Andrea Beccari

According to our database, Andrea Beccari authored at least 41 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

"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.

Candida Manelfi, Valerio Tazzari, Filippo Lunghini, Carmen Cerchia, Anna Fava, Alessandro Pedretti, Pieter F. W. Stouten, Giulio Vistoli, Andrea Rosario Beccari

J. Cheminformatics, December, 2024

Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs.

Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Luigi Crisci, Biagio Cosenza, Andrea Beccari, Gianluca Palermo

J. Supercomput., May, 2024

GPU-optimized approaches to molecular docking-based virtual screening in drug discovery: A comparative analysis.

Emanuele Vitali, Federico Ficarelli, Mauro Bisson, Davide Gadioli, Gianmarco Accordi, Massimiliano Fatica, Andrea Rosario Beccari, Gianluca Palermo

J. Parallel Distributed Comput., April, 2024

Enabling performance portability on the LiGen drug discovery pipeline.

Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Andrea Rosario Beccari

Future Gener. Comput. Syst., 2024

Exploring the future of biopharmaceutical drug discovery: can advanced AI platforms overcome current challenges?

Alberto Bettanti, Andrea Rosario Beccari, Marco Biccarino

Discov. Artif. Intell., 2024

Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers.

Emanuele Triuzzi, Riccardo Mengoni, Domenico Bonanni, Daniele Ottaviani, Andrea Beccari, Gianluca Palermo

CoRR, 2024

A LSTM-enhanced surrogate model to simulate the dynamics of particle-laden fluid systems.

Arash Hajisharifi, Rahul Halder, Michele Girfoglio, Andrea Beccari, Domenico Bonanni, Gianluigi Rozza

CoRR, 2024

A geometric XAI approach to protein pocket detection.

Giovanni Bocchi, Patrizio Frosini, Alessandra Micheletti, Alessandro Pedretti, Gianluca Palermo, Davide Gadioli, Carmen Gratteri, Filippo Lunghini, Andrea Rosario Beccari, Anna Fava, Carmine Talarico

Proceedings of the Joint Proceedings of the xAI 2024 Late-breaking Work, 2024

Unlocking performance portability on LUMI-G supercomputer: A virtual screening case study.

Gianmarco Accordi, Davide Gadioli, Gianluca Palermo, Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Andrea Rosario Beccari

Proceedings of the 12th International Workshop on OpenCL and SYCL, 2024

ZSMILES: An Approach for Efficient SMILES Storage for Random Access in Virtual Screening.

Gianmarco Accordi, Davide Gadioli, Giorgio Seguini, Andrea Rosario Beccari, Gianluca Palermo

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2024

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale.

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

Proceedings of the 21st ACM International Conference on Computing Frontiers, 2024

2023

ProfhEX: AI-based platform for small molecules liability profiling.

Filippo Lunghini, Anna Fava, Vincenzo Pisapia, Francesco Sacco, Daniela Iaconis, Andrea Rosario Beccari

J. Cheminformatics, December, 2023

A non-intrusive data-driven reduced order model for parametrized CFD-DEM numerical simulations.

Arash Hajisharifi, Francesco Romano, Michele Girfoglio, Andrea Beccari, Domenico Bonanni, Gianluigi Rozza

J. Comput. Phys., October, 2023

EXSCALATE: An Extreme-Scale Virtual Screening Platform for Drug Discovery Targeting Polypharmacology to Fight SARS-CoV-2.

Davide Gadioli, Emanuele Vitali, Federico Ficarelli, Chiara Latini, Candida Manelfi, Carmine Talarico, Cristina Silvano, Carlo Cavazzoni, Gianluca Palermo, Andrea Rosario Beccari

IEEE Trans. Emerg. Top. Comput., 2023

Improving computation efficiency using input and architecture features for a virtual screening application.

Gianmarco Accordi, Emanuele Vitali, Davide Gadioli, Luigi Crisci, Biagio Cosenza, Mauro Bisson, Massimiliano Fatica, Andrea Beccari, Gianluca Palermo

CoRR, 2023

Domain-Specific Energy Modeling for Drug Discovery and Magnetohydrodynamics Applications.

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

Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, 2023

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach.

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

Proceedings of the 20th ACM International Conference on Computing Frontiers, 2023

2022

GPU-optimized Approaches to Molecular Docking-based Virtual Screening in Drug Discovery: A Comparative Analysis.

Emanuele Vitali, Federico Ficarelli, Mauro Bisson, Davide Gadioli, Massimiliano Fatica, Andrea Rosario Beccari, Gianluca Palermo

CoRR, 2022

GENEOnet: A new machine learning paradigm based on Group Equivariant Non-Expansive Operators. An application to protein pocket detection.

Giovanni Bocchi, Patrizio Frosini, Alessandra Micheletti, Alessandro Pedretti, Carmen Gratteri, Filippo Lunghini, Andrea Rosario Beccari, Carmine Talarico

CoRR, 2022

Towards a Portable Drug Discovery Pipeline with SYCL 2020.

