In recent years, Foundation Models have emerged as powerful tools for uncovering patterns, relationships, and the intricate statistical properties of biological molecules such proteins, DNA and RNA. By leveraging these models, researchers are poised to revolutionize research in molecular biology, ushering in a new era of discovery and understanding in this field of biology with potential for the development of novel therapeutics and diagnostic tools. The AI Models of Biomolecules focus group is designed to unite two research communities by establishing a forum for dialogue between computer scientists and engineers developing AI technologies for RNA, DNA, and proteins, and experts in molecular biology, life sciences, and clinical sciences who bring forward pressing scientific and translational challenges.
By fostering this bidirectional exchange, we aim to accelerate cross-fertilization, dismantle disciplinary silos, and catalyze the development of AI technologies tailored to today’s most advanced molecular questions.
About the SIB focus groups
The focus groups aim to foster knowledge exchanges and collaborations in the community of 900 SIB Members, around specific scientific and/or transversal topics, from single-cell sequencing to equality, diversity and inclusion. View all focus groups
Foundation models for Biomolecules
Foundation models represent a significant breakthrough in deep learning, featuring large architectures trained on vast amounts of unlabelled data to create general-purpose representations capable of solving a large variety of down-stream tasks. Large Language Models (LLMs) for natural language, such as ChatGPT, serve as prime examples of foundation models. They are often based on the Transformer architecture which enables them to capture the intricate relationships and dependencies within text sequences. As a result, they have ushered in a new era of possibilities in NLP by providing rich representations of text as well as the ability to generate new but faithful natural language.
About the SIB focus groups
The focus groups aim to foster knowledge exchanges and collaborations in the community of 900 SIB Members, around specific scientific and/or transversal topics, from single-cell sequencing to equality, diversity and inclusion. View all focus groups
In biology, similar models are showing great promise, particularly in predicting structures and functions. Recently, models for DNA, RNA and proteins have emerged. However, several challenges remain before this technology can become a research standard. In particular, we must better understand what these models learn and how their representations relate to real biological mechanisms, and augment them to reflect the context-specific nature of biology by integrating LLM technologies with graph-based approaches and knowledge augmentation to incorporate interactions, networks, and prior biological knowledge.
Goals of the focus group
The AI Models of Biomolecules focus group brings together researchers across computational and molecular life sciences who are interested in AI technologies for omics to exchange perspectives on recent advances, best practices, and ongoing challenges in the field. By expanding our reach to national and international researchers, we seek to create a platform for:
- Staying updated: As AI technologies for omics data evolve rapidly, it is challenging to keep pace. This group aims to ensure that SIB members and the broader community remain informed about the latest developments, maintaining an active network of diverse experts to support and train both the Swiss community and beyond.
- Resource sharing: Given that AI technologies for omics demand significant computing and energy resources, this group seeks to build a network of research groups that can share resources, making these models more accessible to the entire community and benefit the greatest number.
- Promoting collaboration: The best development of such technologies occurs through close collaboration between computer scientists and domain experts. The AI Models of Biomolecules focus group brings together Swiss early-career academic researchers — including PhD candidates and postdoctoral fellows — to present their work and scientific challenges, alongside leading international experts who showcase state-of-the-art AI technologies in a hybrid format. This structure enables broad participation from global communities while strengthening local networking through monthly in-person meetings hosted at the EPFL AI Center, the University of Bern Department of Digital Medicine, and Idiap Research Institute in Martigny, three key hubs for artificial intelligence that help ensure strong community representation and access to one of the largest AI research networks.
We encourage members to actively participate by sharing their experiences with the latest tools, reviewing papers, and contributing code to a public GitHub repository dedicated to RNA/DNA foundation models.
The group currently gathers 13 SIB research groups and associated members. If you wish to join, subscribe to the dedicated mailing-list.
The agenda for the academic year 2025/2026 is already nearly finalized, featuring an exciting line-up of speakers covering topics ranging from RNA structure to RNA modification and function prediction using graph-based approaches and RNA language models. The program also includes speakers from industry, notably the Roche RNA Hub, reflecting our commitment to exposing PhD candidates and postdoctoral researchers to real-world challenges while offering opportunities to showcase their work to potential employers. Stay up to date by following us on LinkedIn for the latest news and announcements.
Month | Date | Location | Speaker no.1 | Speaker no.2 |
|---|---|---|---|---|
| October | 8/10/2025 | EPFL AI center | Half-day symposium | |
| November | 19/11/2025 | DDM (Bern) | Cancelled | |
| December | 17/12/2025 | EPFL AI center | Mile Sikic | Sebastian Leidel (Bern University) |
| January | 14/01/2026 | DDM (Bern) | Vamsi Nallapareddy (EPFL) | Parth Bibekar (EPFL) |
| February | 20/02/2026 | EPFL AI center | Marta Szachniuk (Poznan University of Technology) | Rodrigo Siqueira Reis (University of Bern) |
March | 11/03/2026 | DDM (Bern) | Yu Li (confirmed) | Pedro Beltrao (ETH, SIB) |
April | 15/04/2026 | EPFL AI center | Xavier Hernandez-Alias (Max-Planck-Institute of Biochemistry) | Slivi Rouskin (University of California San Francisco) |
May | 06/05/2026 | DDM (Bern) | Amin Tavakoli (Caltech) | Cyril Malbranke (EPFL) |
June | 10/06/2026 | EPFL AI center | Elena Rivas (Harvard University) | Kathi Zarnack (Julius Maximilians University Würzburg) |
July | 08/07/2026 | DDM (Bern) | TBA | TDB |
September | 09/09/2026 | Idiap | TBA - (King Abdullah University of Science and Technology) | Daniel Butnaru (Roche RNA Hub) |
October | 07/10/2026 | DDM (Bern) | Vincent Stimper (Isomorphic) | TBA |
November | 11/11/2026 | EPFL AI center | Christine Mayr (Sloan Kettering Institute) | TBA |
December | 16/12/2026 | DDM (Bern) | TBA - Special event |
Focus group coordinating members
- Raphaëlle Luisier, Chair (Group Leader)
- Janna Hastings, Co-Chair (Group Leader)
- Vincent Jung, Co-Chair (PhD student)
- Charlotte Tumescheit, Co-Chair (Postdoctoral researcher)
Are you a SIB Member and interested in joining? Subscribe to the dedicated mailing-list or contact Raphaëlle Luisier or Janna Hastings to book a date for a future presentation.