---
title: "Tommi Jaakkola — all works — Elamur Research"
description: "All 95 works of Tommi Jaakkola in the Elamur Research library, the most cited first: our summaries where we have them, else the original."
canonical: "https://research.elamur.ai/free/en/authors/tommi-jaakkola/works/"
---
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# Tommi Jaakkola — all works

95 works · [← Tommi Jaakkola](https://md.research.elamur.ai/free/en/authors/tommi-jaakkola/)

1. **[De novo design of protein structure and function with RFdiffusion ↗](https://doi.org/10.1038/s41586-023-06415-8) Nature · no summary yet**Joseph L. Watson et al.*2023 · 2,342 citations*
2. **[Analyzing Learned Molecular Representations for Property Prediction ↗](https://doi.org/10.1021/acs.jcim.9b00237) Journal of Chemical Information and Modeling · no summary yet**Kevin Yang et al.*2019 · 1,932 citations*
3. [**Style Transfer from Non-Parallel Text by Cross-Alignment**Tianxiao Shen, Tao Lei, Regina Barzilay, et al.*Machine translation · 979 citations*](https://md.research.elamur.ai/free/en/papers/shen-2017-style-transfer-non-parallel-text/)
4. **[Rationalizing Neural Predictions](https://md.research.elamur.ai/free/en/papers/lei-2016-rationalizing-neural-predictions/) [Conference on Empirical Methods in Natural Language Processing (EMNLP)](https://md.research.elamur.ai/free/en/venues/emnlp/)**Tao Lei, Regina Barzilay, Tommi Jaakkola*2016 · 949 citations*
5. **[Junction Tree Variational Autoencoder for Molecular Graph Generation ↗](https://arxiv.org/abs/1802.04364) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2018 · 777 citations*
6. **[Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction ↗](https://doi.org/10.1101/2025.06.14.659707) bioRxiv (Cold Spring Harbor Laboratory) · no summary yet**Saro Passaro et al.*2025 · 674 citations*
7. **[Boltz-1 Democratizing Biomolecular Interaction Modeling ↗](https://doi.org/10.1101/2024.11.19.624167) bioRxiv (Cold Spring Harbor Laboratory) · no summary yet**Jeremy Wohlwend et al.*2024 · 491 citations*
8. **[Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction ↗](https://doi.org/10.1021/acs.jcim.6b00601) Journal of Chemical Information and Modeling · no summary yet**Connor W. Coley et al.*2017 · 477 citations*
9. **[Graph neural networks ↗](https://doi.org/10.1038/s43586-024-00294-7) Nature Reviews Methods Primers · no summary yet**Gabriele Corso et al.*2024 · 457 citations*
10. **[DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking ↗](https://arxiv.org/abs/2210.01776) arXiv (Cornell University) · no summary yet**Gabriele Corso et al.*2022 · 355 citations*
11. **[Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii ↗](https://doi.org/10.1038/s41589-023-01349-8) Nature Chemical Biology · no summary yet**Gary Liu et al.*2023 · 353 citations*
12. **[Gromov-Wasserstein Alignment of Word Embedding Spaces](https://md.research.elamur.ai/free/en/papers/melis-2018-gromov-wasserstein-alignment-word-embedding/) [Conference on Empirical Methods in Natural Language Processing (EMNLP)](https://md.research.elamur.ai/free/en/venues/emnlp/)**David Alvarez-Melis, Tommi Jaakkola*2018 · 338 citations*
13. **[Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis ↗](https://doi.org/10.1021/acs.jmedchem.9b02120) Journal of Medicinal Chemistry · no summary yet**Thomas J. Struble et al.*2020 · 245 citations*
14. **[On Dual Decomposition and Linear Programming Relaxations for Natural Language Processing](https://md.research.elamur.ai/free/en/papers/rush-2010-dual-decomposition-linear-programming-relaxations/) [Conference on Empirical Methods in Natural Language Processing (EMNLP)](https://md.research.elamur.ai/free/en/venues/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 ↗](https://aclanthology.org/D17-1042/) Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing · no summary yet**David Alvarez-Melis, Tommi Jaakkola*2017 · 232 citations*
