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#32 Deep tensor factorization and a pitfall for machine learning methods with Jacob Schreiber
In this episode, we hear from Jacob Schreiber about his algorithm,
Avocado.
Avocado uses deep tensor factorization to break a three-dimensional tensor of
epigenomic data into three orthogonal dimensions corresponding to cell types,
assay types, and genomic loci. Avocado can extract a low-dimensional,
information-rich latent representation from the wealth of experimental data
from projects like the Roadmap Epigenomics Consortium and ENCODE. This
representation allows you to impute genome-wide epigenomics experiments that
have not yet been performed.
Jacob also talks about a pitfall he discovered when trying to predict gene
expression from a mix of genomic and epigenomic data. As you increase the
complexity of a machine learning model, its performance may be increasing for
the wrong reason: instead of learning something biologically interesting, your
model may simply be memorizing the average gene expression for that gene
across your training cell types using the nucleotide sequence.
Links:
If you enjoyed this episode, please consider supporting the podcast on Patreon.
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By Roman Cheplyaka
4.8
3434 ratings
In this episode, we hear from Jacob Schreiber about his algorithm,
Avocado.
Avocado uses deep tensor factorization to break a three-dimensional tensor of
epigenomic data into three orthogonal dimensions corresponding to cell types,
assay types, and genomic loci. Avocado can extract a low-dimensional,
information-rich latent representation from the wealth of experimental data
from projects like the Roadmap Epigenomics Consortium and ENCODE. This
representation allows you to impute genome-wide epigenomics experiments that
have not yet been performed.
Jacob also talks about a pitfall he discovered when trying to predict gene
expression from a mix of genomic and epigenomic data. As you increase the
complexity of a machine learning model, its performance may be increasing for
the wrong reason: instead of learning something biologically interesting, your
model may simply be memorizing the average gene expression for that gene
across your training cell types using the nucleotide sequence.
Links:
If you enjoyed this episode, please consider supporting the podcast on Patreon.
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