A selection of recent scientific publications from the research groups of the laboratory

67 entries « 1 of 2 »

2025

Pham, Giang; Milazzo, Paolo

Gene Importance Assessment based on Shapley Values for Boolean Networks: Validation and Scalability Analysis Proceedings Article

In: International Symposium ``from Data to Models and Back'' (DataMod 2024), Springer 2025.

BibTeX

Mastorci, Francesca; Lazzeri, Maria Francesca Lodovica; Ait-Ali, Lamia; Marcheschi, Paolo; Quadrelli, Paola; Mariani, Massimiliano; Margaryan, Rafik; Pennè, Wanda; Savino, Marco; Prencipe, Giuseppe; others,

Home-Based Intervention Tool for Cardiac Telerehabilitation: Protocol for a Controlled Trial Journal Article

In: JMIR Research Protocols, vol. 14, no. 1, pp. e47951, 2025.

BibTeX

2024

Podda, Marco; Bonechi, Simone; Palladino, Andrea; Scaramuzzino, Mattia; Brozzi, Alessandro; Roma, Guglielmo; Muzzi, Alessandro; Priami, Corrado; Sîrbu, Alina; Bodini, Margherita

Classification of Neisseria meningitidis genomes with a bag-of-words approach and machine learning Journal Article

In: iScience, 2024.

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Pingitore, Alessandro; Zhang, Chenxiang; Vassalle, Cristina; Ferragina, Paolo; Landi, Patrizia; Mastorci, Francesca; Sicari, Rosa; Tommasi, Alessandro; Zavattari, Cesare; Prencipe, Giuseppe; others,

Machine learning to identify a composite indicator to predict cardiac death in ischemic heart disease Journal Article

In: International Journal of Cardiology, vol. 404, pp. 131981, 2024.

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Cignoni, Giacomo; Scatena, Cristian; Frascarelli, Chiara; Fusco, Nicola; Naccarato, Antonio Giuseppe; Fanelli, Giuseppe Nicoló; Sîrbu, Alina

PD-L1 Classification of Weakly-Labeled Whole Slide Images of Breast Cancer Journal Article

In: arXiv preprint arXiv:2404.10175, 2024.

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Graziani, Caterina; Drucks, Tamara; Jogl, Fabian; Bianchini, Monica; scarselli,; Gärtner, Thomas

The Expressive Power of Path-Based Graph Neural Networks Proceedings Article

In: Forty-first International Conference on Machine Learning, 2024.

Abstract | Links | BibTeX

Brodo, Linda; Bruni, Roberto; Falaschi, Moreno

A framework for monitored dynamic slicing of Reaction Systems Journal Article

In: Natural Computing, 2024.

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Tolloso, Matteo; Galfrè, Silvia Giulia; Pavone, Arianna; Podda, Marco; S^ırbu, Alina; Priami, Corrado

How Much Do DNA and Protein Deep Embeddings Preserve Biological Information? Proceedings Article

In: International Conference on Computational Methods in Systems Biology, pp. 209–225, Springer 2024.

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Castiglioni, Valentina; Loreti, Michele; Tini, Simone

Bio-Stark: A Tool for the Time-Point Robustness Analysis of Biological Systems Proceedings Article

In: Gori, Roberta; Milazzo, Paolo; Tribastone, Mirco (Ed.): Computational Methods in Systems Biology - 22nd International Conference, CMSB 2024, Pisa, Italy, September 16-18, 2024, Proceedings, pp. 62–70, Springer, 2024.

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Castiglioni, Valentina; Loreti, Michele; Tini, Simone

RobTL: Robustness Temporal Logic for CPS Proceedings Article

In: Majumdar, Rupak; Silva, Alexandra (Ed.): 35th International Conference on Concurrency Theory, CONCUR 2024, September 9-13, 2024, Calgary, Canada, pp. 15:1–15:23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.

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Castiglioni, Valentina; Lanotte, Ruggero; Loreti, Michele; Tini, Simone

Evaluating the Effectiveness of Digital Twins Through Statistical Model Checking with Feedback and Perturbations Proceedings Article

In: Haxthausen, Anne E.; Serwe, Wendelin (Ed.): Formal Methods for Industrial Critical Systems - 29th International Conference, FMICS 2024, Milan, Italy, September 9-11, 2024, Proceedings, pp. 21–39, Springer, 2024.

