AI for drug discovery and cellular profiling

Srijit Seal

Principal Scientist at Human Chemical Company and Visiting Researcher at Uppsala University.

I am a researcher in chemoinformatics and computational biology, centered on using machine learning and Cell Painting to study small-molecule bioactivity, image-based profiling, and drug discovery.
I am Principal Scientist at Human Chemical Company and Visiting Researcher at Uppsala University. Previously, I was Senior Scientist at Merck US and completed my postdoc at the Broad Institute of MIT and Harvard where I was advised by Anne Carpenter and Shantanu Singh.
I obtained my PhD from the University of Cambridge where I was advised by Andreas Bender. I also serve on the Board of Directors at the American Society for Cellular and Computational Toxicology and the Editorial Board of the Journal of Cheminformatics.

AI for Science Cell Painting Bioactivity Modeling Cheminformatics Drug Discovery
31 Publications 1,027 Citations (Google Scholar) 151 GitHub stars Checked Oct 5, 2026
Publications Talks Tutorials Follow on LinkedIn

Selected work

Featured Research

Counting cells can accurately predict small-molecule bioactivity benchmarks
Nature Communications, 2026

Counting cells can accurately predict small-molecule bioactivity benchmarks

Read paper
Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes
Cell Systems, 2026

Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes

Read paper
PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules
Journal of Cheminformatics, 2025

PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules

Read paper
Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World
Chemical Research in Toxicology, 2025

Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World

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Speaking

Talks & Workshops

November 2026

ACT 2026 Continuing Education (CE) Course

From Predictive Models to Collaborative Intelligence: The Role of Agentic AI in the Future of Toxicology (CE2)

, 08:00 to 11:30 CT

CE Course Chair, Human Chemical Company

San Antonio, TX, US
September 2026

Discovery on Target 2026

Agentic AI for Target Safety Assessment Enable Modality-Agnostic Framework for Early Discovery Decision-Making

, 11:50 EDT

Visiting Researcher, Uppsala University

Boston, MA, US
September 2026

BioTechX USA 2026

AI/ML for Drug Discovery

, 15:50 EDT, AI in Drug Discovery and Development

Hynes Convention Center, Boston, MA, US
September 2026

BioTechX USA 2026

Invite Only: Building the Future of AI & Data Strategy in Life Sciences

, 10:40 EDT, Roundtables

Hynes Convention Center, Boston, MA, US
August 2026

ACS Fall 2026

Validation framework for evaluating generalization across diverse chemical data

Chicago, IL, US
August 2026

ACS Fall 2026

Agent-driven research automation: Integrating AI coding assistants into small molecule discovery workflows

Chicago, IL, US
October 2025

Food Standards Agency Workshop

Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World

London, UK
May 2025

University of Delaware

GTA Annual Meeting: The Last Mile: Opportunities to Bridge Research and Increase Impact in Human and Environmental Health Science

Newark, DE, US
March 2025

Society of Toxicology (SOT)

Using Generative AI to ‘Turn’ Safe but Inactive Molecules into Effective Ligands

Orlando, Florida, US
April 2024

ODSC East Conference 2024

Machine Learning in Drug Discovery: How Not to Lie with Computational Models?

Cambridge, US

Featured tools

Tools & Tutorials

Tool

PKSmart

Open-source pharmacokinetic modeling for small-molecule discovery workflows.

Open PKSmart
Course

Introduction to Cheminformatics and AI in Drug Discovery

Hands-on modeling workflows, predictive ML, and AI-assisted cheminformatics.

Open course
Tutorial

Leveraging Cell Painting Morphological Profiles for Machine Learning–Driven Bioactivity Prediction

Practical workflow for turning morphology profiles into bioactivity prediction features.

Open tutorial
Utilities

Drug Discovery and Toxicology Utilities

Small, reusable tools for cheminformatics, Cell Painting, and reproducible research workflows.

