Academic Publications

2025

Branco, Pedro, et al. “Black-box non-interactive zero knowledge from vector trapdoor hash.” Annual International Conference on the Theory and Applications of Cryptographic Techniques. Cham: Springer Nature Switzerland, 2025.

Aydeniz, Ayhan Alp, et al. “Safe Entropic Agents under Team Constraints.” Proceedings of the 24th International Conference on Autonomous Agents and Multiagent Systems. 2025.

Shah, Pranav NM, Ruben Sanchez-Garcia, and David I. Stuart. “TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms.” Biological Crystallography 81.2 (2025).

Alsaadi, Aymen, et al. “Adaptive Protein Design Protocols and Middleware.” 2025 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2025.

Merzky, Andre, et al. “Scalable Runtime Architecture for Data-driven, Hybrid HPC and ML Workflow Applications.” arXiv preprint arXiv:2503.13343 (2025).

Sorzano, COS, Jimenez A, Mota J, Vilas JV, Maluenda D, Martinez M, Ramirez – Aportela E, et al. ‘Survey of the Analysis of Continuous Conformational Variability of Biological Macromolecules by Electron Microsc opy’. Acta Crystallographica Section F: Structural Biology Communications 75, no. 1 (2019): 19 – 32

Groshev, Milan, Luca Zanzi, Carlos Delgado, Xinyu Li, Antonio de la Oliva, and Xavier Costa-Pérez. “Energy-Aware Joint Orchestration of 5G and Robots: Experimental Testbed and Field Validation.” IEEE Transactions on Network and Service Management, 2025, doi:10.1109/TNSM.2025.3555126.

Calvillo-Fernandez, Adrián, Tome Dimitrovski, Milan Groshev, Ananya Ganesh, Constantine Ayimba, and Antonio de la Oliva. “Attention to Virtualization: Making Network Digital Twins Aware of Network Slicing.” IEEE Network, vol. 39, no. 3, May 2025, pp. 134–139, doi:10.1109/MNET.2025.3552137.

Ferla, Matteo P., et al. “Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology.” Journal of Cheminformatics 17.1 (2025): 4.

Dyballa, Luciano, et al. “Learning dynamic representations of the functional connectome in neurobiological networks.” ArXiv (2024): arXiv-2402.

2024

Ballester-Ripoll, Rafael, and Roxana Bujack. “Entropy Coding Compression of Tree Tensor Networks.” (2025).

Marzari, Luca, et al. “Enumerating safe regions in deep neural networks with provable probabilistic guarantees.” Proceedings of the AAAI Conference on Artificial Intelligence. Vol. 38. No. 19. 2024.

Aydeniz, Ayhan Alp, et al. “Entropy Seeking Constrained Multiagent Reinforcement Learning.” Proceedings of the 23rd International Conference on Autonomous Agents and Multiagent Systems. 2024.

On Stateful Value Factorization in Multi-Agent Reinforcement Learning

Sanchez-Garcia, Ruben, et al. “Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation.” International Journal of Molecular Sciences 25.7 (2024): 3959.

Dyballa, Luciano, et al. “Population encoding of stimulus features along the visual hierarchy.” Proceedings of the National Academy of Sciences 121.4 (2024): e2317773121.

Prohaska, Vera, and Eduardo Castelló Ferrer. “Spice: Smart projection interface for cooking enhancement.” arXiv preprint arXiv:2412.03551 (2024).

2023

Wills, Stephanie, et al. “Fragment merging using a graph database samples different catalogue space than similarity search.” Journal of Chemical Information and Modeling 63.11 (2023): 3423-3437.

Baldoni, Gabriele, Luca Cominardi, Milan Groshev, Antonio de la Oliva, and Antonio Corsaro. “Managing the Far-Edge: Are Today’s Centralized Solutions a Good Fit?” IEEE Consumer Electronics Magazine, vol. 12, no. 3, May 2023, pp. 51–61, doi:10.1109/MCE.2021.3082503.

