From LLMs to DNA: A Practical Guide to Genomic Foundation Models in Healthcare
From LLMs to DNA: A Practical Guide to Genomic Foundation Models in Healthcare
Tutorial Overview
As genomic sequencing becomes increasingly integrated into clinical practice, the primary challenge is shifting from data generation to functional interpretation. Recent advances in artificial intelligence have introduced genomic foundation models, deep learning architectures trained on large collections of biological sequences that learn contextual representations of DNA. This tutorial provides a practical introduction to genomic foundation models and their emerging applications in medicine and epidemiology. Participants will explore the conceptual transition from natural language processing models to genomic sequence models, focusing on architectural adaptations required for biological data, including long-range dependencies and large genomic contexts. The tutorial will present recent developments in the field through selected case studies, including large-scale models such as Evo2. Participants will learn how these models can support biomedical tasks such as variant effect prediction, genomic representation learning, and pathogen genome analysis. Learning objectives include: (i) understanding the key architectural differences between NLP language models and genomic foundation models, (ii) evaluating their potential applications in clinical genomics and epidemiology, and (iii) exploring practical workflows for inference, adaptation, and evaluation of genomic AI models. The tutorial combines conceptual lectures with practical demonstrations to provide participants with both theoretical foundations and hands-on exposure to emerging genomic AI methods.
Program
Lecture - Introduction to Genomic Language Models: from NLP to Genomic Foundational Models
Lecture - State of the Art Genomic Language Models: Architectures & Tokenizers for DNA
Hands-on - Lab. 1: Training a Custom Genomic BERT from Scratch
Lecture - Applications of Genomic Language models: From Human Clinical Genetics to Epidemiology
Hands-on - Lab. 2: Genomic Sequence Embeddings & Downstream Tasks
Hands-on - Lab. 3: SARS-CoV-2 Variant Prioritization using Genomic Language Models
Conclusions: Ethical Considerations, Limitations, and Future Work
Important dates
Tutorial Date: July 7, 2026
Location
The tutorial will be held within the AIME 2026 Conference in Ottawa (Canada) on July 7, 2026.
Chairs
Dr. Simone Rancati - Postdoc, University of Pavia, Italy - simone.rancati01@universitadipavia.it
Pablo Arozarena - PhD candidate, University of Piemonte Orientale, Italy - pablo.arozarena@uniupo.it
Co-chairs
Dr. Luigi Portinale - Full Professor, University of Piemonte Orientale, Italy - luigi.portinale@uniupo.it
Dr. Enea Parimbelli - Assistant Professor, University of Pavia, Italy - enea.parimbelli@unipv.it
Dr. Giovanna Nicora - Assistant Professor, University of Pavia, Italy - giovanna.nicora@unipv.it
Dr. Riccardo Bellazzi - Full Professor, University of Pavia, Italy - riccardo.bellazzi@unipv.it