AIMC Topic: Neural Networks, Computer

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ESM-BBB-Pred: a fine-tuned ESM 2.0 and deep neural networks for the identification of blood-brain barrier peptides.

Briefings in bioinformatics
Blood-brain barrier peptides (BBBP) could significantly improve the delivery of drugs to the brain, paving the way for new treatments for central nervous system (CNS) disorders. The primary challenge in treating CNS disorders lies in the difficulty p...

Learning genotype-phenotype associations from gaps in multi-species sequence alignments.

Briefings in bioinformatics
Understanding the genetic basis of phenotypic variation is fundamental to biology. Here we introduce GAP, a novel machine learning framework for predicting binary phenotypes from gaps in multi-species sequence alignments. GAP employs a neural network...

Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.

Briefings in bioinformatics
Existing algorithms for assessing tumor purity are limited to a single omics data, such as gene expression, somatic copy number variations, somatic mutations, and DNA methylation. Here we proposed the machine learning Multi-omics Tumor Purity predict...

Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data.

Briefings in bioinformatics
Cancer is a highly diverse group of diseases, and each type of cancer can be further divided into various subtypes according to specific characteristics, cellular origins, and molecular markers. Subtyping helps in tailoring treatment and prognosis ac...

BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction.

Briefings in bioinformatics
The automatic and accurate extraction of diverse biomedical relations from literature constitutes the core elements of medical knowledge graphs, which are indispensable for healthcare artificial intelligence. Currently, fine-tuning through stacking v...

Predicting transcriptional changes induced by molecules with MiTCP.

Briefings in bioinformatics
Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug di...

scGO: interpretable deep neural network for cell status annotation and disease diagnosis.

Briefings in bioinformatics
Machine learning has emerged as a transformative tool for elucidating cellular heterogeneity in single-cell RNA sequencing. However, a significant challenge lies in the "black box" nature of deep learning models, which obscures the decision-making pr...

A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction.

Briefings in bioinformatics
Many human diseases result from a complex interplay of behavioral, clinical, and molecular factors. Integrating low-dimensional behavioral and clinical features with high-dimensional molecular profiles can significantly improve disease outcome predic...

Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics.

Briefings in bioinformatics
Recent advances in single-cell RNA-Sequencing (scRNA-Seq) technologies have revolutionized our ability to gather molecular insights into different phenotypes at the level of individual cells. The analysis of the resulting data poses significant chall...

VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.

Briefings in bioinformatics
This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus ide...