GenSo-FDSS: a neural-fuzzy decision support system for pediatric ALL cancer subtype identification using gene expression data.
OBJECTIVE
Acute lymphoblastic leukemia (ALL) is the most common malignancy of childhood, representing nearly one third of all pediatric cancers. Currently, the treatment of pediatric ALL is centered on tailoring the intensity of the therapy applied to a patient's risk of relapse, which is linked to the type of leukemia the patient has. Hence, accurate and correct diagnosis of the various leukemia subtypes becomes an important first step in the treatment process. Recently, gene expression profiling using DNA microarrays has been shown to be a viable and accurate diagnostic tool to identify the known prognostically important ALL subtypes. Thus, there is currently a huge interest in developing autonomous classification systems for cancer diagnosis using gene expression data. This is to achieve an unbiased analysis of the data and also partly to handle the large amount of genetic information extracted from the DNA microarrays.


METHODS
Generally, existing medical decision support systems (DSS) for cancer classification and diagnosis are based on traditional statistical methods such as Bayesian decision theory and machine learning models such as neural networks (NN) and support vector machine (SVM). Though high accuracies have been reported for these systems, they fall short on certain critical areas. These included (a) being able to present the extracted knowledge and explain the computed solutions to the users; (b) having a logical deduction process that is similar and intuitive to the human reasoning process; and (c) flexible enough to incorporate new knowledge without running the risk of eroding old but valid information. On the other hand, a neural fuzzy system, which is synthesized to emulate the human ability to learn and reason in the presence of imprecise and incomplete information, has the ability to overcome the above-mentioned shortcomings. However, existing neural fuzzy systems have their own limitations when used in the design and implementation of DSS. Hence, this paper proposed the use of a novel neural fuzzy system: the generic self-organising fuzzy neural network (GenSoFNN) with truth-value restriction (TVR) fuzzy inference, as a fuzzy DSS (denoted as GenSo-FDSS) for the classification of ALL subtypes using gene expression data.


CONCLUSIONS
The performance of the GenSo-FDSS system is encouraging when benchmarked against those of NN, SVM and the K-nearest neighbor (K-NN) classifier. On average, a classification rate of above 90% has been achieved using the GenSo-FDSS system.
Tung
W L
WL
Centre for Computational Intelligence, School of Computer Engineering, Nanyang Technological University, Blk N4 #2A-32, Nanyang Avenue, Singapore 639798, Singapore. wltung@pmail.ntu.edu.sg
Quek
C
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D000465:Algorithms; D002648:Child; D003658:Decision Making, Computer-Assisted; D003663:Decision Trees; D017143:Fuzzy Logic; D015870:Gene Expression; D006801:Humans; D009010:Monte Carlo Method; D016571:Neural Networks, Computer; D020411:Oligonucleotide Array Sequence Analysis; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000175:diagnosis / Q000235:genetics*; D012372:ROC Curve