logo

Modelling and vErification of alkaptonuria and multiple sclerosis Driven by biomedICAl data

The goal of this project is to bridge the gap between data, models and validation, integrating the data-driven and model-driven research directions, so that to develop next generation modelling and analysis approaches for biomedical investigations.

We are developing the MEDICA framework, which combines three analysis phases: (1) extracting existing knowledge from integrated datasets, that will feed into (2) building multilevel mechanistic models, which will then go through (3) validation and model checking.

Biomedical research needs are the driving force of the project. We are tackling open research questions for Multiple Sclerosis (MS) and Alkaptonuria (AKU), for which we have world-leading experts in our consortium.

Our team

  • Vincenzo Lomonaco
  • Silvia Giulia Galfrè
  • Francesca Levi
  • Francesco Massafra
  • Paolo Milazzo
  • Giang Pham
  • Corrado Priami
  • Samuele Punzo
  • Alina Sîrbu (UNIBO)

  • Elvio Amparore
  • Marco Beccuti
  • Marinella Clerico
  • Massimiliano De Pierro
  • Alessandro Maglione
  • Simone Pernice
  • Simona Rolla
  • James Sproston

  • Moreno Falaschi
  • Francesca Ariani
  • Linda Brodo
  • Sara Brunetti
  • Caterina Graziani
  • Veronica Lachi
  • Giulia Palma
  • Alessandra Renieri
  • Simone Rinaldi
  • Bianca Roncaglia
  • Ottavia Spiga
  • Anna Visibelli

  • Simone Tini
  • Ruggero Lanotte
  • Desiree Manicardi
  • Nicoletta Sabadini

Contact: alina.sirbu@unipi.it

Publications

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

2024

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.

Abstract | Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

Ballis, Demis; Brodo, Linda; Falaschi, Moreno

Modeling and Analyzing Reaction Systems in Maude Journal Article

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

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

This project was financed by the European Union – Next-GenerationEU – National Recovery and Resilience Plan (NRRP) – MISSION 4 COMPONENT 2, INVESTMENT N. 1.1, CALL PRIN 2022 D.D. 104 02-02-2022 – MEDICA CUP N. I53D23003720006 .