Related papers: Deep Motif Dashboard: Visualizing and Understandin…
This paper applies a deep convolutional/highway MLP framework to classify genomic sequences on the transcription factor binding site task. To make the model understandable, we propose an optimization driven strategy to extract "motifs", or…
Transcription factors are proteins that regulate the expression of genes by binding to specific genomic regions known as Transcription Factor Binding Sites (TFBSs), typically located in the promoter regions of those genes. Accurate…
Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety…
Deep Neural Network(DNN) techniques have been prevalent in software engineering. They are employed to faciliatate various software engineering tasks and embedded into many software applications. However, analyzing and understanding their…
Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…
Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…
Deep-predictive-coding networks (DPCNs) are hierarchical, generative models. They rely on feed-forward and feed-back connections to modulate latent feature representations of stimuli in a dynamic and context-sensitive manner. A crucial…
Motivation: Deep learning architectures have recently demonstrated their power in predicting DNA- and RNA-binding specificities. Existing methods fall into three classes: Some are based on Convolutional Neural Networks (CNNs), others use…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Deep Recurrent Neural Network (RNN) has gained popularity in many sequence classification tasks. Beyond predicting a correct class for each data instance, data scientists also want to understand what differentiating factors in the data have…
Identification of drug-target interactions (DTIs) plays a key role in drug discovery. The high cost and labor-intensive nature of in vitro and in vivo experiments have highlighted the importance of in silico-based DTI prediction approaches.…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Convolutional neural network (CNN) driven by image recognition has been shown to be able to explain cortical responses to static pictures at ventral-stream areas. Here, we further showed that such CNN could reliably predict and decode…
The goal of our research is to develop methods advancing automatic visual recognition. In order to predict the unique or multiple labels associated to an image, we study different kind of Deep Neural Networks architectures and methods for…
Deep Neural Networks (DNNs) deliver state-of-the-art performance in many image recognition and understanding applications. However, despite their outstanding performance, these models are black-boxes and it is hard to understand how they…
Representations in the hidden layers of Deep Neural Networks (DNN) are often hard to interpret since it is difficult to project them into an interpretable domain. Graph Convolutional Networks (GCN) allow this projection, but existing…
Deep convolutional neural networks have proven their effectiveness, and have been acknowledged as the most dominant method for image classification. However, a severe drawback of deep convolutional neural networks is poor explainability.…
The success of recent deep convolutional neural networks (CNNs) depends on learning hidden representations that can summarize the important factors of variation behind the data. However, CNNs often criticized as being black boxes that lack…
We propose a new, more actionable view of neural network interpretability and data analysis by leveraging the remarkable matching effectiveness of representations derived from deep networks, guided by an approach for class-conditional…