Kipoi - Seminar

The monthly virtual seminar series is designed as a platform for interested Kipoi users and developers and will host talks on the applications of deep learning on biological data. The seminar is held on every first Wednesday of the month at 5:30 p.m. - 6:30 p.m. CET. We are also happy to share the recordings of the seminar on YouTube.

How to take part

The Virtual Seminar Series takes place via Zoom. To take part in the seminar, you can register for the online Zoom conference. Your personal join link will be valid for all upcoming lectures of the series.

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How to apply as a speaker

The seminar is a great opportunity to present your recent work to a large international audience. If you want to apply as a speaker, please use the contact in the registration confirmation email.

Next seminar

Title: A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction

4 March 2026 5:30 p.m. - 6:30 p.m. Central European Time

Speaker: Sam Boshar, Instadeep

Abstract:

We present Nucleotide Transformer v3 (NTv3), a multi-species genomic foundation model that unifies long-range sequence modeling, base-resolution functional prediction, genome annotation, and controllable sequence generation within a single efficient architecture. NTv3 employs a U-Net–like design to model up to 1 Mb of genomic context at single-nucleotide resolution. It is pre-trained on 9 trillion base pairs using masked language modeling and post-trained on ~16,000 functional genomics tracks and annotation labels across 24 animal and plant species. NTv3 achieves state-of-the-art performance on functional-track and genome-annotation benchmarks across species, consolidates shared regulatory grammar for long-range genome-to-function inference, and supports variant interpretation. We fine-tune NTv3 into a controllable generative model via masked diffusion, enabling the design of enhancer sequences with specified activity and promoter selectivity, which we validate experimentally. The NTv3 model family, benchmarks, and practical training and design tools are released to support broad genomic applications.

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