Daily Archives: September 27, 2018

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

Our next meeting will be at 1pm on Oct 1st, in room 4130 of the Discovery building. Our Selected paper is Kipoi: accelerating the community exchange and reuse of predictive models for genomics.
The abstract is as follows.

Advanced machine learning models applied to large-scale genomics datasets hold the promise to be major drivers for genome science. Once trained, such models can serve as a tool to probe the relationships between data modalities, including the effect of genetic variants on phenotype. However, lack of standardization and limited accessibility of trained models have hampered their impact in practice. To address this, we present Kipoi, a collaborative initiative to define standards and to foster reuse of trained models in genomics. Already, the Kipoi repository contains over 2,000 trained models that cover canonical prediction tasks in transcriptional and post-transcriptional gene regulation. The Kipoi model standard grants automated software installation and provides unified interfaces to apply and interpret models. We illustrate Kipoi through canonical use cases, including model benchmarking, transfer learning, variant effect prediction, and building new models from existing ones. By providing a unified framework to archive, share, access, use, and build on models developed by the community, Kipoi will foster the dissemination and use of machine learning models in genomics.

We welcome all who can join us for this discussion. Feel free to begin that discussion in the comments section below.