Publications

Research output of the FRACTALS Research Group

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Journals

2026

  1. Massive stochastic simulation of cosmic rays propagation in the heliosphere: The COSMICA code
    Leone Bacciu, Matteo Grazioso, Giovanni Cavallotto, and 5 more authors
    Astronomy and Computing, 2026
    DOI Code
  2. Improving the Annotation for Spatial Proteomics: A Computational Approach to Enhance Molecular Characterization of Thyroid Nodules
    Vasco Coelho, Nicole Monza, Natalia S Porto, and 4 more authors
    Journal of Proteome Research, 2026
    DOI
  3. Spatial Proteomics Uncovers Region-Specific Proteomic Signatures in Autoimmune Liver Diseases
    Elisa Merelli, Vanna Denti, Giulia Capitoli, and 8 more authors
    Digestive and Liver Disease, 2026
    DOI
  4. Validation of COSMICA code for massive stochastic simulation of cosmic rays propagation in the heliosphere
    Stefano Della Torre, Leone Bacciu, Matteo Grazioso, and 5 more authors
    Astronomy and Computing, 2026
    DOI

2025

  1. COSMICA: a GPU-optimized code for solar modulation studies
    L Bacciu, G Cavallotto, S Della Torre, and 5 more authors
    2025
    DOI Code Slides
  2. MiThyCA: A Computational Pathology Pipeline for the Identification of Microscopic Foci of Papillary Thyroid Carcinoma-Like Nuclear Features with AI in Whole-Slide Histological Images
    Leone Bacciu, Mario Urso, Vasco Coelho, and 8 more authors
    Endocrine Pathology, 2025
    DOI Code
  3. GPNMB marks a quiescent cell population in melanoma and promotes metastasis formation
    Fiorenza Lotti, Marine Melixetian, Thalia Vlachou, and 8 more authors
    EMBO reports, 2025
    DOI
  4. Strain analysis in mitral regurgitation using interpretable machine learning
    Amalia Lupi, Marco Salvatore Nobile, Roberto Bianco, and 3 more authors
    Journal of Cardiovascular Magnetic Resonance, 2025
    DOI
  5. Sudden cardiac arrest prediction via deep learning electrocardiogram analysis
    European Heart Journal-Digital Health, 2025
    DOI
  6. Well begun Is half done: The impact of pre-processing in MALDI mass spectrometry imaging analysis applied to a case study of thyroid nodules
    Giulia Capitoli, Kirsten CJ Abeelen, Isabella Piga, and 4 more authors
    Stats, 2025
    DOI
  7. Machine Learning ensemble algorithms for classification of thyroid nodules through proteomics: Extending the method of Shapley values from binary to multi-class tasks
    Giulia Capitoli, Simone Magnaghi, Andrea D’Amicis, and 6 more authors
    Stats, 2025
    DOI
  8. Multimodal Attention-Aware Fusion for Diagnosing Distal Myopathy: Evaluating Model Interpretability and Clinician Trust
    Mohsen Abbaspour Onari, Lucie Charlotte Magister, Yaoxin Wu, and 8 more authors
    arXiv preprint arXiv:2508.01316, 2025
    DOI
  9. FanFAIR: sensitive data sets semi-automatic fairness assessment
    Chiara Gallese, Teresa Scantamburlo, Luca Manzoni, and 2 more authors
    BMC Medical Informatics and Decision Making, 2025
    DOI
  10. Assisting clinical diagnosis with interpretable fuzzy probabilistic modelling
    Giulia Capitoli, Marco S Nobile, Emma L Ambags, and 3 more authors
    BMC Medical Informatics and Decision Making, 2025
    DOI
  11. Local manipulations of the fitness landscape mitigate stall in particle swarm optimization
    Mario Marino, Daniele M Papetti, Daniela Besozzi, and 1 more author
    Applied Soft Computing, 2025
    DOI
  12. Machine Learning models explanations as interpretations of evidence: A theoretical framework of explainability and its implications on high-stakes biomedical decision-making
    Matteo Rizzo, Alberto Veneri, Matteo Marcuzzo, and 5 more authors
    BMC MEDICAL RESEARCH METHODOLOGY, 2025
    DOI
  13. Supervised and Semi-Supervised Explainable AI applied to Cardiovascular Magnetic Resonance Mapping Techniques
    Matteo Grazioso
    2025
  14. Expert-Guided POMDP Learning for Data-Efficient Modeling in Healthcare
    Marco Locatelli, Arjen Hommersom, Roberto Clemens Cerioli, and 2 more authors
    arXiv preprint arXiv:2511.14619, 2025
    DOI
  15. Distinct neoadjuvant chemotherapy regimens differentially modulate the immune landscape in triple-negative breast cancer, with potential impact on combination with immunotherapy
    Marco Barreca, Marco Mariani, Matteo Dugo, and 8 more authors
    2025
  16. Picture this: Mass Spectrometry Imaging to unveil the multiomic layers of the tumor immune environment
    G Bindi, C Fumagalli, N Porto, and 8 more authors
    2025
  17. TRISOMY 21: development of syndrome-specific growth charts from a wide Italian cohort and validation of BMI as a predictor of increased risk of metabolic derangement
    Alessandro Cattoni, Silvia Molinari, Luisa Calı̀, and 8 more authors
    Journal of Endocrinological Investigation, 2025
    DOI
  18. The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy
    Salvatore Artale, Francesca Filiali, Elena Beretta, and 8 more authors
    JMIR Research Protocols, 2025
    DOI
  19. Biomarker identification through spatial proteomics for the characterization of indeterminate thyroid nodules
    Giulia Capitoli, Antonio Maria Alviano, Nicole Monza, and 8 more authors
    Endocrine, 2025
    DOI
  20. Single-slide detection and typing of AL renal amyloidosis: combining mass spectrometry imaging and digital pathology
    Greta Bindi, Giorgio Cazzaniga, Federico Alberici, and 8 more authors
    Amyloid, 2025
    DOI
  21. # 2459 Risk score for onset of kidney failure in patients with chronic kidney disease
    Michele Provenzano, Lilio Hu, Roberta Arena, and 8 more authors
    Nephrology Dialysis Transplantation, 2025
    DOI
  22. Multiomics tissue segmentation via spatially-informed nested biclustering methods
    Francesco Denti, Cecilia Balocchi, Vanna Denti, and 1 more author
    arXiv preprint arXiv:2509.02482, 2025
    DOI
  23. Archimedean Copulas: A Useful Approach in Biomedical Data—A Review with an Application in Pediatrics
    Giulia Risca, Stefania Galimberti, Paola Rebora, and 3 more authors
    Stats, 2025
    DOI
  24. Machine learning for monoclonal gammopathies of renal significance risk stratification using clinical and pathology data
    Giorgio Cazzaniga, Giulia Capitoli, Raffaella Barretta, and 8 more authors
    Kidney International Reports, 2025
    DOI
  25. The routine use of a digital tool for the tumor cell fraction quantification in molecular pathology: an international validation of QuANTUM
    Vincenzo L’Imperio, Giulia Capitoli, Giorgio Cazzaniga, and 8 more authors
    Pathologica, 2025
    DOI
  26. Transferrin saturation and serum ferritin are main predictors of liver iron content in subjects with hyperferritinemia
    Giulia Risca, Sara Pelucchi, Raffaella Mariani, and 5 more authors
    Clinical Gastroenterology and Hepatology, 2025
    DOI
  27. Spatially informed nonnegative matrix trifactorization for coclustering mass spectrometry data
    Andrea Sottosanti, Francesco Denti, Stefania Galimberti, and 2 more authors
    Biometrical Journal, 2025
    DOI
  28. Limited Knowledge of Toxoplasmosis-Specific Preventive Behaviors in Pregnant Women: A Survey Study in Northern Italy
    Federica Fernicola, Elisabetta Colciago, Giulia Capitoli, and 6 more authors
    International Journal of Environmental Research and Public Health, 2025
    DOI
  29. Correction to: Reference Values of Ceruloplasmin across the Adult Age Range in a Large Italian Healthy Population
    Davide Martinez Garofalo, Raffaella Mariani, Mara Botti, and 3 more authors
    The Journal of Applied Laboratory Medicine, 2025
    DOI

