  Deep neural network (DNN) models have recently obtained state-of-the-art
prediction accuracy for the transcription factor binding (TFBS) site
classification task. However, it remains unclear how these approaches identify
meaningful DNA sequence signals and give insights as to why TFs bind to certain
locations. In this paper, we propose a toolkit called the Deep Motif Dashboard
(DeMo Dashboard) which provides a suite of visualization strategies to extract
motifs, or sequence patterns from deep neural network models for TFBS
classification. We demonstrate how to visualize and understand three important
DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our
first visualization method is finding a test sequence's saliency map which uses
first-order derivatives to describe the importance of each nucleotide in making
the final prediction. Second, considering recurrent models make predictions in
a temporal manner (from one end of a TFBS sequence to the other), we introduce
temporal output scores, indicating the prediction score of a model over time
for a sequential input. Lastly, a class-specific visualization strategy finds
the optimal input sequence for a given TFBS positive class via stochastic
gradient optimization. Our experimental results indicate that a
convolutional-recurrent architecture performs the best among the three
architectures. The visualization techniques indicate that CNN-RNN makes
predictions by modeling both motifs as well as dependencies among them.
