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Simone Spolaor

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2020 – today

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2023
[j14]
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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:
Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning. Frontiers Bioinform. 3 (2023)
[j13]
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  - journals/ploscb/ChiccoSN23
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Davide Chicco, Simone Spolaor, Marco S. Nobile:
Ten quick tips for fuzzy logic modeling of biomedical systems. PLoS Comput. Biol. 19(12) (2023)
2022
[j12]
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  - journals/symmetry/RivaCNSRBT22
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Simone G. Riva, Paolo Cazzaniga, Marco S. Nobile, Simone Spolaor, Leonardo Rundo, Daniela Besozzi, Andrea Tangherloni:
SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks. Symmetry 14(1): 119 (2022)
[c18]
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Caro Fuchs, Simone Spolaor, Uzay Kaymak, Marco S. Nobile:
The Impact of Variable Selection and Transformation on the Interpretability and Accuracy of Fuzzy Models. CIBCB 2022: 1-8
[c17]
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Daniele M. Papetti, Vasco Coelho, Daniel A. Ashlock, Paolo Cazzaniga, Simone Spolaor, Daniela Besozzi, Marco S. Nobile:
Local Bubble Dilation Functions: Hypersphere-bounded Landscape Deformations Simplify Global Optimization. CIBCB 2022: 1-8
2021
[j11]
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  - journals/ploscb/TangherloniNCCS21
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Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Giulia Capitoli, Simone Spolaor, Leonardo Rundo, Giancarlo Mauri, Daniela Besozzi:
FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks. PLoS Comput. Biol. 17(9) (2021)
[c16]
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Andrea Tangherloni, Simone G. Riva, Simone Spolaor, Daniela Besozzi, Marco S. Nobile, Paolo Cazzaniga:
The Impact of Representation on the Optimization of Marker Panels for Single-cell RNA Data. CEC 2021: 1423-1430
[c15]
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Simone Spolaor, Daniele M. Papetti, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile:
A comparison of multi-objective optimization algorithms to identify drug target combinations. CIBCB 2021: 1-8
2020
[b1]
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Simone Spolaor:
Fuzzy logic for the modeling and simulation of complex systems. University of Milan, Italy, 2020
[j10]
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  - journals/bioinformatics/NobileVPSVCRMAC20
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Marco S. Nobile, Giuseppina Votta, Roberta Palorini, Simone Spolaor, Humberto De Vitto, Paolo Cazzaniga, Francesca Ricciardiello, Giancarlo Mauri, Lilia Alberghina, Ferdinando Chiaradonna, Daniela Besozzi:
Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. Bioinform. 36(7): 2181-2188 (2020)
[j9]
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  - journals/entropy/ManzoniPCSMBN20
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Luca Manzoni, Daniele M. Papetti, Paolo Cazzaniga, Simone Spolaor, Giancarlo Mauri, Daniela Besozzi, Marco S. Nobile:
Surfing on Fitness Landscapes: A Boost on Optimization by Fourier Surrogate Modeling. Entropy 22(3): 285 (2020)
[j8]
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Daniela Besozzi, Luca Manzoni, Marco S. Nobile, Simone Spolaor, Mauro Castelli, Leonardo Vanneschi, Paolo Cazzaniga, Stefano Ruberto, Leonardo Rundo, Andrea Tangherloni:
Computational Intelligence for Life Sciences. Fundam. Informaticae 171(1-4): 57-80 (2020)
[j7]
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  - journals/ijcisys/SpolaorFCKBN20
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Simone Spolaor, Caro Fuchs, Paolo Cazzaniga, Uzay Kaymak, Daniela Besozzi, Marco S. Nobile:
Simpful: A User-Friendly Python Library for Fuzzy Logic. Int. J. Comput. Intell. Syst. 13(1): 1687-1698 (2020)
[j6]
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Simone Spolaor, Marco S. Nobile, Giancarlo Mauri, Paolo Cazzaniga, Daniela Besozzi:
Coupling Mechanistic Approaches and Fuzzy Logic to Model and Simulate Complex Systems. IEEE Trans. Fuzzy Syst. 28(8): 1748-1759 (2020)
[j5]
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  - journals/titb/NobileNVSCMPB20
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Marco S. Nobile, Eric Nisoli, Thalia Vlachou, Simone Spolaor, Paolo Cazzaniga, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi:
cuProCell: GPU-Accelerated Analysis of Cell Proliferation With Flow Cytometry Data. IEEE J. Biomed. Health Informatics 24(11): 3173-3181 (2020)
[c14]
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  - conf/cec/NobileSCPBAM20
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Marco S. Nobile, Simone Spolaor, Paolo Cazzaniga, Daniele M. Papetti, Daniela Besozzi, Daniel A. Ashlock, Luca Manzoni:
Which random is the best random? A study on sampling methods in Fourier surrogate modeling. CEC 2020: 1-8
[c13]
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Marco S. Nobile, Paolo Cazzaniga, Simone Spolaor, Daniela Besozzi, Luca Manzoni:
Fourier Surrogate Models of Dilated Fitness Landscapes in Systems Biology : or how we learned to torture optimization problems until they confess. CIBCB 2020: 1-8
[c12]
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  - conf/fuzzIEEE/FuchsSNK20
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Caro Fuchs, Simone Spolaor, Marco S. Nobile, Uzay Kaymak:
pyFUME: a Python Package for Fuzzy Model Estimation. FUZZ-IEEE 2020: 1-8
[c11]
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  - conf/ijcnn/PapettiSBCAN20
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Daniele M. Papetti, Simone Spolaor, Daniela Besozzi, Paolo Cazzaniga, Marco Antoniotti, Marco S. Nobile:
On the automatic calibration of fully analogical spiking neuromorphic chips. IJCNN 2020: 1-8
[c10]
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  - conf/ipmu/FuchsSNK20
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Caro Fuchs, Simone Spolaor, Marco S. Nobile, Uzay Kaymak:
A Graph Theory Approach to Fuzzy Rule Base Simplification. IPMU (1) 2020: 387-401

