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PLOS Computational Biology

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Correction: ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii

by Lakshmipuram S. Swapna, Grant C. Stevens, Aline Sardinha-Silva, Lucas ZhongMing Hu, Verena Brand, Daniel D. Fusca, Cuihong Wan, Xuejian Xiong, Jon P. Boyle, Michael E. Grigg, Andrew Emili, John Parkinson


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Hierarchical abstraction drives human-like 3-D shape processing in deep learning models

by Shuhao Fu, Philip J. Kellman, Hongjing Lu

Both humans and deep learning models can recognize objects from 3D shapes depicted with sparse visual information, such as a set of points randomly sampled from the surfaces of 3D objects (termed a point cloud). Although deep learning models achieve human-like performance in recognizing objects from 3D shapes, it remains uncle...

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Optimizing oral contraceptive timing: Daytime intake reduces doses and enhances efficacy

by Brenda Lyn Gavina, Taeyong Lee, Olive Cawiding, Sunhwa Choi, Sungwook Choi, Soyoung Kim, Jae Kyoung Kim

Contraception is essential for reproductive health and women’s empowerment because it allows informed choices about pregnancy prevention. Oral contraceptives (OCs) are a popular method due to their accessibility and high level of effectiveness in attaining contracep...

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An approximate-copula distribution for statistical modeling

by Sarah S. Ji, Benjamin B. Chu, Hua Zhou, Kenneth Lange

Copulas, generalized estimating equations, and generalized linear mixed models promote the analysis of grouped data where non-normal responses are correlated. Unfortunately, parameter estimation remains challenging in these three frameworks. Based on prior work of Tonda, we derive a new class of probability density...

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CTFacTomo: Reconstructing 3D spatial structures of RNA tomography transcriptomes by collapsed tensor factorization

by Tianci Song, Quoc Nguyen, Charles Broadbent, Rui Kuang

Cells are organized to form three-dimensional structures of complex tissues. To map the complete 3D organization of a tissue, technologies based on tissue microdissections provide deep bulk RNA sequencing of orthographically arranged cryosections of a tissue, such that the full 3D spatial structure could be inferr...

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