Related papers: DNA-Level Splice Junction Prediction using Deep Re…

We introduce segmental recurrent neural networks (SRNNs) which define, given an input sequence, a joint probability distribution over segmentations of the input and labelings of the segments. Representations of the input segments (i.e.,…

The use of deep learning is facilitating a wide range of data processing tasks in many areas. The analysis of fusion data is no exception, since there is a need to process large amounts of data collected from the diagnostic systems attached…

We introduce a deep residual recurrent neural network (DR-RNN) as an efficient model reduction technique for nonlinear dynamical systems. The developed DR-RNN is inspired by the iterative steps of line search methods in finding the residual…

The deep Convolutional Neural Network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following basic principles such as increasing the depth and constructing highway connections, researchers have manually…

A deep neural network (DNN) with piecewise linear activations can partition the input space into numerous small linear regions, where different linear functions are fitted. It is believed that the number of these regions represents the…

One of the main goals of developmental biology is to reveal the gene regulatory networks (GRNs) underlying the robust differentiation of multipotent progenitors into precisely specified cell types. Most existing methods to infer GRNs from…

Accurately reconstructing Gene Regulatory Networks (GRNs) is crucial for understanding gene functions and disease mechanisms. Single-cell RNA sequencing (scRNA-seq) technology provides vast data for computational GRN reconstruction. Since…

Accurate localization of proteins from fluorescence microscopy images is challenging due to the inter-class similarities and intra-class disparities introducing grave concerns in addressing multi-class classification problems. Conventional…

Deploying deep neural networks (DNNs) on IoT and mobile devices is a challenging task due to their limited computational resources. Thus, demanding tasks are often entirely offloaded to edge servers which can accelerate inference, however,…

DNA-binding proteins are a class of proteins which have a specific or general affinity to DNA and include three important components: transcription factors; nucleases, and histones. DNA-binding proteins also perform important roles in many…

We present a novel multi-parent crossover operator in genetic algorithms (GAs) called ``Deep Neural Crossover'' (DNC). Unlike conventional GA crossover operators that rely on a random selection of parental genes, DNC leverages the…

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein…

Recently several deep learning models have been used for DNA sequence based classification tasks. Often such tasks require long and variable length DNA sequences in the input. In this work, we use a sequence-to-sequence autoencoder model to…

Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively…

Deep Neural Networks (DNNs) are widely used for decision making in a myriad of critical applications, ranging from medical to societal and even judicial. Given the importance of these decisions, it is crucial for us to be able to interpret…

Due to cellular heterogeneity, cell nuclei classification, segmentation, and detection from pathological images are challenging tasks. In the last few years, Deep Convolutional Neural Networks (DCNN) approaches have been shown…

Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation,…

Spatial transcriptomics (ST) has emerged as an advanced technology that provides spatial context to gene expression. Recently, deep learning-based methods have shown the capability to predict gene expression from WSI data using ST data.…

Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…