander J. Titus,Curtis L. Petersen,Curtis L. Petersen,Youdinghuan Chen,Lucas A. Salas,Brock C. Christensen +6 more
TL;DR: MethylNet is described, a DNAm deep learning method that can construct embeddings, make predictions, generate new data, and uncover unknown heterogeneity with minimal user supervision that can study cellular differences, grasp higher order information of cancer sub-types, and capture factors associated with smoking in concordance with known differences.
Journal ArticleDOI
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors.
Sean P. Gordon,Bruno Contreras-Moreira,Joshua J. Levy,Joshua J. Levy,Armin Djamei,Armin Djamei,Angelika Czedik-Eysenberg,Virginia S. Tartaglio,Virginia S. Tartaglio,Adam M. Session,Joel Martin,Amy Cartwright,Andrew Katz,Vasanth R. Singan,Eugene Goltsman,Kerrie Barry,Vinh Ha Dinh-Thi,Boulos Chalhoub,Boulos Chalhoub,Antonio Díaz-Pérez,Antonio Díaz-Pérez,Rubén Sancho,Joanna Lusinska,Elzbieta Wolny,Candida Nibau,John H. Doonan,Luis A. J. Mur,Christopher Plott,Jerry Jenkins,Samuel P. Hazen,Scott J. Lee,Shengqiang Shu,David Goodstein,Daniel S. Rokhsar,Daniel S. Rokhsar,Jeremy Schmutz,Robert Hasterok,Pilar Catalán,Pilar Catalán,Pilar Catalán,John P. Vogel,John P. Vogel +41 more
TL;DR: Pan-genomic approach is used to reveal gradual polyploid genome evolution by analyzing of Brachypodium hybridum and its diploid progenitors and results are consistent with a gradual accumulation of genomic changes afterpolyploidization and a lack of subgenome expression dominance.
Journal ArticleDOI
Don't dismiss logistic regression: the case for sensible extraction of interactions in the era of machine learning.
TL;DR: A statistically significant increase in predictive performance when using hybrid procedures and greater clarity in the association with the outcome of terms acquired compared to directly interpreting the random forest output are found.
Proceedings ArticleDOI
Topological Feature Extraction and Visualization of Whole Slide Images using Graph Neural Networks.
TL;DR: In this paper, Graph Neural Networks (GNNs) and Topological Data Analysis (TDA) are combined to identify and quantify key pathogenic information pathways in colon cancer.
Journal ArticleDOI
A large-scale internal validation study of unsupervised virtual trichrome staining technologies on nonalcoholic steatohepatitis liver biopsies.
Joshua J. Levy,Nasim Azizgolshani,Michael J. Andersen,Arief A. Suriawinata,Xiaoying Liu,Mikhail Lisovsky,Bing Ren,Carly A. Bobak,Brock C. Christensen,Louis J. Vaickus +9 more
TL;DR: The results demonstrate that virtual trichrome technologies may offer a software solution that can be employed in the clinical setting as a diagnostic decision aid.