| 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 | 632 | 2025 |
| Ranked reward: Enabling self-play reinforcement learning for combinatorial optimization A Laterre, Y Fu, MK Jabri, AS Cohen, D Kas, K Hajjar, TS Dahl, A Kerkeni, ... arXiv preprint arXiv:1807.01672, 2018 | 134 | 2018 |
| 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 | 80 | 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 |
| 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 |
| 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 |
| Qd-rl: Efficient mixing of quality and diversity in reinforcement learning G Cideron, T Pierrot, N Perrin, K Beguir, O Sigaud arXiv preprint arXiv:2006.08505 36, 2020 | 40 | 2020 |
| Progressive loss of conserved spike protein neutralizing antibody sites in Omicron sublineages is balanced by preserved T cell immunity A Muik, BG Lui, J Quandt, H Diao, Y Fu, M Bacher, J Gordon, A Toker, ... Cell Reports 42 (8), 2023 | 38 | 2023 |
| De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments K Eloff, K Kalogeropoulos, O Morell, A Mabona, JB Jespersen, W Williams, ... bioRxiv, 2023.08. 30.555055, 2023 | 32 | 2023 |
| Mava: A research framework for distributed multi-agent reinforcement learning A Pretorius, K ab Tessera, AP Smit, K Eloff, C Formanek, SJ Grimbly, ... arXiv preprint arXiv:2107.01460 5, 2021 | 31* | 2021 |
| 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 | 24 | 2025 |
| InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments K Eloff, K Kalogeropoulos, A Mabona, O Morell, R Catzel, ... Nature Machine Intelligence, 1-15, 2025 | 23 | 2025 |
| Chatnt: A multimodal conversational agent for dna, rna and protein tasks G Richard, BP de Almeida, H Dalla-Torre, C Blum, L Hexemer, P Pandey, ... bioRxiv, 2024.04. 30.591835, 2024 | 20 | 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 |
| A game-theoretic analysis of networked system control for common-pool resource management using multi-agent reinforcement learning A Pretorius, S Cameron, E Van Biljon, T Makkink, S Mawjee, J du Plessis, ... Advances in neural information processing systems 33, 9983-9994, 2020 | 17 | 2020 |
| 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 |
| The nucleotide transformer: Building and evaluating robust foundation models for human genomics. bioRxiv (2023) H Dalla-Torre, L Gonzalez, J Mendoza-Revilla, NL Carranza, ... URL https://www. biorxiv. org/content/10.1101/2023.01 11, v2, 2023 | 12 | 2023 |
| Framedipt: Se (3) diffusion model for protein structure inpainting C Zhang, A Leach, T Makkink, M Arbesú, I Kadri, D Luo, L Mizrahi, ... biorxiv, 2023.11. 21.568057, 2023 | 10 | 2023 |
