María Rodríguez Martínez

44 papers A* 2A 1B 1Journal 36Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	SurvBoard: standardized benchmarking for multi-omics cancer survival models. Briefings Bioinform. David Wissel, Nikita Janakarajan, Aayush Grover, Enrico Toniato, María Rodríguez Martínez, Valentina Boeva
2024	J	`jnl`	Adaptive Conformal Regression with Split-Jackknife+ Scores. Trans. Mach. Learn. Res. Nicolas Deutschmann, Mattia Rigotti, María Rodríguez Martínez
2024	A*	`conf`	Conformal Autoregressive Generation: Beam Search with Coverage Guarantees. AAAI Nicolas Deutschmann, Marvin Alberts, María Rodríguez Martínez
2024	—	`conf`	HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology. MIDL Elias Baumann, Bastian Dislich, Josef Lorenz Rumberger, Iris D. Nagtegaal, María Rodríguez Martínez, Inti Zlobec
2024	J	`jnl`	Unlearning Information Bottleneck: Machine Unlearning of Systematic Patterns and Biases. CoRR Ling Han, Hao Huang, Dustin Scheinost, Mary-Anne Hartley, María Rodríguez Martínez
2023	J	`jnl`	Adaptive Conformal Regression with Jackknife+ Rescaled Scores. CoRR Nicolas Deutschmann, Mattia Rigotti, María Rodríguez Martínez
2023	A	`conf`	Aligned Diffusion Schrödinger Bridges. UAI Vignesh Ram Somnath, Matteo Pariset, Ya-Ping Hsieh, María Rodríguez Martínez, Andreas Krause, Charlotte Bunne
2023	J	`jnl`	Aligned Diffusion Schrödinger Bridges. CoRR Vignesh Ram Somnath, Matteo Pariset, Ya-Ping Hsieh, María Rodríguez Martínez, Andreas Krause, Charlotte Bunne
2023	J	`jnl`	Conformal Autoregressive Generation: Beam Search with Coverage Guarantees. CoRR Nicolas Deutschmann, Marvin Alberts, María Rodríguez Martínez
2023	J	`jnl`	DockGame: Cooperative Games for Multimeric Rigid Protein Docking. CoRR Vignesh Ram Somnath, Pier Giuseppe Sessa, María Rodríguez Martínez, Andreas Krause
2023	J	`jnl`	FLAN: feature-wise latent additive neural models for biological applications. Briefings Bioinform. An-phi Nguyen, Stefania Vasilaki, María Rodríguez Martínez
2022	—	`conf`	Attention-Based Interpretable Regression of Gene Expression in Histology. iMIMIC@MICCAI Mara Graziani, Niccolò Marini, Nicolas Deutschmann, Nikita Janakarajan, Henning Müller, María Rodríguez Martínez
2022	J	`jnl`	Attention-based Interpretable Regression of Gene Expression in Histology. CoRR Mara Graziani, Niccolò Marini, Nicolas Deutschmann, Nikita Janakarajan, Henning Müller, María Rodríguez Martínez
2022	J	`jnl`	Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. Bioinform. Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
2022	J	`jnl`	DECODE: a computational pipeline to discover T cell receptor binding rules. Bioinform. Iliana Papadopoulou, An-phi Nguyen, Anna Weber, María Rodríguez Martínez
2022	J	`jnl`	Is Attention Interpretation? A Quantitative Assessment On Sets. CoRR Jonathan Haab, Nicolas Deutschmann, María Rodríguez Martínez
2022	—	`conf`	Is Attention Interpretation? A Quantitative Assessment on Sets. PKDD/ECML Workshops (1) Jonathan Haab, Nicolas Deutschmann, María Rodríguez Martínez
2022	J	`jnl`	PCfun: a hybrid computational framework for systematic characterization of protein complex function. Briefings Bioinform. Varun S. Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G. Williams, Zhen Chen, Wenguang Shao, Patrick G. A. Pedrioli, Anthony W. Purcell, María Rodríguez Martínez, Jiangning Song, Matteo Manica, Ruedi Aebersold, Chen Li
2021	J	`jnl`	COSIFER: a Python package for the consensus inference of molecular interaction networks. Bioinform. Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A. Stolovitzky, María Rodríguez Martínez
2021	J	`jnl`	Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2. Mach. Learn. Sci. Technol. Jannis Born, Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius, Nikita Janakarajan, Antonio Cardinale, Teodoro Laino, María Rodríguez Martínez
