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Convolutional Kitchen Sinks for Transcription Factor Binding Site Prediction [article]

Alyssa Morrow, Vaishaal Shankar, Devin Petersohn, Anthony Joseph, Benjamin Recht, Nir Yosef
<span title="2017-05-31">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>

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We present a simple and efficient method for prediction of transcription factor binding sites from DNA sequence. Our method computes a random approximation of a convolutional kernel feature map from DNA sequence and then learns a linear model from the approximated feature map. Our method outperforms state-of-the-art deep learning methods on five out of six test datasets from the ENCODE consortium, while training in less than one eighth the time.
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Alyssa Morrow, Vaishaal Shankar, Devin Petersohn, Anthony Joseph, Benjamin Recht, Nir Yosef. "Convolutional Kitchen Sinks for Transcription Factor Binding Site Prediction." arXiv (2017)