Machine Learning Methods for Cancer Classification Using Gene Expression Data: A Review

DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning

(2022) Tulika Kakati et al.   BMC BIOINFORMATICS

Prediction of Time Series Gene Expression and Structural Analysis of Gene Regulatory Networks Using Recurrent Neural Networks

(2022) Michele Monti et al.   Entropy

PanClassif: Improving pan cancer classification of single cell RNA-seq gene expression data using machine learning

(2022) Kazi Ferdous Mahin et al.   GENOMICS

Hybrid gene selection approach using XGBoost and multi-objective genetic algorithm for cancer classification

(2022) Xiongshi Deng et al.   MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING

A Survey of Machine Learning Approaches Applied to Gene Expression Analysis for Cancer Prediction

(2022) Mahmood Jasim et al.   IEEE Access

Gene Expression Profiling in Early Breast Cancer—Patient Stratification Based on Molecular and Tumor Microenvironment Features

(2022) Gyöngyi Munkácsy et al.   Biomedicines

Graph Based Feature Selection for Reduction of Dimensionality in Next-Generation RNA Sequencing Datasets

(2022) Consolata Gakii et al.   Algorithms

Prediction of lung cancer using gene expression and deep learning with KL divergence gene selection

(2022) Suli Liu et al.   BMC BIOINFORMATICS

A multi-objective optimization approach for the identification of cancer biomarkers from RNA-seq data

(2022) Veredas Coleto-Alcudia et al.   EXPERT SYSTEMS WITH APPLICATIONS

Early detection of cancer

(2022) David Crosby et al.   SCIENCE

A novel liver cancer diagnosis method based on patient similarity network and DenseGCN

(2022) Ge Zhang et al.   Scientific Reports

Optimal Deep Learning Enabled Prostate Cancer Detection Using Microarray Gene Expression

(2022) Abdulrhman M. Alshareef et al.   Journal of Healthcare Engineering

Transfer learning for medical image classification: a literature review

(2022) Hee E. Kim et al.   BMC MEDICAL IMAGING

Red Fox Optimizer with Data-Science-Enabled Microarray Gene Expression Classification Model

(2022) Thavavel Vaiyapuri et al.   Applied Sciences-Basel

Individualized pathway activity algorithm identifies oncogenic pathways in pan-cancer analysis

(2022) Xin Ke et al.   EBioMedicine

Deep Learning-Based Pan-Cancer Classification Model Reveals Tissue-of-Origin Specific Gene Expression Signatures

(2022) Mayur Divate et al.   Cancers

MFRAG: Multi-Fitness RankAggreg Genetic Algorithm for biomarker selection from microarray data

(2022) Weidong Xie et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Computer-aided diagnosis for breast cancer classification using deep neural networks and transfer learning

(2022) Hanan Aljuaid et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Graph-based relevancy-redundancy gene selection method for cancer diagnosis

(2022) Saeid Azadifar et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Use of a graph neural network to the weighted gene co-expression network analysis of Korean native cattle

(2022) Hyo-Jun Lee et al.   Scientific Reports

Hierarchical dynamic convolutional neural network for laryngeal disease classification

(2022) Shaoli Wang et al.   Scientific Reports

GNN-SubNet: disease subnetwork detection with explainable graph neural networks

(2022) Bastian Pfeifer et al.   BIOINFORMATICS

A feature selection-based framework to identify biomarkers for cancer diagnosis: A focus on lung adenocarcinoma

(2022) Omar Abdelwahab et al.   PLoS One

A survey on gene expression data analysis using deep learning methods for cancer diagnosis

(2022) U Ravindran et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Transformer for Gene Expression Modeling (T-GEM): An Interpretable Deep Learning Model for Gene Expression-Based Phenotype Predictions

(2022) Ting-He Zhang et al.   Cancers

Improved swarm-optimization-based filter-wrapper gene selection from microarray data for gene expression tumor classification

(2022) Lin Ke et al.   PATTERN ANALYSIS AND APPLICATIONS

Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer

(2022) Dohoon Lee et al.   Nature Communications

A comprehensive survey on computational learning methods for analysis of gene expression data

(2022) Nikita Bhandari et al.   Frontiers in Molecular Biosciences

A review of deep learning applications for genomic selection

(2021) Osval Antonio Montesinos-López et al.   BMC GENOMICS

Prediction and Interpretation of Cancer Survival Using Graph Convolution Neural Networks

(2021) Ricardo Ramirez et al.   METHODS

Breast Cancer Type Classification Using Machine Learning

(2021) Jiande Wu et al.   Journal of Personalized Medicine

Segment-specific kinetics of mRNA, cRNA and vRNA accumulation during influenza infection