Browse tools

Research record

Publications

Model Validation Protocols for Machine Learning in Small Molecule Drug Discovery

Model Validation Protocols for Machine Learning in Small Molecule Drug Discovery

Srijit Seal et al. 29 authors
Srijit Seal, Akshat Shirish Zalte, David Alencar Araripe, Renan Augusto Gomes, Deepa Korani, Mrinal Shekhar, Vishal B. Siramshetty, Arijit Patra, Zhongyu Mou, Xiang Yu, Daniel Kühn, Nils Weskamp, Jeremy Ash, Alan C. Cheng, Cheng Fang, Daniel J. Price, Matteo Aldeghi, Raquel Rodríguez-Pérez, Djork-Arné Clevert, Ola Engkvist, Kristine Deibler, David Rouquie, Michael Reutlinger, Nicola Richmond, Jon Ainsley, Mark Ledeboer, William H. Green, Andreas Bender, Cas Wognum
bioRxiv, 2026 Cited by 0, OpenAlex
Code PDF bioRxiv
Artificial intelligence in drug discovery: what it is, where we stand and the path forward

Artificial intelligence in drug discovery: what it is, where we stand and the path forward

Andreas Bender et al. 16 authors
Andreas Bender, Morgan C. Thomas, Jack W. Scannell, David A. Shaywitz, Gian Marco Ghiandoni, Joe G. Greener, Lavinia-Lorena Pruteanu, Rachel DeVay Jacobson, Koichi Handa, Mariko Hirano, Srijit Seal, Manas Mahale, Marco F. Schmidt, Tim Ahfeldt, Francesca Grisoni, Isidro Cortés-Ciriano
Nature Reviews Drug Discovery, 2026 Cited by 14, Google Scholar
Paper

Interpreting and Visualizing VSA Descriptors through VSA Explainer

Lucas Attia et al. 8 authors
Lucas Attia, Nelson Evbarunegbe, Thomas A. Kirkland, Vinay V. Nair, Ashutosh S. Jogalekar, Ola Spjuth, Andreas Bender, Srijit Seal
ChemRxiv preprint, 2026 Cited by 0, OpenAlex
Paper
Human-supervised Agentic AI for Hypothesis Generation and Experimental Assistance in Drug Repurposing

Human-supervised Agentic AI for Hypothesis Generation and Experimental Assistance in Drug Repurposing

Dinh Long Huynh et al. 16 authors
Dinh Long Huynh, Elin Asp, Flavio Ballante, Jordi Carreras Puigvert, Alisa Nicole DeGrave, Reagon Karki, Kristen Nader, Päivi Östling, B.K. Pokharel, Jonne Rietdijk, Lars Schlotawa, Lina Schmidt, Srijit Seal, Brinton A. Seashore-Ludlow, Tero A. Aittokallio, Ola Spjuth
bioRxiv, 2026 Cited by 1, OpenAlex
Code PDF bioRxiv
SHOT-CCR: Biologically guided adversarial training for test-time adaptation in cellular morphology

SHOT-CCR: Biologically guided adversarial training for test-time adaptation in cellular morphology

W. Dee et al. 5 authors
W. Dee, Aaron Wenteler, Srijit Seal, Otto Morris, Gregory Slabaugh
MICCAI, 2026 Cited by 0, OpenAlex
Paper PDF Code bioRxiv
CAPRICHO: Interpretable Quality Flagging and Flexible ChEMBL Bioactivity Curation for QSAR Modeling

CAPRICHO: Interpretable Quality Flagging and Flexible ChEMBL Bioactivity Curation for QSAR Modeling

David Alencar Araripe et al. 4 authors
David Alencar Araripe, Srijit Seal, Olivier J. M. Béquignon, Gerard J. P. van Westen
Journal of Chemical Information and Modeling, 2026 Cited by 1, Google Scholar
Paper Code

Application of machine learning and artificial intelligence methods in predictions of absorption, distribution, metabolism, and excretion properties of chemicals