16. **[Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network ↗](https://arxiv.org/abs/1709.04555) arXiv (Cornell University) · no summary yet**Wengong Jin et al.*2017 · 184 citations*
17. **[Rethinking Cooperative Rationalization: Introspective Extraction and Complement Control](https://md.research.elamur.ai/free/en/papers/yu-2019-rethinking-cooperative-rationalization-introspective-extraction/) [Conference on Empirical Methods in Natural Language Processing (EMNLP)](https://md.research.elamur.ai/free/en/venues/emnlp/)**Mo Yu, Shiyu Chang, Yang Zhang, et al.*2019 · 179 citations*
18. **[Low-Rank Tensors for Scoring Dependency Structures ↗](https://aclanthology.org/P14-1130/) Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · no summary yet**Tao Lei et al.*2014 · 162 citations*
19. **[Molding CNNs for text: non-linear, non-consecutive convolutions ↗](https://aclanthology.org/D15-1180/) Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing · no summary yet**Tao Lei, Regina Barzilay, Tommi Jaakkola*2015 · 156 citations*
20. **[Ten Pairs to Tag – Multilingual POS Tagging via Coarse Mapping between Embeddings ↗](https://aclanthology.org/N16-1156/) Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies · no summary yet**Yuan Zhang et al.*2016 · 153 citations*
21. **[Learning Multimodal Graph-to-Graph Translation for Molecular Optimization ↗](https://arxiv.org/abs/1812.01070) arXiv (Cornell University) · no summary yet**Wengong Jin et al.*2018 · 130 citations*
22. **[Semi-supervised Question Retrieval with Gated Convolutions ↗](https://aclanthology.org/N16-1153/) Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies · no summary yet**Tao Lei et al.*2016 · 129 citations*
23. **[Atom-level enzyme active site scaffolding using RFdiffusion2 ↗](https://doi.org/10.1038/s41592-025-02975-x) Nature Methods · no summary yet**Woody Ahern et al.*2025 · 116 citations*
24. **[Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem ↗](https://arxiv.org/abs/2206.04119) arXiv (Cornell University) · no summary yet**Brian L. Trippe et al.*2022 · 114 citations*
25. **[Aspect-augmented Adversarial Networks for Domain Adaptation ↗](https://aclanthology.org/Q17-1036/) Transactions of the Association for Computational Linguistics · no summary yet**Yuan Zhang, Regina Barzilay, Tommi Jaakkola*2017 · 114 citations*
26. **[Crystal Diffusion Variational Autoencoder for Periodic Material Generation ↗](https://arxiv.org/abs/2110.06197) arXiv (Cornell University) · no summary yet**Tian Xie et al.*2021 · 105 citations*
27. **[EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction ↗](https://arxiv.org/abs/2202.05146) arXiv (Cornell University) · no summary yet**Stärk, Hannes et al.*2022 · 98 citations*
28. **[Hierarchical Generation of Molecular Graphs using Structural Motifs ↗](https://arxiv.org/abs/2002.03230) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2020 · 96 citations*
29. **[Torsional Diffusion for Molecular Conformer Generation ↗](https://arxiv.org/abs/2206.01729) arXiv (Cornell University) · no summary yet**Bowen Jing et al.*2022 · 89 citations*
30. **[Multi-Objective Molecule Generation using Interpretable Substructures ↗](https://arxiv.org/abs/2002.03244) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2020 · 89 citations*
31. **[An Unsupervised Method for Uncovering Morphological Chains ↗](https://aclanthology.org/Q15-1012/) Transactions of the Association for Computational Linguistics · no summary yet**Karthik Narasimhan, Regina Barzilay, Tommi Jaakkola*2015 · 88 citations*
32. **[SE(3) diffusion model with application to protein backbone generation ↗](https://arxiv.org/abs/2302.02277) arXiv (Cornell University) · no summary yet**Jason Yim et al.*2023 · 85 citations*
33. **[Dual Decomposition for Parsing with Non-Projective Head Automata](https://md.research.elamur.ai/free/en/papers/koo-2010-dual-decomposition-parsing-non-projective/) [Conference on Empirical Methods in Natural Language Processing (EMNLP)](https://md.research.elamur.ai/free/en/venues/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" ↗](https://doi.org/10.5281/zenodo.6034087) Zenodo (CERN European Organization for Nuclear Research) · no summary yet**Hannes Stark et al.*2022 · 79 citations*
