Category: important_news

Last week, Barbara, Giacomo, Giulia, Gaia, and Matteo attended the 33rd Conference on Intelligent Systems for Molecular Biology & 24th European Conference on Computational Biology (ISMB/ECCB 2025), held in Liverpool, UK, from July 20–24, 2025.

The conference was a valuable opportunity to attend cutting-edge presentations, engage in discussions on the latest advances in bioinformatics, and foster new collaborations.

We’re proud to share that our group contributed to the scientific program with several presentations:

• Giulia Cesaro delivered an oral presentation in the NetBio session titled “Cell-specific Graph Operation Strategy on Signaling Intracellular Pathways” showcasing work done in collaboration with the CostaLab at RWTH Aachen University.
• Giacomo Baruzzo presented the poster “Realistic Simulation of NGS Reads from Tumoral Samples with MOV&RSim”, a project led by Francesca Longhin (former PhD student of our group), in collaboration with AB Analitica.
• Matteo Baldan presented the poster “Integrating Biological Knowledge for Feature Summarization in Spatial Transcriptomics”.
• Gaia Tussardi presented the poster “Multilevel Network Visualization for Deciphering Dysregulated Cellular Signalling”.
• In collaboration with the CostaLab at RWTH Aachen University, we also co-organized the tutorial “Computational Approaches for Deciphering Cell-Cell Communication from Single-Cell and Spatial Transcriptomics Data”.

Last week, our group attended the 23^rd International Conference on Artificial Intelligence in Medicine (AIME 2025) in Pavia, Italy.

It was a fantastic opportunity to follow high-quality presentations and engage with leading researchers and professionals from across the AI and healthcare communities.

We are proud to share that we contributed to the scientific program with four research papers:

• Davide Dei Cas held a short oral presentation entitled “Exploring the Use of Projecting Conflicting Gradients in Multi-Task Neural Networks with an Application to Amyotrophic Lateral Sclerosis.”

• Erica Tavazzi co-authored the poster “Towards Distributed Process Discovery in Healthcare: Testing and Proving the Feasibility of the Federated Alpha+ Algorithm.”

• At the 2^nd International Workshop on Process Mining Applications for Healthcare (PM4H 2025), our group was also involved in two contributions: “Predicting Next Clinical Event in Amyotrophic Lateral Sclerosis using Process-Oriented Machine Learning Models: a Case Study” and “Federated I-PALIA: Privacy-By-Design Distributed Process Discovery for Duplicated Activities in Healthcare” (🏆Best Paper Award – PM4H 2025).

We sincerely thank the conference organizers for hosting this event and for giving us the opportunity to share our research.

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.