(2021) Thu Phan et al.   JOURNAL OF VIROLOGY

(CDRGI)-Cancer detection through relevant genes identification

(2021) Feras Al-Obeidat et al.   NEURAL COMPUTING & APPLICATIONS

Gated Graph Attention Network for Cancer Prediction

(2021) Linling Qiu et al.   SENSORS

Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer

(2021) Hryhorii Chereda et al.   Genome Medicine

Next-generation sequencing technologies: An overview

(2021) Taishan Hu et al.   HUMAN IMMUNOLOGY

Classification of breast cancer using microarray gene expression data: A survey

(2021) Muhammed Abd-Elnaby et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Jaya Ant lion optimization-driven Deep recurrent neural network for cancer classification using gene expression data

(2021) Ramachandro Majji et al.   MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

(2021) Juexin Wang et al.   Nature Communications

Recent Developments in Cancer Systems Biology: Lessons Learned and Future Directions

(2021) Kazim Y. Arga et al.   Journal of Personalized Medicine

Robust biomarker discovery for hepatocellular carcinoma from high-throughput data by multiple feature selection methods

(2021) Zishuang Zhang et al.   BMC Medical Genomics

Cancer statistics for the US Hispanic/Latino population, 2021

(2021) Kimberly D. Miller et al.   CA-A CANCER JOURNAL FOR CLINICIANS

An intelligent ensemble classification method based on multi-layer perceptron neural network and evolutionary algorithms for breast cancer diagnosis

(2021) Saeed Talatian Azad et al.   JOURNAL OF EXPERIMENTAL & THEORETICAL ARTIFICIAL INTELLIGENCE

A deep embedded refined clustering approach for breast cancer distinction based on DNA methylation

(2021) Rocío del Amor et al.   NEURAL COMPUTING & APPLICATIONS

Recurrent Neural Network for Genome Sequencing for Personalized Cancer Treatment in Precision Healthcare

(2021) A. Suresh et al.   NEURAL PROCESSING LETTERS

A stacking ensemble deep learning approach to cancer type classification based on TCGA data

(2021) Mohanad Mohammed et al.   Scientific Reports

Lung adenocarcinoma and lung squamous cell carcinoma cancer classification, biomarker identification, and gene expression analysis using overlapping feature selection methods

(2021) Joe W. Chen et al.   Scientific Reports

Gene Expression-Assisted Cancer Prediction Techniques

(2021) Tanima Thakur et al.   Journal of Healthcare Engineering

Graph Neural Networks and Their Current Applications in Bioinformatics

(2021) Xiao-Meng Zhang et al.   Frontiers in Genetics

Comparison of Selected Immune and Hematological Parameters and Their Impact on Survival in Patients with HPV-Related and HPV-Unrelated Oropharyngeal Cancer

(2021) Adam Brewczyński et al.   Cancers

A Review on Recent Progress in Machine Learning and Deep Learning Methods for Cancer Classification on Gene Expression Data

(2021) Aina Umairah Mazlan et al.   Processes

Gene selection for microarray data classification via multi-objective graph theoretic-based method

(2021) Mehrdad Rostami et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Deep transfer learning for automated liver cancer gene recognition using spectrogram images of digitized DNA sequences

(2021) Bihter Das et al.   Biomedical Signal Processing and Control

MRI radiogenomics for intelligent diagnosis of breast tumors and accurate prediction of neoadjuvant chemotherapy responses-a review

(2021) Xiao-Xia Yin et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Feature selection methods on gene expression microarray data for cancer classification: A systematic review

(2021) Esra'a Alhenawi et al.   COMPUTERS IN BIOLOGY AND MEDICINE

rPAC: Route based pathway analysis for cohorts of gene expression data sets

(2021) Pujan Joshi et al.   METHODS

A Novel Map Reduced Based Parallel Feature Selection and Extreme Learning for Micro Array Cancer Data Classification

(2021) Swati Hira et al.   WIRELESS PERSONAL COMMUNICATIONS

An IoMT-Enabled Smart Healthcare Model to Monitor Elderly People Using Machine Learning Technique

(2021) Muhammad Farrukh Khan et al.   Computational Intelligence and Neuroscience

A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies

(2021) Samarendra Das et al.   Genes

Deep Learning for Human Disease Detection, Subtype Classification, and Treatment Response Prediction Using Epigenomic Data

(2021) Thi Mai Nguyen et al.   Biomedicines

Aspect-based sentiment classification with multi-attention network

(2020) Qiannan Xu et al.   NEUROCOMPUTING

The Application of Deep Learning in Cancer Prognosis Prediction

(2020) Wan Zhu et al.   Cancers

Convolutional neural network models for cancer type prediction based on gene expression