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Castiglioni, Valentina; Lanotte, Ruggero; Loreti, Michele; Manicardi, Desiree; Tini, Simone

[No title] Journal Article

In: Theoretical Computer Science, vol. 1022, pp. 114934, 2024, ISSN: 0304-3975.

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Castiglioni, Valentina; Lanotte, Ruggero; Loreti, Michele; Manicardi, Desiree; Tini, Simone

Robustness for biochemical networks: Step-by-step approach Journal Article

In: Theoretical Computer Science, vol. 1022, pp. 114934, 2024, ISSN: 0304-3975.

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Brodo, Linda; Bruni, Roberto; Falaschi, Moreno; Gori, Roberta; Milazzo, Paolo; Montagna, Valeria; Pulieri, Pasquale

Causal analysis of positive Reaction Systems Journal Article

In: International Journal on Software Tools for Technology Transfer, pp. 1–18, 2024.

BibTeX

Bruni, Roberto; Gori, Roberta; Milazzo, Paolo; Siboulet, Hélène

Melding Boolean networks and reaction systems under synchronous, asynchronous and most permissive semantics Journal Article

In: Natural Computing, vol. 23, no. 2, pp. 235–267, 2024.

BibTeX

Bowles, Juliana; Brodo, Linda; Bruni, Roberto; Falaschi, Moreno; Gori, Roberta; Milazzo, Paolo

Enhancing Reaction Systems with Guards for Analysing Comorbidity Treatment Strategies Proceedings Article

In: International Conference on Computational Methods in Systems Biology (CMSB 2024), pp. 27–44, Springer 2024.

BibTeX

Ballis, Demis; Brodo, Linda; Falaschi, Moreno; Olarte, Carlos

ccReact: a rewriting framework for the formal analysis of reaction systems Journal Article

In: International Journal on Software Tools for Technology Transfer, vol. 26, pp. 707–725, 2024.

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Ballis, Demis; Brodo, Linda; Falaschi, Moreno

Modeling and Analyzing Reaction Systems in Maude Journal Article

In: Electronics, vol. 13, no. 6, 2024.

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Bendjeddou, Asma; Brodo, Linda; Falaschi, Moreno; Tiezzi, Elisa Benedetta Primavera

A Computational Model of the Secondary Hemostasis Pathway in Reaction Systems Journal Article

In: Mathematics, vol. 12, no. 15, 2024.

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Ballis, Demis; Brodo, Linda; Falaschi, Moreno; Olarte, Carlos

Process Calculi and Rewriting Techniques for Analyzing Reaction Systems Proceedings Article

In: Gori, Roberta; Milazzo, Paolo; Tribastone, Mirco (Ed.): Computational Methods in Systems Biology - 22nd International Conference, CMSB 2024, Pisa, Italy, September 16-18, 2024, Proceedings, pp. 1–18, Springer, 2024.

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Brodo, Linda; Bruni, Roberto; Falaschi, Moreno

A framework for monitored dynamic slicing of reaction systems Journal Article

In: Nat. Comput., vol. 23, no. 2, pp. 217–234, 2024.

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Sproston, Jeremy

Clock-Dependent Probabilistic Timed Automata with One Clock and No Memory Proceedings Article

In: Ogata, Kazuhiro; Méry, Dominique; Sun, Meng; Liu, Shaoying (Ed.): Proceedings of the 25th International Conference on Formal Engineering Methods (ICFEM 2024), pp. 70–84, Springer, 2024.

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Graziani, Caterina; Drucks, Tamara; Jogl, Fabian; Bianchini, Monica; scarselli,; Gärtner, Thomas

The Expressive Power of Path-Based Graph Neural Networks Proceedings Article

In: Forty-first International Conference on Machine Learning, 2024.

Links | BibTeX

2023

Brodo, Linda; Bruni, Roberto; Falaschi, Moreno; Gori, Roberta; Milazzo, Paolo

Attractor and Slicing Analysis of a T Cell Differentiation Model Based on Reaction Systems Proceedings Article

In: International Symposium ``from Data to Models and Back'' (DataMod 2023), Springer 2023.

