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Tommi Jaakkola

IIT@MIT · US
Area of research
Artificial Intelligence · Computational Theory and Mathematics
Research interest
Research interests include Computational Drug Discovery Methods, Machine Learning in Materials Science, Topic Modeling, and Machine Learning and Algorithms.
h-index
92
citations
44,871
works
462
NIH funding
primary concept
Computer science
email

Recent publications

Protein FID: improved evaluation of protein structure generative models
Bioinformatics 2026cited by 0position: middledoi
Atom-level enzyme active site scaffolding using RFdiffusion2
Nature Methods 2025cited by 27position: middledoi
AI-driven discovery of synergistic drug combinations against pancreatic cancer
Nature Communications 2025cited by 20position: middledoi
Artificial intelligence for science in quantum, atomistic, and continuum systems
Foundations and Trends® in Machine Learning 2025cited by 10position: middledoi
Structural constraint integration in a generative model for the discovery of quantum materials
Nature Materials 2025cited by 7position: middledoi
Scaling Inference Time Compute for Diffusion Models
2025cited by 4position: middledoi
Diffusion models in protein structure and docking
Wiley Interdisciplinary Reviews Computational Molecular Science 2024cited by 58position: lastdoi
Virtual node graph neural network for full phonon prediction
Nature Computational Science 2024cited by 19position: middledoi
Closing the Execution Gap in Generative AI for Chemicals and Materials: Freeways or Safeguards
2024cited by 7position: middledoi
De novo design of protein structure and function with RFdiffusion
Nature 2023cited by 1,843position: middledoi
Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii
Nature Chemical Biology 2023cited by 312position: middledoi
Autonomous, multiproperty-driven molecular discovery: From predictions to measurements and back
Science 2023cited by 138position: middledoi
Generative models for molecular discovery: Recent advances and challenges
Wiley Interdisciplinary Reviews Computational Molecular Science 2022cited by 302position: middledoi
Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery
Molecular Systems Biology 2022cited by 264position: middledoi
Deep learning identifies synergistic drug combinations for treating COVID-19
Proceedings of the National Academy of Sciences 2021cited by 170position: middledoi
Mol2Image: Improved Conditional Flow Models for Molecule to Image Synthesis
2021cited by 20position: middledoi
A Deep Learning Approach to Antibiotic Discovery
Cell 2020cited by 2,144position: middledoi
Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis
Journal of Medicinal Chemistry 2020cited by 242position: middledoi
Multi-Objective Molecule Generation using Interpretable Substructures
International Conference on Machine Learning 2020cited by 26position: last
Analyzing Learned Molecular Representations for Property Prediction
Journal of Chemical Information and Modeling 2019cited by 1,714position: middledoi
Generative models for graph-based protein design
DSpace@MIT (Massachusetts Institute of Technology) 2019cited by 211position: last
Analyzing Learned Molecular Representations for Property Prediction
ChemRxiv 2019cited by 113position: middledoi
Tight Certificates of Adversarial Robustness for Randomly Smoothed Classifiers
DSpace@MIT (Massachusetts Institute of Technology) 2019cited by 36position: last
Correction to Analyzing Learned Molecular Representations for Property Prediction
Journal of Chemical Information and Modeling 2019cited by 36position: middledoi
Are Learned Molecular Representations Ready for Prime Time?
ChemRxiv 2019cited by 15position: middledoi
Analyzing Learned Molecular Representations for Property Prediction
ChemRxiv 2019cited by 5position: middledoi
A graph-convolutional neural network model for the prediction of chemical reactivity
Chemical Science 2018cited by 691position: middledoi
Approximate Inference in Additive Factorial HMMs with Application to Energy Disaggregation
DSpace@MIT (Massachusetts Institute of Technology) 2018cited by 463position: lastdoi
Junction Tree Variational Autoencoder for Molecular Graph Generation
DSpace@MIT (Massachusetts Institute of Technology) 2018cited by 171position: last
A Graph-Convolutional Neural Network Model for the Prediction of Chemical Reactivity
ChemRxiv 2018cited by 118position: middledoi

Grants

RI: Small: Theory and Algorithms for Learning Perturbation Models
NSF1524427$407,0912015–2018PIRePORTER

Frequent collaborators

Regina Barzilay · IIT@MIT30 papers (2014–2026)Wengong Jin · Broad Institute of MIT and Harvard17 papers (2018–2025)Klavs F. Jensen · Massachusetts Institute of Technology11 papers (2017–2023)Connor W. Coley · IIT@MIT10 papers (2017–2024)Kevin Yang · Microsoft (United States)7 papers (2018–2020)Kyle Swanson · Stanford University7 papers (2019–2023)William H. Green · Moscow Institute of Thermal Technology5 papers (2017–2023) · 5 papers (2019–2019) · 5 papers (2019–2019) · 5 papers (2019–2019)Angel Guzmán-Pérez · Amgen (United States)5 papers (2019–2019)Timothy Hopper · Amgen (United States)5 papers (2019–2019)Hua Gao · Ningbo Center for Disease Control and Prevention5 papers (2019–2019)Andrew Palmer · University of Birmingham5 papers (2019–2019)Tao Leí · Massachusetts Institute of Technology5 papers (2014–2017)James J. Collins · Broad Institute of MIT and Harvard4 papers (2020–2023)Brian Kelley · University of Michigan–Ann Arbor4 papers (2019–2019)Mingda Li · IIT@MIT3 papers (2024–2025)Ryotaro Okabe · Massachusetts Institute of Technology2 papers (2024–2025)Jonathan Stokes · McMaster University2 papers (2020–2021)