Evan Cofer
Evan Cofer
> We present NeuSomatic, the first convolutional neural network approach for somatic mutation detection, which significantly outperforms previous methods on different sequencing platforms, sequencing strategies, and tumor purities. NeuSomatic summarizes...
> Autoencoders provide a powerful framework for learning compressed representations by encoding all of the information needed to reconstruct a data point in a latent code. In some cases, autoencoders...
> The volume and complexity of diagnostic imaging is increasing at a pace faster than the availability of human expertise to interpret it. Artificial intelligence has shown great promise in...
> Rapid diagnosis and treatment of acute neurological illnesses such as stroke, hemorrhage, and hydrocephalus are critical to achieving positive outcomes and preserving neurologic function—‘time is brain’1,2,3,4,5. Although these disorders...
> Millions of human genomes and exomes have been sequenced, but their clinical applications remain limited due to the difficulty of distinguishing disease-causing mutations from benign genetic variation. Here we...
> 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...
Selene encounters an error when the user provides an empty bed file as input to `get_predictions_for_bed_file` (or an empty fasta file for `get_predictions_for_fasta_file`). Specifically, the value `i` (as used on...
In the yml configuration file for `quickstart_training` tutorial, it specifies that `male.hg19.fasta` should be used as the reference sequence, but the archive from zenodo (https://zenodo.org/record/1319886/files/selene_quickstart_tutorial.tar.gz) includes `hg19.fasta`. Interestingly, this file...
At present, Selene assumes chromosomal linearity. Many prokaryotes have circular chromosomes. In the case of circular chromosomes, Selene should allow a sequence feature to wrap from the chromosome "end" in...
At present, Selene does not save a copy of python file containing the model source code. This seems like an oversight; the output directory contents alone should be enough to...