| Efficient and modular implicit differentiation M Blondel, Q Berthet, M Cuturi, R Frostig, S Hoyer, F Llinares-López, ... Advances in neural information processing systems 35, 5230-5242, 2022 | 281 | 2022 |
| Wasserstein weisfeiler-lehman graph kernels M Togninalli, E Ghisu, F Llinares-López, B Rieck, K Borgwardt Advances in neural information processing systems 32, 2019 | 279 | 2019 |
| Graph kernels: State-of-the-art and future challenges K Borgwardt, E Ghisu, F Llinares-López, L O’Bray, B Rieck Foundations and Trends® in Machine Learning 13 (5-6), 531-712, 2020 | 140 | 2020 |
| Prediction of human population responses to toxic compounds by a collaborative competition F Eduati, LM Mangravite, T Wang, H Tang, JC Bare, R Huang, T Norman, ... Nature biotechnology 33 (9), 933-940, 2015 | 121 | 2015 |
| DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer G Baid, DE Cook, K Shafin, T Yun, F Llinares-López, Q Berthet, ... Nature Biotechnology 41 (2), 232-238, 2023 | 111 | 2023 |
| Direct language model alignment from online ai feedback S Guo, B Zhang, T Liu, T Liu, M Khalman, F Llinares, A Rame, T Mesnard, ... arXiv preprint arXiv:2402.04792, 2024 | 96 | 2024 |
| Fast and memory-efficient significant pattern mining via permutation testing F Llinares-López, M Sugiyama, L Papaxanthos, K Borgwardt Proceedings of the 21th ACM SIGKDD international conference on knowledge …, 2015 | 82 | 2015 |
| graphkernels: R and Python packages for graph comparison M Sugiyama, ME Ghisu, F Llinares-López, K Borgwardt Bioinformatics 34 (3), 530-532, 2018 | 72 | 2018 |
| Significant subgraph mining with multiple testing correction M Sugiyama, FL López, N Kasenburg, KM Borgwardt Proceedings of the 2015 SIAM international conference on data mining, 37-45, 2015 | 59* | 2015 |
| Deep embedding and alignment of protein sequences F Llinares-López, Q Berthet, M Blondel, O Teboul, JP Vert Nature Methods 20 (1), 104-111, 2023 | 49 | 2023 |
| Genome-wide detection of intervals of genetic heterogeneity associated with complex traits F Llinares-López, DG Grimm, DA Bodenham, U Gieraths, M Sugiyama, ... Bioinformatics 31 (12), i240-i249, 2015 | 49 | 2015 |
| Finding significant combinations of features in the presence of categorical covariates L Papaxanthos, F Llinares-López, D Bodenham, K Borgwardt Advances in neural information processing systems 29, 2016 | 39 | 2016 |
| Genome-wide genetic heterogeneity discovery with categorical covariates F Llinares-López, L Papaxanthos, D Bodenham, D Roqueiro, ... Bioinformatics 33 (12), 1820-1828, 2017 | 24 | 2017 |
| Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma Y Liu, M Brossard, C Sarnowski, A Vaysse, M Moffatt, ... Scientific reports 7 (1), 938, 2017 | 21 | 2017 |
| Decoding-time Realignment of Language Models T Liu, S Guo, L Bianco, D Calandriello, Q Berthet, F Llinares, J Hoffmann, ... arXiv preprint arXiv:2402.02992, 2024 | 17 | 2024 |
| Deepconsensus: Gap-aware sequence transformers for sequence correction G Baid, DE Cook, K Shafin, T Yun, F Llinares-Lopez, Q Berthet, ... BioRxiv, 2021.08. 31.458403, 2021 | 15 | 2021 |
| CASMAP: detection of statistically significant combinations of SNPs in association mapping F Llinares-López, L Papaxanthos, D Roqueiro, D Bodenham, K Borgwardt Bioinformatics 35 (15), 2680-2682, 2019 | 14 | 2019 |
| InterPro: the protein sequence classification resource in 2025<? mode longmeta?> M Blum, A Andreeva, LC Florentino, SR Chuguransky, T Grego, E Hobbs, ... Nucleic Acids Research 53 (D1), D444-D456, 2025 | 11 | 2025 |
| Differentiable clustering with perturbed spanning forests L Stewart, F Bach, F Llinares-López, Q Berthet Advances in Neural Information Processing Systems 36, 31158-31176, 2023 | 10 | 2023 |
| The Pfam protein families database: embracing AI/ML T Paysan-Lafosse, A Andreeva, M Blum, SR Chuguransky, T Grego, ... Nucleic acids research 53 (D1), D523-D534, 2025 | 9 | 2025 |
Karsten BorgwardtDirector, Max Planck Institute of BiochemistryAdresse e-mail validée de biochem.mpg.de
