🧑‍🔬 Tommi Jaakkola — all works

95 works · ← Tommi Jaakkola

1. De novo design of protein structure and function with RFdiffusion ↗Nature · no summary yetJoseph L. Watson et al.2023 · 2,342 citations
2. Analyzing Learned Molecular Representations for Property Prediction ↗Journal of Chemical Information and Modeling · no summary yetKevin Yang et al.2019 · 1,932 citations
3. Style Transfer from Non-Parallel Text by Cross-AlignmentTianxiao Shen, Tao Lei, Regina Barzilay, et al.Machine translation · 979 citations
4. Rationalizing Neural PredictionsConference on Empirical Methods in Natural Language Processing (EMNLP)Tao Lei, Regina Barzilay, Tommi Jaakkola2016 · 949 citations
5. Junction Tree Variational Autoencoder for Molecular Graph Generation ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2018 · 777 citations
6. Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction ↗bioRxiv (Cold Spring Harbor Laboratory) · no summary yetSaro Passaro et al.2025 · 674 citations
7. Boltz-1 Democratizing Biomolecular Interaction Modeling ↗bioRxiv (Cold Spring Harbor Laboratory) · no summary yetJeremy Wohlwend et al.2024 · 491 citations
8. Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction ↗Journal of Chemical Information and Modeling · no summary yetConnor W. Coley et al.2017 · 477 citations
9. Graph neural networks ↗Nature Reviews Methods Primers · no summary yetGabriele Corso et al.2024 · 457 citations
10. DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking ↗arXiv (Cornell University) · no summary yetGabriele Corso et al.2022 · 355 citations
11. Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii ↗Nature Chemical Biology · no summary yetGary Liu et al.2023 · 353 citations
12. Gromov-Wasserstein Alignment of Word Embedding SpacesConference on Empirical Methods in Natural Language Processing (EMNLP)David Alvarez-Melis, Tommi Jaakkola2018 · 338 citations
13. Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis ↗Journal of Medicinal Chemistry · no summary yetThomas J. Struble et al.2020 · 245 citations
14. On Dual Decomposition and Linear Programming Relaxations for Natural Language ProcessingConference on Empirical Methods in Natural Language Processing (EMNLP)Alexander M. Rush, David Sontag, Michael Collins, et al.2010 · 240 citations
15. A causal framework for explaining the predictions of black-box sequence-to-sequence models ↗Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing · no summary yetDavid Alvarez-Melis, Tommi Jaakkola2017 · 232 citations
16. Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network ↗arXiv (Cornell University) · no summary yetWengong Jin et al.2017 · 184 citations
17. Rethinking Cooperative Rationalization: Introspective Extraction and Complement ControlConference on Empirical Methods in Natural Language Processing (EMNLP)Mo Yu, Shiyu Chang, Yang Zhang, et al.2019 · 179 citations
18. Low-Rank Tensors for Scoring Dependency Structures ↗Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · no summary yetTao Lei et al.2014 · 162 citations
19. Molding CNNs for text: non-linear, non-consecutive convolutions ↗Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing · no summary yetTao Lei, Regina Barzilay, Tommi Jaakkola2015 · 156 citations
20. Ten Pairs to Tag – Multilingual POS Tagging via Coarse Mapping between Embeddings ↗Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies · no summary yetYuan Zhang et al.2016 · 153 citations
21. Learning Multimodal Graph-to-Graph Translation for Molecular Optimization ↗arXiv (Cornell University) · no summary yetWengong Jin et al.2018 · 130 citations
22. Semi-supervised Question Retrieval with Gated Convolutions ↗Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies · no summary yetTao Lei et al.2016 · 129 citations
23. Atom-level enzyme active site scaffolding using RFdiffusion2 ↗Nature Methods · no summary yetWoody Ahern et al.2025 · 116 citations
24. Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem ↗arXiv (Cornell University) · no summary yetBrian L. Trippe et al.2022 · 114 citations
25. Aspect-augmented Adversarial Networks for Domain Adaptation ↗Transactions of the Association for Computational Linguistics · no summary yetYuan Zhang, Regina Barzilay, Tommi Jaakkola2017 · 114 citations
26. Crystal Diffusion Variational Autoencoder for Periodic Material Generation ↗arXiv (Cornell University) · no summary yetTian Xie et al.2021 · 105 citations
27. EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction ↗arXiv (Cornell University) · no summary yetStärk, Hannes et al.2022 · 98 citations
28. Hierarchical Generation of Molecular Graphs using Structural Motifs ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2020 · 96 citations
29. Torsional Diffusion for Molecular Conformer Generation ↗arXiv (Cornell University) · no summary yetBowen Jing et al.2022 · 89 citations
30. Multi-Objective Molecule Generation using Interpretable Substructures ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2020 · 89 citations