Wei-Chun Chou et al. 4 authors
Wei-Chun Chou, Miao Li, Srijit Seal, Zhoumeng Lin
Machine Learning and Artificial Intelligence in Toxicology and Environmental Health (book chapter), Elsevier, 2026 Cited by 4, Google Scholar
Journal
The OASIS Consortium: integrating multi-omics technologies to transform chemical safety assessment

The OASIS Consortium: integrating multi-omics technologies to transform chemical safety assessment

David Rouquie et al. 16 authors
David Rouquie, Andreas Bender, Jaime Cheah, Christine Crute, Deidre A. Dalmas, J.D. Ewald, Aaron M. Fullerton, Joshua Harrill, Sabah Kadri, Nicole Kleinstreuer, Nynke I. Kramer, Jessica L. LaRocca, Constance A. Mitchell, Srijit Seal, Shantanu Singh, Anne E. Carpenter
Toxicological Sciences, 2025 Cited by 13, OpenAlex
Paper

The medicinal chemist's map to deep learning: Concepts, applications, and case studies

Manas Mahale et al. 9 authors
Manas Mahale, Ricardo Scheufen Tieghi, Dea Gogishvili, Dinh Long Huynh, Renan Augusto Gomes, Shagun Krishna, Deidre A. Dalmas, Andreas Bender, Srijit Seal
Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, Elsevier, 2025
Paper
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization

Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization

Miguel García-Ortegón et al. 5 authors
Miguel García-Ortegón, Srijit Seal, Carl Rasmussen, Andreas Bender, Sergio Bacallado
Journal of Cheminformatics, 2024 Cited by 6, Google Scholar
Paper
Out-of-distribution validation for bioactivity prediction in drug discovery: Lessons from materials science

Out-of-distribution validation for bioactivity prediction in drug discovery: Lessons from materials science

Udit Surya Saha et al. 6 authors
Udit Surya Saha, Michele Vendruscolo, Anne E. Carpenter, Shantanu Singh, Andreas Bender, Srijit Seal
ICML 2024 Workshop on ML for Life and Material Sciences Cited by 6, Google Scholar
Paper PDF bioRxiv
AI agents in drug discovery: applications and case studies

AI agents in drug discovery: applications and case studies

Dinh Long Huynh et al. 7 authors
Dinh Long Huynh, Srijit Seal, Dylan Reid, Anne E. Carpenter, Andreas Bender, Ola Spjuth, AIA4S Consortium
Drug Discovery Today, 2026 Cited by 39, Google Scholar
Paper
Earlier Publications
Transfer learning enables discovery of sub-micromolar antibacterials for ESKAPE pathogens from ultra-large chemical spaces

Transfer learning enables discovery of sub-micromolar antibacterials for ESKAPE pathogens from ultra-large chemical spaces

Miguel García-Ortegón et al. 9 authors
Miguel García-Ortegón, Srijit Seal, Emily Geddes, Jenny L. Littler, Collette S. Guy, Jonathan Whiteside, Carl Rasmussen, Andreas Bender, Sergio Bacallado
Chemical Science, 2025 Cited by 5, Google Scholar
Paper
Learning Molecular Representation in a Cell

Learning Molecular Representation in a Cell

Gang Liu et al. 7 authors
Gang Liu, Srijit Seal, John Arevalo, Zhenwen Liang, Anne E. Carpenter, Meng Jiang, Shantanu Singh
ICLR, 2025 Cited by 25, Google Scholar
Project Paper Code PDF arXiv
Progress and new challenges in image-based profiling

Progress and new challenges in image-based profiling

E. Serrano et al. 22 authors
E. Serrano, J. Peters, J. Wagner, R.E. Graham, Z. Chen, B. Feng, G. Miranda, Alexandr A. Kalinin, Loan Vulliard, Jenna Tomkinson, Cameron Mattson, Michael J. Lippincott, Ziqi Kang, Divya Sitani, Dave Bunten, Srijit Seal, Neil O. Carragher, Anne E. Carpenter, Shantanu Singh, Paula A. Marin Zapata, Juan C. Caicedo, Gregory P. Way
Molecular Systems Biology, 2026 Cited by 23, Google Scholar
Paper PDF arXiv
Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World

Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World

Srijit Seal et al. 25 authors
Srijit Seal, Manas Mahale, Miguel García-Ortegón, Chaitanya Joshi, Layla Hosseini Gerami, Alex Beatson, Matthew Greenig, Mrinal Shekhar, Arijit Patra, Caroline Weis, Arash Mehrjou, Adrien Badré, Brianna Paisley, Rhiannon Lowe, Shantanu Singh, Falgun Shah, Bjarki Johannesson, Dominic Williams, David Rouquie, Djork-Arné Clevert, Patrick Schwab, Nicola Richmond, Christos A. Nicolaou, Raymond J. Gonzalez, Andreas Bender
Chemical Research in Toxicology, 2025 Cited by 164, Google Scholar
Paper
Counting cells can accurately predict small-molecule bioactivity benchmarks

Counting cells can accurately predict small-molecule bioactivity benchmarks

Srijit Seal et al. 17 authors
Srijit Seal, W. Dee, A. Shah, Natacha Cerisier, A. Zhang, Esteban Miglietta, K.L. Titterton, Á.A. Cabrera, D.A. Boiko, Alex Beatson, Gregory Slabaugh, Olivier Taboureau, Jordi Carreras Puigvert, Shantanu Singh, Ola Spjuth, Andreas Bender, Anne E. Carpenter
Nature Communications, 2026 Cited by 9, Google Scholar
Paper PDF bioRxiv
Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes

Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes

J.D. Ewald et al. 19 authors
J.D. Ewald, K.L. Titterton, A. Bäuerle, Alex Beatson, D.A. Boiko, Á.A. Cabrera, Jaime Cheah, Beth Cimini, Bram Gorissen, Joshua Harrill, Thouis Jones, Konrad Karczewski, Christine Crute, David Rouquie, Srijit Seal, Erin Weisbart, Brandon White, Anne E. Carpenter, Shantanu Singh
Cell Systems, 2026 Cited by 18, Google Scholar
Paper PDF bioRxiv
Advice for Bad Computational Toxicologists

Advice for Bad Computational Toxicologists

Srijit Seal et al. 2 authors
Srijit Seal, Thomas Hartung
NAM Journal, 2025 Cited by 3, Google Scholar
Paper
Cell Painting: a decade of discovery and innovation in cellular imaging

Cell Painting: a decade of discovery and innovation in cellular imaging

Srijit Seal et al. 8 authors
Srijit Seal, Marianna Trapotsi, Ola Spjuth, Jordi Carreras Puigvert, Nigel Greene, Shantanu Singh, Andreas Bender, Anne E. Carpenter
Nature Methods, 2024 Cited by 190, Google Scholar
Paper Journal
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank

Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank

Srijit Seal et al. 7 authors
Srijit Seal, Ola Spjuth, Layla Hosseini Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter
Journal of Chemical Information and Modeling, 2024 Cited by 65, Google Scholar
Project Paper Code
Integrating Cell Morphology with Gene Expression and Chemical Structure to aid Mitochondrial Toxicity detection

Integrating Cell Morphology with Gene Expression and Chemical Structure to aid Mitochondrial Toxicity detection

Srijit Seal et al. 6 authors
Srijit Seal, Jordi Carreras Puigvert, Marianna Trapotsi, Yang Hongbin, Ola Spjuth, Andreas Bender
Communications Biology, 2022 Cited by 115, Google Scholar
Paper
Comparison of Cellular Morphological descriptors and Molecular Fingerprints for the prediction of Cytotoxicity- and Proliferation-related assays

Comparison of Cellular Morphological descriptors and Molecular Fingerprints for the prediction of Cytotoxicity- and Proliferation-related assays

