Carnegie Mellon University
Please join the NSF AI Planning Institute at Carnegie Mellon University for the 2023 Biophysics and Quantitative Biology in the AI Era Workshop on January 12th and 13th.

The workshop will cover 4 themes: AI for Image Analysis, Quantification of Behavior and Decision Making, Learning Models from Data, and High Throughput Experimental Tools with one half day set aside for each theme.

The organizing committee is pleased to announce the following workshop speakers: 

Register for the Biophysics and Quantitative Biology in the AI Era workshop. 

Abstract submissions welcome. We especially encourage submissions from undergraduates. Some submissions will be selected for talks and others for a poster session on Friday afternoon.

The workshop will be in Rango Room 3 in the Cohen University Center January 12 & 13, 2023 in person and via Zoom. 

The workshop starts daily at 9:00 AM and ends at 5:00 PM.

Campus Maps

Day 1 Workshop Themes: Thursday, January 12th


9:00 - 10:30 AM

  • David Van Valen (Invited) [9:00 - 9:30 (+5')]: "Everything as code"
  • Joel McManus (Contributed) [9:35 - 9:55 (+2')]: "Unraveling rules of post-transcriptional gene regulation using massively parallel reporter assays and quantitative modeling"
  • Keisuke Ishihara (Contributed) [9:55 - 10:13 (+2')]: "Topological morphogenesis of neuroepithelial organoids"
  • Sophia Hu (Contributed) [10:15 - 10:30 (+2')]: "Epithelial-mesenchymal transition couples with both G1/S and G2/M arrest"

10:30 - 10:45 AM: Coffee/Tea Break






10:45 - 12:00 PM

  • Pankaj Mehta (Invited) [10:45-11:10: (+10')]: "Learning order parameters for cell fate from scRNA-seq data":
  • Parisa Mollaei (Contributed) [11:25-11:40 (+2')]: "Learning the Protein Activity Using Structures and Dynamics"
  • Qi Song (Contributed) [11:43-11:58 (+2')]: "scSTEM: clustering pseudo-time ordered single cell data"

12:15 - 1:15: Lunch provided

1:30 - 3:00 PM

  • Jing Zhang (Invited) [1:30-2:00 (+10')]: "Characterizing the brain regulatory grammar at a single-cell resolution to highlight disease-driving genetic and epigenetic dysregulations"
  • Ketaki Ghatole & Arnav Gupta (Contributed) [2:10-2:25 (+2')]: "Multi-omics Analysis of Lung Cancer using Autoencoders"
  • Lauren Luciani (Contributed) [2:27-2:42 (+2')]: "Mathematical Model to Identify Mechanisms behind Severe Influenza Infection in Juvenile Mice"
  • Tatum McGreary (Contributed) [2:44-2:59 (+2')]: Identifying the mechanisms linking sex hormones and influenza infection using computational modeling"




4:00 - 5:00 PM: Poster Session and Reception (light appetizers)


Day 2 Workshop Themes: Friday, January 13th


 9:00 - 10:30 AM

  • Jan Funke (Invited) [9:00-9:30]: "Neurotransmitter Classification from Electron Microscopy"
  • Daisuke Kihara (Invited) [9:30-10:00]: "Building and Validating Biomolecular Structure Models for cryo-EM Maps Using Deep Learning"
  • Jianhua Xing (Contributed) [10:00-10:30]: "Learn cellular dynamics from live cell imaging data"

10:30 - 10:45 AM: Coffee & Tea Break

10:45 - 12:15 PM

  • Li Shen (Invited) [10:45-11:15]: "Brain imaging genetics for Alzheimer’s disease: integrated analysis and machine learning"
  • Shikhar Uttam (Contributed) [11:15-11:45]: "Label-free nanoscale nuclear architecture mapping of early carcinogenesis"
  • Ali Dabouei (Contributed) [11:45-12:15]: "Detecting anomalies in a laboratory setting"



12:15 - 1:15 PM Lunch provided

1:30 - 3:30 PM

  • Gordon Berman [1:30-2:10]:  “Themes and Variations in Animal Behavior” 
  • Alex Hsu [2:10-2:30]: "Behavioral classification for single and multi-agents"
  • Shreya Saxena (Invited) [2:30-3:10]: Elucidating the Neural Control of Movement using AI
  • Kenji Lee [3:10-3:30]: "Multi-modal composition of physiological signals to delineate neuronal cell types in-vivo"

Nearby Hotels:

Hampton Inn University Center
3315 Hamlet Street
Pittsburgh, PA 15213

1.6 miles from CMU

Hilton Garden Inn
University Place
3454 Forbes Avenue
Pittsburgh, PA 15213

1.3 miles from CMU

Holiday Inn Select University Center
100 Lytton Avenue
Pittsburgh, PA 15213

3.5 miles from CMU

Hotel Indigo Pittsburgh University-Oakland
329 Technology Drive
Pittsburgh, PA 15219

1.6 miles from CMU

The Inns on Negley
703 South Negley Avenue
Pittsburgh, PA 15232

1.6 miles from CMU


The Maverick
120 South Whitfield Street
Pittsburgh, PA 15206

2.2 miles from CMU

The Oaklander Hotel
5130 Bigelow Blvd.
Pittsburgh, PA 15213

1 mile from CMU

Residence Inn by Marriott
3896 Bigelow Boulevard
Pittsburgh, PA 15213
412- 621-2200

1.6 miles from CMU

Residence Inn Pittsburgh Oakland/University Place
3341 Forbes Ave.
Pittsburgh, PA 15213

1.6 miles from CMU

Quality Inn University Center Hotel
3401 Boulevard of the Allies
Pittsburgh, PA 15213

1.8 miles from CMU

The 2023 Biophysics and Quantitative Biology in the AI Era Workshop Organizing Committee: 

