Daniela Besozzi

88 papers B 15C 7Misc 1Journal 43Unranked 20

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Local manipulations of the fitness landscape mitigate stall in particle swarm optimization. Appl. Soft Comput. Mario Marino, Daniele M. Papetti, Daniela Besozzi, Marco S. Nobile
2025	J	`jnl`	Expert-Guided POMDP Learning for Data-Efficient Modeling in Healthcare. CoRR Marco Locatelli, Arjen Hommersom, Roberto Clemens Cerioli, Daniela Besozzi, Fabio Stella
2025	—	`conf`	We Are Sending You Back... to the Optimum! Fuzzy Time Travel Particle Swarm Optimization. EvoApplications (2) Daniele M. Papetti, Andrea Tangherloni, Vasco Coelho, Daniela Besozzi, Paolo Cazzaniga, Marco S. Nobile
2024	—	`conf`	Reinforcement Learning and Fuzzy Logic Modelling for Personalized Dynamic Treatment. HC@AIxIA Marco Locatelli, Roberto Clemens Cerioli, Daniela Besozzi, Arjen Hommersom, Fabio Stella
2023	J	`jnl`	An accurate and time-efficient deep learning-based system for automated segmentation and reporting of cardiac magnetic resonance-detected ischemic scar. Comput. Methods Programs Biomed. Daniele M. Papetti, Kirsten van Abeelen, Rhodri H. Davies, Roberto Menè, Francesca Heilbron, Francesco P. Perelli, Jessica Artico, Andreas Seraphim, James C. Moon, Gianfranco Parati, Hui Xue, Peter Kellman, Luigi P. Badano, Daniela Besozzi, Marco S. Nobile, Camilla Torlasco
2023	J	`jnl`	Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning. Frontiers Bioinform. Daniele M. Papetti, Simone Spolaor, Iman Nazari, Andrea Tirelli, Tommaso Leonardi, Chiara Caprioli, Daniela Besozzi, Thalia Vlachou, Pier Giuseppe Pelicci, Paolo Cazzaniga, Marco S. Nobile
2023	B	`conf`	The Domination Game: Dilating Bubbles to Fill Up Pareto Fronts. CEC Vasco Coelho, Daniele M. Papetti, Andrea Tangherloni, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile
2023	J	`jnl`	Unsupervised neural networks as a support tool for pathology diagnosis in MALDI-MSI experiments: A case study on thyroid biopsies. Expert Syst. Appl. Marco S. Nobile, Giulia Capitoli, Virgil Sowirono, Francesca Clerici, Isabella Piga, Kirsten van Abeelen, Fulvio Magni, Fabio Pagni, Stefania Galimberti, Paolo Cazzaniga, Daniela Besozzi
2022	C	`conf`	Local Bubble Dilation Functions: Hypersphere-bounded Landscape Deformations Simplify Global Optimization. CIBCB Daniele M. Papetti, Vasco Coelho, Daniel A. Ashlock, Paolo Cazzaniga, Simone Spolaor, Daniela Besozzi, Marco S. Nobile
2022	J	`jnl`	SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks. Symmetry Simone G. Riva, Paolo Cazzaniga, Marco S. Nobile, Simone Spolaor, Leonardo Rundo, Daniela Besozzi, Andrea Tangherloni
2021	C	`conf`	A comparison of multi-objective optimization algorithms to identify drug target combinations. CIBCB Simone Spolaor, Daniele M. Papetti, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile
2021	J	`jnl`	Analysis of single-cell RNA sequencing data based on autoencoders. BMC Bioinform. Andrea Tangherloni, Federico Ricciuti, Daniela Besozzi, Pietro Liò, Ana Cvejic
2021	J	`jnl`	FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks. PLoS Comput. Biol. Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Giulia Capitoli, Simone Spolaor, Leonardo Rundo, Giancarlo Mauri, Daniela Besozzi
2021	B	`conf`	If You Can't Beat It, Squash It: Simplify Global Optimization by Evolving Dilation Functions. CEC Daniele M. Papetti, Daniel A. Ashlock, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile
2021	J	`jnl`	Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics. BMC Bioinform. Paolo Cazzaniga, Maria Raposo, Daniela Besozzi, Ivan Merelli, Antonino Staiano, Angelo Ciaramella, Riccardo Rizzo, Luca Manzoni
