| Pot: Python optimal transport R Flamary, N Courty, A Gramfort, MZ Alaya, A Boisbunon, S Chambon, ... Journal of Machine Learning Research 22 (78), 1-8, 2021 | 1092 | 2021 |
| Improving and generalizing flow-based generative models with minibatch optimal transport A Tong, N Malkin, G Huguet, Y Zhang, J Rector-Brooks, K Fatras, G Wolf, ... arXiv preprint arXiv:2302.00482, 2023 | 236* | 2023 |
| Quantifying the effect of experimental perturbations at single-cell resolution DB Burkhardt, JS Stanley III, A Tong, AL Perdigoto, SA Gigante, ... Nature biotechnology 39 (5), 619-629, 2021 | 198* | 2021 |
| Trajectorynet: A dynamic optimal transport network for modeling cellular dynamics A Tong, J Huang, G Wolf, D Van Dijk, S Krishnaswamy International conference on machine learning, 9526-9536, 2020 | 166 | 2020 |
| A sandbox for prediction and integration of DNA, RNA, and proteins in single cells MD Luecken, DB Burkhardt, R Cannoodt, C Lance, A Agrawal, H Aliee, ... Thirty-fifth conference on neural information processing systems datasets …, 2021 | 111 | 2021 |
| Multiscale PHATE identifies multimodal signatures of COVID-19 M Kuchroo, J Huang, P Wong, JC Grenier, D Shung, A Tong, C Lucas, ... Nature biotechnology 40 (5), 681-691, 2022 | 80* | 2022 |
| SE (3)-Stochastic Flow Matching for Protein Backbone Generation AJ Bose, T Akhound-Sadegh, G Huguet, K Fatras, J Rector-Brooks, ... International Conference on Learning Representations (spotlight), 2024 | 58 | 2024 |
| Manifold Interpolating Optimal-Transport Flows for Trajectory Inference G Huguet, DS Magruder, A Tong, O Fasina, M Kuchroo, G Wolf, ... Advances in Neural Information Processing Systems, 2022 | 52 | 2022 |
| Simulation-free Schrödinger bridges via score and flow matching A Tong, N Malkin, K Fatras, L Atanackovic, Y Zhang, G Huguet, G Wolf, ... International Conference on Artificial Intelligence and Statistics, 2024 | 43 | 2024 |
| Fixing bias in reconstruction-based anomaly detection with lipschitz discriminators A Tong, G Wolf, S Krishnaswamy Journal of Signal Processing Systems, 1-15, 2021 | 39* | 2021 |
| Single-cell analysis reveals inflammatory interactions driving macular degeneration M Kuchroo, M DiStasio, E Song, E Calapkulu, L Zhang, M Ige, AH Sheth, ... Nature Communications 14 (1), 2589, 2023 | 37 | 2023 |
| Trellis tree-based analysis reveals stromal regulation of patient-derived organoid drug responses MR Zapatero, A Tong, JW Opzoomer, R O’Sullivan, FC Rodriguez, J Sufi, ... Cell 186 (25), 5606-5619. e24, 2023 | 36 | 2023 |
| Iterated Denoising Energy Matching for Sampling from Boltzmann Densities T Akhound-Sadegh, J Rector-Brooks, AJ Bose, S Mittal, P Lemos, CH Liu, ... International Conference on Machine Learning, 2024 | 35 | 2024 |
| Immune cells and their inflammatory mediators modify β cells and cause checkpoint inhibitor–induced diabetes AL Perdigoto, S Deng, KC Du, M Kuchroo, DB Burkhardt, A Tong, G Israel, ... JCI insight 7 (17), e156330, 2022 | 33 | 2022 |
| Diffusion earth mover’s distance and distribution embeddings AY Tong, G Huguet, A Natik, K MacDonald, M Kuchroo, R Coifman, ... International Conference on Machine Learning, 10336-10346, 2021 | 33* | 2021 |
| DynGFN: Towards Bayesian Inference of Gene Regulatory Networks with GFlowNets L Atanackovic, A Tong, B Wang, LJ Lee, Y Bengio, J Hartford Thirty-seventh Conference on Neural Information Processing Systems, 2023 | 32* | 2023 |
| Learnable filters for geometric scattering modules A Tong, F Wenkel, D Bhaskar, K Macdonald, J Grady, M Perlmutter, ... IEEE Transactions on Signal Processing, 2024 | 21* | 2024 |
| Finding archetypal spaces using neural networks D van Dijk, DB Burkhardt, M Amodio, A Tong, G Wolf, S Krishnaswamy 2019 IEEE International Conference on Big Data (Big Data), 2634-2643, 2019 | 21* | 2019 |
| Multimodal data visualization and denoising with integrated diffusion M Kuchroo, A Godavarthi, A Tong, G Wolf, S Krishnaswamy 2021 IEEE 31st International Workshop on Machine Learning for Signal …, 2021 | 19* | 2021 |
| Sequence-Augmented SE (3)-Flow Matching For Conditional Protein Backbone Generation G Huguet, J Vuckovic, K Fatras, E Thibodeau-Laufer, P Lemos, R Islam, ... Thirty-eighth Conference on Neural Information Processing Systems, 2024 | 18 | 2024 |
Smita KrishnaswamyYale UniversityVerificeret mail på yale.edu