2024

  1. An explainable data-driven decision support framework for strategic customer development
    Mohsen Abbaspour Onari, Mustafa Jahangoshai Rezaee, Morteza Saberi, and 1 more author
    Knowledge-Based Systems, 2024
    DOI
  2. Python library for interval-valued fuzzy inference
    Krzysztof Dyczkowski, Piotr Grochowalski, Dawid Kosior, and 6 more authors
    SoftwareX, 2024
    DOI
  3. Machine Learning streamlines the morphometric characterization and multiclass segmentation of nuclei in different follicular thyroid lesions: Everything in a NUTSHELL
    Vincenzo L’Imperio, Vasco Coelho, Giorgio Cazzaniga, and 8 more authors
    Modern Pathology, 2024
    DOI
  4. Small energy benefits of in-wake flying in long-duration migratory flights
    Elisa Perinot, Ortal Mizrahy Rewald, Johannes Fritz, and 5 more authors
    Proceedings of the Royal Society B, 2024
    DOI
  5. Abstract Su803: Sudden cardiac arrest prediction via Deep Learning electrocardiogram analysis
    Luca Neri, Matt Oberdier, Alessandro Orro, and 7 more authors
    Circulation, 2024
    DOI
  6. Meta-problems in global optimization: new perspectives from Computational Intelligence
    DANIELE Papetti
    2024
  7. Development and validation of a gene expression-based Breast Cancer Purity Score
    Marco Barreca, Matteo Dugo, Barbara Galbardi, and 7 more authors
    NPJ precision oncology, 2024
    DOI
  8. Development and validation of a gene expression score to account for tumour purity and improve prognostication in breast cancer
    Marco Barreca, Matteo Dugo, Barbara Galbardi, and 8 more authors
    bioRxiv, 2024
    DOI
  9. Tumour ecosystem and molecular dynamics in clinical triple-negative breast cancer depend on the chemotherapy regimen
    M Barreca, M Mariani, M Dugo, and 8 more authors
    2024
  10. Reference ranges for complete blood count in children and adolescents with Down syndrome
    Martina Lattuada, Giulia Capitoli, Marco Casati, and 7 more authors
    Frontiers in pediatrics, 2024
    DOI
  11. Spatially resolved molecular characterization of Noninvasive Follicular Thyroid Neoplasms with Papillary-Like Nuclear Features (NIFTPs) identifies a distinct proteomic signature associated with RAS-mutant lesions
    Vanna Denti, Angela Greco, Antonio Maria Alviano, and 8 more authors
    International Journal of Molecular Sciences, 2024
    DOI
  12. Matrix-assisted laser desorption/ionization mass spectrometry imaging as a new tool for molecular histopathology in epilepsy surgery
    Cinzia Cagnoli, Dalia De Santis, Claudio Caccia, and 8 more authors
    Epilepsia, 2024
    DOI
  13. Reference values of ceruloplasmin across the adult age range in a large Italian healthy population
    Sara Pelucchi, Giulia Risca, Corradina Lanzafame, and 8 more authors
    The journal of applied laboratory medicine, 2024
    DOI
  14. Pelvic ultrasound and pubertal attainment in girls with sexual precocity: the pivotal role of uterine volume in predicting the timing of menarche
    Alessandro Cattoni, Gianni Russo, Giulia Capitoli, and 8 more authors
    Frontiers in endocrinology, 2024
    DOI
  15. Spatial resolution of renal amyloid deposits through MALDI-MSI: a combined digital and molecular approach to monoclonal gammopathies
    Greta Bindi, Andrew Smith, Glenda Oliveira, and 8 more authors
    Journal of Clinical Pathology, 2024
    DOI
  16. Endocrine, auxological and metabolic profile in children and adolescents with Down syndrome: from infancy to the first steps into adult life
    Silvia Molinari, Chiara Fossati, Maria Laura Nicolosi, and 8 more authors
    Frontiers in endocrinology, 2024
    DOI
  17. Haemochromatosis in children: A national retrospective cohort promoted by the AIEOP (Associazione Italiana Emato-Oncologia Pediatrica) study group
    Paola Corti, Giulia Maria Ferrari, Martha Caterina Faraguna, and 8 more authors
    British Journal of Haematology, 2024
    DOI

2023

  1. Unsupervised neural networks as a support tool for pathology diagnosis in MALDI-MSI experiments: A case study on thyroid biopsies
    Marco S Nobile, Giulia Capitoli, Virgil Sowirono, and 8 more authors
    Expert Systems with Applications, 2023
    DOI
  2. An accurate and time-efficient deep learning-based system for automated segmentation and reporting of cardiac magnetic resonance-detected ischemic scar
    Daniele M Papetti, Kirsten Van Abeelen, Rhodri Davies, and 8 more authors
    Computer methods and programs in biomedicine, 2023
    DOI
  3. Models of representation in Computational Intelligence [guest editorial]
    Marco S Nobile, Luca Manzoni, Daniel A Ashlock, and 1 more author
    IEEE Computational Intelligence Magazine, 2023
    DOI
  4. Characterization of bird formations using fuzzy modelling
    Elisa Perinot, Johannes Fritz, Leonida Fusani, and 2 more authors
    Journal of the Royal Society Interface, 2023
    DOI
  5. Assisting clinical practice with fuzzy probabilistic decision trees
    Emma L Ambags, Giulia Capitoli, Vincenzo L’ Imperio, and 3 more authors
    arXiv preprint arXiv:2304.07788, 2023
    DOI
  6. Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning
    Daniele M Papetti, Simone Spolaor, Iman Nazari, and 8 more authors
    Frontiers in Bioinformatics, 2023
    DOI
  7. Muscle magnetic resonance characterization of STIM1 tubular aggregate myopathy using unsupervised learning
    Amalia Lupi, Simone Spolaor, Alessandro Favero, and 4 more authors
    PLoS ONE, 2023
    DOI
  8. Use of artificial intelligence to automatically predict the optimal patient-specific inversion time for late gadolinium enhancement imaging. Tool development and clinical validation
    C Torlasco, DM Papetti, S Castelletti, and 7 more authors
    European Heart Journal-Cardiovascular Imaging, 2023
    DOI
  9. Measuring perceived trust in XAI-assisted decision-making by eliciting a mental model
    Mohsen Abbaspour Onari, Isel Grau, Marco S Nobile, and 1 more author
    arXiv preprint arXiv:2307.11765, 2023
    DOI
  10. Large T cell clones expressing immune checkpoints increase during multiple myeloma evolution and predict treatment resistance
    Cirino Botta, Cristina Perez, Marta Larrayoz, and 8 more authors
    Nature communications, 2023
    DOI
  11. Ten quick tips for fuzzy logic modeling of biomedical systems
    Davide Chicco, Simone Spolaor, and Marco S Nobile
    PLOS Computational Biology, 2023
    DOI
  12. Simplifying fitness landscapes using dilation functions evolved with genetic programming
    Daniele M Papetti, Andrea Tangherloni, Davide Farinati, and 2 more authors
    IEEE Computational Intelligence Magazine, 2023
    DOI
  13. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data
    Andrea Tangherloni, Simone G. Riva, Brynelle Myers, and 2 more authors
    Journal of Biomedical Informatics, 2023
    DOI
  14. Pubertal attainment and Leydig cell function following pediatric hematopoietic stem cell transplantation: a three-decade longitudinal assessment
    Alessandro Cattoni, Maria Laura Nicolosi, Giulia Capitoli, and 8 more authors
    Frontiers in Endocrinology, 2023
    DOI
  15. Paving the path toward multi-omics approaches in the diagnostic challenges faced in thyroid pathology
    Isabella Piga, Vincenzo L’Imperio, Giulia Capitoli, and 4 more authors
    Expert review of proteomics, 2023
    DOI
  16. Longitudinal Assessment of Pubertal Attainment and Testicular Function Following Pediatric Hematopoietic Stem Cell Transplantation: The Role of the Conditioning Regimen
    Alessandro Cattoni, Maria Laura Nicolosi, Giulia Capitoli, and 11 more authors
    Blood, 2023
    DOI
  17. Thyroid function tests in children and adolescents with trisomy 21: definition of syndrome-specific reference ranges
    Alessandro Cattoni, Silvia Molinari, Giulia Capitoli, and 8 more authors
    The Journal of Clinical Endocrinology & Metabolism, 2023
    DOI
  18. Towards the definition of the molecular hallmarks of idiopathic membranous nephropathy in serum proteome: A DIA-PASEF approach
    Paolo Previtali, Lisa Pagani, Giulia Risca, and 8 more authors
    International Journal of Molecular Sciences, 2023
    DOI
  19. A DNA damage response-like phenotype defines a third of colon cancers at onset
    Stefania Mauro, Maddalena M Bolognesi, Nicoletta Villa, and 8 more authors
    The FASEB Journal, 2023
    DOI
  20. Women’s attitude towards COVID-19 vaccination in pregnancy: A survey study in northern Italy
    Elisabetta Colciago, Giulia Capitoli, Patrizia Vergani, and 1 more author
    International Journal of Gynecology & Obstetrics, 2023
    DOI
  21. Iron overload following hematopoietic stem cell transplantation: prevalence, severity, and management in children and adolescents with malignant and nonmalignant diseases
    Alessandro Cattoni, Giulia Capitoli, Sara Casagranda, and 8 more authors
    Transplantation and Cellular Therapy, 2023
    DOI
  22. Plasma proteomic variables related to COVID-19 severity: an untargeted nLC-MS/MS investigation
    Lisa Pagani, Clizia Chinello, Giulia Risca, and 8 more authors
    International Journal of Molecular Sciences, 2023
    DOI
  23. Spatially resolved molecular approaches for the characterisation of non-invasive follicular tumours with papillary-like features (NIFTPs)
    Isabella Piga, Vincenzo L’Imperio, Lucrezia Principi, and 8 more authors
    International Journal of Molecular Sciences, 2023
    DOI

