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ORCIDAndrea Beccari
Andrea Rosario Beccari
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2020 – today
- 2024
[j15]Luigi Crisci
, Lorenzo Carpentieri, Biagio Cosenza, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Andrea Rosario Beccari:
Enabling performance portability on the LiGen drug discovery pipeline. Future Gener. Comput. Syst. 158: 44-59 (2024)- [j14]Candida Manelfi, Valerio Tazzari, Filippo Lunghini, Carmen Cerchia, Anna Fava, Alessandro Pedretti, Pieter F. W. Stouten, Giulio Vistoli, Andrea Rosario Beccari:
"DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases. J. Cheminformatics 16(1): 21 (2024) - [j13]Emanuele Vitali, Federico Ficarelli, Mauro Bisson, Davide Gadioli, Gianmarco Accordi, Massimiliano Fatica, Andrea Rosario Beccari, Gianluca Palermo:
GPU-optimized approaches to molecular docking-based virtual screening in drug discovery: A comparative analysis. J. Parallel Distributed Comput. 186: 104819 (2024) - [j12]Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Luigi Crisci, Biagio Cosenza, Andrea Beccari, Gianluca Palermo:
Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs. J. Supercomput. 80(8): 11798-11815 (2024) - [c17]Gianluca Palermo, Gianmarco Accordi, Davide Gadioli, Yuedong Zhang, Emanuele Vitali, Bruno Guindani, Danilo Ardagna, Cristina Silvano, Andrea Rosario Beccari, Domenico Bonanni, Carmine Talarico, Filippo Lunghini, Akash Deep Biswas, Jan Martinovic, Martin Golasowski, Paulo Silva, Ada Böhm, Jakub Beránek, Jan Krenek, Branislav Jansik, Peter Thoman, Philip Salzmann, Thomas Fahringer, Torsten Schwede, Leila Tamara Alexander, Gerardo Tauriello, Janani Durairaj, Biagio Cosenza, Luigi Crisci, Andrew Emerson, Federico Ficarelli, Erik Lindahl, Sebastian Wingbermühle, Daniele Gregori, Silvano Coletti, Emanuele Sana, Philipp Gschwandtner:
LIGATE - LIgand Generator and portable drug discovery platform AT Exascale. CF (Companion) 2024 - [c16]Gianmarco Accordi, Davide Gadioli, Giorgio Seguini, Andrea Rosario Beccari, Gianluca Palermo:
ZSMILES: An Approach for Efficient SMILES Storage for Random Access in Virtual Screening. IPDPS (Workshops) 2024: 554-560 - [c15]Gianmarco Accordi, Davide Gadioli, Gianluca Palermo, Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Andrea Rosario Beccari:
Unlocking performance portability on LUMI-G supercomputer: A virtual screening case study. IWOCL 2024: 9:1-9:4 - [c14]Giovanni Bocchi, Patrizio Frosini, Alessandra Micheletti, Alessandro Pedretti, Gianluca Palermo, Davide Gadioli, Carmen Gratteri, Filippo Lunghini, Andrea Rosario Beccari, Anna Fava, Carmine Talarico:
A geometric XAI approach to protein pocket detection. xAI (Late-breaking Work, Demos, Doctoral Consortium) 2024: 217-224 - [i12]Arash Hajisharifi, Rahul Halder, Michele Girfoglio, Andrea Beccari, Domenico Bonanni, Gianluigi Rozza:
A LSTM-enhanced surrogate model to simulate the dynamics of particle-laden fluid systems. CoRR abs/2403.14283 (2024) - [i11]Gianmarco Accordi, Davide Gadioli, Giorgio Seguini, Andrea Rosario Beccari, Gianluca Palermo:
ZSMILES: an approach for efficient SMILES storage for random access in Virtual Screening. CoRR abs/2404.19391 (2024) - [i10]Emanuele Triuzzi, Riccardo Mengoni, Domenico Bonanni, Daniele Ottaviani, Andrea Beccari, Gianluca Palermo:
Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers. CoRR abs/2405.06657 (2024) - 2023
- [j11]Filippo Lunghini, Anna Fava, Vincenzo Pisapia, Francesco Sacco, Daniela Iaconis, Andrea Rosario Beccari:
ProfhEX: AI-based platform for small molecules liability profiling. J. Cheminformatics 15(1): 60 (2023) - [j10]Arash Hajisharifi, Francesco Romano, Michele Girfoglio, Andrea Beccari, Domenico Bonanni, Gianluigi Rozza:
A non-intrusive data-driven reduced order model for parametrized CFD-DEM numerical simulations. J. Comput. Phys. 491: 112355 (2023) - [j9]Davide Gadioli, Emanuele Vitali, Federico Ficarelli, Chiara Latini, Candida Manelfi, Carmine Talarico, Cristina Silvano, Carlo Cavazzoni, Gianluca Palermo, Andrea Rosario Beccari:
EXSCALATE: An Extreme-Scale Virtual Screening Platform for Drug Discovery Targeting Polypharmacology to Fight SARS-CoV-2. IEEE Trans. Emerg. Top. Comput. 11(1): 170-181 (2023) - [c13]Gianluca Palermo, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Cristina Silvano, Bruno Guindani, Danilo Ardagna, Andrea Rosario Beccari, Domenico Bonanni, Carmine Talarico, Filippo Lunghini, Jan Martinovic, Paulo Silva, Ada Bohm, Jakub Beránek, Jan Krenek, Branislav Jansik, Biagio Cosenza, Luigi Crisci, Peter Thoman, Philip Salzmann, Thomas Fahringer, Leila T. Alexander, Gerardo Tauriello, Torsten Schwede, Janani Durairaj, Andrew Emerson, Federico Ficarelli, Sebastian Wingbermühle, Erik Lindahl, Daniele Gregori, Emanuele Sana, Silvano Coletti, Philipp Gschwandtner:
Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. CF 2023: 272-278 - [c12]Lorenzo Carpentieri, Marco D'Antonio, Kaijie Fan, Luigi Crisci, Biagio Cosenza, Federico Ficarelli, Daniele Cesarini, Gianmarco Accordi, Davide Gadioli, Gianluca Palermo, Peter Thoman, Philip Salzmann, Philipp Gschwandtner, Markus Wippler, Filippo Marchetti, Daniele Gregori, Andrea Rosario Beccari:
Domain-Specific Energy Modeling for Drug Discovery and Magnetohydrodynamics Applications. SC Workshops 2023: 1789-1800 - [i9]Arash Hajisharifi, Francesco Romano, Michele Girfoglio, Andrea Beccari, Domenico Bonanni, Gianluigi Rozza:
A Non-Intrusive Data-Driven Reduced Order Model for Parametrized CFD-DEM Numerical Simulations. CoRR abs/2302.12625 (2023) - [i8]Gianmarco Accordi, Emanuele Vitali, Davide Gadioli, Luigi Crisci, Biagio Cosenza, Mauro Bisson, Massimiliano Fatica, Andrea Beccari, Gianluca Palermo:
Improving computation efficiency using input and architecture features for a virtual screening application. CoRR abs/2303.06150 (2023) - [i7]Gianluca Palermo, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Cristina Silvano, Bruno Guindani, Danilo Ardagna, Andrea Rosario Beccari, Domenico Bonanni, Carmine Talarico, Filippo Lunghini, Jan Martinovic, Paulo Silva, Ada Bohm, Jakub Beránek, Jan Krenek, Branislav Jansik, Luigi Crisci, Biagio Cosenza, Peter Thoman, Philip Salzmann, Thomas Fahringer, Leila T. Alexander, Gerardo Tauriello, Torsten Schwede, Janani Durairaj, Andrew Emerson, Federico Ficarelli, Sebastian Wingbermühle, Erik Lindahl, Daniele Gregori, Emanuele Sana, Silvano Coletti, Philipp Gschwandtner:
Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. CoRR abs/2304.09953 (2023) - 2022
- [c11]Davide Gadioli, Emanuele Vitali, Federico Ficarelli, Chiara Latini, Candida Manelfi, Carmine Talarico, Cristina Silvano, Andrea Rosario Beccari, Gianluca Palermo:
An extreme-scale virtual screening platform for drug discovery. CF 2022: 211-212 - [c10]Luigi Crisci, Majid Salimi Beni, Biagio Cosenza, Nicolò Scipione, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Andrea Beccari:
Towards a Portable Drug Discovery Pipeline with SYCL 2020. IWOCL 2022: 5:1-5:2 - [i6]Giovanni Bocchi, Patrizio Frosini, Alessandra Micheletti, Alessandro Pedretti, Carmen Gratteri, Filippo Lunghini, Andrea Rosario Beccari, Carmine Talarico:
GENEOnet: A new machine learning paradigm based on Group Equivariant Non-Expansive Operators. An application to protein pocket detection. CoRR abs/2202.00451 (2022) - [i5]Emanuele Vitali, Federico Ficarelli, Mauro Bisson, Davide Gadioli, Massimiliano Fatica, Andrea Rosario Beccari, Gianluca Palermo:
GPU-optimized Approaches to Molecular Docking-based Virtual Screening in Drug Discovery: A Comparative Analysis. CoRR abs/2209.05069 (2022) - 2021
- [j8]Candida Manelfi, Marica Gemei, Carmine Talarico, Carmen Cerchia, Anna Fava, Filippo Lunghini, Andrea Rosario Beccari:
"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool. J. Cheminformatics 13(1): 54 (2021) - [j7]Davide Gadioli, Gianluca Palermo, Stefano Cherubin, Emanuele Vitali, Giovanni Agosta, Candida Manelfi, Andrea Rosario Beccari, Carlo Cavazzoni, Nico Sanna, Cristina Silvano:
Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App. J. Supercomput. 77(1): 841-869 (2021) - [i4]Davide Gadioli, Emanuele Vitali, Federico Ficarelli, Chiara Latini, Candida Manelfi, Carmine Talarico, Cristina Silvano, Carlo Cavazzoni, Gianluca Palermo, Andrea Rosario Beccari:
EXSCALATE: An extreme-scale in-silico virtual screening platform to evaluate 1 trillion compounds in 60 hours on 81 PFLOPS supercomputers. CoRR abs/2110.11644 (2021)
2010 – 2019
- 2019
- [j6]Cristina Silvano, Giovanni Agosta, Andrea Bartolini, Andrea Rosario Beccari, Luca Benini, Loïc Besnard, João Bispo, Radim Cmar, João M. P. Cardoso, Carlo Cavazzoni, Daniele Cesarini, Stefano Cherubin, Federico Ficarelli, Davide Gadioli, Martin Golasowski, Antonio Libri, Jan Martinovic, Gianluca Palermo, Emanuele Vitali:
The ANTAREX domain specific language for high performance computing. Microprocess. Microsystems 68: 58-73 (2019) - [j5]Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano:
Exploiting OpenMP and OpenACC to accelerate a geometric approach to molecular docking in heterogeneous HPC nodes. J. Supercomput. 75(7): 3374-3396 (2019) - [c9]Emanuele Vitali, Davide Gadioli, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano, Gianluca Palermo:
An hybrid approach to accelerate a molecular docking application for virtual screening in heterogeneous nodes: POSTER. CF 2019: 298-299 - [c8]Cristina Silvano, Giovanni Agosta, Andrea Bartolini, Andrea Rosario Beccari, Luca Benini, Loïc Besnard, João Bispo, Radim Cmar, João M. P. Cardoso, Carlo Cavazzoni, Daniele Cesarini, Stefano Cherubin, Federico Ficarelli, Davide Gadioli, Martin Golasowski, Imane Lasri, Antonio Libri, Candida Manelfi, Jan Martinovic, Gianluca Palermo, Pedro Pinto, Erven Rohou, Nico Sanna, Katerina Slaninová, Emanuele Vitali:
Supporting the Scale-Up of High Performance Application to Pre-Exascale Systems: The ANTAREX Approach. PDP 2019: 116-123 - [i3]Cristina Silvano, Giovanni Agosta, Andrea Bartolini, Andrea Rosario Beccari, Luca Benini, Loïc Besnard, João Bispo, Radim Cmar, João M. P. Cardoso, Carlo Cavazzoni, Daniele Cesarini, Stefano Cherubin, Federico Ficarelli, Davide Gadioli, Martin Golasowski, Antonio Libri, Jan Martinovic, Gianluca Palermo, Pedro Pinto, Erven Rohou, Katerina Slaninová, Emanuele Vitali:
The ANTAREX Domain Specific Language for High Performance Computing. CoRR abs/1901.06175 (2019) - [i2]Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano:
Exploiting OpenMP & OpenACC to Accelerate a Molecular Docking Mini-App in Heterogeneous HPC Nodes. CoRR abs/1901.06229 (2019) - [i1]Davide Gadioli, Gianluca Palermo, Stefano Cherubin, Emanuele Vitali, Giovanni Agosta, Candida Manelfi, Andrea Rosario Beccari, Carlo Cavazzoni, Nico Sanna, Cristina Silvano:
Tunable Approximations to Control Time-to-Solution in an HPC Molecular Docking Mini-App. CoRR abs/1901.06363 (2019) - 2018
