Category: important_news

On March 20th, 2025, we proudly celebrated the achievements of Isotta Trescato, Giulia Cesaro, and Francesca Longhin, who successfully defended their Ph.D. theses in Information Engineering at the University of Padua. 🎉

Each of them conducted outstanding research on cutting-edge topics in computational medicine and bioinformatics, contributing valuable knowledge and tools to their respective fields.

🔬 Giulia Cesaro focused her PhD research on the development of computational methods to infer cell-cell communication using single-cell RNA sequencing data. Her work allows for a deeper understanding of how cells interact with each other in complex tissues—knowledge that is critical for interpreting biological processes such as development, immune response, and disease progression.

🧬 Francesca Longhin worked on enhancing variant calling and interpretation pipelines through data-driven in-silico simulations and artificial intelligence techniques. Her project improves the accuracy and reliability of genetic variant analysis, a fundamental aspect of personalized medicine and genomic diagnostics.

📊 Isotta Trescato dedicated her thesis to transparent artificial intelligence approaches for modeling disease progression using real-world clinical registry data. Her goal was to build predictive models that are not only accurate but also interpretable by clinicians—an essential requirement for integrating AI into real-world healthcare settings.

Last week, Giacomo attended the 33rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (March 10-12, 2025 – Turin, Italy).

It was a great opportunity to attend insightful talks and engage in discussions about the present and future of high-performance computing!

We are also proud to share that our work, “quickSparseM: a library for memory- and time-efficient computation on large, sparse matrices with application to omics data” by Giacomo Baruzzo, Giulia Cesaro, and Barbara Di Camillo, received the Best Paper Award in the “High Performance Computing in Modelling and Simulation” session. The article will soon be available in the conference proceedings on the IEEE website (https://www.computer.org/csdl/proceedings/1000543).

We extend our sincere thanks to the conference and session organizers for hosting this event and giving us the opportunity to present our research!

On Tuesday, 21 January 2025, the Aula Morgagni at the Policlinico Universitario of Padua hosted the event “Introduction to Artificial Intelligence in Medicine.” Organised by the Departments of Information Engineering (DEI) and Medicine (DIMED), the meeting brought together experts and researchers to discuss the transformative role of AI in healthcare.

The session was opened by Professors Gaudenzio Meneghesso, Director of the DEI, and Paolo Simioni, Director of the DIMED, who welcomed attendees and highlighted the interdisciplinary collaboration driving AI innovation.

The scientific programme included a series of engaging presentations:

• Introduction to Machine Learning by Prof. Barbara Di Camillo (DEI) provided a comprehensive overview of the fundamentals of machine learning and its applications in medical research.
• Applications to Clinical Records by Dr. Erica Tavazzi (DEI), a researcher from our group, explored AI-driven approaches to extracting insights from patient data.
• Applications to Imaging Data by Dr. Marco Castellaro (DEI) demonstrated how AI enhances diagnostic imaging techniques.
• Large Language Models and Generative AI and Chatbots were expertly discussed by Prof. Giorgio Satta (DEI), who highlighted their potential to revolutionise communication and support activities.
• Data Representation and Knowledge in Generative AI by Prof. Nicola Ferro (DEI) delved into the technical challenges and opportunities in knowledge-based systems.

The event concluded with a dynamic Q&A session, fostering lively discussions among attendees and speakers.

The SysBioBig group wishes you a Merry Christmas and Happy Holidays!
Best of luck and success in the New Year! 🎄🎅🏻🎁✨

We are proud to announce that five of our PhD students recently presented their innovative research during the 2nd edition of the “Young Minds at Work: Blending Biomedical Sciences and Bioinformatics” conference. Their contributions included two oral presentations and three poster presentations, showcasing the depth and breadth of their scientific work.

Oral Presentations:

• Matteo Baldan: “Simulation of bacteria interaction networks: from topology to species abundance.”
• Gaia Tussardi: “Addressing the Biological Interpretation of High-Dimensional Cell-Cell Communication Data from Single Cell Transcriptomics Through an Interactive Web Application.”

Poster Presentations:

This conference offered an exceptional platform for our students to share their insights, gain valuable feedback, and engage with the broader scientific community working at the intersection of biomedical sciences and bioinformatics.

Congratulations to our team for their outstanding contributions and impactful research presentations! Let’s keep pushing the boundaries of scientific discovery.

On November 20 and 21, 2024, the Department of Information Engineering of the University of Padova, in collaboration with Fondazione UniSMART, organized two events on Artificial Intelligence: “AI@DEI for Industry” and “AI@DEI for Biomeds and Health”.

The events focused on innovative topics such as Generative AI, Data Analytics, AI in biomedical research and healthcare, Bioinformatics, and Health Informatics, showcasing practical applications and future perspectives for collaboration between University and Industry.

During the event, our researcher Giacomo Baruzzo presented the AI activities in Bioinformatics and Health Informatics carried out by the computer engineering group, including some research projects conducted by our research group.

