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Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…
Molecular docking is a structure-based computational drug design technique for predicting the interaction between a small molecule (ligand) and a macromolecule (receptor). Over the past three decades various docking software programs have…
With the continuous growth in the number of parameters of transformer-based pretrained language models (PLMs), particularly the emergence of large language models (LLMs) with billions of parameters, many natural language processing (NLP)…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
Prompt learning is an effective method to customize Vision-Language Models (VLMs) for various downstream tasks, involving tuning very few parameters of input prompt tokens. Recently, prompt pretraining in large-scale dataset (e.g.,…
By coupling peptides with DNA tags (i.e., 'barcodes'), it is now possible to harness high-throughput sequencing (HTS) technologies to enable highly multiplexed peptide-based assays, which have a variety of potential applications including…
Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual…
Pre-trained language models have demonstrated powerful capabilities in the field of natural language processing (NLP). Recently, code pre-trained model (PTM), which draw from the experiences of the NLP field, have also achieved…
The accurate identification of antiviral peptides (AVPs) is crucial for novel drug development. However, existing methods still have limitations in capturing complex sequence dependencies and distinguishing confusing samples with high…
Foundation models have significantly advanced medical image analysis through the pre-train fine-tune paradigm. Among various fine-tuning algorithms, Parameter-Efficient Fine-Tuning (PEFT) is increasingly utilized for knowledge transfer…
Photoplethysmography (PPG) is a widely used non-invasive sensing modality for continuous cardiovascular and physiological monitoring across clinical, laboratory, and wearable settings. While existing PPG datasets support a broad range of…
Nanopore resistive pulse sensors are emerging technologies for single-molecule protein sequencing. But they can hardly detect small post-translational modifications (PTMs) such as hydroxylation in single-molecule level. While a combination…
Protein interactions constitute the fundamental building block of almost every life activity. Identifying protein communities from Protein-Protein Interaction (PPI) networks is essential to understand the principles of cellular organization…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
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…
Large language models (LLMs) frequently achieve impressive scores on standardized benchmarks, yet accuracy alone offers a limited view of their capabilities. Evaluating open-source LLMs through leaderboards faces persistent issues like data…
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…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
Inspired by its success in natural language processing and computer vision, pre-training has attracted substantial attention in cheminformatics and bioinformatics, especially for molecule based tasks. A molecule can be represented by either…
Photoplethysmography is a non-invasive optical technique that measures changes in blood volume within tissues. It is commonly and increasingly used for in a variety of research and clinical application to assess vascular dynamics and…