Epistasis Blog

From the Computational Genetics Laboratory at the University of Pennsylvania (www.epistasis.org)

Sunday, October 04, 2015

ExSTraCS 2.0: Description and Evaluation of a Scalable Learning Classifier System

Our latest paper on the development, evaluation, and application of learning classifier systems (LCS) to the detection and characterization of genetic effects that are heterogeneous. This work has been lead by my former graduate student and postdoc Dr. Ryan Urbanowicz. See his web page for more information.

Urbanowicz RJ, Moore JH. ExSTraCS 2.0: Description and Evaluation of a Scalable Learning Classifier System. Evol Intell. 2015 Sep;8(2):89-116. [PubMed] [Springer]


Algorithmic scalability is a major concern for any machine learning strategy in this age of 'big data'. A large number of potentially predictive attributes is emblematic of problems in bioinformatics, genetic epidemiology, and many other fields. Previously, ExS-TraCS was introduced as an extended Michigan-style supervised learning classifier system that combined a set of powerful heuristics to successfully tackle the challenges of classification, prediction, and knowledge discovery in complex, noisy, and heterogeneous problem domains. While Michigan-style learning classifier systems are powerful and flexible learners, they are not considered to be particularly scalable. For the first time, this paper presents a complete description of the ExS-TraCS algorithm and introduces an effective strategy to dramatically improve learning classifier system scalability. ExSTraCS 2.0 addresses scalability with (1) a rule specificity limit, (2) new approaches to expert knowledge guided covering and mutation mechanisms, and (3) the implementation and utilization of the TuRF algorithm for improving the quality of expert knowledge discovery in larger datasets. Performance over a complex spectrum of simulated genetic datasets demonstrated that these new mechanisms dramatically improve nearly every performance metric on datasets with 20 attributes and made it possible for ExSTraCS to reliably scale up to perform on related 200 and 2000-attribute datasets. ExSTraCS 2.0 was also able to reliably solve the 6, 11, 20, 37, 70, and 135 multiplexer problems, and did so in similar or fewer learning iterations than previously reported, with smaller finite training sets, and without using building blocks discovered from simpler multiplexer problems. Furthermore, ExS-TraCS usability was made simpler through the elimination of previously critical run parameters.


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