2022

  1. Salp Swarm Optimization: a critical review
    Mauro Castelli, Luca Manzoni, Luca Mariot, and 2 more authors
    Expert Systems with Applications, 2022
    DOI
  2. SMGen: A generator of synthetic models of biochemical reaction networks
    Simone G Riva, Paolo Cazzaniga, Marco S Nobile, and 4 more authors
    Symmetry, 2022
    DOI
  3. Modeling calcium signaling in S. cerevisiae highlights the role and regulation of the calmodulin-calcineurin pathway in response to hypotonic shock
    S Spolaor, M Rovetta, MS Nobile, and 3 more authors
    Frontiers in Molecular Biosciences, 2022
    DOI
  4. Shaping and dilating the fitness landscape for parameter estimation in stochastic biochemical models
    Marco S Nobile, Daniele M Papetti, Simone Spolaor, and 2 more authors
    Applied Sciences, 2022
    DOI
  5. Fuzzy Sets in Probability Trees for Interpretable AI Decision Making
    EL Ambags, L Genga, MS Nobile, and 3 more authors
    2022
  6. 506 TECHNIQUES OF ARTIFICIAL INTELLIGENCE FOR THE DETERMINATION OF THE OPTIMAL INVERSION TIME: THE THAITI PROJECT
    Camilla Torlasco, Daniele M Papetti, Maria Sabatini, and 8 more authors
    European Heart Journal Supplements, 2022
    DOI
  7. MSR32 COVID-19 Beds’ Occupancy and Hospital Complaints: A Predictive Model
    E Foglia, LB Ferrario, D Bellavia, and 5 more authors
    Value in Health, 2022
    DOI
  8. Dissecting the histological features of lupus nephritis highlights new common patterns of injury in class III/IV
    Maddalena Maria Bolognesi, Giulia Capitoli, Stefania Galimberti, and 8 more authors
    Annals of the Rheumatic Diseases, 2022
    DOI
  9. Spatial multiomics of lipids, N-glycans, and tryptic peptides on a single FFPE tissue section
    Vanna Denti, Giulia Capitoli, Isabella Piga, and 8 more authors
    Journal of Proteome Research, 2022
    DOI
  10. Definition of IgG subclass-specific glycopatterns in idiopathic membranous nephropathy: aberrant IgG glycoforms in blood
    Clizia Chinello, Noortje Haan, Giulia Capitoli, and 8 more authors
    International Journal of Molecular Sciences, 2022
    DOI
  11. Cytomolecular classification of thyroid nodules using fine-needle washes aspiration biopsies
    Giulia Capitoli, Isabella Piga, Vincenzo L’Imperio, and 7 more authors
    International Journal of Molecular Sciences, 2022
    DOI

2021

  1. FiCoS: a fine- and coarse-grained GPU-powered deterministic simulator for biochemical networks
    Andrea Tangherloni, Marco S Nobile, Paolo Cazzaniga, and 5 more authors
    bioRxiv, 2021
    DOI
  2. A CUDA-powered method for the feature extraction and unsupervised analysis of medical images
    Leonardo Rundo, Andrea Tangherloni, Paolo Cazzaniga, and 6 more authors
    The Journal of Supercomputing, 2021
    DOI
  3. The Multi-Level Mechanism of Action of a Pan-Ras Inhibitor Explains its Antiproliferative Activity on Cetuximab-Resistant Cancer Cells
    Renata Tisi, Michela Spinelli, Alessandro Palmioli, and 8 more authors
    Frontiers in Molecular Biosciences, 2021
    DOI
  4. Screening for combination cancer therapies with dynamic fuzzy modeling and multi-objective optimization
    Simone Spolaor, Martijn Scheve, Murat Firat, and 3 more authors
    Frontiers in Genetics, 2021
    DOI
  5. HyperBeta: characterizing the structural dynamics of proteins and self-assembling peptides
    Marco S Nobile, Federico Fontana, Luca Manzoni, and 5 more authors
    Scientific Reports, 2021
    DOI
  6. Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models
    Marco S Nobile, Vasco Coelho, Dario Pescini, and 1 more author
    BMC Bioinformatics, 2021
    DOI
  7. Tremor assessment using smartphone sensor data and fuzzy reasoning
    Caro Fuchs, Marco S Nobile, Guillaume Zamora, and 3 more authors
    BMC Bioinformatics, 2021
    DOI
  8. Dark blood ischemic LGE segmentation using a deep learning approach
    C Torlasco, D Papetti, R Mene, and 8 more authors
    European Heart Journal-Cardiovascular Imaging, 2021
    DOI
  9. Investigating the performance of multi-objective optimization when learning Bayesian Networks
    Marco S Nobile, Paolo Cazzaniga, and Daniele Ramazzotti
    Neurocomputing, 2021
    DOI
  10. Analysis of single-cell RNA sequencing data based on autoencoders
    Andrea Tangherloni, Federico Ricciuti, Daniela Besozzi, and 2 more authors
    BMC bioinformatics, 2021
    DOI
  11. OMICS in chronic kidney disease: focus on prognosis and prediction
    Michele Provenzano, Raffaele Serra, Carlo Garofalo, and 8 more authors
    International Journal of Molecular Sciences, 2021
    DOI
  12. Does the urinary proteome reflect ccRCC stage and grade progression?
    Lucia Santorelli, Martina Stella, Clizia Chinello, and 7 more authors
    Diagnostics, 2021
    DOI
  13. Use of diagnostic criteria from ACR and EU-TIRADS systems to improve the performance of cytology in thyroid nodule triage
    Davide Seminati, Giulia Capitoli, Davide Leni, and 6 more authors
    Cancers, 2021
    DOI
  14. Lipidomic typing of colorectal cancer tissue containing tumour-infiltrating lymphocytes by MALDI mass spectrometry imaging
    Vanna Denti, Allia Mahajneh, Giulia Capitoli, and 8 more authors
    Metabolites, 2021
    DOI
  15. Cytopathology of bronchoalveolar lavages in COVID-19 pneumonia: a pilot study
    Valentina Canini, Francesca Bono, Paolo Calzavacca, and 8 more authors
    Cancer cytopathology, 2021
    DOI
  16. Diagnostic performances of the ACR-TIRADS system in thyroid nodules triage: a prospective single center study
    Davide Leni, Davide Seminati, Davide Fior, and 7 more authors
    Cancers, 2021
    DOI
  17. Urinary extracellular vesicle protein profiles discriminate different clinical subgroups of children with idiopathic nephrotic syndrome
    Lucia Santorelli, William Morello, Elisa Barigazzi, and 8 more authors
    Diagnostics, 2021
    DOI
  18. Ex vivo thyroid fine needle aspirations as an alternative for MALDI-MSI proteomic investigation: intra-patient comparison
    Isabella Piga, Giulia Capitoli, Francesca Clerici, and 8 more authors
    Analytical and bioanalytical chemistry, 2021
    DOI

