AIMC Topic: Deep Learning

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Introducing TEC-LncMir for prediction of lncRNA-miRNA interactions through deep learning of RNA sequences.

Briefings in bioinformatics
The interactions between long noncoding RNA (lncRNA) and microRNA (miRNA) play critical roles in life processes, highlighting the necessity to enhance the performance of state-of-the-art models. Here, we introduced TEC-LncMir, a novel approach for pr...

DeepPFP: a multi-task-aware architecture for protein function prediction.

Briefings in bioinformatics
Deriving protein function from protein sequences poses a significant challenge due to the intricate relationship between sequence and function. Deep learning has made remarkable strides in predicting sequence-function relationships. However, models t...

Classification-based pathway analysis using GPNet with novel P-value computation.

Briefings in bioinformatics
Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted lim...

Inferring the genetic relationships between unsupervised deep learning-derived imaging phenotypes and glioblastoma through multi-omics approaches.

Briefings in bioinformatics
This study aimed to investigate the genetic association between glioblastoma (GBM) and unsupervised deep learning-derived imaging phenotypes (UDIPs). We employed a combination of genome-wide association study (GWAS) data, single-nucleus RNA sequencin...

Deep learning-based design and experimental validation of a medicine-like human antibody library.

Briefings in bioinformatics
Antibody generation requires the use of one or more time-consuming methods, namely animal immunization, and in vitro display technologies. However, the recent availability of large amounts of antibody sequence and structural data in the public domain...

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...

Therapeutic gene target prediction using novel deep hypergraph representation learning.

Briefings in bioinformatics
Identifying therapeutic genes is crucial for developing treatments targeting genetic causes of diseases, but experimental trials are costly and time-consuming. Although many deep learning approaches aim to identify biomarker genes, predicting therape...

scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data.

Briefings in bioinformatics
Single-cell high-throughput chromosome conformation capture (Hi-C) technology enables capturing chromosomal spatial structure information at the cellular level. However, to effectively investigate changes in chromosomal structure across different cel...

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...