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2017 ; 2
(1
): ä Nephropedia Template TP
gab.com Text
Twit Text FOAVip
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Learning Parsimonious Classification Rules from Gene Expression Data Using
Bayesian Networks with Local Structure
#MMPMID28331847
Lustgarten JL
; Balasubramanian JB
; Visweswaran S
; Gopalakrishnan V
Data (Basel)
2017[Mar]; 2
(1
): ä PMID28331847
show ga
The comprehensibility of good predictive models learned from high-dimensional
gene expression data is attractive because it can lead to biomarker discovery.
Several good classifiers provide comparable predictive performance but differ in
their abilities to summarize the observed data. We extend a Bayesian Rule
Learning (BRL-GSS) algorithm, previously shown to be a significantly better
predictor than other classical approaches in this domain. It searches a space of
Bayesian networks using a decision tree representation of its parameters with
global constraints, and infers a set of IF-THEN rules. The number of parameters
and therefore the number of rules are combinatorial to the number of predictor
variables in the model. We relax these global constraints to a more generalizable
local structure (BRL-LSS). BRL-LSS entails more parsimonious set of rules because
it does not have to generate all combinatorial rules. The search space of local
structures is much richer than the space of global structures. We design the
BRL-LSS with the same worst-case time-complexity as BRL-GSS while exploring a
richer and more complex model space. We measure predictive performance using Area
Under the ROC curve (AUC) and Accuracy. We measure model parsimony performance by
noting the average number of rules and variables needed to describe the observed
data. We evaluate the predictive and parsimony performance of BRL-GSS, BRL-LSS
and the state-of-the-art C4.5 decision tree algorithm, across 10-fold
cross-validation using ten microarray gene-expression diagnostic datasets. In
these experiments, we observe that BRL-LSS is similar to BRL-GSS in terms of
predictive performance, while generating a much more parsimonious set of rules to
explain the same observed data. BRL-LSS also needs fewer variables than C4.5 to
explain the data with similar predictive performance. We also conduct a
feasibility study to demonstrate the general applicability of our BRL methods on
the newer RNA sequencing gene-expression data.