2020

  1. Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells
    Marco S Nobile, Giuseppina Votta, Roberta Palorini, and 8 more authors
    Bioinformatics, 2020
    DOI
  2. Surfing on fitness landscapes: A boost on optimization by Fourier surrogate modeling
    Luca Manzoni, Daniele M Papetti, Paolo Cazzaniga, and 4 more authors
    Entropy, 2020
    DOI
  3. cuProCell: GPU-accelerated analysis of cell proliferation with flow cytometry data
    Marco S. Nobile, Eric Nisoli, Thalia Vlachou, and 5 more authors
    IEEE Journal of Biomedical and Health Informatics, 2020
    DOI
  4. ACDC: Automated cell detection and counting for time-lapse fluorescence microscopy
    Leonardo Rundo, Andrea Tangherloni, Darren R Tyson, and 8 more authors
    Applied Sciences, 2020
    DOI
  5. Simpful: a user-friendly python library for fuzzy logic
    Simone Spolaor, Caro Fuchs, Paolo Cazzaniga, and 3 more authors
    International Journal of Computational Intelligence Systems, 2020
    DOI
  6. Molecular trait of follicular-patterned thyroid neoplasms defined by MALDI-imaging
    Isabella Piga, Giulia Capitoli, Francesca Clerici, and 8 more authors
    Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2020
    DOI
  7. Analysis of Hashimoto’s thyroiditis on fine needle aspiration samples by MALDI-Imaging
    Giulia Capitoli, Isabella Piga, Francesca Clerici, and 8 more authors
    Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2020
    DOI
  8. Recent Advances in MALDI Mass Spectrometry Imaging: A Cutting-Edge Tool for the Diagnosis of Thyroid Nodules
    Isabella Piga, Giulia Capitoli, Francesca Clerici, and 3 more authors
    Toxic Chemical and Biological Agents: Detection, Diagnosis and Health Concerns, 2020
    DOI
  9. Precision nephrology is a non-negligible state of mind in clinical research: remember the past to face the future
    Michele Provenzano, Luca De Nicola, Michelle J Pena, and 6 more authors
    Nephron, 2020
    DOI
  10. In-depth mapping of the urinary N-glycoproteome: distinct signatures of ccRCC-related progression
    Lucia Santorelli, Giulia Capitoli, Clizia Chinello, and 8 more authors
    Cancers, 2020
    DOI

2019

  1. GenHap: a novel computational method based on genetic algorithms for haplotype assembly
    Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, and 6 more authors
    BMC Bioinformatics, 2019
    DOI
  2. ginSODA: massive parallel integration of stiff ODE systems on GPUs.
    Marco S Nobile, Paolo Cazzaniga, Daniela Besozzi, and 1 more author
    Journal of Supercomputing, 2019
  3. MedGA: a novel evolutionary method for image enhancement in medical imaging systems
    Leonardo Rundo, Andrea Tangherloni, Marco S Nobile, and 4 more authors
    Expert Systems with Applications, 2019
    DOI
  4. Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena
    Daniele Ramazzotti, Marco S Nobile, Marco Antoniotti, and 1 more author
    Journal of computational science, 2019
    DOI
  5. Modeling cell proliferation in human acute myeloid leukemia xenografts
    Marco S Nobile, Thalia Vlachou, Simone Spolaor, and 6 more authors
    Bioinformatics, 2019
    DOI
  6. A novel framework for MR image segmentation and quantification by using MedGA
    Leonardo Rundo, Andrea Tangherloni, Paolo Cazzaniga, and 7 more authors
    Computer methods and programs in biomedicine, 2019
    DOI
  7. USE-Net: Incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets
    Leonardo Rundo, Changhee Han, Yudai Nagano, and 8 more authors
    Neurocomputing, 2019
    DOI
  8. Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design
    Andrea Tangherloni, Simone Spolaor, Paolo Cazzaniga, and 4 more authors
    Applied Soft Computing, 2019
    DOI
  9. Coupling mechanistic approaches and fuzzy logic to model and simulate complex systems
    Simone Spolaor, Marco S Nobile, Giancarlo Mauri, and 2 more authors
    IEEE Transactions on Fuzzy Systems, 2019
    DOI
  10. Computational intelligence for life sciences
    Daniela Besozzi, Luca Manzoni, Marco S Nobile, and 7 more authors
    Fundamenta Informaticae, 2019
    DOI
  11. scAEspy: a tool for autoencoder-based analysis of single-cell RNA sequencing data
    Andrea Tangherloni, Federico Ricciuti, Daniela Besozzi, and 2 more authors
    BioRxiv, 2019
    DOI
  12. Results of a multicentre, randomized, controlled open-label study on the use of anti-t-lymphocyte globulin (ATLG) and rituximab for immunomodulation of graft-versus-host disease (GvHD) and graft failure (GF) in patients with non-malignant disorders
    Mattia Algeri, Stefania Galimberti, Maria Ester Bernardo, and 8 more authors
    Blood, 2019
    DOI
  13. MALDI-MSI as a complementary diagnostic tool in cytopathology: a pilot study for the characterization of thyroid nodules
    Giulia Capitoli, Isabella Piga, Stefania Galimberti, and 8 more authors
    Cancers, 2019
    DOI
  14. Clinical-pathological issues in thyroid pathology: study on the routine application of NIFTP diagnostic criteria
    Valentina Canini, Davide Leni, Angela Ida Pincelli, and 8 more authors
    Scientific Reports, 2019
    DOI
  15. The management of haemoglobin interference for the MALDI-MSI proteomics analysis of thyroid fine needle aspiration biopsies
    Isabella Piga, Giulia Capitoli, Vanna Denti, and 8 more authors
    Analytical and bioanalytical chemistry, 2019
    DOI
  16. Molecular signatures of medullary thyroid carcinoma by matrix-assisted laser desorption/ionisation mass spectrometry imaging
    Andrew Smith, Manuel Galli, Isabella Piga, and 8 more authors
    Journal of proteomics, 2019
    DOI
  17. Feasibility study for the MALDI-MSI analysis of thyroid fine needle aspiration biopsies: evaluating the morphological and proteomic stability over time
    Isabella Piga, Giulia Capitoli, Silvia Tettamanti, and 8 more authors
    PROTEOMICS–Clinical Applications, 2019
    DOI