31. An Unsupervised Method for Uncovering Morphological Chains ↗Transactions of the Association for Computational Linguistics · no summary yetKarthik Narasimhan, Regina Barzilay, Tommi Jaakkola2015 · 88 citations
32. SE(3) diffusion model with application to protein backbone generation ↗arXiv (Cornell University) · no summary yetJason Yim et al.2023 · 85 citations
33. Dual Decomposition for Parsing with Non-Projective Head AutomataConference on Empirical Methods in Natural Language Processing (EMNLP)Terry Koo, Alexander M. Rush, Michael Collins, et al.2010 · 82 citations
34. Data used for training in "EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction" ↗Zenodo (CERN European Organization for Nuclear Research) · no summary yetHannes Stark et al.2022 · 79 citations
35. Blank Language Models ↗Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP) · no summary yetTianxiao Shen et al.2020 · 78 citations
36. Diffusion models in protein structure and docking ↗Wiley Interdisciplinary Reviews Computational Molecular Science · no summary yetJason Yim et al.2024 · 72 citations
37. Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design ↗arXiv (Cornell University) · no summary yetWengong Jin et al.2021 · 71 citations
38. Chapter 11. Junction Tree Variational Autoencoder for Molecular Graph Generation ↗RSC drug discovery/RSC drug discovery series · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2020 · 63 citations
39. Educating Text Autoencoders: Latent Representation Guidance via Denoising ↗arXiv (Cornell University) · no summary yetTianxiao Shen et al.2019 · 63 citations
40. Greed is Good if Randomized: New Inference for Dependency Parsing ↗Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP) · no summary yetYuan Zhang et al.2014 · 63 citations
41. GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles ↗arXiv (Cornell University) · no summary yetOctavian-Eugen Ganea et al.2021 · 58 citations
42. Consistent Accelerated Inference via Confident Adaptive Transformers ↗Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing · no summary yetTal Schuster et al.2021 · 56 citations
43. Conformal Language Modeling ↗arXiv:2306.10193 · no summary yetVictor Quach et al.2023 · 48 citations
44. Steps to Excellence: Simple Inference with Refined Scoring of Dependency Trees ↗Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · no summary yetYuan Zhang et al.2014 · 48 citations
45. Path-Augmented Graph Transformer Network ↗ChemRxiv · no summary yetBenson Chen, Regina Barzilay, Tommi Jaakkola2019 · 37 citations
46. Deriving Neural Architectures from Sequence and Graph Kernels ↗arXiv (Cornell University) · no summary yetTao Lei et al.2017 · 36 citations
47. Learning to Make Generalizable and Diverse Predictions for Retrosynthesis ↗arXiv (Cornell University) · no summary yetBenson Chen et al.2019 · 34 citations
48. AI-driven discovery of synergistic drug combinations against pancreatic cancer ↗Nature Communications · no summary yetMohsen Pourmousa et al.2025 · 33 citations
49. Fast protein backbone generation with SE(3) flow matching ↗arXiv (Cornell University) · no summary yetJason Yim et al.2023 · 30 citations
50. DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models ↗arXiv (Cornell University) · no summary yetMohamed Amine Ketata et al.2023 · 29 citations
51. Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking ↗arXiv (Cornell University) · no summary yetOctavian-Eugen Ganea et al.2021 · 29 citations
52. Are Learned Molecular Representations Ready for Prime Time? ↗ChemRxiv · no summary yetKevin Yang et al.2019 · 29 citations
53. Deep Confident Steps to New Pockets: Strategies for Docking Generalization ↗PubMed · no summary yetGabriele Corso et al.2024 · 28 citations
54. Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design ↗PubMed · no summary yetCampbell, Andrew et al.2024 · 27 citations
55. Optimal Transport Graph Neural Networks ↗arXiv (Cornell University) · no summary yetBenson Chen et al.2020 · 23 citations
56. Hierarchical Graph-to-Graph Translation for Molecules ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2019 · 22 citations
57. Scaling Inference Time Compute for Diffusion Models ↗IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings · no summary yetNanye Ma et al.2025 · 18 citations
58. Inference-Time Scaling for Diffusion Models beyond Scaling Denoising Steps ↗arXiv (Cornell University) · no summary yetNanye Ma et al.2025 · 16 citations
59. Dirichlet Flow Matching with Applications to DNA Sequence Design ↗PubMed · no summary yetStark, Hannes et al.2024 · 14 citations
60. Blind protein-ligand docking with diffusion-based deep generative models ↗Biophysical Journal · no summary yetGabriele Corso et al.2022 · 13 citations
61. Improving Molecular Design by Stochastic Iterative Target Augmentation ↗ChemRxiv · no summary yetKevin Yang et al.2020 · 13 citations