Participant List

  • Agustin Cruz: University of Pittsburgh
  • Aidan Lakshman: University of Pittsburgh Biomedical Informatics
  • Akanksha Sachan : Carnegie Mellon University
  • Akash Kishore: Carnegie Mellon University
  • Akhil V:
  • Alex Hsu: Carnegie Mellon University
  • Ali Dabouei: Carnegie Mellon University
  • Amanda Merkley: Carnegie Mellon University, College of Engineering
  • Angad Singh Chopra: CU
  • Ann Lee: Carnegie Mellon University
  • Anrui Liu: Carnegie Mellon University
  • Antara Titikhsha : Carnegie Mellon University
  • Anush Devadhasan: Carnegie Mellon University
  • Arnav Gupta: Carnegie Mellon University MSCB
  • Arun Das: University of Pittsburgh
  • Arun Lekshmi Narayanan: University of Pittsburgh
  • Arvind Rao: University of Michigan, Ann Arbor
  • Ashish Singh : Indian Institute of technology Roorkee
  • Balaji Iyer: University of Cincinnati
  • Carl Kingsford: Carnegie Mellon University
  • Chad Schafer: Carnegie Mellon University
  • Christopher Aldrich: Carnegie Mellon University
  • Cristian Alirio Parra : Universidad de Antioquia/Colombia
  • Daisuke Kihara: Purdue University
  • Dani Lavage: UPMC / Pitt
  • Daniel Sium:
  • David Van Valen: Caltech
  • Deb S Banerjee: Carnegie Mellon University/ MCS(Physics)
  • Deyi Li:
  • Dhenenjay Yadav: Chaudhary Charan Singh Haryana Agricultural University
  • Dongshunyi "Dora" Li:
  • Dr. Sara Khan: COMSATS university Pakistan
  • Drew Bridges: Carnegie Mellon University
  • Edwin Rodriguez: University of Pittsburgh
  • Elizabeth Finney : University of California Riverside
  • Elizabeth Meinert-Spyker: Carnegie Mellon University
  • Emma DiBernardo: Carnegie Mellon University
  • Eric Yttri: Carnegie Mellon University
  • Eshaan Mandal: Thapar Institute Of Engineering and Technology
  • Fangwei Si: Carnegie Mellon University
  • Gordon Berman: Boston University
  • Haley Fuller: University of Pittsburgh
  • Hanna Salman: University of Pittsburgh
  • Hisako Masuda: Indiana University Kokomo
  • Hugh Galloway: University of Pittsburgh
  • Hy Trac: Carnegie Mellon University
  • Jackie Vo: Carnegie Mellon University
  • Jacob Rast: Carnegie Mellon University
  • James Rooney: University of Pittsburgh School of Medicine
  • Jan Funke:
  • Jan Janecka: Duquesne University
  • Jasmine Crawford: Berkeley
  • Jason Shoemaker: University of Pittsburgh
  • Jason Xiaotian Dou: University of Pittsburgh
  • Jianhua Xing: University of Pittsburgh
  • Jiayi Li: Carnegie Mellon University
  • Jiefei Wang: University of Pittsburgh
  • Jing Zhang: UCI
  • Joel Disu: Carnegie Mellon University
  • Joel McManus: Carnegie Mellon University Associate Professor of Biological Sciences
  • John Hall: Temple University
  • Jojo Prentice: Carnegie Mellon
  • Jonathan Fritz: Ohio State University
  • Jonathan Rubin: University of Pittsburgh
  • Ju-Chun Huang: Carnegie Mellon University
  • Kai Shimagaki: UC Riverside / University of Pittsburgh
  • Kartik Pande: Thapar University
  • Ke Ni: CPCB (University of Pittsburgh, School of Medicine/ Carnegie Mellon University, SCS CBD)
  • Keisuke Ishihara: University of Pittsburgh
  • Keith Callenberg :
  • Kenji Lee: Department of Psychological and Brain Sciences, Boston University
  • Ketaki Ghatole: Carnegie Mellon University
  • Lara Abdelmohsen: Carnegie Mellon University
  • Lauren Luciani: University of Pittsburgh
  • Leandro Lopez:
  • Li Shen: University of Pennsylvania
  • Logan Carpenter: Carnegie Mellon University
  • Mangyin Mo: Carnegie Mellon University
  • Mark DeAngelis: Carnegie Mellon University
  • Michael Gee: Carnegie Mellon University
  • Mikaéla Murph: Rutgers University
  • Min Xu: Carnegie Mellon University
  • Mio Chen:
  • Monica Dayao: Carnegie Mellon University
  • Motasem ElGamel:
  • Nahom Mossazghi: Carnegie Mellon University
  • Najibul Haque Sarker: Bangladesh University of Engineering and Technology
  • Nanami Kubota: University of Pittsburgh
  • Narayanan Puthillathu Vasudevan: Ohio State University
  • Nathan Lord: University of Pittsburgh
  • Olexandr Isayev: Carnegie Mellon University, Chemistry
  • Owen Lucas: University of Pittsburgh
  • Palanisamy Kandhan : SRM Institute of Science and Technology
  • Pankaj Mehta: Boston University
  • Parisa Mollaei: Carnegie Mellon University
  • Qi Song: Carnegie Mellon University
  • Rajdeep Pawar: Carnegie Mellon University
  • Ramakrishna Suresh: University of Pittsburgh, Swanson School of Engineering
  • Rumana (Ru) Rashid: University of Pittsburgh
  • Rupprecht Jean-François: CNRS/Aix-Marseille University
  • Russell Schwartz: Carnegie Mellon University
  • Ryan LeFebre: University of Pittsburgh
  • Saheli Mitra: Carnegie Mellon University
  • Sanni Joseph Adaviruku: Adekunle Ajasin University Akungba Akoko
  • Santiago Rodriguez: University of California, Berkeley
  • Sanya Sinha : Birla Institute of Technology
  • Sarah Baalbaki: Carnegie Mellon University
  • Scott Dodelson: Carnegie Mellon University
  • Shalini Panthangi: Carnegie Mellon University
  • Sharadhi Bharadwaj: Carnegie Mellon university
  • Shikhar Uttam: University of Pittsburgh
  • Shiladitya Banerjee: Carnegie Mellon University
  • Shreya Saxena: University of Florida
  • Shruthi Venkatesh: University of Pittsburgh
  • Siddhant:
  • Silvia Liu: University of Pittsburgh
  • Sophia Hu: University of Pittsburgh
  • Spencer Krieger: Carnegie Mellon University, Computational Biology Department
  • Srujana Prasanna Neelavar : Carnegie Mellon University
  • Stephanie Tristram-Nagle: Carnegie Mellon University/Mellon College of Science
  • Surya Prasath: University of Cincinnati/CCHMC
  • Tatum McGeary : University of Pittsburgh
  • Thomas Tam: Carnegie Mellon University
  • Tianyue Zhang: Carnegie Mellon University
  • Tiffany Nakai: Carnegie Mellon University
  • Tresha: Carnegie Mellon University
  • Trevor Grandpre: Princeton University
  • Vaughn Cooper: University of Pittsburgh School of Medicine
  • Wanzi Xiao: Carnegie Mellon University
  • Wenduo Cheng: Carnegie Mellon University
  • Yajushi Khurana: University of Pittsburgh
  • Yang Liu: University of Pittsburgh
  • Yihang Shen: Carnegie Mellon University
  • Yongxin (Leon) Zhao: Biological Sciences
  • Yu Fang: Carnegie Mellon University, Dietrich
  • Yuan Chen: Carnegie Mellon University
  • Yurun Tian: Carnegie Mellon University, ECE
  • Yuxuan Shen: Carnegie Mellon University
  • Zhentao Liu: Pitt/UPMC