2018

  1. Fuzzy Self-Tuning PSO: A settings-free algorithm for global optimization
    Marco S Nobile, Paolo Cazzaniga, Daniela Besozzi, and 3 more authors
    Swarm and Evolutionary Computation, 2018
    DOI
  2. Multi-objective optimization to explicitly account for model complexity when learning Bayesian Networks
    Paolo Cazzaniga, Marco S Nobile, and Daniele Ramazzotti
    CoRR, 2018
  3. GPU Powered Parameter Estimation of Large-scale kinetic metabolic model
    Niccolo Totis, Andrea Tangherloni, Marco Beccuti, and 6 more authors
    Proceedings of CIBB, 2018
    DOI
  4. GenHap: Evolutionary Computation For Haplotype Assembly
    Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, and 7 more authors
    Proceedings of CIBB, 2018
    DOI

2017

  1. Gillespie’s stochastic simulation algorithm on MIC coprocessors
    Andrea Tangherloni, Marco S Nobile, Paolo Cazzaniga, and 2 more authors
    The Journal of Supercomputing, 2017
    DOI
  2. LASSIE: simulating large-scale models of biochemical systems on GPUs
    Andrea Tangherloni, Marco S Nobile, Daniela Besozzi, and 2 more authors
    BMC Bioinformatics, 2017
    DOI
  3. GPU-powered model analysis with PySB/cupSODA
    Leonard A Harris, Marco S Nobile, James C Pino, and 5 more authors
    Bioinformatics, 2017
    DOI
  4. Efficient simulation of reaction systems on graphics processing units
    Marco S Nobile, Antonio E Porreca, Simone Spolaor, and 4 more authors
    Fundamenta Informaticae, 2017
    DOI

2016

  1. GPU-powered evolutionary design of mass-action-based models of gene regulation
    Marco S Nobile, Davide Cipolla, Paolo Cazzaniga, and 1 more author
    Evolutionary Computation in Gene Regulatory Network Research, 2016
    DOI
  2. Graphics Processing Units in Bioinformatics, Computational Biology and Systems Biology
    Marco S Nobile, Paolo Cazzaniga, Andrea Tangherloni, and 1 more author
    Briefings in Bioinformatics, 2016
    DOI
  3. COSYS: Computational Systems Biology Infrastructure
    Fabio Cumbo, Marco S Nobile, Chiara Damiani, and 3 more authors
    Proceedings of CIBB, 2016
    DOI
  4. Learning the probabilistic structure of cumulative phenomena with suppes-bayes causal networks
    Daniele Ramazzotti, Marco S Nobile, Marco Antoniotti, and 1 more author
    arXiv preprint arXiv:1703.03074, 2016
    DOI
  5. Strategies for structuring interdisciplinary education in systems biology: an European perspective
    Marija Cvijovic, Thomas Höfer, Jure Aćimović, and 8 more authors
    NPJ systems biology and applications, 2016
    DOI

2015

  1. Evolutionary inference of biological systems accelerated on Graphics Processing Units
    M Nobile and others
    2015

2014

  1. cuTauLeaping: A GPU-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems
    Marco S Nobile, Paolo Cazzaniga, Daniela Besozzi, and 2 more authors
    PLoS One, 2014
    DOI
  2. Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization
    Paolo Cazzaniga, Marco S Nobile, Daniela Besozzi, and 2 more authors
    BioMed research international, 2014
    DOI
  3. GPU-accelerated simulations of mass-action kinetics models with cupSODA
    Marco S Nobile, Paolo Cazzaniga, Daniela Besozzi, and 1 more author
    The Journal of Supercomputing, 2014
    DOI
  4. Computational strategies for a system-level understanding of metabolism
    Paolo Cazzaniga, Chiara Damiani, Daniela Besozzi, and 8 more authors
    Metabolites, 2014
    DOI

2013

  1. Modeling and Simulation of the Blood Coagulation Cascade
    Matteo Bellini, Daniela Besozzi, Paolo Cazzaniga, and 2 more authors
    Egyptian Computer Science Journal, 2013
  2. GPU-powered sensitivity analysis and parameter estimation of a reaction-based model of the post replication repair pathway in yeast
    Paolo Cazzaniga, Riccardo Colombo, MARCO S Nobile, and 4 more authors
    TICSP SERIES, 2013
  3. In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae
    Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, and 5 more authors
    BMC Systems Biology, 2013
    DOI
  4. Computational methods in systems biology: case studies and biological insights
    Daniela Besozzi and others
    Electronic Proceedings in Theoretical Computer Science, 2013
    DOI

2012

  1. A GPU-based multi-swarm PSO method for parameter estimation in stochastic biological systems exploiting discrete-time target series
    Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, and 2 more authors
    Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 2012
    DOI
  2. An excursion in reaction systems: from computer science to biology
    Luca Corolli, Carlo Maj, Fabrizio Marini, and 2 more authors
    Theoretical computer science, 2012
    DOI
  3. The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae
    Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, and 3 more authors
    EURASIP Journal on Bioinformatics and Systems Biology, 2012
    DOI
  4. Simulation of the Ras/cAMP/PKA pathway in budding yeast highlights the establishment of stable oscillatory states
    Dario Pescini, Paolo Cazzaniga, Daniela Besozzi, and 4 more authors
    Biotechnology advances, 2012

2011

  1. PCNA ubiquitylation as the wet readout of a Post-Replication Repair computational model
    F Amara, R Colombo, F Spadaro, and 4 more authors
    2011
  2. Investigating oscillatory regimens in the Ras/cAMP/PKA pathway in S. cerevisiae: the role of feedback control mechanisms
    DARIO Pescini, Paolo Cazzaniga, DANIELA Besozzi, and 4 more authors
    Tampere International Center for Signal Processing series, 2011
  3. Modeling diffusion in a signal transduction pathway: the use of virtual volumes in P systems
    Daniela Besozzi, Paolo Cazzaniga, Stefania Cocolo, and 2 more authors
    International Journal of Foundations of Computer Science, 2011
    DOI