62. Improved motif-scaffolding with SE(3) flow matching ↗PubMed · no summary yetJason Yim et al.2024 · 12 citations
63. Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2022 · 12 citations
64. Learning to refine text based recommendations ↗Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing · no summary yetYouyang Gu et al.2016 · 12 citations
65. Conformal Prediction Sets with Limited False Positives ↗arXiv (Cornell University) · no summary yetFisch, Adam et al.2022 · 11 citations
66. Few-shot Conformal Prediction with Auxiliary Tasks ↗arXiv (Cornell University) · no summary yetFisch, Adam et al.2021 · 10 citations
67. Multi-Resolution Autoregressive Graph-to-Graph Translation for Molecules ↗ChemRxiv · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2019 · 10 citations
68. Domain Extrapolation via Regret Minimization. ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2020 · 9 citations
69. Deep Transfer in Reinforcement Learning by Language Grounding. ↗arXiv (Cornell University) · no summary yetKarthik Narasimhan, Regina Barzilay, Tommi Jaakkola2017 · 9 citations
70. Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models ↗arXiv (Cornell University) · no summary yetGabriele Corso et al.2023 · 7 citations
71. Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design ↗arXiv (Cornell University) · no summary yetStärk, Hannes et al.2023 · 7 citations
72. Graph Adversarial Networks: Protecting Information against Adversarial Attacks ↗no summary yetPeiyuan Liao et al.2021 · 7 citations
73. Information Obfuscation of Graph Neural Networks ↗arXiv (Cornell University) · no summary yetPeiyuan Liao et al.2020 · 7 citations
74. Calibrated Selective Classification ↗arXiv (Cornell University) · no summary yetFisch, Adam, Tommi Jaakkola, Regina Barzilay2022 · 6 citations
75. Efficiently Controlling Multiple Risks with Pareto Testing ↗arXiv (Cornell University) · no summary yetBracha Laufer-Goldshtein et al.2022 · 5 citations
76. Relaxed Conformal Prediction Cascades for Efficient Inference Over Many Labels. ↗arXiv (Cornell University) · no summary yetAdam Fisch et al.2020 · 5 citations
77. Adaptive Invariance for Molecule Property Prediction ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2020 · 5 citations
78. Improved Conditional Flow Models for Molecule to Image Synthesis ↗arXiv (Cornell University) · no summary yetKarren Yang et al.2020 · 5 citations
79. Protein FID: improved evaluation of protein structure generative models ↗Bioinformatics · no summary yetFelix Faltings et al.2026 · 4 citations
80. Improving Protein Optimization with Smoothed Fitness Landscapes ↗arXiv (Cornell University) · no summary yetAndrew Kirjner et al.2023 · 4 citations
81. Syfer: Neural Obfuscation for Private Data Release ↗arXiv (Cornell University) · no summary yetAdam Yala et al.2022 · 4 citations
82. CRAFT: ClusteR-specific Assorted Feature selecTion ↗arXiv (Cornell University) · no summary yetVikas Garg, Cynthia D Rudin, Tommi Jaakkola2015 · 4 citations
83. Sample, estimate, aggregate: A recipe for causal discovery foundation models ↗arXiv (Cornell University) · no summary yetMenghua Wu et al.2024 · 3 citations
84. Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models ↗arXiv (Cornell University) · no summary yetWengong Jin, Regina Barzilay, Tommi Jaakkola2020 · 3 citations
85. Hierarchical protein backbone generation with latent and structure diffusion ↗arXiv (Cornell University) · no summary yetJason Yim et al.2025 · 2 citations
86. NeuraCrypt: Hiding Private Health Data via Random Neural Networks for Public Training ↗arXiv (Cornell University) · no summary yetAdam Yala et al.2021 · 2 citations
87. Identifying biological perturbation targets through causal differential networks ↗arXiv (Cornell University) · no summary yetMenghua Wu et al.2024 · 1 citation
88. Fast non-autoregressive inverse folding with discrete diffusion ↗arXiv (Cornell University) · no summary yetJohn Jeongseok Yang et al.2023 · 1 citation
89. Using Deep Reinforcement Learning to Generate Rationales for Molecules ↗no summary yetBenson Chen et al.2018 · 1 citation
90. ProxelGen: Generating Proteins as 3D Densities ↗PubMed · no summary yetFelix Faltings et al.2025
91. PEOPL: Characterizing Privately Encoded Open Datasets with Public Labels ↗arXiv (Cornell University) · no summary yetHoma Esfahanizadeh et al.2023
92. Risk-Controlling Model Selection via Guided Bayesian Optimization ↗arXiv (Cornell University) · no summary yetBracha Laufer-Goldshtein et al.2023
93. Denoising Improves Latent Space Geometry in Text Autoencoders ↗no summary yetTianxiao Shen et al.2019
94. Iterative Target Augmentation for Effective Conditional Generation ↗no summary yetKevin Yang et al.2019
95. An Unsupervised Method for Uncovering Morphological Chains (Open Access, Publisher's Version) ↗no summary yetKarthik Narasimhan, Regina Barzilay, Tommi Jaakkola2015

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