AIMC Topic: Deep Learning

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Coevolutionary signals in multiple sequence alignments improve virulence factor prediction with an MSA Transformer.

Scientific reports
Identification of virulence factors (VFs) is critical for expanding our knowledge on bacterial pathogenesis and also for developing targeted strategies for the prevention and treatment of related infectious diseases. Understanding virulence factors r...

AttenUNeT X with iterative feedback mechanisms for robust deep learning skin lesion segmentation.

Scientific reports
Accurate skin lesion segmentation is critical for improving early diagnosis of skin cancer. In this study, we propose AttenUNeT X, a novel extension of the U-Net architecture that integrates three key enhancements: (i) a feedback mechanism within dec...

A multi-representation deep-learning framework for accurate multicancer classification.

Journal of translational medicine
BACKGROUND: Accurate multicancer classification constitutes a cornerstone of modern oncology, offering critical insights into diagnosis, therapeutic decision-making, and prognostication. Numerous existing approaches, however, remain restricted to lim...

MCLCBA: multi-view contrastive learning network for RNA methylation site prediction.

BMC bioinformatics
BACKGROUND: RNA methylation (RM) regulates gene expression regulation, RNA stability, and protein translation. Accurate prediction of RM modification sites is essential for understanding their biological functions. However, existing wet-lab detection...

MPIDNN-GPPI: multi-protein language model with an improved deep neural network for generalized protein‒protein interaction prediction.

BMC genomics
Predicting protein‒protein interactions (PPIs) plays a crucial role in understanding biological processes. Although biological experimental methods can identify PPIs, they are costly, time-consuming, labor-intensive, and often lack stability. In cont...

Denoising single-cell RNA-seq data with a deep learning-embedded statistical framework.

BMC bioinformatics
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) provides extensive opportunities to explore cellular heterogeneity but is often limited by substantial technical noise and variability. The prevalence of zero counts, arising from both biological var...

Deep learning-based noise reduction method for the system matrix in magnetic particle imaging.

Physics in medicine and biology
. Magnetic particle imaging (MPI) is an emerging imaging technique based on superparamagnetic iron oxide nanoparticles, offering high sensitivity and rapid imaging. However, in measurement-based MPI, image quality is degraded by noise arising during ...

MGCL-CAP: Masked Graph Contrastive Learning with Gated Cross-Attention for Chemical Allergenicity Prediction.

Journal of chemical information and modeling
Chemical allergens are prevalent in both consumer and industrial products, often triggering hypersensitivity reactions with significant public health and regulatory implications. Traditional experimental screening is time-consuming and labor-intensiv...

Impact of contrast enhancement boost and super-resolution deep learning reconstruction on pediatric congenital heart disease CTA scans: ultra-low contrast dose.

BMC medical imaging
OBJECTIVE: To evaluate the feasibility of using contrast enhancement boost (CE-Boost) combined with super-resolution deep learning reconstruction (SR-DLR) to reduce contrast agent dosage in pediatric patients with congenital heart disease (CHD).

Opportunities for AI-based Model-informed Drug Development: A Comparative Analysis of NONMEM and AI-based Models for Population Pharmacokinetic Prediction.

The AAPS journal
Model-informed drug development (MIDD) plays an important role in pharmacometrics by leveraging mathematical models to optimize drug dosing strategies. Traditional methods such as nonlinear mixed effects modeling (NONMEM) have long been the gold stan...