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Pilot1/NT3/README.md

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The Pilot1 Benchmark 4, commonly referred to as NT3, is a 1D convolutional network for classifying RNA-seq gene expression profiles into normal or tumor tissue categories.
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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 on the balanced 700 matched normal-tumor gene expression profile pairs available 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 difference and transformation of latent representation between normal and tumor tissues.
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The model also acts as a quality control check for synthetically generated gene expression profiles.

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