AIMC Topic: Software

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A multi-view graph convolutional network framework based on adaptive adjacency matrix and multi-strategy fusion mechanism for identifying spatial domains.

Bioinformatics (Oxford, England)
MOTIVATION: Spatial transcriptomics (ST) addresses the loss of spatial context in single-cell RNA-sequencing by simultaneously capturing gene expression and spatial location information. A critical task of ST is the identification of spatial domains....

GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes.

Bioinformatics (Oxford, England)
MOTIVATION: Leveraging deep learning for the representation learning of Gene Ontology (GO) and Gene Ontology Annotation (GOA) holds significant promise for enhancing downstream biological tasks such as protein-protein interaction prediction. Prior ap...

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization.

Bioinformatics (Oxford, England)
SUMMARY: In single-cell transcriptomics, inconsistent cell type annotations due to varied naming conventions and hierarchical granularity impede data integration, machine learning applications, and meaningful evaluations. To address this challenge, w...

Lit-OTAR framework for extracting biological evidences from literature.

Bioinformatics (Oxford, England)
SUMMARY: The lit-OTAR framework, developed through a collaboration between Europe PMC and Open Targets, leverages deep learning to revolutionize drug discovery by extracting evidence from scientific literature for drug target identification and valid...

H2GnnDTI: hierarchical heterogeneous graph neural networks for drug-target interaction prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Identifying drug-target interactions (DTIs) is a crucial step in drug repurposing and drug discovery. The significant increase in demand and the expensive nature for experimentally identifying DTIs necessitate computational tools for auto...

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.

Nucleic acids research
Ribonucleic Acid (RNA) is the central conduit for information transfer in the cell. Identifying potential RNA targets in disease conditions is a challenging task, given the vast repertoire of functional non-coding RNAs in a human cell. A potential dr...

MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human.

Briefings in bioinformatics
In post-translational modification, covalent bonds on lysine and attached chemical groups significantly change proteins' physical and chemical properties. They shape protein structures, enhance function and stability, and are vital for physiological ...

IDP-EDL: enhancing intrinsically disordered protein prediction by combining protein language model and ensemble deep learning.

Briefings in bioinformatics
Identification of intrinsically disordered regions (IDRs) in proteins is essential for understanding fundamental cellular processes. The IDRs can be divided into long disordered regions (LDRs) and short disordered regions (SDRs) according to their le...

FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis.

Briefings in bioinformatics
Single-cell multi-omics technologies have revolutionized the study of cell states and functions by simultaneously profiling multiple molecular layers within individual cells. However, existing methods for integrating these data struggle to preserve c...