Nima Aghaeepour

According to our database, Nima Aghaeepour authored at least 27 papers between 2005 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

MedHELM: Holistic Evaluation of Large Language Models for Medical Tasks.

Suhana Bedi, Hejie Cui, Miguel Fuentes, Alyssa Unell, Michael Wornow, Juan M. Banda, Nikesh Kotecha, Timothy Keyes, Yifan Mai, Mert Oez, Hao Qiu, Shrey Jain, Leonardo Schettini, Mehr Kashyap, Jason Alan Fries, Akshay Swaminathan, Philip Chung, Fateme Nateghi, Asad Aali, Ashwin Nayak, Shivam Vedak, Sneha S. Jain, Birju S. Patel, Oluseyi Fayanju, Shreya J. Shah, Ethan Goh, Dong-han Yao, Brian Soetikno, Eduardo Pontes Reis, Sergios Gatidis, Vasu Divi, Robson Capasso, Rachna Saralkar, Chia-Chun Chiang, Jenelle A. Jindal, Tho Pham, Faraz Ghoddusi, Steven Lin, Albert S. Chiou, Christy Hong, Mohana Roy, Michael F. Gensheimer, Hinesh Patel, Kevin Schulman, Dev Dash, Danton Char, Lance Downing, François Grolleau, Kameron C. Black, Bethel Mieso, Aydin Zahedivash, Wen-wai Yim, Harshita Sharma, Tony Lee, Hannah Kirsch, Jennifer Lee, Nerissa Ambers, Carlene Lugtu, Aditya Sharma, Bilal Mawji, Alex Alekseyev, Vicky Zhou, Vikas Kakkar, Jarrod Helzer, Anurang Revri, Yair Bannett, Roxana Daneshjou, Jonathan H. Chen, Emily Alsentzer, Keith E. Morse, Nirmal Ravi, Nima Aghaeepour, Vanessa Kennedy, Akshay Chaudhari, Thomas Wang, Sanmi Koyejo, Matthew P. Lungren, Eric Horvitz, Percy Liang, Mike Pfeffer, Nigam H. Shah

CoRR, May, 2025

VeriFact: Verifying Facts in LLM-Generated Clinical Text with Electronic Health Records.

Philip Chung, Akshay Swaminathan, Alex J. Goodell, Yeasul Kim, S. Momsen Reincke, Lichy Han, Ben Deverett, Mohammad Amin Sadeghi, Abdel-Badih Ariss, Marc Ghanem, David Seong, Andrew A. Lee, Caitlin E. Coombes, Brad Bradshaw, Mahir A. Sufian, Hyo Jung Hong, Teresa P. Nguyen, Mohammad R. Rasouli, Komal Kamra, Mark A. Burbridge, James McAvoy, Roya Saffary, Stephen P. Ma, Dev Dash, James Xie, Ellen Y. Wang, Clifford A. Schmiesing, Nigam Shah, Nima Aghaeepour

CoRR, January, 2025

Impact of digital health interventions on glycemic control and weight management.

Arvind Veluvali, Ashkan Dehghani Zahedani, Amir Hosseinian, Nima Aghaeepour, Tracey McLaughlin, Mark Woodward, Alex Ditullio, Noosheen Hashemi, Michael P. Snyder

npj Digit. Medicine, 2025

Author Correction: A machine learning approach to leveraging electronic health records for enhanced omics analysis.

Samson Mataraso, Camilo Espinosa, David Seong, S. Momsen Reincke, Eloïse Berson, Jonathan D. Reiss, Yeasul Kim, Marc Ghanem, Chi-Hung Shu, Tomin James, Yuqi Tan, Sayane Shome, Ina A. Stelzer, Dorien Feyaerts, Ronald J. Wong, Gary M. Shaw, Martin S. Angst, Brice Gaudilliere, David K. Stevenson, Nima Aghaeepour

Nat. Mac. Intell., 2025

A machine learning approach to leveraging electronic health records for enhanced omics analysis.

Samson Mataraso, Camilo Espinosa, David Seong, S. Momsen Reincke, Eloïse Berson, Jonathan D. Reiss, Yeasul Kim, Marc Ghanem, Chi-Hung Shu, Tomin James, Yuqi Tan, Sayane Shome, Ina A. Stelzer, Dorien Feyaerts, Ronald J. Wong, Gary M. Shaw, Martin S. Angst, Brice Gaudilliere, David K. Stevenson, Nima Aghaeepour

Nat. Mac. Intell., 2025

Mitigation of outcome conflation in predicting patient outcomes using electronic health records.

S. Momsen Reincke, Camilo Espinosa, Philip Chung, Tomin James, Eloïse Berson, Nima Aghaeepour

J. Am. Medical Informatics Assoc., 2025

2024

Correction: Digital health application integrating wearable data and behavioral patterns improves metabolic health.

