
ACROSS
Actionable, Collaborative, Reusable, interOperable Sepsis System

Abstract
Standardizing heterogeneous healthcare data is essential for understanding complex diseases and improving treatment. In line with the national sepsis program, the SDSC is collaborating with the University Hospital of Lausanne (CHUV), the University Hospital Bern (Inselspital) and the Children Hospital in Zurich (Kispi) to develop an AI-powered data pipeline for sepsis quality-of-care monitoring. Deployed at CHUV, the tool provides caregivers and hospital managers with timely feedback on clinical practice and enables benchmarking of key measures.
This strategic project aims to create a standardized software solution that enables hospitals to organize and share sepsis-related data in a consistent way. By implementing the same approach across partner hospitals, the project will improve data quality, support expansion to additional healthcare settings – including pediatric care – and lay the foundation for a national sepsis program that is compatible with international standards and, more broadly, for OMOP-based infrastructure in Switzerland. [1]
People
Collaborators


As an EPFL Life Science Engineer, my main interest is to do science with an impact. FAIR principals guide my work style, and I strive for user-centric infrastructure to encompass data science in the biomedical and governmental spheres. I have experience in Global Health, working with multi-hospital surveillance system for pandemics, as well as training data scientist (thegraphcourses.org). My core side-interests lie in ocean conservation notably cetacean conservation, biodiversity, and untreated health problematics from lower and middle income countries. I have solid hard skills in problem-solving, data engineering in AI/ML, and have developed soft skills in creativity and social integration. I have acquired domain knowledge in a diversity of fields: from biology-related sciences such as human gut microbiology, epidemiology, and environmental sciences, as well as social sciences such as anthropology and psychology. I am always happy to engage with new people on innovative and impactful thematics so please do reach out!


Stefan has a background in Biology and decided to move towards evolutionary bioinformatics for both his MSc and PhD.Over the years, he developed a passion for the entire data analysis process: from collecting data, to analyzing and presenting results. Presentations, particularly opportunities for public speaking, are activities he enjoys since he values communication a lot. In order to follow this passion and deepen his knowledge on systems to collect and manage data, he joined SDSC in 2023 as a Biomedical Data Engineer.Outside work, Stefan is an avid reader of sci-fi books (but not only!), enjoys swimming, running, and biking both competitively and casually and enjoys plenty of activities with friends, especially when beer is involved.


Almut Lütge joined the ORDES team in Zurich as Biomedical Data Engineer, in January 2024.
Almut did both her Bachelor and Master in molecular biotechnology with a major in bioinformatics at the University of Heidelberg in Germany.
After her masters she worked as a research assistant on population genetics at the NTNU in Trondheim, Norway.
In 2018 Almut started her PhD about benchmarking of single cell analysis tools at the University of Zürich, followed by a short PostDoc in pharmaceutical immunology at ETH Zürich.
Almut enjoys data-driven problem-solving and highly value open science.


Isione Bonvalot joined the SDSC in October 2025 as a Data Scientist in the Innovation team, based in Lausanne.
Isione holds a Bachelor’s degree in Microengineering and a Master’s in Robotics from EPFL. She gained international and industry experience through a Master’s internship in Sri Lanka and her Master’s thesis project at Melexis in Switzerland, supervised by the Swiss Data Science Center. Isione has also been a volunteer firefighter for five years. Passionate about the outdoors, Isione enjoys climbing, ski touring, alpinism, and mountain adventures, and when indoors, she is an avid strategy board game player.


Luana Martelli worked as a Security Expert for the ORDES / Infrastructure team. After completing her M.Sc. in IT security at the HES-SO, Luana worked a few years in the industry as a consultant, doing security assessment for companies. She has a great interest in programming and cryptography.


Raphaël Matusiak joined the SDSC in January 2021 as a Data Scientist in the Innovation team, based in Lausanne.
Raphaël worked for 6 years as an engineer in biomedical research labs. Performing a lot of image analysis for microscopy experiments, its curiosity led him to learn about Data Science. Therefore, he joined a consulting company and worked on several projects, notably one within Air France Company, on a predictive maintenance project and a shorter one on an NLP PoC. Since the beginning of 2021, Raphaël is working in the SDSC industry team.


Oksana is a disruptive innovator bringing her positive energy to projects. Driven by her curiosity and can-do attitude she excels in industrial and academic contexts. Oksana earned her PhD in Life Sciences and Bioinformatics from the University of Lausanne after two MSc in Bioinformatics and in Information Systems from the University of Geneva. For more than 10 years, she has been committed to actively promoting the value of data science and advocating the best practices for reproducible and ethical research. She believes that Swiss Data Science Center is a key player in building a competitive data economy in Switzerland leveraging its innovative potential and renown commitment to quality.