2021	B	`conf`	The Impact of Representation on the Optimization of Marker Panels for Single-cell RNA Data. CEC Andrea Tangherloni, Simone G. Riva, Simone Spolaor, Daniela Besozzi, Marco S. Nobile, Paolo Cazzaniga
2020	—	`ed.`	Computational Intelligence Methods for Bioinformatics and Biostatistics - 16th International Meeting, CIBB 2019, Bergamo, Italy, September 4-6, 2019, Revised Selected Papers CIBB Paolo Cazzaniga, Daniela Besozzi, Ivan Merelli, Luca Manzoni
2020	J	`jnl`	Computational Intelligence for Life Sciences. Fundam. Informaticae Daniela Besozzi, Luca Manzoni, Marco S. Nobile, Simone Spolaor, Mauro Castelli, Leonardo Vanneschi, Paolo Cazzaniga, Stefano Ruberto, Leonardo Rundo, Andrea Tangherloni
2020	J	`jnl`	Coupling Mechanistic Approaches and Fuzzy Logic to Model and Simulate Complex Systems. IEEE Trans. Fuzzy Syst. Simone Spolaor, Marco S. Nobile, Giancarlo Mauri, Paolo Cazzaniga, Daniela Besozzi
2020	C	`conf`	Fourier Surrogate Models of Dilated Fitness Landscapes in Systems Biology : or how we learned to torture optimization problems until they confess. CIBCB Marco S. Nobile, Paolo Cazzaniga, Simone Spolaor, Daniela Besozzi, Luca Manzoni
2020	J	`jnl`	Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. Bioinform. Marco S. Nobile, Giuseppina Votta, Roberta Palorini, Simone Spolaor, Humberto De Vitto, Paolo Cazzaniga, Francesca Ricciardiello, Giancarlo Mauri, Lilia Alberghina, Ferdinando Chiaradonna, Daniela Besozzi
2020	B	`conf`	On the automatic calibration of fully analogical spiking neuromorphic chips. IJCNN Daniele M. Papetti, Simone Spolaor, Daniela Besozzi, Paolo Cazzaniga, Marco Antoniotti, Marco S. Nobile
2020	J	`jnl`	Simpful: A User-Friendly Python Library for Fuzzy Logic. Int. J. Comput. Intell. Syst. Simone Spolaor, Caro Fuchs, Paolo Cazzaniga, Uzay Kaymak, Daniela Besozzi, Marco S. Nobile
2020	J	`jnl`	Surfing on Fitness Landscapes: A Boost on Optimization by Fourier Surrogate Modeling. Entropy Luca Manzoni, Daniele M. Papetti, Paolo Cazzaniga, Simone Spolaor, Giancarlo Mauri, Daniela Besozzi, Marco S. Nobile
2020	B	`conf`	Which random is the best random? A study on sampling methods in Fourier surrogate modeling. CEC Marco S. Nobile, Simone Spolaor, Paolo Cazzaniga, Daniele M. Papetti, Daniela Besozzi, Daniel A. Ashlock, Luca Manzoni
2020	J	`jnl`	cuProCell: GPU-Accelerated Analysis of Cell Proliferation With Flow Cytometry Data. IEEE J. Biomed. Health Informatics Marco S. Nobile, Eric Nisoli, Thalia Vlachou, Simone Spolaor, Paolo Cazzaniga, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi
2019	J	`jnl`	A novel framework for MR image segmentation and quantification by using MedGA. Comput. Methods Programs Biomed. Leonardo Rundo, Andrea Tangherloni, Paolo Cazzaniga, Marco S. Nobile, Giorgio Russo, Maria Carla Gilardi, Salvatore Vitabile, Giancarlo Mauri, Daniela Besozzi, Carmelo Militello
2019	J	`jnl`	Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design. Appl. Soft Comput. Andrea Tangherloni, Simone Spolaor, Paolo Cazzaniga, Daniela Besozzi, Leonardo Rundo, Giancarlo Mauri, Marco S. Nobile
2019	J	`jnl`	GenHap: a novel computational method based on genetic algorithms for haplotype assembly. BMC Bioinform. Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli, Daniela Besozzi
2019	J	`jnl`	MedGA: A novel evolutionary method for image enhancement in medical imaging systems. Expert Syst. Appl. Leonardo Rundo, Andrea Tangherloni, Marco S. Nobile, Carmelo Militello, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga
2019	J	`jnl`	Modeling cell proliferation in human acute myeloid leukemia xenografts. Bioinform. Marco S. Nobile, Thalia Vlachou, Simone Spolaor, Daniela Bossi, Paolo Cazzaniga, Luisa Lanfrancone, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi
2019	C	`conf`	ProCell: Investigating cell proliferation with Swarm Intelligence. CIBCB Marco S. Nobile, Thalia Vlachou, Simone Spolaor, Paolo Cazzaniga, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi
2019	J	`jnl`	USE-Net: Incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets. Neurocomputing Leonardo Rundo, Changhee Han, Yudai Nagano, Jin Zhang, Ryuichiro Hataya, Carmelo Militello, Andrea Tangherloni, Marco S. Nobile, Claudio Ferretti, Daniela Besozzi, Maria Carla Gilardi, Salvatore Vitabile, Giancarlo Mauri, Hideki Nakayama, Paolo Cazzaniga
2019	J	`jnl`	USE-Net: incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets. CoRR Leonardo Rundo, Changhee Han, Yudai Nagano, Jin Zhang, Ryuichiro Hataya, Carmelo Militello, Andrea Tangherloni, Marco S. Nobile, Claudio Ferretti, Daniela Besozzi, Maria Carla Gilardi, Salvatore Vitabile, Giancarlo Mauri, Hideki Nakayama, Paolo Cazzaniga
2019	J	`jnl`	ginSODA: massive parallel integration of stiff ODE systems on GPUs. J. Supercomput. Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
2018	B	`conf`	Computational Intelligence for Parameter Estimation of Biochemical Systems. CEC Marco S. Nobile, Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga
2018	—	`conf`	Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization. CIBB Niccoló Totis, Andrea Tangherloni, Marco Beccuti, Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Marzio Pennisi, Francesco Pappalardo
2018	J	`jnl`	Fuzzy Self-Tuning PSO: A settings-free algorithm for global optimization. Swarm Evol. Comput. Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Riccardo Colombo, Giancarlo Mauri, Gabriella Pasi
2018	—	`conf`	GPU Accelerated Analysis of Treg-Teff Cross Regulation in Relapsing-Remitting Multiple Sclerosis. Euro-Par Workshops Marco Beccuti, Paolo Cazzaniga, Marzio Pennisi, Daniela Besozzi, Marco S. Nobile, Simone Pernice, Giulia Russo, Andrea Tangherloni, Francesco Pappalardo
2018	—	`conf`	High Performance Computing for Haplotyping: Models and Platforms. Euro-Par Workshops Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, Marco S. Nobile, Ivan Merelli, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Pietro Liò
2017	J	`jnl`	Efficient Simulation of Reaction Systems on Graphics Processing Units. Fundam. Informaticae Marco S. Nobile, Antonio E. Porreca, Simone Spolaor, Luca Manzoni, Paolo Cazzaniga, Giancarlo Mauri, Daniela Besozzi
2017	J	`jnl`	GPU-powered model analysis with PySB/cupSODA. Bioinform. Leonard A. Harris, Marco S. Nobile, James C. Pino, Alexander L. R. Lubbock, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Carlos F. Lopez
2017	J	`jnl`	GenHap: A novel computational method based on genetic algorithms for haplotype assembly. PeerJ Prepr. Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Ivan Merelli, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri, Pietro Liò
2017	J	`jnl`	Gillespie's Stochastic Simulation Algorithm on MIC coprocessors. J. Supercomput. Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
2017	J	`jnl`	Graphics processing units in bioinformatics, computational biology and systems biology. Briefings Bioinform. Marco S. Nobile, Paolo Cazzaniga, Andrea Tangherloni, Daniela Besozzi