Sanchez-Garcia, Ruben, et al. “CESPED: A benchmark for supervised particle pose estimation in cryo-EM.” Physical Review Research 6.2 (2024): 023245.

Dyballa, Luciano, and Steven W. Zucker. “IAN: Iterated Adaptive Neighborhoods for manifold learning and dimensionality estimation.” Neural Computation 35.3 (2023): 453-524.

Groshev, Milan, et al. “Edge robotics: Are we ready? An experimental evaluation of current vision and future directions.” Digital Communications and Networks 9.1 (2023): 166-174.

2022

Rafael Ballester-Ripoll and Manuele Leonelli (2022). You only derive once (YODO): Automatic differentiation for efficient sensitivity analysis in Bayesian networks. In Proceedings of the 11th International Conference on Probabilistic Graphical Models (PGM), pp. 169-180. PMLR. 5-7 September 2022, Almería, Spain.

Martín-Pérez, Jorge, Fabrizio Malandrino, Carla-Fabiana Chiasserini, Milan Groshev, and Carlos J. Bernardos. “KPI Guarantees in Network Slicing.” IEEE/ACM Transactions on Networking, vol. 30, no. 2, Apr. 2022, pp. 655–668, doi:10.1109/TNET.2021.3120318.

Zuccotto, M., Piccinelli, M., Castellini, A., Marchesini, E., & Farinelli, A. (2022). Learning state-variable relationships in POMCP: A framework for mobile robots. Frontiers in Robotics and Al, 9, 2296-9144.

Groshev, Milan, Carlos Guimarães, Jorge Martín-Pérez, and Antonio de la Oliva. “Toward Intelligent Cyber-Physical Systems: Digital Twin Meets Artificial Intelligence.” IEEE Communications Magazine, vol. 59, no. 8, Aug. 2021, pp. 14–20, doi:10.1109/MCOM.001.2001237.

Sanchez-Garcia, Ruben, et al. “DeepEMhancer: a deep learning solution for cryo-EM volume post-processing.” Communications biology 4.1 (2021): 874.

Costa, Bruno, et al. “Randomized oblivious transfer for secure multiparty computation in the quantum setting.” Entropy 23.8 (2021): 1001.

Groshev, Milan, Carlos Guimarães, Antonio de la Oliva, and Robert Gazda. “Dissecting the Impact of Information and Communication Technologies on Digital Twins as a Service.” IEEE Access, vol. 9, 2021, pp. 102862–102876, doi:10.1109/ACCESS.2021.3098109.

Sanchez – Garcia R, Segura J, Maluenda D, Sorzano COS, and Carazo JM. ‘MicrographCleaner: A Python Package for Cryo – EM Micrograph Cleaning Using Deep Learning’. Journal of Structural Biology 210, no. 3 (2020): 10749 8.

Segura J, Sanchez – Garcia R, Sorzano COS, and Carazo JM. ‘3DBIONOTES v3.0: Crossing Molecular and Structural Biology Data with Genomic Variations’. Bioinformatics 35, no. 18 (2019): 3512 – 13.

Sorzano, COS, Jimenez A, Mota J, Vilas JV, Maluenda D, Martinez M, Ramirez – Aportela E, et al. ‘Survey of the Analysis of Continuous Conformational Variability of Biological Macromolecules by Electron Microsc opy’. Acta Crystallographica Section F: Structural Biology Communications 75, no. 1 (2019): 19 – 32

Jimenez A, Jonic S, Majtner T, Oton J, Vilas JV, Maluenda D, Mota J, et al. ‘Validation of Electron Microscopy Initial Models via Small Angle X – Ray Scattering Cur ves’. Bioinformatics 35, no. 14 (2019): 2427 – 33.

Sanchez – Garcia R, Sorzano COS., Carazo J M., & Segura, J (2019). BIPSPI: a method for the predicti on of partner – specific protein – protein interfaces. Bioinformatics , 35 , no. 3 (2019): 470 – 477.

Sanchez-Garcia, Ruben, et al. “BIPSPI: a method for the prediction of partner-specific protein–protein interfaces.” Bioinformatics 35.3 (2019): 470-477.

