Assessing reproducibility and veracity across machine learning techniques in biomedicine: A case study using TCGA data

International Journal of Medical Informatics
Ahyoung Amy KimVignesh Subbian

Abstract

Many studies that aim to identify gene biomarkers using statistical methods and translate them into FDA-approved drugs have faced challenges due to lack of clinical validity and methodological reproducibility. Since genomic data analysis relies heavily on these statistical learning tools more than before, it is vital to address the limitations of these computational techniques. Our study demonstrates these methodological gaps among most common statistical learning techniques used in gene expression analysis. To assess the classification ability and reproducibility of statistical learning tools for gene biomarker detection, six state-of-the-art machine learning models were trained on four different cancer data retrieved from The Cancer Genome Atlas (TCGA). Standard performance metrics including specificity, sensitivity, precision, and F1 score were evaluated to investigate the classification ability. For analysis of reproducibility, the identifiability of gene classifiers was examined by quantifying the consistency of the chosen classifier genes. Among the six state-of-the-art machine learning methods, the random forest had the best classification ability overall. Very few genes were selected by multiple methods, which suggests ...Continue Reading

References

Jan 19, 2007·The New England Journal of Medicine·Joan Massagué
Jun 3, 2010·Scandinavian Journal of Clinical and Laboratory Investigation. Supplementum·Adam S Ptolemy, Nader Rifai
May 24, 2013·Nature·C Glenn Begley
Nov 27, 2014·Neoplasia : an International Journal for Oncology Research·Iris H WeiArul M Chinnaiyan
Jan 31, 2015·The New England Journal of Medicine·Francis S Collins, Harold Varmus
Mar 10, 2015·Genetic Testing and Molecular Biomarkers·Sharon F Terry
Nov 17, 2015·Bioinformatics·Ying-Wooi WanZhandong Liu
Aug 25, 2016·Seminars in Cell & Developmental Biology·Diane Catherine Wang, Xiangdong Wang
Nov 20, 2016·Cancer·Edmund A Mroz, James W Rocco
Nov 25, 2016·BMC Medical Research Methodology·Maarten van SmedenJohannes B Reitsma
Jan 18, 2017·Clinical and Translational Science·L M McShane
Feb 25, 2019·Artificial Intelligence in Medicine·Maisa Daoud, Michael Mayo
Apr 23, 2019·Bioinformatics and Biology Insights·Haitao Zhao, Zhong-Hui Duan
Jul 7, 2019·Scientific Reports·Colin A TargonskiF Alex Feltus

❮ Previous
Next ❯

Citations

Apr 2, 2021·Biotechnology Advances·Parminder S ReelEmily Jefferson

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.