BibTeX

Pham, Giang; Milazzo, Paolo

Preliminary Results on Shapley Value Notions and Propagation Methods for Boolean Networks Proceedings Article

In: International Symposium ``from Data to Models and Back'' (DataMod 2023), Springer 2023.

BibTeX

Pernice, Simone; Maglione, Alessandro; Tortarolo, Dora; Sirovich, Roberta; Clerico, Marinella; Rolla, Simona; Beccuti, Marco; Cordero, Francesca

A new computational workflow to guide personalized drug therapy Journal Article

In: Journal of Biomedical Informatics, vol. 148, pp. 104546, 2023, ISSN: 1532-0464.

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Testa, Irene; Prencipe, Giuseppe; Priami, Corrado; Sîrbu, Alina

Comparison of Machine Learning Classifiers on Integrated Transcriptomic Data Proceedings Article

In: 2023 IEEE International Conference on Big Data (BigData), pp. 4987–4996, IEEE 2023.

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Graziani, Caterina; Drucks, Tamara; Bianchini, Monica; scarselli,; Gärtner, Thomas

No PAIN no Gain: More Expressive GNNs with Paths Proceedings Article

In: NeurIPS 2023 Workshop: New Frontiers in Graph Learning, 2023.

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2021

Sîrbu, Alina; Barbieri, Greta; Faita, Francesco; Ferragina, Paolo; Gargani, Luna; Ghiadoni, Lorenzo; Priami, Corrado

Early outcome detection for COVID-19 patients Journal Article

In: Scientific Reports, vol. 11, no. 1, pp. 18464, 2021.

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2020

Prezza, Nicola; Pisanti, Nadia; Sciortino, Marinella; Rosone, Giovanna

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform Journal Article

In: BMC Bioinformatics, vol. 21, no. S8, 2020.

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Guerrini, Veronica; Louza, Felipe A; Rosone, Giovanna

Metagenomic analysis through the extended Burrows-Wheeler transform Journal Article

In: BMC Bioinformatics, vol. 21, no. S8, 2020.

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Kocian, Alexander; Carmassi, Giulia; Cela, Fatjon; Incrocci, Luca; Milazzo, Paolo; Chessa, Stefano

Bayesian Sigmoid-Type Time Series Forecasting with Missing Data for Greenhouse Crops Journal Article

In: Sensors, vol. 20, no. 11, pp. 3246, 2020.

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Kocian, Alexander; Massa, Daniele; Cannazzaro, Samantha; Incrocci, Luca; Lonardo, Sara Di; Milazzo, Paolo; Chessa, Stefano

Dynamic Bayesian network for crop growth prediction in greenhouses Journal Article

In: Computers and Electronics in Agriculture, vol. 169, pp. 105167, 2020.

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Barbuti, Roberto; Gori, Roberta; Milazzo, Paolo

Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation Journal Article

In: Theoretical Computer Science, 2020.

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Muscolino, Alessandro; Maria, Antonio Di; Alaimo, Salvatore; Borzì, Stefano; Ferragina, Paolo; Ferro, Alfredo; Pulvirenti, Alfredo

NETME: On-the-fly knowledge network construction from biomedical literature Book Section

In: International Conference on Complex Networks and their Applications (COMPLEX), Springer International Publishing, 2020.

BibTeX

Ferragina, Paolo; Vinciguerra, Giorgio

The PGM-index: a fully-dynamic compressed learned index with provable worst-case bounds Journal Article

In: Proceedings of the VLDB Endowment, vol. 13, no. 10, pp. 1162–1175, 2020.

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Rossi, Alessio; Pozzo, Eleonora Da; Menicagli, Dario; Tremolanti, Chiara; Priami, Corrado; Sirbu, Alina; Clifton, David A; Martini, Claudia; Morelli, Davide

A Public Dataset of 24-h Multi-Levels Psycho-Physiological Responses in Young Healthy Adults Journal Article

In: Data, vol. 5, no. 4, pp. 91, 2020.