Sorzano COS, Vargas J, Vilas JL, Jimenez – Moreno A, Mot a J, Majtner T, Maluenda D, et al. ‘Swarm Optimization as a Consensus Technique for Electron Microscopy Initial Volume’. Appl. Anal. Optim 2 (2018): 299 – 313.

Sanchez – Garcia R, Segura J, Maluenda D, Carazo JM, and Sorzano COS. ‘Deep Consensus, a Deep Learning – Based Approach for Particle Pruning in Cryo – Electron Microscopy’. IUCrJ 5, no. 6 (2018): 854 – 65.

2025

Aydeniz, Ayhan Alp, et al. “Safe Entropic Agents under Team Constraints.” Proceedings of the 24th International Conference on Autonomous Agents and Multiagent Systems. 2025.

Shah, Pranav NM, Ruben Sanchez-Garcia, and David I. Stuart. “TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms.” Biological Crystallography 81.2 (2025).

Merzky, Andre, et al. “Scalable Runtime Architecture for Data-driven, Hybrid HPC and ML Workflow Applications.” arXiv preprint arXiv:2503.13343 (2025).

Lin, Y., Kopp, R. E., Reedy, A., Turilli, M., Jha, S., and Ashe, E. L.: PaleoSTeHM v1.0: a modern, scalable spatiotemporal hierarchical modeling framework for paleo-environmental data, Geosci. Model Dev., 18, 2609–2637, https://doi.org/10.5194/gmd-18-2609-2025, 2025.

Dyballa, Luciano, et al. “Learning dynamic representations of the functional connectome in neurobiological networks.” ArXiv (2024): arXiv-2402.

2024

Aydeniz, Ayhan Alp, et al. “Entropy Seeking Constrained Multiagent Reinforcement Learning.” Proceedings of the 23rd International Conference on Autonomous Agents and Multiagent Systems. 2024.

On Stateful Value Factorization in Multi-Agent Reinforcement Learning

Alsaadi, Aymen, Shantenu Jha, and Matteo Turilli. “Hydra: Brokering Cloud and HPC Resources to Support the Execution of Heterogeneous Workloads at Scale.” Proceedings of the 14th Workshop on AI and Scientific Computing at Scale using Flexible Computing Infrastructures. 2024.

Dyballa, Luciano, et al. “Population encoding of stimulus features along the visual hierarchy.” Proceedings of the National Academy of Sciences 121.4 (2024): e2317773121.

2023

Sanchez-Garcia, Ruben, et al. “CESPED: A benchmark for supervised particle pose estimation in cryo-EM.” Physical Review Research 6.2 (2024): 023245.

Dyballa, Luciano, and Steven W. Zucker. “IAN: Iterated Adaptive Neighborhoods for manifold learning and dimensionality estimation.” Neural Computation 35.3 (2023): 453-524.

Groshev, Milan, et al. “Edge robotics: Are we ready? An experimental evaluation of current vision and future directions.” Digital Communications and Networks 9.1 (2023): 166-174.

2025

Aydeniz, Ayhan Alp, et al. “Safe Entropic Agents under Team Constraints.” Proceedings of the 24th International Conference on Autonomous Agents and Multiagent Systems. 2025.

de la Jara, Javier Jimenez, et al. “HADAD: Hexagonal A-Star with Differential Algorithm Designed for weather routing.” Ocean Engineering 319 (2025): 120050.

Groshev, Milan, Luca Zanzi, Carlos Delgado, Xinyu Li, Antonio de la Oliva, and Xavier Costa-Pérez. “Energy-Aware Joint Orchestration of 5G and Robots: Experimental Testbed and Field Validation.” IEEE Transactions on Network and Service Management, 2025, doi:10.1109/TNSM.2025.3555126.

Calvillo-Fernandez, Adrián, Tome Dimitrovski, Milan Groshev, Ananya Ganesh, Constantine Ayimba, and Antonio de la Oliva. “Attention to Virtualization: Making Network Digital Twins Aware of Network Slicing.” IEEE Network, vol. 39, no. 3, May 2025, pp. 134–139, doi:10.1109/MNET.2025.3552137.

