Genetics

A Cascade Flexible Neural Forest Model for Cancer Subtypes Classification on Gene Expression Data.

The correct classification of cancer subtypes is of great significance for the in-depth study of cancer pathogenesis and the realization of accurate treatment for cancer patients. In recent years, the classification of cancer subtypes using deep neural networks and gene expression data has become a hot topic. However, most classifiers may face the challenges of overfitting and low classification a...

Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes.

BACKGROUND: Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionality reduction (MDR) is a popular approach for detecting gene-gene interactions that has been extended in various forms to handle binary and continuous phenotypes. However, only few...

Effective gene expression prediction from sequence by integrating long-range interactions.

How noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human geneti...

Deep convolutional neural network-based algorithm for muscle biopsy diagnosis.

Histopathologic evaluation of muscle biopsy samples is essential for classifying and diagnosing muscle diseases. However, the numbers of experienced s...

COVID-19 detection from lung CT-Scans using a fuzzy integral-based CNN ensemble.

The COVID-19 pandemic has collapsed the public healthcare systems, along with severely damaging the economy of the world. The SARS-CoV-2 virus also kn...

Advances in for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence.

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, whe...

Intelligent Optimization Algorithm-Based Path Planning for a Mobile Robot.

The purpose of mobile robot path planning is to produce the optimal safe path. However, mobile robots have poor real-time obstacle avoidance in local ...

PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks.

Advances in genome sequencing have accelerated the growth of sequenced genomes but at a cost in the quality of genome annotation. At the same time, co...

Hyperspectral Image Classification Using Deep Genome Graph-Based Approach.

Recently developed hybrid models that stack 3D with 2D CNN in their structure have enjoyed high popularity due to their appealing performance in hyper...

AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome.

In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable...

4mC-RF: Improving the prediction of 4mC sites using composition and position relative features and statistical moment.

N4-methylcytosine (4 mC) is an important epigenetic modification that occurs enzymatically by the action of DNA methyltransferases. 4 mC sites exist i...

Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships.

Inferring phenotypic outcomes from genomic features is both a promise and challenge for systems biology. Using gene expression data to predict phenoty...

EditPredict: Prediction of RNA editable sites with convolutional neural network.

RNA editing exerts critical impacts on numerous biological processes. While millions of RNA editings have been identified in humans, much more are exp...

Analyses of child cardiometabolic phenotype following assisted reproductive technologies using a pragmatic trial emulation approach.

Assisted reproductive technologies (ART) are increasingly used, however little is known about the long-term health of ART-conceived offspring. Weak se...

Mutations of PHOX2B Gene in Patients of Obesity Hypoventilation Syndrome in Central India.

 Paired-like homeobox 2B (PHOX2B) gene on chromosome 4p12 codes for a transcription factor having a role in the formation of noradrenergic neuronal c...

Machine learning model for predicting Major Depressive Disorder using RNA-Seq data: optimization of classification approach.

Considering human brain disorders, Major Depressive Disorder (MDD) is seen as a lethal disease in which a person goes to the extent of suicidal behavi...

Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data.

BACKGROUND: With the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompt...

Multimodal deep learning models for the prediction of pathologic response to neoadjuvant chemotherapy in breast cancer.

The achievement of the pathologic complete response (pCR) has been considered a metric for the success of neoadjuvant chemotherapy (NAC) and a powerfu...

Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment.

HIV molecular epidemiology estimates the transmission patterns from clustering genetically similar viruses. The process involves connecting geneticall...

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network.

Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long ...