SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations

Autor: Yi-Ching Tang, Rongbin Li, Jing Tang, W. Jim Zheng, Xiaoqian Jiang

Publikováno v: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-19 (2024)

Abstract Background The potential benefits of drug combination synergy in cancer medicine are significant, yet the risks must be carefully managed due to the possibility of increased toxicity. Although artificial intelligence applications have demons

Externí odkaz: https://doaj.org/article/c54b658f28264d4380f2212e21308682

Crowd-sourced machine learning prediction of long COVID using data from the National COVID Cohort CollaborativeResearch in context

Autor: Timothy Bergquist, Johanna Loomba, Emily Pfaff, Fangfang Xia, Zixuan Zhao, Yitan Zhu, Elliot Mitchell, Biplab Bhattacharya, Gaurav Shetty, Tamanna Munia, Grant Delong, Adbul Tariq, Zachary Butzin-Dozier, Yunwen Ji, Haodong Li, Jeremy Coyle, Seraphina Shi, Rachael V. Philips, Andrew Mertens, Romain Pirracchio, Mark van der Laan, John M. Colford, Jr., Alan Hubbard, Jifan Gao, Guanhua Chen, Neelay Velingker, Ziyang Li, Yinjun Wu, Adam Stein, Jiani Huang, Zongyu Dai, Qi Long, Mayur Naik, John Holmes, Danielle Mowery, Eric Wong, Ravi Parekh, Emily Getzen, Jake Hightower, Jennifer Blase, Ataes Aggarwal, Joseph Agor, Amera Al-Amery, Oluwatobiloba Aminu, Adit Anand, Corneliu Antonescu, Mehak Arora, Sayed Asaduzzaman, Tanner Asmussen, Mahdi Baghbanzadeh, Frazier Baker, Bridget Bangert, Laila Bekhet, Jenny Blase, Brian Caffo, Hao Chang, Zeyuan Chen, Jiandong Chen, Jeffrey Chiang, Peter Cho, Robert Cockrell, Parker Combs, Ciara Crosby, Ran Dai, Anseh Danesharasteh, Elif Yildirim, Ryan Demilt, Kaiwen Deng, Sanjoy Dey, Rohan Dhamdhere, Andrew Dickson, Phoebe Dijour, Dong Dinh, Richard Dixon, Albi Domi, Souradeep Dutta, Mirna Elizondo, Zeynep Ertem, Solomon Feuerwerker, Danica Fliss, Jennifer Fowler, Sunyang Fu, Kelly Gardner, Neil Getty, Mohamed Ghalwash, Logan Gloster, Phil Greer, Yuanfang Guan, Colby Ham, Samer Hanoudi, Jeremy Harper, Nathaniel Hendrix, Leeor Hershkovich, Junjie Hu, Yu Huang, Tongtong Huang, Junguk Hur, Monica Isgut, Hamid Ismail, Grant Izmirlian, Kuk Jang, Christianah Jemiyo, Hayoung Jeong, Xiayan Ji, Ming Jiang, Sihang Jiang, Xiaoqian Jiang, Yuye Jiang, Akin Johnson, Zach Analyst, Saarthak Kapse, Uri Kartoun, Dukka KC, Zahra Fard, Tim Kosfeld, Spencer Krichevsky, Mike Kuo, Dale Larie, Lauren Lederer, Shan Leng, Hongyang Li, Jianfu Li, Tiantian Li, Xinwen Liang, Hengyue Liang, Feifan Liu, Daniel Liu, Gang Luo, Ravi Madduri, Vithal Madhira, Shivali Mani, Farzaneh Mansourifard, Robert Matson, Vangelis Metsis, Pablo Meyer, Catherine Mikhailova, Dante Miller, Christopher Milo, Gourav Modanwal, Ronald Moore, David Morgenthaler, Rasim Musal, Vinit Nalawade, Rohan Narain, Saideep Narendrula, Alena Obiri, Satoshi Okawa, Chima Okechukwu, Toluwanimi Olorunnisola, Tim Ossowski, Harsh Parekh, Jean Park, Saaya Patel, Jason Patterson, Chetan Paul, Le Peng, Diana Perkins, Suresh Pokharel, Dmytro Poplavskiy, Zach Pryor, Sarah Pungitore, Hong Qin, Salahaldeen Rababa, Mahbubur Rahman, Elior Rahmani, Gholamali Rahnavard, Md Raihan, Suraj Rajendran, Sarangan Ravichandran, Chandan Reddy, Abel Reyes, Ali Roghanizad, Sean Rouffa, Xiaoyang Ruan, Arpita Saha, Sahil Sawant, Melody Schiaffino, Diego Seira, Saurav Sengupta, Ruslan Shalaev, Linh Shinguyen, Karnika Singh, Soumya Sinha, Damien Socia, Halen Stalians, Charalambos Stavropoulos, Jan Strube, Devika Subramanian, Jiehuan Sun, Ju Sun, Chengkun Sun, Prathic Sundararajan, Salmonn Talebi, Edward Tawiah, Jelena Tesic, Mikaela Thiess, Raymond Tian, Luke Torre-Healy; Ming-Tse Tsai, David Tyus, Madhurima Vardhan, Benjamin Walzer, Jacob Walzer, Junda Wang, Lu Wang, Will Wang, Jonathan Wang, Yisen Wang, Chad Weatherly, Fanyou Wu, Yifeng Wu, Hao Yan, Zhichao Yang, Biao Ye, Rui Yin, Changyu Yin, Yun Yoo, Albert You, June Yu, Martin Zanaj, Zachary Zaiman, Kai Zhang, Xiaoyi Zhang, Tianmai Zhang, Degui Zhi, Yishan Zhong, Huixue Zhou, Andrea Zhou, Yuanda Zhu, Sophie Zhu, Meredith Adams, Caleb Alexander, Benjamin Amor, Alfred Anzalone, Benjamin Bates, Will Beasley, Tellen Bennett, Mark Bissell, Eilis Boudreau, Samuel Bozzette, Katie Bradwell, Carolyn Bramante, Don Brown, Penny Burgoon, John Buse, Tiffany Callahan, Kenrick Cato, Scott Chapman, Christopher Chute, Jaylyn Clark, Marshall Clark, Will Cooper, Lesley Cottrell, Karen Crowley, Mariam Deacy, Christopher Dillon, David Eichmann, Mary Emmett, Rebecca Erwin-Cohen, Patricia Francis, Evan French, Rafael Fuentes, Davera Gabriel, Joel Gagnier, Nicole Garbarini, Jin Ge, Kenneth Gersing, Andrew Girvin, Valery Gordon, Alexis Graves, Justin Guinney, Melissa Haendel, J.W. Hayanga, Brian Hendricks, Wenndy Hernandez, Elaine Hill, William Hillegass, Stephanie Hong, Dan Housman, Robert Hurley, Jessica Islam, Randeep Jawa, Steve Johnson, Rishi Kamaleswaran, Warren Kibbe, Farrukh Koraishy, Kristin Kostka, Michael Kurilla, Adam Lee, Harold Lehmann, Hongfang Liu, Charisse Madlock-Brown; Sandeep Mallipattu, Amin Manna, Federico Mariona, Emily Marti, Greg Martin, Jomol Mathew, Diego Mazzotti, Julie McMurry, Hemalkumar Mehta, Sam Michael, Robert Miller, Leonie Misquitta, Richard Moffitt, Michele Morris, Kimberly Murray, Lavance Northington, Shawn O’Neil, Amy Olex, Matvey Palchuk, Brijesh Patel, Rena Patel, Philip Payne, Jami Pincavitch, Lili Portilla, Fred Prior, Saiju Pyarajan, Lee Pyles, Nabeel Qureshi, Peter Robinson, Joni Rutter, Ofer Sadan, Nasia Safdar, Amit Saha, Joel Saltz, Mary Saltz, Clare Schmitt, Soko Setoguchi, Noha Sharafeldin, Anjali Sharathkumar, Usman Sheikh, Hythem Sidky, George Sokos, Andrew Southerland, Heidi Spratt, Justin Starren, Vignesh Subbian, Christine Suver, Cliff Takemoto, Meredith Temple-O'Connor, Umit Topaloglu, Satyanarayana Vedula, Anita Walden, Kellie Walters, Cavin Ward-Caviness, Adam Wilcox, Ken Wilkins, Andrew Williams, Chunlei Wu, Elizabeth Zampino, Xiaohan Zhang, Richard Zhu