2024

Branco, Pedro, et al. “Roted: Random oblivious transfer for embedded devices.” IACR Transactions on Cryptographic Hardware and Embedded Systems (2021): 215-238.

2023

Coretti-Sanchez, N., et al. “Urban Mobility Swarms: Towards a Decentralized Autonomous Bicycle-Sharing System.” 2023 IEEE 26th International Conference on Intelligent Transportation Systems (ITSC). IEEE, 2023.

Castelló Ferrer, E., Berman, I., Kapitonov, A., Manaenko, V., Chernyaev, M., & Tarasov, P. (2023). “Gaka-chu: a self-employed autonomous robot artist”. Proceedings of the IEEE International Conference on Robotics and Automation (ICRA), 11583-11589.

Ferrer, Eduardo Castelló. “If blockchain is the solution, robot security is the problem.” Frontiers in Blockchain 6 (2023): 1181820.

Groshev, Milan, et al. “Edge robotics: Are we ready? An experimental evaluation of current vision and future directions.” Digital Communications and Networks 9.1 (2023): 166-174.

2022

Castelló Ferrer, E., Jiménez, E., Lopez-Presa, J. L., & Martín-Rueda, J. (2022). “Following Leaders in Byzantine Multi-Robot Systems by Using Blockchain Technology”. IEEE Transactions on Robotics.

Martín-Pérez, Jorge, Fabrizio Malandrino, Carla-Fabiana Chiasserini, Milan Groshev, and Carlos J. Bernardos. “KPI Guarantees in Network Slicing.” IEEE/ACM Transactions on Networking, vol. 30, no. 2, Apr. 2022, pp. 655–668, doi:10.1109/TNET.2021.3120318.

Groshev, Milan, Carlos Guimarães, Jorge Martín-Pérez, and Antonio de la Oliva. “Toward Intelligent Cyber-Physical Systems: Digital Twin Meets Artificial Intelligence.” IEEE Communications Magazine, vol. 59, no. 8, Aug. 2021, pp. 14–20, doi:10.1109/MCOM.001.2001237.

Castelló Ferrer, E., Hardjono, T., Pentland, A. S., & Dorigo, M. (2021). “Secure and secret cooperation in robotic swarms”. Science Robotics, 4(29), eaaw3739.

Branco, Pedro. “A post-quantum UC-commitment scheme in the global random oracle model from code-based assumptions.” Cryptology ePrint Archive (2019).

Branco, P., Mateus, P., Salema, C., Souto, A. Using Low – Density Parity – Check codes to improve the McEliece cryptosystem. Information Sciences, Volume 510, 2020, Pages 243 – 255, ISSN 0020 – 0 255

Jimenez A, Jonic S, Majtner T, Oton J, Vilas JV, Maluenda D, Mota J, et al. ‘Validation of Electron Microscopy Initial Models via Small Angle X – Ray Scattering Cur ves’. Bioinformatics 35, no. 14 (2019): 2427 – 33.

Castelló Ferrer, Eduardo. “The blockchain: a new framework for robotic swarm systems.” Proceedings of the Future Technologies Conference (FTC) 2018: Volume 2. Springer International Publishing, 2019.

Strobel, Volker, Eduardo Castelló Ferrer, and Marco Dorigo. “Managing byzantine robots via blockchain technology in a swarm robotics collective decision making scenario.” (2018).

Sorzano COS, Vargas J, Vilas JL, Jimenez – Moreno A, Mot a J, Majtner T, Maluenda D, et al. ‘Swarm Optimization as a Consensus Technique for Electron Microscopy Initial Volume’. Appl. Anal. Optim 2 (2018): 299 – 313.

2025

Branco, Pedro, Nico Döttling, and Akshayaram Srinivasan. “Two-Round Maliciously-Secure Oblivious Transfer with Optimal Rate.” Annual International Conference on the Theory and Applications of Cryptographic Techniques. Cham: Springer Nature Switzerland, 2024.

