WP5 Progress Presented at the REDDIE Project Stakeholder Meeting in Madrid

On Sunday, 8th September 2024, the 2nd Stakeholder Meeting of the REDDIE project took place at the IFEMA Convention Centre in Madrid. During the event, our tenure-track researcher and PI, Martina Vettoretti, presented the activities related to Work Package 5 (WP5), Advanced Methodological Frameworks for Enhancing Clinical Trials with Real-World and Virtual Evidence, for which our group is the leader.

The presentation focused on the progress made in two key methodological tasks. The first is the enhancement of methodologies for conducting retrospective observational studies, where we have performed a systematic review to identify and evaluate available methods on a set of artificial datasets. This work aims to define guidelines for selecting appropriate methods in various contexts and develop a fully-automated analysis pipeline to improve reproducibility and scalability.
The second task involves advancing tools for building data-driven simulation models. These models are becoming increasingly important as the simulated data they can create provide a complementary perspective to real-world data and clinical trial data. Simulated data can be generated using computational models, such as dynamic Bayesian networks (DBNs), a technique in which our group has both methodological expertise and practical experience. Within the REDDIE project, we are advancing the use of DBNs to simulate long-term outcomes in patients with type 1 and type 2 diabetes, leveraging RWD sourced from national diabetes registries to build more accurate models.
These efforts will ultimately contribute to more personalised approaches in diabetes management, while also improving the scalability and robustness of the simulation models used in healthcare research.

We extend our gratitude to the organisers for a well-executed and insightful meeting, and for the valuable feedback received from key stakeholders, whose input is essential to the success of this project.

Sharing Our Research at CIBB 2024 in Benevento

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.

Our PhD Candidates Highlight Their Research Milestones in Formal Review

Last week, our PhD students Francesca Longhin, Giulia Cesaro, Isotta Trescato (3rd year), Mikele Milia (2nd year), and Sara Poletto (1st year) presented their research progress to a departmental commission. This formal step in their doctoral journey offered the entire group, as well as attendees, a valuable opportunity to reflect on the progress of our young researchers. It also provided a platform to share and discuss the diverse research directions currently being developed within our team, highlighting the breadth and depth of work being undertaken in our international projects.

Highlights from IEEE EMBC 2024

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.

University of Padova Hosts Danish Medicines Agency for REDDIE Project Technical Meeting

On July 10-12, 2024, our group had the pleasure of hosting Dr. Tirdad Seifi Ala, our esteemed partner from the Danish Medicines Agency (Lægemiddelstyrelsen, DMA), for an in-depth technical meeting within the REDDIE project. This visit was a significant milestone in our ongoing collaboration and provided an excellent opportunity to delve into the details of the current activities in Work Package 5 (WP5), titled “Advanced Methodological Frameworks for Enhancing Clinical Trials with Real-World and Virtual Evidence.”

The WP5 is led by our research group under the supervision of Principal Investigator Dr. Martina Vettoretti, with active involvement from both UNIPD and DMA. During the meeting, we had the opportunity to discuss some of the latest methodologies developed by our team, focusing on predictive models for the progression of chronic diseases and the conduction of retrospective observational studies.

The discussions were highly productive and insightful. Dr. Seifi Ala provided valuable feedback and shared his expertise, which helped refine our approaches and identify new avenues for future research. The collaborative atmosphere facilitated a deeper understanding of the challenges and opportunities in leveraging real-world evidence to enhance clinical trials.

As our partnership with DMA continues to strengthen, we are excited about the potential to contribute significantly to the use of real-world evidence for complementing randomized controlled trials. Our joint efforts aim to improve the efficacy, safety, and cost-effectiveness of technologies designed to prevent and treat diabetes, ultimately benefiting patients and healthcare systems alike.

We look forward to continuing this fruitful collaboration and are eager to see the impact of our combined contributions to the REDDIE project.

