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The Pilot1 Benchmark 5, commonly referred to as TC1, is a 1D convolutional network for classifying RNA-seq gene expression profiles into 18 balanced tumor types (e.g., breast cancer, melanoma, etc).
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The network follows the classic architecture of convolutional models with multiple 1D convolutional layers interleaved with pooling layers followed by final dense layers.
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The network can optionally use 1D locally connected layers in place of convolution layers as well as dropout layers for regularization.
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The model is trained and cross-validated on a total of 5,400 RNA-seq profiles from the NCI genomic data commons.
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The full set of expression features contains 60,483 float columns transformed from RNA-seq FPKM-UQ values. This model achieves around 98% classification accuracy.
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It is useful for studying the relationships between latent representations of different tumor types as well as classifying synthetically generated gene expression profiles.
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The model has also been used to flag incorrectly typed gene expression profiles from the databases
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