Publikováno v: EBioMedicine, Vol 108, Iss , Pp 105333- (2024)

Summary: Background: While many patients seem to recover from SARS-CoV-2 infections, many patients report experiencing SARS-CoV-2 symptoms for weeks or months after their acute COVID-19 ends, even developing new symptoms weeks after infection. These

Externí odkaz: https://doaj.org/article/fc8b927c62764ca1b7f11ebc4c7f5aba

FedGMMAT: Federated generalized linear mixed model association tests.

Autor: Wentao Li, Han Chen, Xiaoqian Jiang, Arif Harmanci

Publikováno v: PLoS Computational Biology, Vol 20, Iss 7, p e1012142 (2024)

Increasing genetic and phenotypic data size is critical for understanding the genetic determinants of diseases. Evidently, establishing practical means for collaboration and data sharing among institutions is a fundamental methodological barrier for

Externí odkaz: https://doaj.org/article/dad99edfdd764ecdba189c97ff815314

CancerGPT for few shot drug pair synergy prediction using large pretrained language models

Autor: Tianhao Li, Sandesh Shetty, Advaith Kamath, Ajay Jaiswal, Xiaoqian Jiang, Ying Ding, Yejin Kim

Publikováno v: npj Digital Medicine, Vol 7, Iss 1, Pp 1-10 (2024)

Abstract Large language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biol

Externí odkaz: https://doaj.org/article/2860f1902e664e25827b2ed1f438a540

Deep learning to predict rapid progression of Alzheimer's disease from pooled clinical trials: A retrospective study.

Autor: Xiaotian Ma, Madison Shyer, Kristofer Harris, Dulin Wang, Yu-Chun Hsu, Christine Farrell, Nathan Goodwin, Sahar Anjum, Avram S Bukhbinder, Sarah Dean, Tanveer Khan, David Hunter, Paul E Schulz, Xiaoqian Jiang, Yejin Kim

Publikováno v: PLOS Digital Health, Vol 3, Iss 4, p e0000479 (2024)

The rate of progression of Alzheimer's disease (AD) differs dramatically between patients. Identifying the most is critical because when their numbers differ between treated and control groups, it distorts the outcome, making it impossible to tell wh

Externí odkaz: https://doaj.org/article/d2f144709464433c9f556b2060b689d3