Conferences

2025

  1. Improving the Efficiency and the Validity of Molecular Transformers
    Leone Bacciu, Matteo Grazioso, Silvia Multari, and 3 more authors
    In 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2025
    DOI
  2. Assessing Cardiac Functionality by Means of Interpretable AI and Myocardial Strain
    Marco S Nobile, Amalia Lupi, Leone Bacciu, and 4 more authors
    In 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2025
    DOI
  3. Investigating fairness with FanFAIR: is pre-processing useful only for performances?
    Michele Rispoli, Marco S Nobile, Luca Manzoni, and 6 more authors
    In 2025 IEEE Symposium on Computational Intelligence in Health and Medicine (CIHM), 2025
    DOI
  4. A survey of modern hybrid particle swarm optimization algorithms
    Matteo Grazioso, Chiara Gallese, Leonardo Vanneschi, and 1 more author
    In International Conference on the Applications of Evolutionary Computation (Part of EvoStar), 2025
    DOI
  5. We are sending you back... to the optimum! Fuzzy Time Travel Particle Swarm Optimization
    Daniele M Papetti, Andrea Tangherloni, Vasco Coelho, and 3 more authors
    In International Conference on the Applications of Evolutionary Computation (Part of EvoStar), 2025
    DOI
  6. Assessing and Quantifying Perceived Trust in Interpretable Clinical Decision Support
    Mohsen Abbaspour Onari, Isel Grau, Chao Zhang, and 2 more authors
    In World Conference on Explainable Artificial Intelligence, 2025
    DOI
  7. The Dynamics of Trust in XAI: Assessing Perceived and Demonstrated Trust Across Interaction Modes and Risk Treatments
    Mohsen Abbaspour Onari, Gregor Baer, Chao Zhang, and 3 more authors
    In World Conference on Explainable Artificial Intelligence, 2025
    DOI
  8. Assessing the value of Explainable Artificial Intelligence for Magnetic Resonance Imaging
    Giada Frasson, Matteo Rizzo, Marco Salvatore Nobile, and 2 more authors
    In World Conference on Explainable Artificial Intelligence, 2025
    DOI
  9. Inclusive Play Through Robotic Toys and Accessible Design: A Child-Centered Approach
    Stefano D’Ambrosio, Sara Cecchetti, Lorenzo Guerrieri, and 5 more authors
    In International Conference of the Association for the Advancement of Assistive Technology in Europe, 2025
    DOI
  10. Inclusive Play Through Robots: Insights from Early Experimentation
    Stefano D’Ambrosio, Antonella Gilardoni, Mabel Giraldo, and 2 more authors
    In International Conference of the Association for the Advancement of Assistive Technology in Europe, 2025
    DOI

2024

  1. Our Fruitful Relationship with Sugeno Inference, from FUMOSO to pyFUME
    Leone Bacciu, Paolo Cazzaniga, Chiara Gallese, and 4 more authors
    In International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems, 2024
    DOI Code
  2. Applications of IFIS python library in interval-valued fuzzy inference problems
    Barbara Pékala, Piotr Grochowalskii, Dawid Kosior, and 6 more authors
    In 2024 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE), 2024
    DOI
  3. A fast feature selection for interpretable modeling based on Fuzzy Inference Systems
    Andrea Tangherloni, Paolo Cazzaniga, Nicolò Stranieri, and 2 more authors
    In 2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2024
    DOI
  4. Predicting metabolic reactions with a Molecular Transformer for drug design optimization
    Silvia Multari, Rıza Özçelik, Angelica Mazzolari, and 2 more authors
    In 2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2024
    DOI
  5. Reinforcement Learning and Fuzzy Logic Modelling for Personalized Dynamic Treatment
    Marco Locatelli, R Cerioli, Daniela Besozzi, and 3 more authors
    In CEUR WORKSHOP PROCEEDINGS, 2024
  6. A modified EACOP implementation for real-parameter single objective optimization problems
    Andrea Tangherloni, Vasco Coelho, Francesca M Buffa, and 1 more author
    In 2024 IEEE Congress on Evolutionary Computation (CEC), 2024
    DOI
  7. MALDI-MS imaging in niftp diagnosis: an alternative approach
    Fabio Pagni, Angela Greco, Vanna Denti, and 7 more authors
    In Endocrine Abstracts, 2024
    DOI
  8. Bayesian Biclustering on a Renal Cell Carcinoma Tissue Section
    Giulia Capitoli, Vanna Denti, Cecilia Balocchi, and 1 more author
    In Scientific Meeting of the Italian Statistical Society, 2024
    DOI

2023

  1. A theoretical framework for AI models explainability with application in biomedicine
    Matteo Rizzo, Alberto Veneri, Andrea Albarelli, and 3 more authors
    In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2023
    DOI
  2. The Domination Game: Dilating Bubbles to Fill Up Pareto Fronts
    Vasco Coelho, Daniele M Papetti, Andrea Tangherloni, and 3 more authors
    In 2023 IEEE Congress on Evolutionary Computation (CEC), 2023
    DOI
  3. Trustworthy Machine Learning predictions to support clinical research and decisions
    Andrea Bianchi, Antinisca Di Marco, Francesca Marzi, and 7 more authors
    In 2023 IEEE 36th International Symposium on Computer-Based Medical Systems (CBMS), 2023
    DOI
  4. Investigating semi-automatic assessment of data sets fairness by means of fuzzy logic
    Chiara Gallese, Teresa Scantamburlo, Luca Manzoni, and 1 more author
    In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2023
    DOI
  5. Estimation of fuzzy models from mixed data sets with pyFUME
    Daniele M Papetti, Caro Fuchs, Vasco Coelho, and 2 more authors
    In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2023
    DOI
  6. Trustworthy artificial intelligence in medical applications: A mini survey
    Mohsen Abbaspour Onari, Isel Grau, Marco S Nobile, and 1 more author
    In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2023
  7. Advantages of GPU-accelerated approach for solving the Parker equation in the heliosphere
    Giuseppe La Vacca, Stefano Della Torre, Giovanni Cavallotto, and 5 more authors
    In Proceedings of the 38th International Cosmic Ray Conference (ICRC2023), 2023
    DOI
  8. Evolving Dilation Functions for Parameter Estimation
    Daniele M Papetti and Vasco Coelho
    In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2023
    DOI
  9. Consensus Clustering Strategy for Cell Type Assignments of scRNA-seq Data
    Simone G. Riva, Brynelle Myers, Paolo Cazzaniga, and 2 more authors
    In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2023
    DOI
  10. Segmenting Brain MALDI-MSI Data Under Separate Exchangeability
    Francesco Denti, Cecilia Balocchi, and Giulia Capitoli
    In Interational Conference on Bayesian Young Statistician Meeting, 2023
    DOI

2022

  1. Local bubble dilation functions: Hypersphere-bounded landscape deformations simplify global optimization
    Daniele M Papetti, Vasco Coelho, Daniel A Ashlock, and 4 more authors
    In 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2022
    DOI
  2. Predicting and characterizing legal claims of hospitals with computational intelligence: the legal and ethical implications
    Chiara Gallese, Caro Fuchs, Simone G Riva, and 5 more authors
    In 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2022
    DOI
  3. The impact of variable selection and transformation on the interpretability and accuracy of fuzzy models
    Caro Fuchs, Simone Spolaor, Uzay Kaymak, and 1 more author
    In 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2022
    DOI
  4. Comparing interpretable AI approaches for the clinical environment: an application to COVID-19
    Mohsen Abbaspour Onari, Marco S Nobile, Isel Grau, and 4 more authors
    In 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2022
    DOI
  5. Building interpretable and parsimonious fuzzy models using a multi-objective approach
    Caro Fuchs, Uzay Kaymak, and Marco S Nobile
    In 2022 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE), 2022
    DOI
  6. Multi-objective Optimization for Marker Panel Identification in Single-cell Data
    Andrea Tangherloni, Simone G. Riva, Brynelle Myers, and 1 more author
    In 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2022
    DOI
  7. A Deep Learning Pipeline for the Automatic cell type Assignment of scRNA-seq Data
    Simone G. Riva, Brynelle Myers, Paolo Cazzaniga, and 1 more author
    In 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2022
    DOI

2021

  1. The impact of representation on the optimization of marker panels for single-cell RNA data
    Andrea Tangherloni, Simone G Riva, Simone Spolaor, and 3 more authors
    In 2021 IEEE Congress on Evolutionary Computation (CEC), 2021
    DOI
  2. If you can’t beat it, squash it: Simplify global optimization by evolving dilation functions
    Daniele M Papetti, Daniel A Ashlock, Paolo Cazzaniga, and 2 more authors
    In 2021 IEEE Congress on Evolutionary Computation (CEC), 2021
    DOI
  3. A comparison of multi-objective optimization algorithms to identify drug target combinations
    Simone Spolaor, Daniele M Papetti, Paolo Cazzaniga, and 2 more authors
    In 2021 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2021
    DOI
  4. Characterizing the flying behaviour of bird flocks with fuzzy reasoning.
    Elisa Perinot, Johannes Fritz, Leonida Fusani, and 2 more authors
    In WILF, 2021
    DOI
  5. Integration of Multiple scRNA-Seq Datasets on the Autoencoder Latent Space
    Simone G. Riva, Paolo Cazzaniga, and Andrea Tangherloni
    In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2021
    DOI

