AIMC Topic: Deep Learning

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ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images.

Briefings in bioinformatics
Structural information for chemical compounds is often described by pictorial images in most scientific documents, which cannot be easily understood and manipulated by computers. This dilemma makes optical chemical structure recognition (OCSR) an ess...

Adapt-Kcr: a novel deep learning framework for accurate prediction of lysine crotonylation sites based on learning embedding features and attention architecture.

Briefings in bioinformatics
Protein lysine crotonylation (Kcr) is an important type of posttranslational modification that is associated with a wide range of biological processes. The identification of Kcr sites is critical to better understanding their functional mechanisms. H...

Deep learning-based identification of genetic variants: application to Alzheimer's disease classification.

Briefings in bioinformatics
Deep learning is a promising tool that uses nonlinear transformations to extract features from high-dimensional data. Deep learning is challenging in genome-wide association studies (GWAS) with high-dimensional genomic data. Here we propose a novel t...

ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning.

Briefings in bioinformatics
Protein secretion has a pivotal role in many biological processes and is particularly important for intercellular communication, from the cytoplasm to the host or external environment. Gram-positive bacteria can secrete proteins through multiple secr...

Accelerating the discovery of antifungal peptides using deep temporal convolutional networks.

Briefings in bioinformatics
The application of machine intelligence in biological sciences has led to the development of several automated tools, thus enabling rapid drug discovery. Adding to this development is the ongoing COVID-19 pandemic, due to which researchers working in...

Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.

Briefings in bioinformatics
With the rapid progress of deep learning in cryo-electron microscopy and protein structure prediction, improving the accuracy of the protein structure model by using a density map and predicted contact/distance map through deep learning has become an...

Multimodal deep learning for biomedical data fusion: a review.

Briefings in bioinformatics
Biomedical data are becoming increasingly multimodal and thereby capture the underlying complex relationships among biological processes. Deep learning (DL)-based data fusion strategies are a popular approach for modeling these nonlinear relationship...

A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data.

Briefings in bioinformatics
Inferring gene regulatory networks (GRNs) based on gene expression profiles is able to provide an insight into a number of cellular phenotypes from the genomic level and reveal the essential laws underlying various life phenomena. Different from the ...

Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning.

Briefings in bioinformatics
Accurate prediction of atomic partial charges with high-level quantum mechanics (QM) methods suffers from high computational cost. Numerous feature-engineered machine learning (ML)-based predictors with favorable computability and reliability have be...

CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics.

Briefings in bioinformatics
Two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) provides a large amount of molecular information from biological samples. However, the lack of a comprehensive compound library or customizable bioinformatics tool is...