The linear neuron as marker selector and clinical predictor in cancer gene analysis

Computer Methods and Programs in Biomedicine
Michalis E Blazadonakis, Michalis E Zervakis

Abstract

The problem of gene selection has been extensively studied in a number of scientific works using various kinds of methods. However, the application of a linear neuron is a novel approach possessing several advantages. In this work we propose to study the behavior of such a linear neuron, appropriately adapted and trained to the problem of gene selection in the DNA microarray experiment. We explore the proposed approach in terms of an accuracy evaluation criterion, which is used to assess the performance of the proposed methodology, but we also evaluate the produced results in terms of cluster quality and survival prediction. Cluster quality reflects the ability of the method to select differentially expressed genes, which in turn leads to better clustering and survival prediction. We directly compare the proposed methodology with RFE-SVM, a well known and broadly accepted method demonstrating remarkable performance on various data sets of clinical interest. Conducted computational experiments show that the proposed approach can be efficiently used within the field of gene selection producing high-quality results in terms of accuracy and robustness.

References

Feb 2, 2002·Nature·Laura J van 't VeerStephen H Friend
Feb 16, 2002·Bioinformatics·F Azuaje
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Christophe Ambroise, Geoffrey J McLachlan
Dec 20, 2002·The New England Journal of Medicine·Marc J van de VijverRené Bernards
Jan 2, 2003·Journal of the National Cancer Institute·Richard SimonLisa M McShane
Aug 25, 2005·Bioinformatics·Fan Li, Yiming Yang
Sep 13, 2007·Journal of the National Cancer Institute·Hong JiangJuan Fueyo
Feb 6, 2008·IEEE Transactions on Neural Networks·J Vesanto, E Alhoniemi
Feb 7, 2008·IEEE Transactions on Neural Networks·V N Vapnik
Feb 1, 1979·IEEE Transactions on Pattern Analysis and Machine Intelligence·D L Davies, D W Bouldin

❮ Previous
Next ❯

Citations

Feb 18, 2011·Australasian Physical & Engineering Sciences in Medicine·Hamid MahmoodianIqbal Saripan
Feb 10, 2009·BMC Bioinformatics·Michalis ZervakisDimitris Kafetzopoulos
Jul 20, 2011·Artificial Intelligence in Medicine·Michalis E BlazadonakisDimitrios Kafetzopoulos
Sep 4, 2010·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Michalis E BlazadonakisDimitris Kafetzopoulos

❮ 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.