AIMC Topic: Algorithms

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Kolmogorov-Arnold networks for genomic tasks.

Briefings in bioinformatics
Kolmogorov-Arnold networks (KANs) emerged as a promising alternative for multilayer perceptrons (MLPs) in dense fully connected networks. Multiple attempts have been made to integrate KANs into various deep learning architectures in the domains of co...

deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model.

Briefings in bioinformatics
MOTIVATION: Topologically associated domains (TADs) play a key role in the 3D organization and function of genomes, and accurate detection of TADs is essential for revealing the relationship between genomic structure and function. Most current method...

PCLSurv: a prototypical contrastive learning-based multi-omics data integration model for cancer survival prediction.

Briefings in bioinformatics
Accurate cancer survival prediction remains a critical challenge in clinical oncology, largely due to the complex and multi-omics nature of cancer data. Existing methods often struggle to capture the comprehensive range of informative features requir...

Relational similarity-based graph contrastive learning for DTI prediction.

Briefings in bioinformatics
As part of the drug repurposing process, it is imperative to predict the interactions between drugs and target proteins in an accurate and efficient manner. With the introduction of contrastive learning into drug-target prediction, the accuracy of dr...

BAMBI integrates biostatistical and artificial intelligence methods to improve RNA biomarker discovery.

Briefings in bioinformatics
RNA biomarkers enable early and precise disease diagnosis, monitoring, and prognosis, facilitating personalized medicine and targeted therapeutic strategies. However, identification of RNA biomarkers is hindered by the challenge of analyzing relative...

Benchmarking ensemble machine learning algorithms for multi-class, multi-omics data integration in clinical outcome prediction.

Briefings in bioinformatics
The complementary information found in different modalities of patient data can aid in more accurate modelling of a patient's disease state and a better understanding of the underlying biological processes of a disease. However, the analysis of multi...

Scaling up drug combination surface prediction.

Briefings in bioinformatics
Drug combinations are required to treat advanced cancers and other complex diseases. Compared with monotherapy, combination treatments can enhance efficacy and reduce toxicity by lowering the doses of single drugs-and there especially synergistic com...

DRAG: design RNAs as hierarchical graphs with reinforcement learning.

Briefings in bioinformatics
The rapid development of RNA vaccines and therapeutics puts forward intensive requirements on the sequence design of RNAs. RNA sequence design, or RNA inverse folding, aims to generate RNA sequences that can fold into specific target structures. To d...

Optimizing sample size for supervised machine learning with bulk transcriptomic sequencing: a learning curve approach.

Briefings in bioinformatics
Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate classification accuracy without undue resource allocat...

Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis.

Briefings in bioinformatics
High-throughput sequencing technologies have facilitated a deeper exploration of prognostic biomarkers. While many deep learning (DL) methods primarily focus on feature extraction or employ simplistic fully connected layers within prognostic modules,...