| Nucleotide Transformer: building and evaluating robust foundation models for human genomics H Dalla-Torre, L Gonzalez, J Mendoza-Revilla, N Lopez Carranza, ... Nature Methods 22 (2), 287-297, 2025 | 634 | 2025 |
| Diversity policy gradient for sample efficient quality-diversity optimization T Pierrot, V Macé, F Chalumeau, A Flajolet, G Cideron, K Beguir, A Cully, ... Proceedings of the Genetic and Evolutionary Computation Conference, 1075-1083, 2022 | 116* | 2022 |
| A foundational large language model for edible plant genomes J Mendoza-Revilla, E Trop, L Gonzalez, M Roller, H Dalla-Torre, ... Communications Biology 7 (1), 835, 2024 | 63 | 2024 |
| Simple guidance mechanisms for discrete diffusion models Y Schiff, SS Sahoo, H Phung, G Wang, S Boshar, H Dalla-torre, ... arXiv preprint arXiv:2412.10193, 2024 | 62 | 2024 |
| Multi-objective quality diversity optimization T Pierrot, G Richard, K Beguir, A Cully Proceedings of the genetic and evolutionary computation conference, 139-147, 2022 | 55 | 2022 |
| Learning compositional neural programs with recursive tree search and planning T Pierrot, G Ligner, SE Reed, O Sigaud, N Perrin, A Laterre, D Kas, ... Advances in Neural Information Processing Systems 32, 2019 | 48 | 2019 |
| A multimodal conversational agent for DNA, RNA and protein tasks BP de Almeida, G Richard, H Dalla-Torre, C Blum, L Hexemer, P Pandey, ... Nature Machine Intelligence, 1-14, 2025 | 44* | 2025 |
| Early computational detection of potential high-risk SARS-CoV-2 variants K Beguir, MJ Skwark, Y Fu, T Pierrot, NL Carranza, A Laterre, I Kadri, ... Computers in biology and medicine 155, 106618, 2023 | 44 | 2023 |
| Neuroevolution is a competitive alternative to reinforcement learning for skill discovery F Chalumeau, R Boige, B Lim, V Macé, M Allard, A Flajolet, A Cully, ... arXiv preprint arXiv:2210.03516, 2022 | 37 | 2022 |
| QDax: A library for quality-diversity and population-based algorithms with hardware acceleration F Chalumeau, B Lim, R Boige, M Allard, L Grillotti, M Flageat, V Macé, ... Journal of Machine Learning Research 25 (108), 1-16, 2024 | 34 | 2024 |
| Advancing dna language models: The genomics long-range benchmark CH Kao, E Trop, MK Polen, Y Schiff, BP de Almeida, A Gokaslan, T Pierrot, ... ICLR 2024 Workshop on Machine Learning for Genomics Explorations 5, 2024 | 21* | 2024 |
| Are genomic language models all you need? Exploring genomic language models on protein downstream tasks S Boshar, E Trop, BP de Almeida, L Copoiu, T Pierrot Bioinformatics 40 (9), btae529, 2024 | 19 | 2024 |
| Annotating the genome at single-nucleotide resolution with DNA foundation models BP De Almeida, H Dalla-Torre, G Richard, C Blum, L Hexemer, M Gélard, ... Nature Methods, 1-15, 2025 | 18 | 2025 |
| The quality-diversity transformer: Generating behavior-conditioned trajectories with decision transformers V Macé, R Boige, F Chalumeau, T Pierrot, G Richard, N Perrin-Gilbert Proceedings of the Genetic and Evolutionary Computation Conference, 1221-1229, 2023 | 17 | 2023 |
| Fast population-based reinforcement learning on a single machine A Flajolet, CB Monroc, K Beguir, T Pierrot International Conference on Machine Learning, 6533-6547, 2022 | 16 | 2022 |
| Offline reinforcement learning hands-on L Monier, J Kmec, A Laterre, T Pierrot, V Courgeau, O Sigaud, K Beguir arXiv preprint arXiv:2011.14379, 2020 | 16 | 2020 |
| Learning the language of protein structure B Gaujac, J Donà, L Copoiu, T Atkinson, T Pierrot, TD Barrett arXiv preprint arXiv:2405.15840, 2024 | 15 | 2024 |
| Evolving populations of diverse RL agents with MAP-elites T Pierrot, A Flajolet arXiv preprint arXiv:2303.12803, 2023 | 13 | 2023 |
| First-order and second-order variants of the gradient descent in a unified framework T Pierrot, N Perrin-Gilbert, O Sigaud International Conference on Artificial Neural Networks, 197-208, 2021 | 13 | 2021 |
| Multi-modal transfer learning between biological foundation models JJ Garau-Luis, P Bordes, L Gonzalez, M Roller, B de Almeida, C Blum, ... Advances in Neural Information Processing Systems 37, 78431-78450, 2024 | 12 | 2024 |
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