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, towards enabling full scientific discovery pipelines via novel agentic assistants. 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 one-day course will give a gentle introduction into LLMs, going from theoretical concepts towards practical, hands-on experience interacting with LLMs for exploring biodata through a series of exercises provided in Jupyter Notebooks. These will include programmatically interacting with an LLM to construct a simple Retrieval Augmented Generation (RAG) application for answering biological questions using existing SIB resources.

Audience

This course is addressed to life scientists and bioinformaticians, in academia and industry, who are interested in LLMs and who already have prior experience using Python through Jupyter Notebooks.

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
Programmatically interact with LLMs in Jupyter Notebooks (Python)
Build a simple RAG application for answering questions over biodata

Prerequisites

Knowledge / competencies

This course is designed for beginners. Participants are expected to have at least one year experience with Python (intermediate level).

Technical

You are required to bring your own computer with an Internet connection and a recent version of Python (3.12 or higher) installed. Optionally you can also have Jupyter Notebook installed.

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.

Applications will close as soon as the places will be filled up, but not later than 05/05/2025. Deadline for free-of-charge cancellation is set to 05/05/2025. Cancellation after this date will not be reimbursed.

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.

Venue and Time

This course will take place at the University of Lausanne.

It will start at 9:00 CEST and end around 17:00 CEST.

Precise information will be provided to the participants before the course.

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