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The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…

Molecular dynamics (MD) is a powerful tool for exploring the behavior of atomistic systems, but its reliance on sequential numerical integration limits simulation efficiency. We present a novel neural network architecture, MDtrajNet, and a…

Masked diffusion models (MDMs) have achieved notable progress in modeling discrete data, while their potential in molecular generation remains underexplored. In this work, we explore their potential and introduce the surprising result that…

Ensemble of machine learning models yields improved performance as well as robustness. However, their memory requirements and inference costs can be prohibitively high. Knowledge distillation is an approach that allows a single model to…

Machine learning (ML) is revolutionising drug discovery by expediting the prediction of small molecule properties essential for developing new drugs. These properties -- including absorption, distribution, metabolism and excretion (ADME)--…

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying…

Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent…

In drug discovery, predicting the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of small-molecule drugs is critical for ensuring safety and efficacy. However, the process of accurately predicting these…

Advanced Persistent Threats (APTs) pose a significant security risk to organizations and industries. These attacks often lead to severe data breaches and compromise the system for a long time. Mitigating these sophisticated attacks is…

Background: Pharmacokinetic evaluation is one of the key processes in drug discovery and development. However, current absorption, distribution, metabolism, excretion prediction models still have limited accuracy. Aim: This study aims to…

The versatility of multimodal deep learning holds tremendous promise for advancing scientific research and practical applications. As this field continues to evolve, the collective power of cross-modal analysis promises to drive…

We introduce a machine learning method in which energy solutions from the Schrodinger equation are predicted using symmetry adapted atomic orbitals features and a graph neural-network architecture. \textsc{OrbNet} is shown to outperform…

Few-shot learning is a promising approach to molecular property prediction as supervised data is often very limited. However, many important molecular properties depend on complex molecular characteristics -- such as the various 3D…

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail…

In order to characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine learning method to characterize…

The thermoelectric performance of materials exhibits complex nonlinear dependencies on both elemental types and their proportions, rendering traditional trial-and-error approaches inefficient and time-consuming for material discovery. In…

Caco-2 permeability serves as a critical in vitro indicator for predicting the oral absorption of drug candidates during early-stage drug discovery. To enhance the accuracy and efficiency of computational predictions, we systematically…

A central challenge in computational catalysis is the identification of low-energy and chemically plausible adsorption configurations, as these directly affect adsorption energies, reaction pathways, and catalytic performance. Existing…

In silico drug-target interaction (DTI) prediction is an important and challenging problem in biomedical research with a huge potential benefit to the pharmaceutical industry and patients. Most existing methods for DTI prediction including…

Prediction of complete step-by-step chemical reaction mechanisms (CRMs) remains a major challenge. Whereas the traditional approaches in CRM tasks rely on expert-driven experiments or costly quantum chemical computations, contemporary deep…