2021	J	`jnl`	It's FLAN time! Summing feature-wise latent representations for interpretability. CoRR An-phi Nguyen, María Rodríguez Martínez
2021	J	`jnl`	On the feasibility of deep learning applications using raw mass spectrometry data. Bioinform. Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez
2021	J	`jnl`	SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
2021	J	`jnl`	TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks. CoRR Anna Weber, Jannis Born, María Rodríguez Martínez
2021	J	`jnl`	TITAN: T-cell receptor specificity prediction with bimodal attention networks. Bioinform. Anna Weber, Jannis Born, María Rodríguez Martínez
2021	J	`jnl`	The Multiple Dimensions of Networks in Cancer: A Perspective. Symmetry Cristian Axenie, Roman Bauer, María Rodríguez Martínez
2020	J	`jnl`	FPGA Accelerated Analysis of Boolean Gene Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Matteo Manica, Raphael Polig, Mitra Purandare, Roland Mathis, Christoph Hagleitner, María Rodríguez Martínez
2020	J	`jnl`	Learning Invariances for Interpretability using Supervised VAE. CoRR An-phi Nguyen, María Rodríguez Martínez
2020	—	`ed.`	Mathematical and Computational Oncology - Second International Symposium, ISMCO 2020, San Diego, CA, USA, October 8-10, 2020, Proceedings ISMCO George Bebis, Max A. Alekseyev, Heyrim Cho, Jana Gevertz, María Rodríguez Martínez
2020	J	`jnl`	On quantitative aspects of model interpretability. CoRR An-phi Nguyen, María Rodríguez Martínez
2020	B	`conf`	PaccMann RECOMB Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez
2020	J	`jnl`	PaccMann CoRR Jannis Born, Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius, María Rodríguez Martínez
2020	J	`jnl`	PaccMann: a web service for interpretable anticancer compound sensitivity prediction. Nucleic Acids Res. Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
2020	J	`jnl`	Pre-training Protein Language Models with Label-Agnostic Binding Pairs Enhances Performance in Downstream Tasks. CoRR Modestas Filipavicius, Matteo Manica, Joris Cadow, María Rodríguez Martínez
2019	J	`jnl`	Context-specific interaction networks from vector representation of words. Nat. Mach. Intell. Matteo Manica, Roland Mathis, Joris Cadow, María Rodríguez Martínez
2019	J	`jnl`	DeStress: Deep Learning for Unsupervised Identification of Mental Stress in Firefighters from Heart-rate Variability (HRV) Data. CoRR Ali Oskooei, Sophie Mai Chau, Jonas R. M. Weiss, Arvind Sridhar, María Rodríguez Martínez, Bruno Michel
2019	J	`jnl`	MonoNet: Towards Interpretable Models by Learning Monotonic Features. CoRR An-phi Nguyen, María Rodríguez Martínez
2019	J	`jnl`	Reinforcement learning-driven de-novo design of anticancer compounds conditioned on biomolecular profiles. CoRR Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
2019	J	`jnl`	Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders. CoRR Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
2019	J	`jnl`	edGNN: a Simple and Powerful GNN for Directed Labeled Graphs. CoRR Guillaume Jaume, An-phi Nguyen, María Rodríguez Martínez, Jean-Philippe Thiran, Maria Gabrani
2018	J	`jnl`	Inference of the three-dimensional chromatin structure and its temporal behavior. CoRR Bianca-Cristina Cristescu, Zalán Borsos, John Lygeros, María Rodríguez Martínez, Maria Anna Rapsomaniki
2018	J	`jnl`	Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer. CoRR Ali Oskooei, Matteo Manica, Roland Mathis, María Rodríguez Martínez
2018	J	`jnl`	PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks. CoRR Ali Oskooei, Jannis Born, Matteo Manica, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
2016	A*	`conf`	Marginalized Continuous Time Bayesian Networks for Network Reconstruction from Incomplete Observations. AAAI Lukas Studer, Loïc Paulevé, Christoph Zechner, Matthias Reumann, María Rodríguez Martínez, Heinz Koeppl