Luigi Crisci, Majid Salimi Beni, Biagio Cosenza, Nicolò Scipione, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Andrea Beccari

Proceedings of the IWOCL'22: International Workshop on OpenCL, Bristol, United Kingdom, May 10, 2022

An extreme-scale virtual screening platform for drug discovery.

Davide Gadioli, Emanuele Vitali, Federico Ficarelli, Chiara Latini, Candida Manelfi, Carmine Talarico, Cristina Silvano, Andrea Rosario Beccari, Gianluca Palermo

Proceedings of the CF '22: 19th ACM International Conference on Computing Frontiers, Turin, Italy, May 17, 2022

2021

Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App.

Davide Gadioli, Gianluca Palermo, Stefano Cherubin, Emanuele Vitali, Giovanni Agosta, Candida Manelfi, Andrea Rosario Beccari, Carlo Cavazzoni, Nico Sanna, Cristina Silvano

J. Supercomput., 2021

"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool.

Candida Manelfi, Marica Gemei, Carmine Talarico, Carmen Cerchia, Anna Fava, Filippo Lunghini, Andrea Rosario Beccari

J. Cheminformatics, 2021

EXSCALATE: An extreme-scale in-silico virtual screening platform to evaluate 1 trillion compounds in 60 hours on 81 PFLOPS supercomputers.

Davide Gadioli, Emanuele Vitali, Federico Ficarelli, Chiara Latini, Candida Manelfi, Carmine Talarico, Cristina Silvano, Carlo Cavazzoni, Gianluca Palermo, Andrea Rosario Beccari

CoRR, 2021

2019

Exploiting OpenMP and OpenACC to accelerate a geometric approach to molecular docking in heterogeneous HPC nodes.

Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano

J. Supercomput., 2019

The ANTAREX domain specific language for high performance computing.

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

Microprocess. Microsystems, 2019

Exploiting OpenMP & OpenACC to Accelerate a Molecular Docking Mini-App in Heterogeneous HPC Nodes.

Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano

CoRR, 2019

The ANTAREX Domain Specific Language for High Performance Computing.

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

CoRR, 2019

Supporting the Scale-Up of High Performance Application to Pre-Exascale Systems: The ANTAREX Approach.

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

Proceedings of the 27th Euromicro International Conference on Parallel, 2019

An hybrid approach to accelerate a molecular docking application for virtual screening in heterogeneous nodes: POSTER.

Emanuele Vitali, Davide Gadioli, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano, Gianluca Palermo

Proceedings of the 16th ACM International Conference on Computing Frontiers, 2019

2018

ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors.

Matteo Lo Monte, Candida Manelfi, Marica Gemei, Daniela Corda, Andrea Rosario Beccari

Bioinform., 2018

Accelerating a Geometric Approach to Molecular Docking with OpenACC.

Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Cristina Silvano

Proceedings of the 6th International Workshop on Parallelism in Bioinformatics, 2018

ANTAREX: A DSL-Based Approach to Adaptively Optimizing and Enforcing Extra-Functional Properties in High Performance Computing.

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

Proceedings of the 21st Euromicro Conference on Digital System Design, 2018

Autotuning and adaptivity in energy efficient HPC systems: the ANTAREX toolbox.

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

Proceedings of the 15th ACM International Conference on Computing Frontiers, 2018

2017

The ANTAREX tool flow for monitoring and autotuning energy efficient HPC systems.

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

Proceedings of the 2017 International Conference on Embedded Computer Systems: Architectures, 2017

2016

Autotuning and adaptivity approach for energy efficient Exascale HPC systems: The ANTAREX approach.

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

Proceedings of the 2016 Design, Automation & Test in Europe Conference & Exhibition, 2016

The ANTAREX approach to autotuning and adaptivity for energy efficient HPC systems.

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

Proceedings of the ACM International Conference on Computing Frontiers, CF'16, 2016

2015

ANTAREX - AutoTuning and Adaptivity appRoach for Energy Efficient eXascale HPC Systems.

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

Proceedings of the 18th IEEE International Conference on Computational Science and Engineering, 2015

2013

LiGen: A High Performance Workflow for Chemistry Driven de Novo Design.

Andrea Beccari, Carlo Cavazzoni, Claudia Beato, Gabriele Costantino

J. Chem. Inf. Model., 2013

Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program.

Claudia Beato, Andrea Beccari, Carlo Cavazzoni, Simone Lorenzi, Gabriele Costantino

J. Chem. Inf. Model., 2013

2011

Discovering HDAC class II selective inhibitors by multidisciplinary approach.

Simone Lorenzi, Andrea Beccari, D. Carettoni, M. Rubino, Vanessa Nardese

J. Cheminformatics, 2011