The 4th edition of the Brain Innovation Days, organised by the European Brain Council, will take place on 13-14 November 2024 in Brussels, Belgium, under the overarching theme “Navigating the Brain Across a Lifetime“.
This event aims to bring the wider brain ecosystem together to foster dialogue, exchange knowledge, accelerate investment in research & innovation, and facilitate business development.

The main theme will revolve around 5 subthemes:

🧠 Blossoming Brains: Early Brain Development
🏫 Building Brains: Schools and Workplaces
🏥 Timeless Brains: Nurturing Resilience, Embracing Change
⚙️ Holistic Brains: Strategies for Brain Health in a Dynamic Society
🚀 Advancements in Neurotechnology: Pioneering Innovations

The programme will include a wide array of session types, including plenary sessions, inspiring Brain Talks, Poster and Innovation Showcase, matchmaking and networking activities, the Brain Innovation Days Pitch Competition, breakout sessions, panels, and how-to sessions.

Our PI Prof. Barbara Di Camillo will take part in the “Harnessing AI for brain health: lab to market to society” panel, an event that marks the conclusion of the BRAINTEASER project, celebrating its advances in remote prediction, prevention, and care for people with multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Key sessions will cover the transition of BRAINTEASER’s technology (an app and wearables) from the lab to the market, and the potential impact on patient-centred care. There will also be a showcase of the project’s clinical app and insights on its application to other neurodegenerative diseases like Parkinson’s.

The Brain Innovation Days offer an exciting opportunity to engage with the latest innovations in brain health, and we are proud to see Prof. Di Camillo contribute to the discussion on AI’s role in advancing care from lab to market, reinforcing our commitment to impactful, patient-centred research.

These days our group is attending the 19th conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2024) in Benevento, Italy.

We are proud to contribute to the event with the special session “Informatics research in bioinformatics: Contributions from the CINI-InfoLife network” co-organised and co-chaired by our researchers Giacomo Baruzzo and Mikele Milia, part of Young-InfoLife, and the following 5 oral presentations, most of them developed within the projects we are involved in (PNC/PNRR DARE initiative, H2020 BRAINTEASER project, Horizon Europe REDDIE project):

• “Comprehensive benchmarking of network inference methods for 16S rDNA-Seq data”, Piero Mariotto, Matteo Baldan, Barbara Di Camillo, and Giacomo Baruzzo
• “Comparing Propensity Score-Based Methods in Estimating the Treatment Effects: A Simulation Study“, Sara Poletto, Enrico Longato, Erica Tavazzi, and Martina Vettoretti
• “Effect of Clinical History on Predictive Model Performance for Renal Complications of Diabetes”, Davide Dei Cas, Barbara Di Camillo, Gian Paolo Fadini, Giovanni Sparacino and Enrico Longato
• “Exploring the Impact of Environmental Pollutants on Multiple Sclerosis Progression“, Elena Marinello, Erica Tavazzi, Enrico Longato, Pietro Bosoni, Arianna Dagliati, Mahin Vazifehdan, Riccardo Bellazzi, Isotta Trescato, Alessandro Guazzo, Martina Vettoretti, Eleonora Tavazzi, Lara Ahmad, Roberto Bergamaschi, Paola Cavalla, Umberto Manera, Adriano Chiò and Barbara Di Camillo
• “Network-Based Cross-Entropy Approach for Continuous Genotype-Phenotype Association Analysis”, Mikele Milia, Giacomo Baruzzo, and Barbara Di Camillo

We extend our sincere thanks to the conference organisers for facilitating this event and for providing us with the opportunity to present our research.

From July 15th to 19th, 2024, our group participated in the 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) held in Orlando, Florida.

Our group was represented in the Health Informatics track with a poster presentation titled “Characterization of Chronic Kidney Disease Progression in Patients with Diabetes via Group-Based Multi-Trajectory Modeling”, authored by Alessandro Guazzo, Enrico Longato, Gian Paolo Fadini, Giovanni Sparacino, Rema Padman, and Barbara Di Camillo.

Additionally, our Principal Investigator, Prof. Barbara Di Camillo, was an organizer and speaker for two impactful mini-symposia.
The first mini-symposium, “Trustworthy AI in Medicine: Implications for Data, Algorithms and Systems,” took place on Wednesday, July 17th. This session addressed the critical issue of trustworthiness in AI systems used in clinical settings. The discussion covered various aspects, from data collection and preprocessing to algorithm reliability and explainability, drawing on practical examples from international projects such as the 4CE consortium and the BRAINTEASER project.
The second mini-symposium, “Fostering Equity in Science, Technology and Innovation: Insights and Best Practices in Co-Creating Policy Recommendations,” was held on Friday, July 19th. This session focused on promoting equity in these disciplines through collaborative policy-making. Experts from diverse backgrounds shared their experiences and best practices. The symposium provided valuable insights into the co-creation process, highlighting the importance of inclusivity and diversity in shaping effective policies.

We extend our gratitude to the organizers for making our participation in EMBC 2024 a fruitful experience, marked by engaging discussions and potential collaborations.