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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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## Data
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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 from RNA-seq [FPKM-UQ](https://docs.gdc.cancer.gov/Encyclopedia/pages/HTSeq-FPKM-UQ/) values. This model achieves around 98% classification accuracy.
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The associated metadata for the samples can be found [here](http://ftp.mcs.anl.gov/pub/candle/public/benchmarks/Pilot1/normal-tumor/matched_normal_samples.metadata.tsv).
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## Profile runs
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We have run the same configuration across multiple machines and compared the resource utilization.
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