35. **[Blank Language Models ↗](https://aclanthology.org/2020.emnlp-main.420/) Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP) · no summary yet**Tianxiao Shen et al.*2020 · 78 citations*
36. **[Diffusion models in protein structure and docking ↗](https://doi.org/10.1002/wcms.1711) Wiley Interdisciplinary Reviews Computational Molecular Science · no summary yet**Jason Yim et al.*2024 · 72 citations*
37. **[Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design ↗](https://arxiv.org/abs/2110.04624) arXiv (Cornell University) · no summary yet**Wengong Jin et al.*2021 · 71 citations*
38. **[Chapter 11. Junction Tree Variational Autoencoder for Molecular Graph Generation ↗](https://doi.org/10.1039/9781788016841-00228) RSC drug discovery/RSC drug discovery series · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2020 · 63 citations*
39. **[Educating Text Autoencoders: Latent Representation Guidance via Denoising ↗](https://arxiv.org/abs/1905.12777) arXiv (Cornell University) · no summary yet**Tianxiao Shen et al.*2019 · 63 citations*
40. **[Greed is Good if Randomized: New Inference for Dependency Parsing ↗](https://aclanthology.org/D14-1109/) Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP) · no summary yet**Yuan Zhang et al.*2014 · 63 citations*
41. **[GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles ↗](https://arxiv.org/abs/2106.07802) arXiv (Cornell University) · no summary yet**Octavian-Eugen Ganea et al.*2021 · 58 citations*
42. **[Consistent Accelerated Inference via Confident Adaptive Transformers ↗](https://aclanthology.org/2021.emnlp-main.406/) Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing · no summary yet**Tal Schuster et al.*2021 · 56 citations*
43. **[Conformal Language Modeling ↗](https://arxiv.org/abs/2306.10193) arXiv:2306.10193 · no summary yet**Victor Quach et al.*2023 · 48 citations*
44. **[Steps to Excellence: Simple Inference with Refined Scoring of Dependency Trees ↗](https://aclanthology.org/P14-1019/) Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · no summary yet**Yuan Zhang et al.*2014 · 48 citations*
45. **[Path-Augmented Graph Transformer Network ↗](https://doi.org/10.26434/chemrxiv.8214422) ChemRxiv · no summary yet**Benson Chen, Regina Barzilay, Tommi Jaakkola*2019 · 37 citations*
46. **[Deriving Neural Architectures from Sequence and Graph Kernels ↗](https://arxiv.org/abs/1705.09037) arXiv (Cornell University) · no summary yet**Tao Lei et al.*2017 · 36 citations*
47. **[Learning to Make Generalizable and Diverse Predictions for Retrosynthesis ↗](https://arxiv.org/abs/1910.09688) arXiv (Cornell University) · no summary yet**Benson Chen et al.*2019 · 34 citations*
48. **[AI-driven discovery of synergistic drug combinations against pancreatic cancer ↗](https://doi.org/10.1038/s41467-025-56818-6) Nature Communications · no summary yet**Mohsen Pourmousa et al.*2025 · 33 citations*
49. **[Fast protein backbone generation with SE(3) flow matching ↗](https://arxiv.org/abs/2310.05297) arXiv (Cornell University) · no summary yet**Jason Yim et al.*2023 · 30 citations*
50. **[DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models ↗](https://arxiv.org/abs/2304.03889) arXiv (Cornell University) · no summary yet**Mohamed Amine Ketata et al.*2023 · 29 citations*
51. **[Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking ↗](https://arxiv.org/abs/2111.07786) arXiv (Cornell University) · no summary yet**Octavian-Eugen Ganea et al.*2021 · 29 citations*
52. **[Are Learned Molecular Representations Ready for Prime Time? ↗](https://doi.org/10.26434/chemrxiv.7940594.v1) ChemRxiv · no summary yet**Kevin Yang et al.*2019 · 29 citations*
53. **[Deep Confident Steps to New Pockets: Strategies for Docking Generalization ↗](https://arxiv.org/abs/2402.18396) PubMed · no summary yet**Gabriele Corso et al.*2024 · 28 citations*