Ashkan Dehghani Zahedani, Tracey McLaughlin, Arvind Veluvali, Nima Aghaeepour, Amir Hosseinian, Saransh Agarwal, Jingyi Ruan, Shital Tripathi, Mark Woodward, Noosheen Hashemi, Michael Snyder

npj Digit. Medicine, 2024

Large Language Model Capabilities in Perioperative Risk Prediction and Prognostication.

Philip Chung, Christine T. Fong, Andrew M. Walters, Nima Aghaeepour, Meliha Yetisgen, Vikas N. O'Reilly-Shah

CoRR, 2024

Generating pregnant patient biological profiles by deconvoluting clinical records with electronic health record foundation models.

David Seong, Samson Mataraso, Camilo Espinosa, Eloïse Berson, S. Momsen Reincke, Lei Xue, Chloe Kashiwagi, Yeasul Kim, Chi-Hung Shu, Philip Chung, Marc Ghanem, Feng Xie, Ronald J. Wong, Martin S. Angst, Brice Gaudilliere, Gary M. Shaw, David K. Stevenson, Nima Aghaeepour

Briefings Bioinform., 2024

MedAlign: A Clinician-Generated Dataset for Instruction Following with Electronic Medical Records.

Scott L. Fleming, Alejandro Lozano, William J. Haberkorn, Jenelle A. Jindal, Eduardo Pontes Reis, Rahul Thapa, Louis Blankemeier, Julian Z. Genkins, Ethan Steinberg, Ashwin Nayak, Birju S. Patel, Chia-Chun Chiang, Alison Callahan, Zepeng Huo, Sergios Gatidis, Scott J. Adams, Oluseyi Fayanju, Shreya J. Shah, Thomas Savage, Ethan Goh, Akshay S. Chaudhari, Nima Aghaeepour, Christopher D. Sharp, Michael A. Pfeffer, Percy Liang, Jonathan H. Chen, Keith E. Morse, Emma P. Brunskill, Jason A. Fries, Nigam H. Shah

Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024

2023

Digital health application integrating wearable data and behavioral patterns improves metabolic health.

Ashkan Dehghani Zahedani, Arvind Veluvali, Tracey McLaughlin, Nima Aghaeepour, Amir Hosseinian, Saransh Agarwal, Jingyi Ruan, Shital Tripathi, Mark Woodward, Noosheen Hashemi, Michael Snyder

npj Digit. Medicine, 2023

Deep representation learning identifies associations between physical activity and sleep patterns during pregnancy and prematurity.

Neal G. Ravindra, Camilo Espinosa, Eloïse Berson, Thanaphong Phongpreecha, Peinan Zhao, Martin Becker, Alan L. Chang, Sayane Shome, Ivana Maric, Davide De Francesco, Samson Mataraso, Geetha Saarunya, Melan Thuraiappah, Lei Xue, Brice Gaudilliere, Martin S. Angst, Gary M. Shaw, Erik D. Herzog, David K. Stevenson, Sarah K. England, Nima Aghaeepour

npj Digit. Medicine, 2023

Large-scale correlation network construction for unraveling the coordination of complex biological systems.

Martin Becker, Huda Nassar, Camilo Espinosa, Ina A. Stelzer, Dorien Feyaerts, Eloïse Berson, Neda Hajiakhoond Bidoki, Alan L. Chang, Geetha Saarunya, Anthony Culos, Davide De Francesco, Ramin Fallahzadeh, Qun Liu, Yeasul Kim, Ivana Maric, Samson Mataraso, Seyedeh Neelufar Payrovnaziri, Thanaphong Phongpreecha, Neal G. Ravindra, Natalie Stanley, Sayane Shome, Yuqi Tan, Melan Thuraiappah, Maria Xenochristou, Lei Xue, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour

Nat. Comput. Sci., 2023

2022

Early prediction and longitudinal modeling of preeclampsia from multiomics.

Ivana Maric, Kévin Contrepois, Mira N. Moufarrej, Ina A. Stelzer, Dorien Feyaerts, Xiaoyuan Han, Andy Tang, Natalie Stanley, Ronald J. Wong, Gavin M. Traber, Mathew Ellenberger, Alan L. Chang, Ramin Fallahzadeh, Huda Nassar, Martin Becker, Maria Xenochristou, Camilo Espinosa, Davide De Francesco, Mohammad S. Ghaemi, Elizabeth K. Costello, Anthony Culos, Xuefeng Bruce Ling, Karl G. Sylvester, Gary L. Darmstadt, Virginia D. Winn, Gary M. Shaw, David A. Relman, Stephen R. Quake, Martin S. Angst, Michael P. Snyder, David K. Stevenson, Brice Gaudilliere, Nima Aghaeepour

Patterns, 2022

2021

Heart Rate and CGM Feature Representation Diabetes Detection From Heart Rate: Learning Joint Features of Heart Rate and Continuous Glucose Monitors Yields Better Representations.

