| Multimodal learning with graphs Y Ektefaie, G Dasoulas, A Noori, M Farhat, M Zitnik Nature Machine Intelligence 5 (4), 340-350, 2023 | 100 | 2023 |
| A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis AG Green, CH Yoon, ML Chen, Y Ektefaie, M Fina, L Freschi, MI Gröschel, ... Nature communications 13, 2022 | 52 | 2022 |
| Globally diverse Mycobacterium tuberculosis resistance acquisition: a retrospective geographical and temporal analysis of whole genome sequences Y Ektefaie, A Dixit, L Freschi, MR Farhat The Lancet Microbe 2 (3), e96-e104, 2021 | 44 | 2021 |
| Empowering biomedical discovery with AI agents S Gao, A Fang, Y Huang, V Giunchiglia, A Noori, JR Schwarz, Y Ektefaie, ... Cell 187 (22), 6125-6151, 2024 | 43 | 2024 |
| Integrative multiomics-histopathology analysis for breast cancer classification Y Ektefaie, W Yuan, DA Dillon, NU Lin, JA Golden, IS Kohane, KH Yu NPJ Breast Cancer 7 (1), 147, 2021 | 30 | 2021 |
| Evaluating generalizability of artificial intelligence models for molecular datasets Y Ektefaie, A Shen, D Bykova, MG Marin, M Zitnik, M Farhat Nature Machine Intelligence 6 (12), 1512-1524, 2024 | 8 | 2024 |
| PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction A Wenteler, M Occhetta, N Branson, M Huebner, V Curean, W Dee, ... bioRxiv, 2024.10. 02.616248, 2024 | 5 | 2024 |
| Enriching the study population for ischemic stroke therapeutic trials using a machine learning algorithm J Maharjan, Y Ektefaie, L Ryan, S Mataraso, G Barnes, S Shokouhi, ... Frontiers in Neurology 12, 784250, 2022 | 5 | 2022 |
| 1397. Modern Lineages of Mycobacterium tuberculosis Were Recently Introduced in Western India and Demonstrate Increased Transmissibility A Dixit, A Kagal, Y Ektefaie, L Freschi, R Lokhande, M Groeschel, ... Open Forum Infectious Diseases 8 (Supplement_1), S783-S784, 2021 | 3 | 2021 |
| Percent of lung involved in disease on chest X-ray predicts unfavorable treatment outcome in pulmonary tuberculosis M Ghanem, R Srivastava, Y Ektefaie, D Hoppes, G Rosenfeld, Z Yaniv, ... medRxiv, 2024.08. 19.24311411, 2024 | 2 | 2024 |
| Is ignorance bliss? the role of post hoc explanation faithfulness and alignment in model trust in laypeople and domain experts T Han, Y Ektefaie, M Farhat, M Zitnik, H Lakkaraju arXiv preprint arXiv:2312.05690, 2023 | 2 | 2023 |
| Sa102 A MACHINE LEARNING ALGORITHM TO PREDICT GASTROINTESTINAL BLEEDING REQUIRING INTERVENTION A Allen, Y Ektefaie, A Garikipati, C Lam, A Green-Saxena, A Siefkas, ... Gastroenterology 160 (6), S-422, 2021 | 2 | 2021 |
| Tuberculosis resistance acquisition in space and time: an analysis of globally diverse M. tuberculosis whole genome sequences Y Ektefaie, A Dixit, L Freschi, M Farhat bioRxiv, 837096, 2019 | 2 | 2019 |
| Drug Resistance and Epidemiological Success of Modern Mycobacterium tuberculosis Lineages in Western India A Dixit, Y Ektefaie, A Kagal, L Freschi, R Karyakarte, R Lokhande, ... The Journal of Infectious Diseases 231 (1), 84-93, 2025 | 1 | 2025 |
| Systematic review and meta-analysis of protocols and yield of direct from sputum sequencing of Mycobacterium tuberculosis BC Mann, J Loubser, S Omar, C Glanz, Y Ektefaie, KR Jacobson, ... bioRxiv, 2024.12. 04.625621, 2024 | 1 | 2024 |
| Controllable Sequence Editing for Counterfactual Generation MM Li, K Li, Y Ektefaie, S Messica, M Zitnik arXiv preprint arXiv:2502.03569, 2025 | | 2025 |
| Phyla: Towards a Foundation Model for Phylogenetic Inference A Shen, Y Ektefaie, L Jain, MR Farhat, M Zitnik bioRxiv, 2025.01. 17.633626, 2025 | | 2025 |
| Reinforcement learning on structure-conditioned categorical diffusion for protein inverse folding Y Ektefaie, O Viessmann, S Narayanan, D Dresser, JM Kim, A Mkrtchyan arXiv preprint arXiv:2410.17173, 2024 | | 2024 |
| ProCyon: A multimodal foundation model for protein phenotypes O Queen, Y Huang, R Calef, V Giunchiglia, T Chen, G Dasoulas, LA Tai, ... bioRxiv, 2024.12. 10.627665, 2024 | | 2024 |
| Geometric multimodal representation learning Y Ektefaie, G Dasoulas, A Noori, M Farhat, M Zitnik arXiv preprint arXiv:2209.03299, 2022 | | 2022 |