2017	J	`jnl`	LASSIE: simulating large-scale models of biochemical systems on GPUs. BMC Bioinform. Andrea Tangherloni, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga
2016	B	`conf`	GPU-powered and settings-free parameter estimation of biochemical systems. CEC Marco S. Nobile, Andrea Tangherloni, Daniela Besozzi, Paolo Cazzaniga
2016	C	`conf`	Reaction-Based Models of Biochemical Networks. CiE Daniela Besozzi
2015	B	`conf`	Parallelizing Biochemical Stochastic Simulations: A Comparison of GPUs and Intel Xeon Phi Processors. PaCT Paolo Cazzaniga, F. Ferrara, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri
2015	B	`conf`	Proactive Particles in Swarm Optimization: A self-tuning algorithm based on Fuzzy Logic. FUZZ-IEEE Marco S. Nobile, Gabriella Pasi, Paolo Cazzaniga, Daniela Besozzi, Riccardo Colombo, Giancarlo Mauri
2015	C	`conf`	The impact of particles initialization in PSO: Parameter estimation as a case in point. CIBCB Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi
2014	B	`conf`	A memetic hybrid method for the Molecular Distance Geometry Problem with incomplete information. IEEE Congress on Evolutionary Computation Marco S. Nobile, Andrea G. Citrolo, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
2014	J	`jnl`	GPU-accelerated simulations of mass-action kinetics models with cupSODA. J. Supercomput. Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
2014	C	`conf`	Simulation and Analysis of the Blood Coagulation Cascade Accelerated on GPU. PDP Matteo Bellini, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Marco S. Nobile
2013	—	`conf`	GPU-powered Simulation Methodologies for Biological Systems. WIVACE Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco S. Nobile, Dario Pescini, Alessandro Re
2013	J	`jnl`	In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. BMC Syst. Biol. Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, Dario Pescini, Attila Csikász-Nagy, Marco Falconi, Daniela Besozzi, Paolo Plevani
2013	B	`conf`	Reverse engineering of kinetic reaction networks by means of Cartesian Genetic Programming and Particle Swarm Optimization. IEEE Congress on Evolutionary Computation Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
2013	—	`conf`	The foundation of Evolutionary Petri Nets. BioPPN@Petri Nets Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri
2013	B	`conf`	cupSODA: A CUDA-Powered Simulator of Mass-Action Kinetics. PaCT Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
2012	—	`conf`	A GPU-Based Multi-swarm PSO Method for Parameter Estimation in Stochastic Biological Systems Exploiting Discrete-Time Target Series. EvoBIO Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
2012	J	`jnl`	An excursion in reaction systems: From computer science to biology. Theor. Comput. Sci. Luca Corolli, Carlo Maj, Fabrizio Marini, Daniela Besozzi, Giancarlo Mauri
2012	—	`conf`	Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs. GECCO (Companion) Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
2012	J	`jnl`	The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae. EURASIP J. Bioinform. Syst. Biol. Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Sonia Colombo, Enzo Martegani
2011	J	`jnl`	Modeling Diffusion in a Signal Transduction Pathway: the Use of Virtual Volumes in P Systems. Int. J. Found. Comput. Sci. Daniela Besozzi, Paolo Cazzaniga, Stefania Cocolo, Giancarlo Mauri, Dario Pescini
2010	—	`conf`	An Analysis on the Influence of Network Topologies on Local and Global Dynamics of Metapopulation Systems AMCA-POP Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