Federico holds a M.Sc. in Engineering and a Ph.D. in Sustainable Development and Innovation Engineering. After a three-year Postdoc in Environmental Data Mining at the University of Lausanne, in 2021 he joined the Swiss Data Science Centre, where he now works as Principal Data Scientist supporting the acceleration of the digital transformation within industries, NGOs and public bodies. Over the years he worked on the development of methodological tools to mine and model big spatiotemporal datasets. He has deep competencies in applied statistics, machine learning, geocomputation, spatial statistics, remote sensing.
PI | Partners:
University Hospital of Lausanne (CHUV):
- Dr. Sylvain Meylan (main applicant and sepsis expert)
- Jéremie Despraz (principal data scientist)
- Gauthier Le Bosse (data engineer)
University Hospital Bern (Inselspital):
- Prof. Olga Endrich (infrastructure and OMOP project lead)
- Dr. Christine Thurnheer (medical doctor)
- Marcel Messerli (OMOP implementation consultant at Insel)
- Dr. Benjamin Ellenberger (lead data scientist)
University Children’s Hospital Zürich (KiSpi):
- Dr. Luregn Schlapbach (pediatrician)
- Dr. Nora Lüthi (pediatrician)
- Manuel Schweighofer (data engineer)
description
Motivation & Objectives
CHUV and SDSC have co-developed an AI-powered data pipeline for sepsis quality-of-care monitoring. Currently deployed at CHUV, this tool provides caregivers and hospital managers with timely and precise feedback on the clinical practice and allows benchmarking on clinical measures.
In this project, we aim to:
- Standardize the data pipeline to make it interoperable by porting it to the OMOP common data model.
- Package it into production-ready software, enabling its national and international deployment.
- Deploy the standardized pipeline at CHUV, Insel, and KiSpi and validate its performance as a proof-of-concept for a wider dissemination.
This packaged pipeline should eventually enable the creation of a national standardized sepsis registry, with international interoperability.
SDSC Contribution
The SDSC team will have a dual role: on the one hand, our data scientists and engineers are involved in re-modelling, adapting and industrializing the existing AI data pipeline. On the other hand, the team will play a critical role in infrastructure build and deployment.
The modelling work includes:
- Improving the existing AI module
- Generalizing and/or modularizing the pre-processing steps of the source data with the help of the OMOP common data model [1]
- Adapt AI module to a pediatric context
- Refactoring and packaging source code with industry standards and OMOP, ensuring data quality, traceability, privacy and robustness
The infrastructure work includes:
- Understand the IT architecture and context for each hospital
- Coordinate with data engineers to find the most fitting deploying option
- Ensure services are set up and/or ready for a smooth and secure deployment
- Include upstream changes to the modelling/infrastructure code when necessary
Impact
This project extends the reach and impact of the previously validated and operational HERACLES sepsis model at CHUV by adapting it for use with Inselspital patients, laying the groundwork for harmonizing sepsis prevention and treatment protocols between Inselspital and CHUV.
Beyond this initial application, the underlying solution is designed for broader scalability: any Swiss hospital capable of standardizing its data in OMOP format can adopt it, extending its clinical value across the national healthcare system.
Footnote:
[1] OMOP - Observational Medical Outcomes Partnership – is known for OMOP Common Data Model (CDM), an open-source standard designed to normalize and structure complex, fragmented healthcare data (such as electronic health records and insurance claims) into a single, predictable, relational database format.
Presentation
Gallery
Annexe
Additional resources
Bibliography
Publications
Related Pages
- CHUV Heracles Project: https://www.datascience.ch/projects/chuv-heracles-sepsis-model
- OMOP Common Data Model explanation: https://www.ohdsi.org/data-standardization
More projects
Dedgeflow
CHUV: Heracles - Sepsis Model
AI-Driven Political Monitoring
More projects
News
Latest news


Coding the Future: Energy Data Hackdays Expand to French-speaking Switzerland
Coding the Future: Energy Data Hackdays Expand to French-speaking Switzerland
Science des données : le SDSC et le Canton de Vaud soutiennent quatre projets appliqués
Science des données : le SDSC et le Canton de Vaud soutiennent quatre projets appliqués
Le Swiss Data Science Center inaugure son siège au Biopôle de Lausanne
Le Swiss Data Science Center inaugure son siège au Biopôle de Lausanne
Contact us
Let’s talk Data Science
Do you need our services or expertise?
Contact us for your next Data Science project!