2010 – 2019

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2019
[j4]
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  - journals/asc/TangherloniSCBR19
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Andrea Tangherloni, Simone Spolaor, Paolo Cazzaniga, Daniela Besozzi, Leonardo Rundo, Giancarlo Mauri, Marco S. Nobile:
Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design. Appl. Soft Comput. 81 (2019)
[j3]
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  - journals/bioinformatics/NobileVSBCLMPB19
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Marco S. Nobile, Thalia Vlachou, Simone Spolaor, Daniela Bossi, Paolo Cazzaniga, Luisa Lanfrancone, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi:
Modeling cell proliferation in human acute myeloid leukemia xenografts. Bioinform. 35(18): 3378-3386 (2019)
[j2]
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  - journals/bmcbi/TangherloniSRNC19
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Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli, Daniela Besozzi:
GenHap: a novel computational method based on genetic algorithms for haplotype assembly. BMC Bioinform. 20-S(4): 172:1-172:14 (2019)
[c9]
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Marco S. Nobile, Thalia Vlachou, Simone Spolaor, Paolo Cazzaniga, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi:
ProCell: Investigating cell proliferation with Swarm Intelligence. CIBCB 2019: 1-8
[c8]
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Caro Fuchs, Simone Spolaor, Marco S. Nobile, Uzay Kaymak:
A Swarm Intelligence Approach to Avoid Local Optima in Fuzzy C-Means Clustering. FUZZ-IEEE 2019: 1-6
[c7]
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Simone Spolaor:
Bridging Qualitative and Quantitative Modeling with FuzzX. ICTCS 2019: 14-19
[c6]
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  - conf/ssci/SpolaorFKN19
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Simone Spolaor, Caro Fuchs, Uzay Kaymak, Marco S. Nobile:
A Novel Multi-objective Approach to Fuzzy Clustering. SSCI 2019: 850-857
[p1]
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  - series/lncs/SpolaorGIKOMPSSTVVZN19
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Simone Spolaor, Marco Gribaudo, Mauro Iacono, Tomas Kadavy, Zuzana Komínková Oplatková, Giancarlo Mauri, Sabri Pllana, Roman Senkerik, Natalija Stojanovic, Esko Turunen, Adam Viktorin, Salvatore Vitabile, Ales Zamuda, Marco S. Nobile:
Towards Human Cell Simulation. High-Performance Modelling and Simulation for Big Data Applications 2019: 221-249
2018
[c5]
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  - conf/cec/NobileTRSBMC18
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Marco S. Nobile, Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga:
Computational Intelligence for Parameter Estimation of Biochemical Systems. CEC 2018: 1-8
[c4]
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  - conf/europar/TangherloniRSNM18
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Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, Marco S. Nobile, Ivan Merelli, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Pietro Liò:
High Performance Computing for Haplotyping: Models and Platforms. Euro-Par Workshops 2018: 650-661
[c3]
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Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, Paolo Cazzaniga, Marco S. Nobile:
GPU-Powered Multi-Swarm Parameter Estimation of Biological Systems: A Master-Slave Approach. PDP 2018: 698-705
2017
[j1]
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Marco S. Nobile, Antonio E. Porreca, Simone Spolaor, Luca Manzoni, Paolo Cazzaniga, Giancarlo Mauri, Daniela Besozzi:
Efficient Simulation of Reaction Systems on Graphics Processing Units. Fundam. Informaticae 154(1-4): 307-321 (2017)
[c2]
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Simone Spolaor, Andrea Tangherloni, Leonardo Rundo, Paolo Cazzaniga, Marco S. Nobile:
Estimation of Kinetic Reaction Constants: Exploiting Reboot Strategies to Improve PSO's Performance. CIBB 2017: 92-102
[c1]
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Simone Spolaor, Andrea Tangherloni, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga:
Reboot strategies in particle swarm optimization and their impact on parameter estimation of biochemical systems. CIBCB 2017: 1-8
[i1]
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  - journals/peerjpre/TangherloniSRNM17
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Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Ivan Merelli, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri, Pietro Liò:
GenHap: A novel computational method based on genetic algorithms for haplotype assembly. PeerJ Prepr. 5: e3246 (2017)

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