(2020) Milad Mostavi et al.   BMC Medical Genomics

Integrating genomic features for non-invasive early lung cancer detection

(2020) Jacob J. Chabon et al.   NATURE

Transfer learning with convolutional neural networks for cancer survival prediction using gene-expression data

(2020) Guillermo López-García et al.   PLoS One

Using Class-Specific Feature Selection for Cancer Detection with Gene Expression Profile Data of Platelets

(2020) Lei-ming Yuan et al.   SENSORS

Overall survival prediction of non-small cell lung cancer by integrating microarray and clinical data with deep learning

(2020) Yu-Heng Lai et al.   Scientific Reports

Changing Technologies of RNA Sequencing and Their Applications in Clinical Oncology

(2020) Ye Wang et al.   Frontiers in Oncology

Analysis of gene expression profiles of lung cancer subtypes with machine learning algorithms

(2020) Fei Yuan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

An effective feature engineering for DNN using hybrid PCA-GWO for intrusion detection in IoMT architecture

(2020) Swarna Priya R.M. et al.   COMPUTER COMMUNICATIONS

Bayesian Hyper-LASSO Classification for Feature Selection with Application to Endometrial Cancer RNA-seq Data

(2020) Lai Jiang et al.   Scientific Reports

Prediction of breast cancer molecular subtypes on DCE-MRI using convolutional neural network with transfer learning between two centers

(2020) Yang Zhang et al.   EUROPEAN RADIOLOGY

Disease prediction based on micro array classification using deep learning techniques

(2020) V. Chandrasekar et al.   MICROPROCESSORS AND MICROSYSTEMS

DECAB-LSTM: Deep Contextualized Attentional Bidirectional LSTM for cancer hallmark classification

(2020) Longquan Jiang et al.   KNOWLEDGE-BASED SYSTEMS

Prediction of lncRNA-disease associations via an embedding learning HOPE in heterogeneous information networks

(2020) Ji-Ren Zhou et al.   Molecular Therapy-Nucleic Acids

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

Insights into Molecular Classifications of Triple-Negative Breast Cancer: Improving Patient Selection for Treatment

(2019) Ana C. Garrido-Castro et al.   Cancer Discovery

Past, present, and future of circ RNA s

(2019) Ines Lucia Patop et al.   EMBO JOURNAL

Reconstructing gene regulatory networks via memetic algorithm and LASSO based on recurrent neural networks

(2019) Luowen Liu et al.   SOFT COMPUTING

Wx: a neural network-based feature selection algorithm for transcriptomic data

(2019) Sungsoo Park et al.   Scientific Reports

DeepCC: a novel deep learning-based framework for cancer molecular subtype classification

(2019) Feng Gao et al.   Oncogenesis

A comparative study of topology-based pathway enrichment analysis methods

(2019) Jing Ma et al.   BMC BIOINFORMATICS

Unsupervised feature selection algorithm for multiclass cancer classification of gene expression RNA-Seq data

(2019) Pilar García-Díaz et al.   GENOMICS

Investigating the Impact of Biostimulants on the Row Crops Corn and Soybean Using High-Efficiency Phenotyping and Next Generation Sequencing

(2019) Nunzio Briglia et al.   Agronomy-Basel

Deep learning-based clustering approaches for bioinformatics

(2019) Md Rezaul Karim et al.   BRIEFINGS IN BIOINFORMATICS

A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data

(2018) Yunchuan Kong et al.   BIOINFORMATICS

A deep learning-based multi-model ensemble method for cancer prediction

(2018) Yawen Xiao et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Transfer Learning for Molecular Cancer classification using Deep Neural Networks

(2018) Rahul Kumar Sevakula et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Splicing mutations in human genetic disorders: examples, detection, and confirmation

(2018) Abramowicz Anna et al.   JOURNAL OF APPLIED GENETICS

Integrating Feature Selection and Feature Extraction Methods With Deep Learning to Predict Clinical Outcome of Breast Cancer

(2018) Dejun Zhang et al.   IEEE Access

Feature selection of gene expression data for Cancer classification using double RBF-kernels

(2018) Shenghui Liu et al.   BMC BIOINFORMATICS

Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Networks

(2018) Mahboobeh Ghorbani et al.   Frontiers in Physiology

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens

(2013) Hufeng Zhou et al.   BMC Systems Biology

A Classification Framework Applied to Cancer Gene Expression Profiles

(2013) Hussein Hijazi et al.   Journal of Healthcare Engineering

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

(2009) Anna Bauer-Mehren et al.   Molecular Systems Biology