REDDIE Technical Meeting between UNIPD and NOH on Diabetes Outcome Analysis

On July 3-4, 2024, our group hosted a productive technical meeting between UNIPD and NOH in the context of the REDDIE project. This significant event was focused on exploring collaborative opportunities and discussing the utilisation of data from Danmarks Statistik.
The meeting brought together key researchers from both institutions, who engaged in in-depth discussions on the methodologies for analysing diabetes outcomes using real-world data. The exchange of ideas and expertise was stimulating, as participants identified numerous points of contact and potential synergies.
Throughout the two days, the researchers delved into various aspects of diabetes research, emphasising the importance of leveraging real-world data to enhance the understanding of diabetes outcomes. The discussions underscored the potential benefits of integrating diverse datasets and employing advanced analytical techniques to improve research quality and impact. The event concluded with a shared vision of developing innovative solutions and methodologies that will ultimately benefit patients and healthcare providers.
This meeting marks a promising step forward in the collaboration between our group and NOH. The partners expressed enthusiasm about the future possibilities and are committed to continuing their joint efforts to advance diabetes research. 

Great moments at BITS 2024 conference in Trento

Our group has attended the 20th Annual Meeting of the Bioinformatics Italian Society (BITS 2024) in Trento. It was an incredibly successful event!
We are proud to have contributed to the event with 2 oral presentations from Gaia and Piero:

  • “Limitations of the co-occurrence-based approach in the inference of microbiota interaction networks” Piero Mariotto, Matteo Baldan, Barbara Di Camillo, Giacomo Baruzzo
  • “Interactive exploration of cell-cell communication results from single-cell RNA sequencing data through a webapp” Gaia Tussardi, Giulia Cesaro, Barbara Di Camillo, Giacomo Baruzzo

Also, Gaia co-chaired the “YOUNG BITS, RSG-Italy & CINI Young-InfoLife” Symposium, a supporting and stimulating forum for undergraduate, master, PhD students and early stage researchers to present their research and to connect with the wider Italian Bioinformatics Community.

Meeting Between Information Engineering and Women’s and Children’s Health Departments

Yesterday, June 4, 2024, a meeting took place between the Department of Information Engineering and the Department of Women’s and Children’s Health at the University of Padova. The objective of this meeting was to present our respective research areas and explore potential synergies and points of collaboration.
Our researchers, Martina Vettoretti and Giacomo Baruzzo, showcased the research directions of our group, highlighting ongoing projects and key topics. Their presentations were well-received and sparked a lively discussion, with numerous insightful questions from attendees.
This productive meeting demonstrated a strong interest in potential collaborations between the two departments. We are optimistic that this initial exchange will lead to fruitful cooperative opportunities in the near future.

Exciting conference announcements

We are thrilled to announce that our team will be actively participating in the upcoming BITS 2024 and CIBB 2024 conferences! These events present a significant opportunity for us to share our research, connect with fellow professionals in the field, and discover the latest innovations in bioinformatics and computational biology. We hope to see you there!

We are also excited to share some fantastic news: our Principal Investigator, Barbara Di Camillo, will be part of the organizing committee for IEEE ICHI 2025! Stay tuned for more updates.

Key Takeaways from Our Team’s Participation at the World Health Forum Veneto 2024

On 21-22 March 2024, our team had the pleasure of attending the Artificial Intelligence for Medicine conference, hosted within the World Health Forum Veneto in Padova.

Our PI Prof. Barbara Di Camillo delivered an insightful talk titled “Bringing AI into clinical practice: A deep dive into the BRAINTEASER project”, where she presented our work to bring responsible AI into clinical practice. On this occasion, Professor Di Camillo was also interviewed by the prestigious Corriere della Sera, as featured in the article below.

This event was also an opportunity to present some of our group’s latest work. Our senior researchers Erica Tavazzi and Enrico Longato presented a poster titled “Improving Discrimination Performance in Artificial Intelligence Models for Rare Diseases: Strategies for Dealing with Data Scarcity”, sharing insights into strategies for enhancing predictive model performance with limited data.

This event, designed to examine the current state and explore the future of medical sciences and technologies aimed at enhancing care and life quality, was a great opportunity to network and foster new collaborations.

Systems Biology and Bioinformatics Group
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