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Motivation: Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their…

Histone modifications play a critical role in gene regulation. Consequently, predicting gene expression from histone modification signals is a highly motivated problem in epigenetics. We build upon the work of DeepChrome by Singh et al.…

The past decade has seen a revolution in genomic technologies that enable a flood of genome-wide profiling of chromatin marks. Recent literature tried to understand gene regulation by predicting gene expression from large-scale chromatin…

Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…

The attention mechanism is one of the most important priori knowledge to enhance convolutional neural networks. Most attention mechanisms are bound to the convolutional layer and use local or global contextual information to recalibrate the…

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…

Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pathway states. However, most existing deep learning approaches treat chemical and…

Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is vital in protein engineering and therapeutic discovery. However, the scarcity of…

This paper presents a novel deep learning-based approach named RealDiffFusionNet incorporating Neural Controlled Differential Equations (Neural CDE) - time series models that are robust in handling irregularly sampled data - and multi-head…

Equipping a deep model the abaility of few-shot learning, i.e., learning quickly from only few examples, is a core challenge for artificial intelligence. Gradient-based meta-learning approaches effectively address the challenge by learning…

Type inference for dynamic programming languages such as Python is an important yet challenging task. Static type inference techniques can precisely infer variables with enough static constraints but are unable to handle variables with…

Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…

Drug combination therapy has become a increasingly promising method in the treatment of cancer. However, the number of possible drug combinations is so huge that it is hard to screen synergistic drug combinations through wet-lab…

Time series prediction with deep learning methods, especially long short-term memory neural networks (LSTMs), have scored significant achievements in recent years. Despite the fact that the LSTMs can help to capture long-term dependencies,…

Background: Drug-drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible…

Medical image segmentation has been significantly advanced with the rapid development of deep learning (DL) techniques. Existing DL-based segmentation models are typically discriminative; i.e., they aim to learn a mapping from the input…

Efficient deployment of Deep Neural Networks (DNNs), such as Large Language Models (LLMs), on tensor accelerators is essential for maximizing computational efficiency in modern AI systems. However, achieving this is challenging due to the…

Data-driven deep learning models have enabled tremendous progress in change detection (CD) with the support of pixel-level annotations. However, collecting diverse data and manually annotating them is costly, laborious, and…

Understanding how residue variations affect protein stability is crucial for designing functional proteins and deciphering the molecular mechanisms underlying disease-related mutations. Recent advances in protein language models (PLMs) have…

In this paper, we present a physics-based deep learning framework for data-driven prediction of wave propagation in fluid media. The proposed approach, termed Multistep Integration-Inspired Attention (MI2A), combines a denoising-based…