AIMC Topic: Deep Learning

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SGANRDA: semi-supervised generative adversarial networks for predicting circRNA-disease associations.

Briefings in bioinformatics
Emerging research shows that circular RNA (circRNA) plays a crucial role in the diagnosis, occurrence and prognosis of complex human diseases. Compared with traditional biological experiments, the computational method of fusing multi-source biologica...

Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.

Briefings in bioinformatics
Single-cell RNA sequencing (scRNA-Seq) is an emerging strategy for characterizing immune cell populations. Compared to flow or mass cytometry, scRNA-Seq could potentially identify cell types and activation states that lack precise cell surface marker...

Feature extraction approaches for biological sequences: a comparative study of mathematical features.

Briefings in bioinformatics
As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced. Although machine learning algorithms have been successfully applied to a large number of genomic sequence-related problems,...

Prediction and collection of protein-metabolite interactions.

Briefings in bioinformatics
Interactions between proteins and small molecule metabolites play vital roles in regulating protein functions and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporters and membrane receptors ...

A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information.

Briefings in bioinformatics
Recently, language representation models have drawn a lot of attention in the natural language processing field due to their remarkable results. Among them, bidirectional encoder representations from transformers (BERT) has proven to be a simple, yet...

Anticancer peptides prediction with deep representation learning features.

Briefings in bioinformatics
Anticancer peptides constitute one of the most promising therapeutic agents for combating common human cancers. Using wet experiments to verify whether a peptide displays anticancer characteristics is time-consuming and costly. Hence, in this study, ...

Identification of haploinsufficient genes from epigenomic data using deep forest.

Briefings in bioinformatics
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been develop...

DeepCNV: a deep learning approach for authenticating copy number variations.

Briefings in bioinformatics
Copy number variations (CNVs) are an important class of variations contributing to the pathogenesis of many disease phenotypes. Detecting CNVs from genomic data remains difficult, and the most currently applied methods suffer from an unacceptably hig...

A deep learning based automatic segmentation approach for anatomical structures in intensity modulation radiotherapy.

Mathematical biosciences and engineering : MBE
OBJECTIVE: To evaluate the automatic segmentation approach for organ at risk (OARs) and compare the parameters of dose volume histogram (DVH) in radiotherapy.