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Ferrari, Elisa; Retico, Alessandra; Bacciu, Davide

Measuring the effects of confounders in medical supervised classification problems: the Confounding Index (CI) Journal Article

In: Artificial Intelligence in Medicine, vol. 103, pp. 101804, 2020.

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Bove, Pasquale; Micheli, Alessio; Milazzo, Paolo; Podda, Marco

Prediction of Dynamical Properties of Biochemical Pathways with Graph Neural Networks Proceedings Article

In: Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies, SCITEPRESS - Science and Technology Publications, 2020.

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Torrado, Juan C; Wold, Ida; Jaccheri, Letizia; Pelagatti, Susanna; Chessa, Stefano; Gomez, Javier; Hartvigsen, Gunnar; Michalsen, Henriette

Developing Software for Motivating Individuals with Intellectual Disabilities to Do Outdoor Physical Activity Proceedings Article

In: Proceedings of the ACM/IEEE 42nd International Conference on Software Engineering: Software Engineering in Society, pp. 81–84, Association for Computing Machinery, Seoul, South Korea, 2020, ISBN: 9781450371244.

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Kocian, Alexander; Chessa, Stefano; Grolman, Wilko

Monitoring Practitioner's Skills in Pure-Tone Audiometry Journal Article

In: International Journal of E-Health and Medical Communications, vol. 11, no. 2, pp. 38–63, 2020.

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2019

Pappalardo, Luca; Cintia, Paolo; Ferragina, Paolo; Massucco, Emanuele; Pedreschi, Dino; Giannotti, Fosca

PlayeRank: Data-driven Performance Evaluation and Player Ranking in Soccer via a Machine Learning Approach Journal Article

In: ACM Transactions on Intelligent Systems and Technology, vol. 10, no. 5, pp. 1–27, 2019.

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Misselbeck, Karla; Parolo, Silvia; Lorenzini, Francesca; Savoca, Valeria; Leonardelli, Lorena; Bora, Pranami; Morine, Melissa J; Mione, Maria Caterina; Domenici, Enrico; Priami, Corrado

A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome Journal Article

In: Nature Communications, vol. 10, no. 1, 2019.

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Morelli, Davide; Rossi, Alessio; Cairo, Massimo; Clifton, David A

Analysis of the Impact of Interpolation Methods of Missing RR-intervals Caused by Motion Artifacts on HRV Features Estimations Journal Article

In: Sensors, vol. 19, no. 14, pp. 3163, 2019.

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Bondioli, Mariasole; Chessa, Stefano; Narzisi, Antonio; Pelagatti, Susanna; Piotrowicz, Dario

Capturing Play Activities of Young Children to Detect Autism Red Flags Book Section

In: Advances in Intelligent Systems and Computing, pp. 71–79, Springer International Publishing, 2019.

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Ciuffoletti, Augusto

Design of an Open Remote Electrocardiogram (ECG) Service Journal Article

In: Future Internet, vol. 11, no. 4, pp. 101, 2019.

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Rossi, Alessio; Perri, Enrico; Pappalardo, Luca; Cintia, Paolo; Iaia, Fedon Marcello

Relationship between External and Internal Workloads in Elite Soccer Players: Comparison between Rate of Perceived Exertion and Training Load Journal Article

In: Applied Sciences, vol. 9, no. 23, pp. 5174, 2019.

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Pappalardo, Luca; Cintia, Paolo; Rossi, Alessio; Massucco, Emanuele; Ferragina, Paolo; Pedreschi, Dino; Giannotti, Fosca

A public data set of spatio-temporal match events in soccer competitions Journal Article

In: Scientific Data, vol. 6, no. 1, 2019.

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Simoni, Giulia; Vo, Hong Thanh; Priami, Corrado; Marchetti, Luca

A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology Journal Article

In: Briefings in Bioinformatics, vol. 21, no. 2, pp. 527–540, 2019.

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Franco, Giuseppe; Cerina, Luca; Gallicchio, Claudio; Micheli, Alessio; Santambrogio, Marco Domenico

Continuous Blood Pressure Estimation Through Optimized Echo State Networks Book Section

In: Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions, pp. 48–61, Springer International Publishing, 2019.

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67 entries « 1 of 2 »