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Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states…

MicroRNAs (miRNAs) are short sequences of ribonucleic acids that control the expression of target messenger RNAs (mRNAs) by binding them. Robust prediction of miRNA-mRNA pairs is of utmost importance in deciphering gene regulations but has…

The field of RNA secondary structure prediction has made significant progress with the adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep learning model using axial attention and recycling in the…

Non-orthogonal communications are expected to play a key role in future wireless systems. In downlink transmissions, the data symbols are broadcast from a base station to different users, which are superimposed with different power to…

Deep learning is a topic of considerable current interest. The availability of massive data collections and powerful software resources has led to an impressive amount of results in many application areas that reveal essential but hidden…

Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a…

Small interfering RNA (siRNA) is a short double-stranded RNA molecule (about 21-23 nucleotides) with the potential to cure diseases by silencing the function of target genes. Due to its well-understood mechanism, many siRNA-based drugs have…

Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…

Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…

This paper introduces StutterNet, a novel deep learning based stuttering detection capable of detecting and identifying various types of disfluencies. Most of the existing work in this domain uses automatic speech recognition (ASR) combined…

Deep convolutional neural networks (CNNs) have recently achieved great success for single image super-resolution (SISR) task due to their powerful feature representation capabilities. The most recent deep learning based SISR methods focus…

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…

Deep learning is an emerging technology that is considered one of the most promising directions for reaching higher levels of artificial intelligence. Among the other achievements, building computers that understand speech represents a…

This paper presents a new methodology to alleviate the fundamental trade-off between accuracy and latency in spiking neural networks (SNNs). The approach involves decoding confidence information over time from the SNN outputs and using it…

This paper proposes a novel saliency detection method by developing a deeply-supervised recurrent convolutional neural network (DSRCNN), which performs a full image-to-image saliency prediction. For saliency detection, the local, global,…

In this paper, we introduce SeizNet, a closed-loop system for predicting epileptic seizures through the use of Deep Learning (DL) method and implantable sensor networks. While pharmacological treatment is effective for some epilepsy…

Nowadays deep learning is dominating the field of machine learning with state-of-the-art performance in various application areas. Recently, spiking neural networks (SNNs) have been attracting a great deal of attention, notably owning to…

Saliency methods have been widely used to highlight important input features in model predictions. Most existing methods use backpropagation on a modified gradient function to generate saliency maps. Thus, noisy gradients can result in…

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…

Self-supervised pretraining (SSP) has been recognized as a method to enhance prediction accuracy in various downstream tasks. However, its efficacy for DNA sequences remains somewhat constrained. This limitation stems primarily from the…