2010	—	`conf`	BioSimWare: A Software for the Modeling, Simulation and Analysis of Biological Systems. Int. Conf. on Membrane Computing Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
2010	J	`jnl`	Computing with energy and chemical reactions. Nat. Comput. Alberto Leporati, Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Claudio Ferretti
2009	J	`jnl`	(Tissue) P systems with cell polarity. Math. Struct. Comput. Sci. Daniela Besozzi, Nadia Busi, Paolo Cazzaniga, Claudio Ferretti, Alberto Leporati, Giancarlo Mauri, Dario Pescini, Claudio Zandron
2009	—	`conf`	A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems. EvoBIO Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini, Leonardo Vanneschi
2009	—	`conf`	A Multi-volume Approach to Stochastic Modeling with Membrane Systems. Algorithmic Bioprocesses Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
2009	—	`conf`	A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis COMPMOD Daniela Besozzi, Paolo Cazzaniga, Matteo Dugo, Dario Pescini, Giancarlo Mauri
2008	J	`jnl`	Modelling metapopulations with stochastic membrane systems. Biosyst. Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
2007	J	`jnl`	Cycles and communicating classes in membrane systems and molecular dynamics. Theor. Comput. Sci. Michael Muskulus, Daniela Besozzi, Robert Brijder, Paolo Cazzaniga, Sanne Houweling, Dario Pescini, Grzegorz Rozenberg
2006	J	`jnl`	Dynamical probabilistic P systems. Int. J. Found. Comput. Sci. Dario Pescini, Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
2006	—	`conf`	Formalizing Spherical Membrane Structures and Membrane Proteins Populations. Workshop on Membrane Computing Daniela Besozzi, Grzegorz Rozenberg
2006	—	`ch.`	P System Models for Mechanosensitive Channels. Applications of Membrane Computing Ioan I. Ardelean, Daniela Besozzi, Max H. Garzon, Giancarlo Mauri, Sujoy Roy
2006	—	`conf`	Tau Leaping Stochastic Simulation Method in P Systems. Workshop on Membrane Computing Paolo Cazzaniga, Dario Pescini, Daniela Besozzi, Giancarlo Mauri
2005	B	`conf`	Analysis and Simulation of Dynamics in Probabilistic P Systems. DNA Dario Pescini, Daniela Besozzi, Claudio Zandron, Giancarlo Mauri
2005	Misc	`conf`	Investigating Local Evolutions in Dynamical Probabilistic P Systems. SYNASC Dario Pescini, Daniela Besozzi, Giancarlo Mauri
2005	J	`jnl`	On the power and size of extended gemmating P systems. Soft Comput. Daniela Besozzi, Erzsébet Csuhaj-Varjú, Giancarlo Mauri, Claudio Zandron
2004	—	`conf`	A P System Description of the Sodium-Potassium Pump. Workshop on Membrane Computing Daniela Besozzi, Gabriel Ciobanu
2004	J	`jnl`	Hierarchies of Parallel Rewriting P Systems - A Survey. New Gener. Comput. Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
2003	—	`conf`	Collapsing Hierarchies of Parallel Rewriting P Systems without Target Conflicts. Workshop on Membrane Computing Daniela Besozzi, Giancarlo Mauri, György Vaszil, Claudio Zandron
2003	B	`conf`	Deadlock Decidability in Partial Parallel P Systems. DNA Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
2003	J	`jnl`	Gemmating P systems: collapsing hierarchies. Theor. Comput. Sci. Daniela Besozzi, Giancarlo Mauri, Gheorghe Paun, Claudio Zandron
2002	B	`conf`	Parallel Rewriting P Systems with Deadlock. DNA Daniela Besozzi, Claudio Ferretti, Giancarlo Mauri, Claudio Zandron
2002	—	`conf`	Parallel Rewriting P Systems without Target Conflicts. WMC-CdeA Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
2001	—	`conf`	P Systems with Gemmation of Mobile Membranes. ICTCS Daniela Besozzi, Claudio Zandron, Giancarlo Mauri, Nicoletta Sabadini