2020

  1. A graph theory approach to fuzzy rule base simplification
    Caro Fuchs, Simone Spolaor, Marco S Nobile, and 1 more author
    In International conference on information processing and management of uncertainty in knowledge-based systems, 2020
    DOI
  2. pyFUME: a Python package for fuzzy model estimation
    Caro Fuchs, Simone Spolaor, Marco S Nobile, and 1 more author
    In 2020 IEEE international conference on fuzzy systems (FUZZ-IEEE), 2020
    DOI
  3. Which random is the best random? A study on sampling methods in Fourier surrogate modeling
    Marco S Nobile, Simone Spolaor, Paolo Cazzaniga, and 4 more authors
    In 2020 IEEE Congress on Evolutionary Computation (CEC), 2020
    DOI
  4. On the automatic calibration of fully analogical spiking neuromorphic chips
    Daniele M Papetti, Simone Spolaor, Daniela Besozzi, and 3 more authors
    In 2020 International Joint Conference on Neural Networks (IJCNN), 2020
    DOI
  5. Fourier Surrogate Models of Dilated Fitness Landscapes in Systems Biology: Or how we learned to torture optimization problems until they confess
    Marco S Nobile, Paolo Cazzaniga, Simone Spolaor, and 2 more authors
    In 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2020
    DOI
  6. Fuzzy self-tuning PSO: Single-objective global optimization without moving a finger
    Marco S Nobile
    In Workshop on Evolutionary and Population-based Optimization (WEPO 2020), 19th International Conference of the Italian Association for Artificial Intelligence (AIxIA), 2020
  7. Preventing litigation with a predictive model of COVID-19 ICUs occupancy
    Chiara Gallese, Elena Falletti, Marco S Nobile, and 3 more authors
    In 2020 IEEE International Conference on Big Data (Big Data), 2020
    DOI

2019

  1. CNN-based prostate zonal segmentation on T2-weighted MR images: a cross-dataset study
    Leonardo Rundo, Changhee Han, Jin Zhang, and 8 more authors
    In Neural Approaches to Dynamics of Signal Exchanges, 2019
    DOI
  2. A swarm intelligence approach to avoid local optima in fuzzy c-means clustering
    Caro Fuchs, Simone Spolaor, Marco S Nobile, and 1 more author
    In 2019 IEEE international conference on fuzzy systems (FUZZ-IEEE), 2019
    DOI
  3. HaraliCU: GPU-powered Haralick feature extraction on medical images exploiting the full dynamics of gray-scale levels
    Leonardo Rundo, Andrea Tangherloni, Simone Galimberti, and 5 more authors
    In International Conference on Parallel Computing Technologies, 2019
    DOI
  4. Dilation functions in global optimization
    Marco S Nobile, Paolo Cazzaniga, and Daniel A Ashlock
    In 2019 IEEE Congress on Evolutionary Computation (CEC), 2019
    DOI
  5. ProCell: Investigating cell proliferation with swarm intelligence
    Marco S Nobile, Thalia Vlachou, Simone Spolaor, and 4 more authors
    In 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2019
    DOI
  6. A novel multi-objective approach to fuzzy clustering
    Simone Spolaor, Caro Fuchs, Uzay Kaymak, and 1 more author
    In 2019 IEEE Symposium Series on Computational Intelligence (SSCI), 2019
    DOI

2018

  1. Structural learning of probabilistic graphical models of cumulative phenomena
    Daniele Ramazzotti, Marco S Nobile, Marco Antoniotti, and 1 more author
    In International Conference on Computational Science, 2018
    DOI
  2. GPU-powered multi-swarm parameter estimation of biological systems: A master-slave approach
    Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, and 2 more authors
    In 2018 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP), 2018
    DOI
  3. Computational intelligence for parameter estimation of biochemical systems
    Marco S Nobile, Andrea Tangherloni, Leonardo Rundo, and 4 more authors
    In 2018 IEEE congress on evolutionary computation (CEC), 2018
    DOI
  4. GPU accelerated analysis of treg-teff cross regulation in relapsing-remitting multiple sclerosis
    Marco Beccuti, Paolo Cazzaniga, Marzio Pennisi, and 6 more authors
    In European Conference on Parallel Processing, 2018
    DOI
  5. High performance computing for haplotyping: models and platforms
    Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, and 6 more authors
    In European Conference on Parallel Processing, 2018
    DOI
  6. Efficient and settings-free calibration of detailed kinetic metabolic models with enzyme isoforms characterization
    Niccolò Totis, Andrea Tangherloni, Marco Beccuti, and 5 more authors
    In International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 2018
    DOI
  7. Global sensitivity analysis of constraint-based metabolic models
    Chiara Damiani, Dario Pescini, and Marco S Nobile
    In International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 2018
    DOI

2017

  1. Proactive particles in swarm optimization: A settings-free algorithm for real-parameter single objective optimization problems
    Andrea Tangherloni, Leonardo Rundo, and Marco S Nobile
    In 2017 IEEE Congress on Evolutionary Computation (CEC), 2017
    DOI
  2. Accelerated analysis of biological parameters space using GPUs
    Marco S Nobile and Giancarlo Mauri
    In International Conference on Parallel Computing Technologies, 2017
    DOI
  3. Reboot strategies in particle swarm optimization and their impact on parameter estimation of biochemical systems
    Simone Spolaor, Andrea Tangherloni, Leonardo Rundo, and 2 more authors
    In 2017 IEEE conference on computational intelligence in bioinformatics and computational biology (CIBCB), 2017
    DOI
  4. Estimation of kinetic reaction constants: exploiting reboot strategies to improve PSO’s performance
    Simone Spolaor, Andrea Tangherloni, Leonardo Rundo, and 2 more authors
    In International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 2017
    DOI

2016

  1. GPU-powered and settings-free parameter estimation of biochemical systems
    Marco S Nobile, Andrea Tangherloni, Daniela Besozzi, and 1 more author
    In 2016 IEEE Congress on Evolutionary Computation (CEC), 2016
    DOI
  2. GPU-powered bat algorithm for the parameter estimation of biochemical kinetic values
    Andrea Tangherloni, Marco S Nobile, and Paolo Cazzaniga
    In 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2016
    DOI
  3. Parallel implementation of efficient search schemes for the inference of cancer progression models
    Daniele Ramazzotti, Marco S Nobile, Paolo Cazzaniga, and 2 more authors
    In 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2016
    DOI
  4. COSYS: A computational infrastructure for systems biology
    Fabio Cumbo, Marco S Nobile, Chiara Damiani, and 3 more authors
    In International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 2016
    DOI