Hootan Rashtian, Solmaz Shariat Torbaghan, Salar Rahili, Michael P. Snyder, Nima Aghaeepour

IEEE Access, 2021

2020

Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions.

Anthony Culos, Amy Tsai, Natalie Stanley, Martin Becker, Mohammad Sajjad Ghaemi, David Mcilwain, Ramin Fallahzadeh, Athena Tanada, Huda Nassar, Camilo Espinosa, Maria Xenochristou, Edward Ganio, Laura Peterson, Xiaoyuan Han, Ina A. Stelzer, Kazuo Ando, Dyani Gaudilliere, Thanaphong Phongpreecha, Ivana Maric, Alan L. Chang, Gary M. Shaw, David K. Stevenson, Sean Bendall, Kara L. Davis, Wendy J. Fantl, Garry P. Nolan, Trevor Hastie, Robert Tibshirani, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour

Nat. Mach. Intell., 2020

Feature-weighted elastic net: using "features of features" for better prediction.

J. Kenneth Tay, Nima Aghaeepour, Trevor Hastie, Robert Tibshirani

CoRR, 2020

2019

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

Mohammad Sajjad Ghaemi, Daniel B. DiGiulio, Kévin Contrepois, Benjamin J. Callahan, Thuy T. M. Ngo, Brittany Lee-McMullen, Benoit Lehallier, Anna Robaczewska, David Mcilwain, Yael Rosenberg-Hasson, Ronald J. Wong, Cecele Quaintance, Anthony Culos, Natalie Stanley, Athena Tanada, Amy Tsai, Dyani Gaudilliere, Edward Ganio, Xiaoyuan Han, Kazuo Ando, Leslie McNeil, Martha Tingle, Paul H. Wise, Ivana Maric, Marina Sirota, Tony Wyss-Coray, Virginia D. Winn, Maurice L. Druzin, Ronald Gibbs, Gary L. Darmstadt, David B. Lewis, Vahid Partovi Nia, Bruno Agard, Robert Tibshirani, Garry P. Nolan, Michael P. Snyder, David A. Relman, Stephen R. Quake, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour

Bioinform., 2019

2018

GateFinder: projection-based gating strategy optimization for flow and mass cytometry.

Nima Aghaeepour, Erin F. Simonds, David J. H. F. Knapp, Robert V. Bruggner, Karen Sachs, Anthony Culos, Pier Federico Gherardini, Nikolay Samusik, Gabriela K. Fragiadakis, Sean Bendall, Brice Gaudilliere, Martin S. Angst, Connie J. Eaves, William A. Weiss, Wendy J. Fantl, Garry P. Nolan

Bioinform., 2018

2017

Session Introduction.

Nikolay Samusik, Nima Aghaeepour, Sean Bendall

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

2015

Deep profiling of multitube flow cytometry data.

Kieran O'Neill, Nima Aghaeepour, Jeremy Parker, Donna Hogge, Aly Karsan, Bakul Dalal, Ryan Remy Brinkman

Bioinform., 2015

2014

Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data.

Kieran O'Neill, Adrin Jalali, Nima Aghaeepour, Holger H. Hoos, Ryan Remy Brinkman

Bioinform., 2014

2013

Flow Cytometry Bioinformatics.

Kieran O'Neill, Nima Aghaeepour, Josef Spidlen, Ryan Remy Brinkman

PLoS Comput. Biol., 2013

Ensemble-based prediction of RNA secondary structures.

Nima Aghaeepour, Holger H. Hoos

BMC Bioinform., 2013

2012

Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.

Nima Aghaeepour, Pratip K. Chattopadhyay, Anuradha Ganesan, Kieran O'Neill, Habil Zare, Adrin Jalali, Holger H. Hoos, Mario Roederer, Ryan Remy Brinkman

Bioinform., 2012

2009

Support Vector Clustering: From Local Constraint to Global Stability.

Bahman Yari Saeed Khanloo, Daryanaz Dargahi, Nima Aghaeepour, Ali Masoudi-Nejad

Proceedings of the Foundations of Computational Intelligence - Volume 6: Data Mining, 2009

2005

Dynamic Positioning Based on Voronoi Cells (DPVC).

HesamAddin Dashti, Nima Aghaeepour, Sahar Asadi, Meysam Bastani, Zahra Delafkar, Fatemeh Miri Disfani, Serveh Ghaderi, Shahin Kamali, Sepideh Pashami, Alireza Siahpirani

Proceedings of the RoboCup 2005: Robot Soccer World Cup IX, 2005