[Bioperl-l] Gene expression model using TensorFlow, BioPerl, and PDL
Zakariyya Mughal
I just wanted to post this example notebook <https://nbviewer.org/github/EntropyOrg/perl-AI-TensorFlow-Libtensorflow/blob/master/notebook/InferenceUsingTFHubEnformerGeneExprPredModel.ipynb>
from the <https://metacpan.org/pod/AI::TensorFlow::Libtensorflow>
binding which uses the Enformer gene expression prediction model from
Avsec Ž, Agarwal V, Visentin D, Ledsam JR, Grabska-Barwinska A, Taylor
KR, Assael Y, Jumper J, Kohli P, Kelley DR. Effective gene expression
prediction from sequence by integrating long-range interactions. Nat
Methods. 2021 Oct;18(10):1196-1203. doi: 10.1038/s41592-021-01252-x.
It uses a pre-trained model and replicates the Enformer data from the
first figure in the paper.
This notebook is mainly meant to show the early capabilities of the
TensorFlow low-level `libtensorflow` bindings. In the future, I'll be
working on more high-level bindings to make it easier to build custom
models in addition to the inference that can already be performed.
Best regards,
- Zakariyya Mughal
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