54. **[Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design ↗](https://arxiv.org/abs/2402.04997) PubMed · no summary yet**Campbell, Andrew et al.*2024 · 27 citations*
55. **[Optimal Transport Graph Neural Networks ↗](https://arxiv.org/abs/2006.04804) arXiv (Cornell University) · no summary yet**Benson Chen et al.*2020 · 23 citations*
56. **[Hierarchical Graph-to-Graph Translation for Molecules ↗](https://arxiv.org/abs/1907.11223) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2019 · 22 citations*
57. **[Scaling Inference Time Compute for Diffusion Models ↗](https://doi.org/10.1109/cvpr52734.2025.00241) IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings · no summary yet**Nanye Ma et al.*2025 · 18 citations*
58. **[Inference-Time Scaling for Diffusion Models beyond Scaling Denoising Steps ↗](https://arxiv.org/abs/2501.09732) arXiv (Cornell University) · no summary yet**Nanye Ma et al.*2025 · 16 citations*
59. **[Dirichlet Flow Matching with Applications to DNA Sequence Design ↗](https://arxiv.org/abs/2402.05841) PubMed · no summary yet**Stark, Hannes et al.*2024 · 14 citations*
60. **[Blind protein-ligand docking with diffusion-based deep generative models ↗](https://doi.org/10.1016/j.bpj.2022.11.937) Biophysical Journal · no summary yet**Gabriele Corso et al.*2022 · 13 citations*
61. **[Improving Molecular Design by Stochastic Iterative Target Augmentation ↗](https://doi.org/10.26434/chemrxiv.11839230) ChemRxiv · no summary yet**Kevin Yang et al.*2020 · 13 citations*
62. **[Improved motif-scaffolding with SE(3) flow matching ↗](https://arxiv.org/abs/2401.04082) PubMed · no summary yet**Jason Yim et al.*2024 · 12 citations*
63. **[Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement ↗](https://arxiv.org/abs/2207.06616) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2022 · 12 citations*
64. **[Learning to refine text based recommendations ↗](https://aclanthology.org/D16-1227/) Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing · no summary yet**Youyang Gu et al.*2016 · 12 citations*
65. **[Conformal Prediction Sets with Limited False Positives ↗](https://arxiv.org/abs/2202.07650) arXiv (Cornell University) · no summary yet**Fisch, Adam et al.*2022 · 11 citations*
66. **[Few-shot Conformal Prediction with Auxiliary Tasks ↗](https://arxiv.org/abs/2102.08898) arXiv (Cornell University) · no summary yet**Fisch, Adam et al.*2021 · 10 citations*
67. **[Multi-Resolution Autoregressive Graph-to-Graph Translation for Molecules ↗](https://doi.org/10.26434/chemrxiv.8266745.v1) ChemRxiv · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2019 · 10 citations*
68. **[Domain Extrapolation via Regret Minimization. ↗](https://arxiv.org/abs/2006.03908) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2020 · 9 citations*
69. **[Deep Transfer in Reinforcement Learning by Language Grounding. ↗](https://arxiv.org/abs/1708.00133) arXiv (Cornell University) · no summary yet**Karthik Narasimhan, Regina Barzilay, Tommi Jaakkola*2017 · 9 citations*
70. **[Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models ↗](https://arxiv.org/abs/2310.13102) arXiv (Cornell University) · no summary yet**Gabriele Corso et al.*2023 · 7 citations*
71. **[Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design ↗](https://arxiv.org/abs/2310.05764) arXiv (Cornell University) · no summary yet**Stärk, Hannes et al.*2023 · 7 citations*
72. **[Graph Adversarial Networks: Protecting Information against Adversarial Attacks ↗](https://openalex.org/W3088237946) no summary yet**Peiyuan Liao et al.*2021 · 7 citations*
73. **[Information Obfuscation of Graph Neural Networks ↗](https://arxiv.org/abs/2009.13504) arXiv (Cornell University) · no summary yet**Peiyuan Liao et al.*2020 · 7 citations*
74. **[Calibrated Selective Classification ↗](https://arxiv.org/abs/2208.12084) arXiv (Cornell University) · no summary yet**Fisch, Adam, Tommi Jaakkola, Regina Barzilay*2022 · 6 citations*
