AIMC Topic: Deep Learning

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Molecular design in drug discovery: a comprehensive review of deep generative models.

Briefings in bioinformatics
Deep generative models have been an upsurge in the deep learning community since they were proposed. These models are designed for generating new synthetic data including images, videos and texts by fitting the data approximate distributions. In the ...

Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture.

Briefings in bioinformatics
Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is ...

De novo generation of dual-target ligands using adversarial training and reinforcement learning.

Briefings in bioinformatics
Artificial intelligence, such as deep generative methods, represents a promising solution to de novo design of molecules with the desired properties. However, generating new molecules with biological activities toward two specific targets remains an ...

RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks.

Briefings in bioinformatics
Genotype imputation is a statistical method for estimating missing genotypes from a denser haplotype reference panel. Existing methods usually performed well on common variants, but they may not be ideal for low-frequency and rare variants. Previous ...

XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data.

Briefings in bioinformatics
The lack of explainability is one of the most prominent disadvantages of deep learning applications in omics. This 'black box' problem can undermine the credibility and limit the practical implementation of biomedical deep learning models. Here we pr...

Comparative analysis of molecular fingerprints in prediction of drug combination effects.

Briefings in bioinformatics
Application of machine and deep learning methods in drug discovery and cancer research has gained a considerable amount of attention in the past years. As the field grows, it becomes crucial to systematically evaluate the performance of novel computa...

High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data.

Briefings in bioinformatics
In this study, we proposed a deep learning (DL) model for classifying individuals from mixtures of DNA samples using 27 short tandem repeats and 94 single nucleotide polymorphisms obtained through massively parallel sequencing protocol. The model was...

Deep fusion learning facilitates anatomical therapeutic chemical recognition in drug repurposing and discovery.

Briefings in bioinformatics
The advent of large-scale biomedical data and computational algorithms provides new opportunities for drug repurposing and discovery. It is of great interest to find an appropriate data representation and modeling method to facilitate these studies. ...

DeepFeature: feature selection in nonimage data using convolutional neural network.

Briefings in bioinformatics
Artificial intelligence methods offer exciting new capabilities for the discovery of biological mechanisms from raw data because they are able to detect vastly more complex patterns of association that cannot be captured by classical statistical test...

iDeepSubMito: identification of protein submitochondrial localization with deep learning.

Briefings in bioinformatics
Mitochondria are membrane-bound organelles containing over 1000 different proteins involved in mitochondrial function, gene expression and metabolic processes. Accurate localization of those proteins in the mitochondrial compartments is critical to t...