Branco P., Lai R.W.F., Maitra M., Malavolta G., Rahimi A., Woo I.K.Y. (2025) “Traitor Tracing Without Trusted Authority from Registered Functional Encryption.” In Advances in Cryptology – ASIACRYPT 2024, LNCS 15486, Springer, Singapore.

Branco, Pedro, et al. “Black-box non-interactive zero knowledge from vector trapdoor hash.” Annual International Conference on the Theory and Applications of Cryptographic Techniques. Cham: Springer Nature Switzerland, 2025.

Calvillo-Fernandez, Adrián, Tome Dimitrovski, Milan Groshev, Ananya Ganesh, Constantine Ayimba, and Antonio de la Oliva. “Attention to Virtualization: Making Network Digital Twins Aware of Network Slicing.” IEEE Network, vol. 39, no. 3, May 2025, pp. 134–139, doi:10.1109/MNET.2025.3552137.

2024

Marzari, Luca, et al. “Enumerating safe regions in deep neural networks with provable probabilistic guarantees.” Proceedings of the AAAI Conference on Artificial Intelligence. Vol. 38. No. 19. 2024.

Yokelson, Dewi, et al. “Enabling performance observability for heterogeneous hpc workflows with SOMA.” Proceedings of the 53rd International Conference on Parallel Processing. 2024.

Alsaadi, Aymen, Shantenu Jha, and Matteo Turilli. “Hydra: Brokering Cloud and HPC Resources to Support the Execution of Heterogeneous Workloads at Scale.” Proceedings of the 14th Workshop on AI and Scientific Computing at Scale using Flexible Computing Infrastructures. 2024.

2023

Branco P., Döttling N., Lysyanskaya A., Handschuh H. (2023) “A Framework for Statistically Sender-Private OT with Optimal Rate.” In Advances in Cryptology – CRYPTO 2023, LNCS 14081, Springer, Cham. Tags: Security & Privacy, Scientific Computing

2022

Martín-Pérez, Jorge, Fabrizio Malandrino, Carla-Fabiana Chiasserini, Milan Groshev, and Carlos J. Bernardos. “KPI Guarantees in Network Slicing.” IEEE/ACM Transactions on Networking, vol. 30, no. 2, Apr. 2022, pp. 655–668, doi:10.1109/TNET.2021.3120318.

Costa, Bruno, Pedro Branco, Manuel Goulão, Mariano Lemus, and Paulo Mateus. “Randomized Oblivious Transfer for Secure Multiparty Computation in the Quantum Setting.” Entropy, vol. 23, no. 8, 2021, p. 1001.

2025

Seijo, Francisco, et al. “Contrasting state land and fire use policies condition fire regime seasonality and size in two Central Spain forest landscapes.” Land Use Policy 147 (2024): 107338.

Branco, Pedro, Nico Döttling, and Akshayaram Srinivasan. “Two-Round Maliciously-Secure Oblivious Transfer with Optimal Rate.” Annual International Conference on the Theory and Applications of Cryptographic Techniques. Cham: Springer Nature Switzerland, 2024.

Branco, Pedro, et al. “Black-box non-interactive zero knowledge from vector trapdoor hash.” Annual International Conference on the Theory and Applications of Cryptographic Techniques. Cham: Springer Nature Switzerland, 2025.

Shah, Pranav NM, Ruben Sanchez-Garcia, and David I. Stuart. “TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms.” Biological Crystallography 81.2 (2025).

Alsaadi, Aymen, et al. “Adaptive Protein Design Protocols and Middleware.” 2025 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2025.

Merzky, Andre, et al. “Scalable Runtime Architecture for Data-driven, Hybrid HPC and ML Workflow Applications.” arXiv preprint arXiv:2503.13343 (2025).

de la Jara, Javier Jimenez, et al. “HADAD: Hexagonal A-Star with Differential Algorithm Designed for weather routing.” Ocean Engineering 319 (2025): 120050.

