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Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and…

Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent…

Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…

Detecting complex interactions among risk factors in case-control studies is a fundamental task in clinical and population research. However, though hypothesis testing using logistic regression (LR) is a convenient solution, the LR…

The previously applied independent atom model (IAM) for highly charged ion-molecule collisions which implemented the suppression of multiple ionization and capture on the basis of geometric overlaps of cross-sectional areas representing…

Traditional detection methods of C-reactive protein (CRP) inflammation biomarker, in blood are expensive, time-consuming and labor-intensive. Such existing point-of-care CRP detection devices remain invasive, since they need blood sampling…

Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…

IR absorption spectroscopy of hemoglobin was performed using an IR optical parametric oscillator laser and a commercial atomic force microscope in a novel experimental arrangement based on the use of a bottom-up excitation alignment. This…

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate…

Quantum imaging, one of the pillars of quantum technologies, is well-suited to study sensitive samples which require low-light conditions, like biological tissues. In this context, interaction-free measurements (IFM) allow us infer the…

Large language models (LLMs) have revolutionized machine learning due to their ability to capture complex interactions between input features. Popular post-hoc explanation methods like SHAP provide marginal feature attributions, while their…

Accurate interaction potentials between microscopic components such as colloidal particles or cells are crucial to understanding a range of processes, including colloidal crystallization, bacterial colony formation, and cancer metastasis.…

The viability of a new drug molecule is a time and resource intensive task that makes computer-aided assessments a vital approach to rapid drug discovery. Here we develop a machine learning algorithm, iMiner, that generates novel inhibitor…

Large pre-trained language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields,…

Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…

Large language models ($\textbf{LLMs}$) have emerged as a powerful method for discovery. Instead of utilizing numerical data, LLMs utilize associated variable $\textit{semantic metadata}$ to predict variable relationships. Simultaneously,…

Virtual screening (VS) is widely used during computational drug discovery to reduce costs. Chemogenomics-based virtual screening (CGBVS) can be used to predict new compound-protein interactions (CPIs) from known CPI network data using…

Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…

In this paper, we propose a novel design for molecular communication in which both the transmitter and the receiver have, in a 3-dimensional environment, multiple bulges (in RF communication this corresponds to antenna). The proposed system…

Fluorescence Lifetime Imaging Microscopy (FLIM) using multiphoton excitation techniques is now finding an important place in quantitative imaging of protein-protein interactions and intracellular physiology. We review here the recent…