The next OCBE Biostatistics seminar will be held on Thursday, May 23rd, at 14:30-15:30 in Auditorium 13 (Domus Medica, Oslo).
Ksenia Sokolova, Department of Computer Science, Princeton University (USA), will present about
Deep learning for sequence based gene expression prediction
Abstract: Human biology is defined by specialized cell types driven by a common genome, 98% of which is outside of genes. This noncoding genetic space is linked to the majority of disease risk but remains poorly understood. In this talk, I will discuss how deep learning can be used to predict the effects of noncoding variants on gene expression in primary human cell types. I will introduce ExPectoSC, an atlas of deep-learning models that predict cell-type-specific gene expression from genomic sequences, covering 105 primary cell types across seven organ systems, and how it can be used in the disease context. Additionally, I will present a novel genomic-centered contrastive pre-training method, cGen, to improve training of the models from sequence alone in limited-data contexts. Utilizing sequence augmentations, after pre-training cGen generates unsupervised embeddings that highlight functional clusters and are informative of gene expression in the absence of any labeled information.
The OCBE Biostatistics seminar series is organized by the Oslo Centre for Biostatistics and Epidemiology and is an arena for presenting new interesting work in biostatistics, both on the methodological and applied side, from researchers in Oslo, from Norway and abroad.
See also: https://www.med.uio.no/imb/english/research/centres/ocbe/events/biostat-seminar/ for updates or for subscribing to the events. If you'd like to be added in the "biostat-ext" mailing list, just let us know.
Other upcoming seminars this semester:
May 30th, 2024: Sonia Petrone, Department of Decision Sciences, Bocconi University of Milano, Italy
June 27th, 2024: Alan Hubbard, Center for Targeted Machine Learning and Causal Inference, University of California, Berkeley, USA
Welcome!
Best wishes,
Valeria Vitelli
Associate Professor
Oslo Centre for Biostatistics and Epidemiology,
Department of Biostatistics, University of Oslo, Norway
mailto: valeria.vitelli@medisin.uio.no
