Related papers: ProteoKnight: Convolution-based phage virion prote…

Motivation: As viruses that mainly infect bacteria, phages are key players across a wide range of ecosystems. Analyzing phage proteins is indispensable for understanding phages' functions and roles in microbiomes. High-throughput sequencing…

Although using convolutional neural networks (CNNs) as backbones achieves great successes in computer vision, this work investigates a simple backbone network useful for many dense prediction tasks without convolutions. Unlike the…

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…

Directed evolution plays an indispensable role in protein engineering that revises existing protein sequences to attain new or enhanced functions. Accurately predicting the effects of protein variants necessitates an in-depth understanding…

Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window…

Venn Prediction (VP) is a new machine learning framework for producing well-calibrated probabilistic predictions. In particular it provides well-calibrated lower and upper bounds for the conditional probability of an example belonging to…

The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…

This study introduces PV-RNN, a novel variational RNN inspired by the predictive-coding ideas. The model learns to extract the probabilistic structures hidden in fluctuating temporal patterns by dynamically changing the stochasticity of its…

Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning…

Flow-Imaging Microscopy (FIM) is commonly used in both academia and industry to characterize subvisible particles (those $\le 25 \mu m$ in size) in protein therapeutics. Pharmaceutical companies are required to record vast volumes of FIM…

This paper presents a framework for Convolutional Neural Network (CNN)-based quality enhancement task, by taking advantage of coding information in the compressed video signal. The motivation is that normative decisions made by the encoder…

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…

Uncertainty estimation is an important task for critical problems, such as robotics and autonomous driving, because it allows creating statistically better perception models and signaling the model's certainty in its predictions to the…

Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…

We introduce VPNet, a novel model-driven neural network architecture based on variable projection (VP). Applying VP operators to neural networks results in learnable features, interpretable parameters, and compact network structures. This…

Convolution-based and Transformer-based vision backbone networks process images into the grid or sequence structures, respectively, which are inflexible for capturing irregular objects. Though Vision GNN (ViG) adopts graph-level features…

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a…

Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are…

Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg.…

Predicting protein properties is paramount for biological and medical advancements. Current protein engineering mutates on a typical protein, called the wild-type, to construct a family of homologous proteins and study their properties.…