AIMC Topic: Algorithms

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Integrated multimodal hierarchical fusion and meta-learning for enhanced molecular property prediction.

Briefings in bioinformatics
Accurately predicting the pharmacological and toxicological properties of molecules is a critical step in the drug development process. Owing to the heterogeneity of molecular property prediction tasks, most of the current methods rely on building a ...

scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery.

Briefings in bioinformatics
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) produces vast amounts of individual cell profiling data. Its analysis presents a significant challenge in accurately annotating cell types and their associated biomarkers. Different pipelines ...

Large-scale information retrieval and correction of noisy pharmacogenomic datasets through residual thresholded deep matrix factorization.

Briefings in bioinformatics
Pharmacogenomics studies are attracting an increasing amount of interest from researchers in precision medicine. The advances in high-throughput experiments and multiplexed approaches allow the large-scale quantification of drug sensitivities in mole...

Machine learning-augmented m6A-Seq analysis without a reference genome.

Briefings in bioinformatics
Methylated RNA m6A immunoprecipitation sequencing (m6A-Seq) is a powerful technique for investigating transcriptome-wide m6A modification. However, most of the existing m6A-Seq protocols rely on reference genomes, limiting their use in species lackin...

GAEDGRN: reconstruction of gene regulatory networks based on gravity-inspired graph autoencoders.

Briefings in bioinformatics
Reconstructing high-resolution gene regulatory networks (GRNs) based on single-cell RNA sequencing data provides an opportunity to gain insight into disease pathogenesis. At present, there are a large number of GRN reconstruction methods based on gra...

Pitfalls and Best Practices in Evaluation of AI Algorithmic Biases in Radiology.

Radiology
Despite growing awareness of problems with fairness in artificial intelligence (AI) models in radiology, evaluation of algorithmic biases, or AI biases, remains challenging due to various complexities. These include incomplete reporting of demographi...

Software with artificial intelligence-derived algorithms for detecting and analysing lung nodules in CT scans: systematic review and economic evaluation.

Health technology assessment (Winchester, England)
BACKGROUND: Lung cancer is one of the most common types of cancer and the leading cause of cancer death in the United Kingdom. Artificial intelligence-based software has been developed to reduce the number of missed or misdiagnosed lung nodules on co...

NNKcat: deep neural network to predict catalytic constants (Kcat) by integrating protein sequence and substrate structure with enhanced data imbalance handling.

Briefings in bioinformatics
Catalytic constant (Kcat) is to describe the efficiency of catalyzing reactions. The Kcat value of an enzyme-substrate pair indicates the rate an enzyme converts saturated substrates into product during the catalytic process. However, it is challengi...

MMsurv: a multimodal multi-instance multi-cancer survival prediction model integrating pathological images, clinical information, and sequencing data.

Briefings in bioinformatics
Accurate prediction of patient survival rates in cancer treatment is essential for effective therapeutic planning. Unfortunately, current models often underutilize the extensive multimodal data available, affecting confidence in predictions. This stu...

Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering.

Briefings in bioinformatics
Clustering is pivotal in deciphering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data. However, it suffers from several challenges in handling the high dimensionality and complexity of scRNA-seq data. Especially when employing gr...