- [j4]Matteo Lo Monte, Candida Manelfi, Marica Gemei, Daniela Corda, Andrea Rosario Beccari:
ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors. Bioinform. 34(15): 2566-2574 (2018) - [c7]Cristina Silvano, Gianluca Palermo, Giovanni Agosta, Amir H. Ashouri, Davide Gadioli, Stefano Cherubin, Emanuele Vitali, Luca Benini, Andrea Bartolini, Daniele Cesarini, João M. P. Cardoso, João Bispo, Pedro Pinto, Ricardo Nobre, Erven Rohou, Loïc Besnard, Imane Lasri, Nico Sanna, Carlo Cavazzoni, Radim Cmar, Jan Martinovic, Katerina Slaninová, Martin Golasowski, Andrea Rosario Beccari, Candida Manelfi:
Autotuning and adaptivity in energy efficient HPC systems: the ANTAREX toolbox. CF 2018: 270-275 - [c6]Cristina Silvano, Giovanni Agosta, Andrea Bartolini, Andrea Rosario Beccari, Luca Benini, Loïc Besnard, João Bispo, Radim Cmar, João M. P. Cardoso, Carlo Cavazzoni, Stefano Cherubin, Davide Gadioli, Martin Golasowski, Imane Lasri, Jan Martinovic, Gianluca Palermo, Pedro Pinto, Erven Rohou, Nico Sanna, Katerina Slaninová, Emanuele Vitali:
ANTAREX: A DSL-Based Approach to Adaptively Optimizing and Enforcing Extra-Functional Properties in High Performance Computing. DSD 2018: 600-607 - [c5]Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Cristina Silvano:
Accelerating a Geometric Approach to Molecular Docking with OpenACC. PBio@EuroMPI 2018: 45-51 - 2017
- [c4]Cristina Silvano, Giovanni Agosta, Jorge G. Barbosa, Andrea Bartolini, Andrea Rosario Beccari, Luca Benini, João Bispo, João M. P. Cardoso, Carlo Cavazzoni, Stefano Cherubin, Radim Cmar, Davide Gadioli, Candida Manelfi, Jan Martinovic, Ricardo Nobre, Gianluca Palermo, Martin Palkovic, Pedro Pinto, Erven Rohou, Nico Sanna, Katerina Slaninová:
The ANTAREX tool flow for monitoring and autotuning energy efficient HPC systems. SAMOS 2017: 308-316 - 2016
- [c3]Cristina Silvano, Giovanni Agosta, Stefano Cherubin, Davide Gadioli, Gianluca Palermo, Andrea Bartolini, Luca Benini, Jan Martinovic, Martin Palkovic, Katerina Slaninová, João Bispo, João M. P. Cardoso, Rui Abreu, Pedro Pinto, Carlo Cavazzoni, Nico Sanna, Andrea Rosario Beccari, Radim Cmar, Erven Rohou:
The ANTAREX approach to autotuning and adaptivity for energy efficient HPC systems. Conf. Computing Frontiers 2016: 288-293 - [c2]Cristina Silvano, Giovanni Agosta, Andrea Bartolini, Andrea Rosario Beccari, Luca Benini, João Bispo, Radim Cmar, João M. P. Cardoso, Carlo Cavazzoni, Jan Martinovic, Gianluca Palermo, Martin Palkovic, Pedro Pinto, Erven Rohou, Nico Sanna, Katerina Slaninová:
Autotuning and adaptivity approach for energy efficient Exascale HPC systems: The ANTAREX approach. DATE 2016: 708-713 - 2015
- [c1]Cristina Silvano, Giovanni Agosta, Andrea Bartolini, Andrea Beccari, Luca Benini, João M. P. Cardoso, Carlo Cavazzoni, Radim Cmar, Jan Martinovic, Gianluca Palermo, Martin Palkovic, Erven Rohou, Nico Sanna, Katerina Slaninová:
ANTAREX - AutoTuning and Adaptivity appRoach for Energy Efficient eXascale HPC Systems. CSE 2015: 343-346 - 2013
- [j3]Claudia Beato, Andrea Beccari, Carlo Cavazzoni, Simone Lorenzi, Gabriele Costantino:
Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program. J. Chem. Inf. Model. 53(6): 1503-1517 (2013) - [j2]Andrea Beccari, Carlo Cavazzoni, Claudia Beato, Gabriele Costantino:
LiGen: A High Performance Workflow for Chemistry Driven de Novo Design. J. Chem. Inf. Model. 53(6): 1518-1527 (2013) - 2011
- [j1]Simone Lorenzi, Andrea Beccari, D. Carettoni, M. Rubino, Vanessa Nardese:
Discovering HDAC class II selective inhibitors by multidisciplinary approach. J. Cheminformatics 3(S-1): 2 (2011)
Coauthor Index
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