2015

  1. Parallelizing biochemical stochastic simulations: a comparison of GPUs and Intel Xeon Phi processors
    Paolo Cazzaniga, F Ferrara, Marco S Nobile, and 2 more authors
    In International Conference on Parallel Computing Technologies, 2015
    DOI
  2. A double swarm methodology for parameter estimation in oscillating gene regulatory networks
    Marco S Nobile and Hitoshi Iba
    In 2015 IEEE Congress on Evolutionary Computation (CEC), 2015
    DOI
  3. The impact of particles initialization in PSO: parameter estimation as a case in point
    Paolo Cazzaniga, Marco S Nobile, and Daniela Besozzi
    In 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2015
    DOI
  4. Proactive particles in swarm optimization: a self-tuning algorithm based on fuzzy logic
    Marco S Nobile, Gabriella Pasi, Paolo Cazzaniga, and 3 more authors
    In 2015 IEEE international conference on fuzzy systems (FUZZ-IEEE), 2015
    DOI
  5. Deterministic simulations of large-scale models of cellular processes accelerated on Graphics Processing Units
    Andrea Tangherloni, Paolo Cazzaniga, M Nobile, and 3 more authors
    In Proceedings of CIBB 2015, 2015
  6. Towards a GPU-powered toolbox for the computational analysis of biological systems
    Paolo Cazzaniga, Marco S Nobile, Daniela Besozzi, and 5 more authors
    In Bioinformatics ITalian Society. BITS2015 Conference Proceedings. 12th BITS Annual Meeting. June 3-5 2015 Milano, Italy, 2015
  7. GPU-powered sensitivity analysis of a large-scale model of death cell signaling and proliferation in cancer cells
    Marco S Nobile, Leonard Harris, Erin Shockley, and 5 more authors
    In Third Annual Winter q-bio Meeting. All abstracts., 2015
  8. GPU computing for accelerated analyses of a large-scale model of cell fate in cancer cells
    Marco S Nobile, Leonard Harris, Erin Shockley, and 6 more authors
    In Bioinformatics Italian Society. BITS2015 Conference Proceedings. 12th BITS Annual Meeting. June 3-5 2015 Milano, Italy, 2015

2014

  1. Simulation and analysis of the blood coagulation cascade accelerated on GPU
    Matteo Bellini, Daniela Besozzi, Paolo Cazzaniga, and 2 more authors
    In 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, 2014
    DOI
  2. A memetic hybrid method for the molecular distance geometry problem with incomplete information
    Marco S Nobile, Andrea G Citrolo, Paolo Cazzaniga, and 2 more authors
    In 2014 IEEE Congress on Evolutionary Computation (CEC), 2014
    DOI
  3. Enhancing simulation of chemical reactions at mesoscales
    D Pescini, G Caravagna, M Nobile, and 2 more authors
    In 11th annual meeting of the Bioinformatics Italian Society, Rome, Italy, 2014., 2014

2013

  1. The foundation of Evolutionary Petri Nets
    Marco Salvatore Nobile, Daniela Besozzi, Paolo Cazzaniga, and 1 more author
    In 4th International Workshop on Biological Processes & Petri Nets (BioPPN 2013), 2013
  2. Reverse engineering of kinetic reaction networks by means of cartesian genetic programming and particle swarm optimization
    Marco S Nobile, Daniela Besozzi, Paolo Cazzaniga, and 2 more authors
    In 2013 IEEE Congress on Evolutionary Computation, 2013
    DOI
  3. cupSODA: a CUDA-powered simulator of mass-action kinetics
    Marco S Nobile, Daniela Besozzi, Paolo Cazzaniga, and 2 more authors
    In International Conference on Parallel Computing Technologies, 2013
    DOI
  4. Evolutionary inference of biochemical reaction networks accelerated on graphics processing units
    Marco S Nobile and Giancarlo Mauri
    In 2013 International Conference on High Performance Computing & Simulation (HPCS), 2013
    DOI
  5. A GPU-powered computational analysis of PCNA ubiquitylation processes involved in UV-induced DNA lesions bypass
    Daniela Besozzi, Riccardo Colombo, Paolo Cazzaniga, and 4 more authors
    In 14th International Conference on Systems Biology. Abstract book., 2013
  6. Accelerating the computational analysis of biological systems by means of Graphics Processing Units
    Daniela Besozzi, Paolo Cazzaniga, Riccardo Colombo, and 4 more authors
    In 14th International Conference on Systems Biology. Abstract book., 2013

2012

  1. Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs
    Marco S Nobile, Daniela Besozzi, Paolo Cazzaniga, and 2 more authors
    In Proceedings of the 14th annual conference companion on Genetic and evolutionary computation, 2012
    DOI

2010

  1. BioSimWare: a software for the modeling, simulation and analysis of biological systems
    Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, and 1 more author
    In International Conference on Membrane Computing, 2010
    DOI

Book Chapters

2024

  1. Fuzzy logic for knowledge-driven and data-driven modeling in biomedical sciences
    Paolo Cazzaniga, Simone Spolaor, Caro Fuchs, and 2 more authors
    In Big Data Analysis and Artificial Intelligence for Medical Sciences, 2024
    DOI

2020

  1. An experimental and computational protocol to study cell proliferation in human acute myeloid leukemia xenografts
    Thalia Vlachou, Marco S Nobile, Chiara Ronchini, and 2 more authors
    In Leukemia Stem Cells: Methods and Protocols, 2020
    DOI

2019

  1. Towards human cell simulation
    Simone Spolaor, Marco Gribaudo, Mauro Iacono, and 7 more authors
    In High-Performance Modelling and Simulation for Big Data Applications: Selected Results of the COST Action IC1406 cHiPSet, 2019
    DOI

2018

  1. Accelerating stochastic simulations using Graphics Processing Units
    P Cazzaniga, M Nobile, A Tangherloni, and 2 more authors
    In Quantitative Biology. Theory, Computational Methods and Models, 2018
  2. Le sentenze antiscientifiche: un mito creato dai media
    Chiara Gallese and Daniela Besozzi
    In Ius dicere in a globalized world: A comparative overview, 2018
    DOI
  3. Accelerating stochastic simulations of mechanistic models of biological systems: advantages and issues in the parallelization on graphics processing units
    Paolo Cazzaniga, Marco S Nobile, Andrea Tangherloni, and 1 more author
    In Quantitative Biology: Computational Methods and Examples, 2018

2016

  1. GPU-powered evolutionary design of mass-action based models of gene regulation
    M. S. Nobile, D. Cipolla, P. Cazzaniga, and 1 more author
    In Evolutionary Computation in Gene Regulatory Network Research, 2016

2015

  1. Modeling and Analysis of Cellular Processes with Dynamical Probabilistic P Systems: Questions, Methods and Results
    D Besozzi, P Cazzaniga, G Mauri, and 2 more authors
    In Multidisciplinary Creativity, 2015

2013

  1. Molecular diffusion and compartmentalization in signal transduction pathways: An application of membrane systems to the study of bacterial chemotaxis
    Paolo Cazzaniga, Daniela Besozzi, Dario Pescini, and 1 more author
    In Applications of membrane computing in systems and synthetic biology, 2013
    DOI

Abstracts & Posters

2026

  1. The Role of Solar Modulation on Cosmic Ray Spectra at GV Rigidities
    Stefano Della Torre, Rachele Guidetti, Massimo Gervasi, and 7 more authors
    2026
    46th COSPAR Scientific Assembly, Florence, Italy
  2. Why Performance Matters: Accelerating Solar Modulation of Galactic Cosmic Rays with High-Performance Computing
    Leone Bacciu, Matteo Grazioso, Giovanni Cavallotto, and 5 more authors
    2026
    EGU (European Geosciences Union), Wien, Austria
    DOI

2025

  1. A novel integrated cyclic peptide-based platform for precision delivery of nucleic acid-based therapeutics
    Cristian Fregonese, Matteo Grazioso, Sara Linciano, and 10 more authors
    2025
    StatPhys29 Satellite Meeting: Molecular biophysics at the transition state: from statistical mechanics to AI, University of Trento, Italy
  2. Optimized solar modulation studies using COSMICA GPU-enhanced code
    Leone Bacciu, Giovanni Cavallotto, Stefano Della Torre, and 5 more authors
    2025
    ESWW2025 (European Space Weather Week), Umeå, Sweden