Groshev, Milan, Luca Zanzi, Carlos Delgado, Xinyu Li, Antonio de la Oliva, and Xavier Costa-Pérez. “Energy-Aware Joint Orchestration of 5G and Robots: Experimental Testbed and Field Validation.” IEEE Transactions on Network and Service Management, 2025, doi:10.1109/TNSM.2025.3555126.

Seijo, Francisco, et al. “Contrasting state land and fire use policies condition fire regime seasonality and size in two Central Spain forest landscapes.” Land Use Policy 147 (2024): 107338.

Lin, Y., Kopp, R. E., Reedy, A., Turilli, M., Jha, S., and Ashe, E. L.: PaleoSTeHM v1.0: a modern, scalable spatiotemporal hierarchical modeling framework for paleo-environmental data, Geosci. Model Dev., 18, 2609–2637, https://doi.org/10.5194/gmd-18-2609-2025, 2025.

Calvillo-Fernandez, Adrián, Tome Dimitrovski, Milan Groshev, Ananya Ganesh, Constantine Ayimba, and Antonio de la Oliva. “Attention to Virtualization: Making Network Digital Twins Aware of Network Slicing.” IEEE Network, vol. 39, no. 3, May 2025, pp. 134–139, doi:10.1109/MNET.2025.3552137.

Ballester-Ripoll, Rafael. “Computing statistical moments via tensorization of polynomial chaos expansions.” SIAM/ASA Journal on Uncertainty Quantification 12.2 (2024): 289-308.

2024

Marzari, Luca, et al. “Enumerating safe regions in deep neural networks with provable probabilistic guarantees.” Proceedings of the AAAI Conference on Artificial Intelligence. Vol. 38. No. 19. 2024.

On Stateful Value Factorization in Multi-Agent Reinforcement Learning

Yokelson, Dewi, et al. “Enabling performance observability for heterogeneous hpc workflows with SOMA.” Proceedings of the 53rd International Conference on Parallel Processing. 2024.

Alsaadi, Aymen, Shantenu Jha, and Matteo Turilli. “Hydra: Brokering Cloud and HPC Resources to Support the Execution of Heterogeneous Workloads at Scale.” Proceedings of the 14th Workshop on AI and Scientific Computing at Scale using Flexible Computing Infrastructures. 2024.

Prohaska, Vera, and Eduardo Castelló Ferrer. “Spice: Smart projection interface for cooking enhancement.” arXiv preprint arXiv:2412.03551 (2024).

2023

Baldoni, Gabriele, Luca Cominardi, Milan Groshev, Antonio de la Oliva, and Antonio Corsaro. “Managing the Far-Edge: Are Today’s Centralized Solutions a Good Fit?” IEEE Consumer Electronics Magazine, vol. 12, no. 3, May 2023, pp. 51–61, doi:10.1109/MCE.2021.3082503.

Branco P., Döttling N., Lysyanskaya A., Handschuh H. (2023) “A Framework for Statistically Sender-Private OT with Optimal Rate.” In Advances in Cryptology – CRYPTO 2023, LNCS 14081, Springer, Cham. Tags: Security & Privacy, Scientific Computing

Sanchez-Garcia, Ruben, et al. “CESPED: A benchmark for supervised particle pose estimation in cryo-EM.” Physical Review Research 6.2 (2024): 023245.

2022

Martín-Pérez, Jorge, Fabrizio Malandrino, Carla-Fabiana Chiasserini, Milan Groshev, and Carlos J. Bernardos. “KPI Guarantees in Network Slicing.” IEEE/ACM Transactions on Networking, vol. 30, no. 2, Apr. 2022, pp. 655–668, doi:10.1109/TNET.2021.3120318.

Groshev, Milan, Carlos Guimarães, Antonio de la Oliva, and Robert Gazda. “Dissecting the Impact of Information and Communication Technologies on Digital Twins as a Service.” IEEE Access, vol. 9, 2021, pp. 102862–102876, doi:10.1109/ACCESS.2021.3098109.