DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer von Baid, Gunjan, Cook, Daniel E., Shafin, Kishwar, Yun, Taedong, Llinares-López, Felipe, Berthet, Quentin, Belyaeva, Anastasiya, Töpfer, Armin, Wenger, Aaron M., Rowell, William J., Yang, Howard, Kolesnikov, Alexey, Ammar, Waleed, Vert, Jean-Philippe, Vaswani, Ashish, McLean, Cory Y., Nattestad, Maria, Chang, Pi-Chuan, Carroll, Andrew

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graphkernels: R and Python packages for graph comparison von Sugiyama, Mahito, Ghisu, M Elisabetta, Llinares-López, Felipe, Borgwardt, Karsten

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CASMAP: detection of statistically significant combinations of SNPs in association mapping von Llinares-López, Felipe, Papaxanthos, Laetitia, Roqueiro, Damian, Bodenham, Dean, Borgwardt, Karsten

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The Pfam protein families database: embracing AI/ML von Paysan-Lafosse, Typhaine, Andreeva, Antonina, Blum, Matthias, Chuguransky, Sara Rocio, Grego, Tiago, Pinto, Beatriz Lazaro, Salazar, Gustavo A, Bileschi, Maxwell L, Llinares-López, Felipe, Meng-Papaxanthos, Laetitia, Colwell, Lucy J, Grishin, Nick V, Schaeffer, R Dustin, Clementel, Damiano, Tosatto, Silvio C E, Sonhammer, Erik, Wood, Valerie, Bateman, Alex

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Deep embedding and alignment of protein sequences von Llinares-López, Felipe, Berthet, Quentin, Blondel, Mathieu, Teboul, Olivier, Vert, Jean-Philippe

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Genome-wide genetic heterogeneity discovery with categorical covariates von Llinares-López, Felipe, Papaxanthos, Laetitia, Bodenham, Dean, Roqueiro, Damian, Borgwardt, Karsten

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Genome-wide detection of intervals of genetic heterogeneity associated with complex traits von Llinares-López, Felipe, Grimm, Dominik G, Bodenham, Dean A, Gieraths, Udo, Sugiyama, Mahito, Rowan, Beth, Borgwardt, Karsten

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InterPro: the protein sequence classification resource in 2025 von Blum, Matthias, Andreeva, Antonina, Florentino, Laise Cavalcanti, Chuguransky, Sara Rocio, Grego, Tiago, Hobbs, Emma, Pinto, Beatriz Lazaro, Orr, Ailsa, Paysan-Lafosse, Typhaine, Ponamareva, Irina, Salazar, Gustavo A, Bordin, Nicola, Bork, Peer, Bridge, Alan, Colwell, Lucy, Gough, Julian, Haft, Daniel H, Letunic, Ivica, Llinares-López, Felipe, Marchler-Bauer, Aron, Meng-Papaxanthos, Laetitia, Mi, Huaiyu, Natale, Darren A, Orengo, Christine A, Pandurangan, Arun P, Piovesan, Damiano, Rivoire, Catherine, Sigrist, Christian J A, Thanki, Narmada, Thibaud-Nissen, Françoise, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex

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Prediction of human population responses to toxic compounds by a collaborative competition von Eduati, Federica, Mangravite, Lara M, Wang, Tao, Tang, Hao, Bare, J Christopher, Huang, Ruili, Norman, Thea, Kellen, Mike, Menden, Michael P, Yang, Jichen, Zhan, Xiaowei, Zhong, Rui, Xiao, Guanghua, Xia, Menghang, Abdo, Nour, Kosyk, Oksana, Friend, Stephen, Dearry, Allen, Simeonov, Anton, Tice, Raymond R, Rusyn, Ivan, Wright, Fred A, Stolovitzky, Gustavo, Xie, Yang, Saez-Rodriguez, Julio

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Direct antimicrobial resistance prediction from clinical MALDI-TOF mass spectra using machine learning von Weis, Caroline, Cuénod, Aline, Rieck, Bastian, Dubuis, Olivier, Graf, Susanne, Lang, Claudia, Oberle, Michael, Brackmann, Maximilian, Søgaard, Kirstine K., Osthoff, Michael, Borgwardt, Karsten, Egli, Adrian

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Differentiable Clustering with Perturbed Spanning Forests von Stewart, Lawrence, Bach, Francis S, López, Felipe Llinares, Berthet, Quentin

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Implicit Diffusion: Efficient Optimization through Stochastic Sampling von Marion, Pierre, Korba, Anna, Bartlett, Peter, Blondel, Mathieu, De Bortoli, Valentin, Doucet, Arnaud, Llinares-López, Felipe, Paquette, Courtney, Berthet, Quentin

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Learning Energy Networks with Generalized Fenchel-Young Losses von Blondel, Mathieu, Llinares-López, Felipe, Dadashi, Robert, Hussenot, Léonard, Geist, Matthieu

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Differentiable Clustering with Perturbed Spanning Forests von Stewart, Lawrence, Bach, Francis S, Felipe Llinares López, Berthet, Quentin

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Graph Kernels: State-of-the-Art and Future Challenges von Borgwardt, Karsten, Ghisu, Elisabetta, Llinares-López, Felipe, O'Bray, Leslie, Rieck, Bastian

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Efficient and Modular Implicit Differentiation von Blondel, Mathieu, Berthet, Quentin, Cuturi, Marco, Frostig, Roy, Hoyer, Stephan, Llinares-López, Felipe, Pedregosa, Fabian, Vert, Jean-Philippe

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Implicit Diffusion: Efficient Optimization through Stochastic Sampling von Marion, Pierre, Korba, Anna, Bartlett, Peter, Blondel, Mathieu, De Bortoli, Valentin, Doucet, Arnaud, Llinares-López, Felipe, Paquette, Courtney, Berthet, Quentin

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Wasserstein Weisfeiler-Lehman Graph Kernels von Togninalli, Matteo, Ghisu, Elisabetta, Llinares-López, Felipe, Rieck, Bastian, Borgwardt, Karsten

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Learning Energy Networks with Generalized Fenchel-Young Losses von Blondel, Mathieu, Llinares-López, Felipe, Dadashi, Robert, Léonard Hussenot, Geist, Matthieu

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Efficient and Modular Implicit Differentiation von Blondel, Mathieu, Berthet, Quentin, Cuturi, Marco, Frostig, Roy, Hoyer, Stephan, Llinares-López, Felipe, Pedregosa, Fabian, Vert, Jean-Philippe

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