75. **[Efficiently Controlling Multiple Risks with Pareto Testing ↗](https://arxiv.org/abs/2210.07913) arXiv (Cornell University) · no summary yet**Bracha Laufer-Goldshtein et al.*2022 · 5 citations*
76. **[Relaxed Conformal Prediction Cascades for Efficient Inference Over Many Labels. ↗](https://arxiv.org/abs/2007.03114) arXiv (Cornell University) · no summary yet**Adam Fisch et al.*2020 · 5 citations*
77. **[Adaptive Invariance for Molecule Property Prediction ↗](https://arxiv.org/abs/2005.03004) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2020 · 5 citations*
78. **[Improved Conditional Flow Models for Molecule to Image Synthesis ↗](https://arxiv.org/abs/2006.08532) arXiv (Cornell University) · no summary yet**Karren Yang et al.*2020 · 5 citations*
79. **[Protein FID: improved evaluation of protein structure generative models ↗](https://doi.org/10.1093/bioinformatics/btag156) Bioinformatics · no summary yet**Felix Faltings et al.*2026 · 4 citations*
80. **[Improving Protein Optimization with Smoothed Fitness Landscapes ↗](https://arxiv.org/abs/2307.00494) arXiv (Cornell University) · no summary yet**Andrew Kirjner et al.*2023 · 4 citations*
81. **[Syfer: Neural Obfuscation for Private Data Release ↗](https://arxiv.org/abs/2201.12406) arXiv (Cornell University) · no summary yet**Adam Yala et al.*2022 · 4 citations*
82. **[CRAFT: ClusteR-specific Assorted Feature selecTion ↗](https://arxiv.org/abs/1506.07609) arXiv (Cornell University) · no summary yet**Vikas Garg, Cynthia D Rudin, Tommi Jaakkola*2015 · 4 citations*
83. **[Sample, estimate, aggregate: A recipe for causal discovery foundation models ↗](https://arxiv.org/abs/2402.01929) arXiv (Cornell University) · no summary yet**Menghua Wu et al.*2024 · 3 citations*
84. **[Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models ↗](https://arxiv.org/abs/2011.04651) arXiv (Cornell University) · no summary yet**Wengong Jin, Regina Barzilay, Tommi Jaakkola*2020 · 3 citations*
85. **[Hierarchical protein backbone generation with latent and structure diffusion ↗](https://arxiv.org/abs/2504.09374) arXiv (Cornell University) · no summary yet**Jason Yim et al.*2025 · 2 citations*
86. **[NeuraCrypt: Hiding Private Health Data via Random Neural Networks for Public Training ↗](https://arxiv.org/abs/2106.02484) arXiv (Cornell University) · no summary yet**Adam Yala et al.*2021 · 2 citations*
87. **[Identifying biological perturbation targets through causal differential networks ↗](https://arxiv.org/abs/2410.03380) arXiv (Cornell University) · no summary yet**Menghua Wu et al.*2024 · 1 citation*
88. **[Fast non-autoregressive inverse folding with discrete diffusion ↗](https://arxiv.org/abs/2312.02447) arXiv (Cornell University) · no summary yet**John Jeongseok Yang et al.*2023 · 1 citation*
89. **[Using Deep Reinforcement Learning to Generate Rationales for Molecules ↗](https://openalex.org/W2787290402) no summary yet**Benson Chen et al.*2018 · 1 citation*
90. **[ProxelGen: Generating Proteins as 3D Densities ↗](https://arxiv.org/abs/2506.19820) PubMed · no summary yet**Felix Faltings et al.*2025*
91. **[PEOPL: Characterizing Privately Encoded Open Datasets with Public Labels ↗](https://arxiv.org/abs/2304.00047) arXiv (Cornell University) · no summary yet**Homa Esfahanizadeh et al.*2023*
92. **[Risk-Controlling Model Selection via Guided Bayesian Optimization ↗](https://arxiv.org/abs/2312.01692) arXiv (Cornell University) · no summary yet**Bracha Laufer-Goldshtein et al.*2023*
93. **[Denoising Improves Latent Space Geometry in Text Autoencoders ↗](https://openalex.org/W3005488132) no summary yet**Tianxiao Shen et al.*2019*
94. **[Iterative Target Augmentation for Effective Conditional Generation ↗](https://openalex.org/W3004495729) no summary yet**Kevin Yang et al.*2019*
95. **[An Unsupervised Method for Uncovering Morphological Chains (Open Access, Publisher's Version) ↗](https://openalex.org/W2776643988) no summary yet**Karthik Narasimhan, Regina Barzilay, Tommi Jaakkola*2015*