Overview

Large Language Models (LLMs) are creating a shift of paradigm in how we interact with data across domains. Bioinformatics is one of the fields most prominently impacted by the advent of LLMs, whether for biodata exploration, via LLM-based AI assistants, or for dedicated, domain-specific LLMs such as Protein Language Models or even “ChatGPT for CRISPR”. But how are these models trained? How do we choose among the plethora of options for a target use case? And how do we adapt an existing model to our needs?

This course will give an introduction into LLMs, how they are trained and how they can be fine-tuned for specific applications, with a focus on their uses in bioinformatics. Participants will be able to get hands-on experience interacting with an LLM for exploring biodata, while understanding the important role that structured bio datasets (such as the leading SIB datasets) play in ensuring factual accuracy of answers provided by LLMs.

The course will include 2 Q&A sessions and references for further reading.

Audience

This course is addressed to life scientists and bioinformaticians, in academia and industry, who are interested in LLMs.

Learning outcomes

At the end of the course, the participants are expected to:

Understand the basics of Large Language Models
List some existing LLMs and their applications in bioinformatics
State the pros and cons of closed source vs open source LLMs
Interact with an LLM for exploring biodata

Prerequisites

Knowledge / competencies

This course is designed for beginners. Participants are expected to be familiar with Python (only for the hands-on exercise).

Technical

You are required to have your own computer with an Internet connection.

Application

The registration fees for academics are 100 CHF and 500 CHF for for-profit companies.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days. Applications close on 12/05/2025. Deadline for free-of-charge cancellation is set to 05/05/2025. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will take place at the University of Lausanne. It will start at 9:00 CET and end around 17:00 CET.

Additional information

Coordination: Diana Marek, SIB Training group.

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.

Using Large Language Models for Biodata Exploration: From Theory to Practice