Srijit Seal et al. 4 authors
Srijit Seal, Yang Hongbin, Luis Vollmers, Andreas Bender
Chemical Research in Toxicology, 2021 Cited by 62, Google Scholar
Project PDF Journal
Understanding biology with machine learning: compression, intelligibility, and dependency

Understanding biology with machine learning: compression, intelligibility, and dependency

Elsa Lawrence et al. 10 authors
Elsa Lawrence, Adham El-Shazly, Srijit Seal, Chaitanya Joshi, Pietro Lio, Andreas Bender, Shantanu Singh, Pietro Sormanni, Ola Spjuth, Matthew Greenig
Artificial Intelligence in the Life Sciences, 2026 Cited by 20, Google Scholar
Project Paper PDF arXiv
Using Chemical and Biological data to Predict Drug Toxicity

Using Chemical and Biological data to Predict Drug Toxicity

Anika Liu et al. 4 authors
Anika Liu, Srijit Seal, Yang Hongbin, Andreas Bender
SLAS Discovery, 2023 Cited by 64, Google Scholar
Paper
Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint models using Similarity to Training data

Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint models using Similarity to Training data

Srijit Seal et al. 7 authors
Srijit Seal, Yang Hongbin, Marianna Trapotsi, Shantanu Singh, Jordi Carreras Puigvert, Ola Spjuth, Andreas Bender
Journal of Cheminformatics, 2023 Cited by 47, Google Scholar
Paper Code
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability

From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability

Srijit Seal et al. 6 authors
Srijit Seal, Jordi Carreras Puigvert, Shantanu Singh, Anne E. Carpenter, Ola Spjuth, Andreas Bender
Molecular Biology of the Cell, 2024 Cited by 36, Google Scholar
Project Paper Code
Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity

Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity

Robert Horne et al. 9 authors
Robert Horne, Jared Wilson-Godber, Alicia Gonzalez Diaz, Z. Faidon Brotzakis, Srijit Seal, Rebecca C. Gregory, Andrea Possenti, Sean Chia, Michele Vendruscolo
Journal of Chemical Information and Modeling, 2024 Cited by 20, Google Scholar
Paper Code
Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data

Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data

Srijit Seal et al. 7 authors
Srijit Seal, Dominic Williams, Layla Hosseini Gerami, Manas Mahale, Anne E. Carpenter, Ola Spjuth, Andreas Bender
Chemical Research in Toxicology, 2024 Cited by 58, Google Scholar
Project Paper Code PDF bioRxiv
PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules

PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules

Srijit Seal et al. 7 authors
Srijit Seal, Marianna Trapotsi, Manas Mahale, Vigneshwari Subramanian, Nigel Greene, Ola Spjuth, Andreas Bender
Journal of Cheminformatics, 2025 Cited by 19, Google Scholar
Project Paper Code PDF bioRxiv
Calibrated prediction of scarce adverse drug reaction labels with conditional neural processes

Calibrated prediction of scarce adverse drug reaction labels with conditional neural processes

Miguel García-Ortegón et al. 5 authors
Miguel García-Ortegón, Srijit Seal, Shantanu Singh, Andreas Bender, Sergio Bacallado
ICLR 2024 DMLR Workshop Cited by 1, Google Scholar
Paper

Updates

News

SHOT-CCR is published in the MICCAI 2026 proceedings.

VSA Explainer describes how to interpret molecular surface-area descriptors at the atom level.

pip install infoalign! Add biological information to your chemical fingerprints, using only SMILES as input! Our paper Learning Molecular Representation in a Cell has been accepted to ICLR 2025! We introduce InfoAlign, a new approach for learning molecular representations from cellular response data, integrating features like cell morphology and gene expression. By combining information bottleneck methods with context graphs, we’re able to extract minimal yet sufficient representations of molecules that lead to better predictions and generalization in downstream tasks like molecular property prediction and zero-shot molecule-morphology matching.

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