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A Mixed Discrete-Continuous Attribute List Representation for Large Scale Classification Domains
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A Mixed Discrete-Continuous Attribute List Representation for Large Scale Classification Domains

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This work assesses the performance of the BioHEL data mining method to handle large-scale datasets, and proposes a representation to deal efficiently with domains with mixed discrete-continuous …

This work assesses the performance of the BioHEL data mining method to handle large-scale datasets, and proposes a representation to deal efficiently with domains with mixed discrete-continuous attributes

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  • 1. A Mixed Discrete-Continuous Attribute List Representation for Large Scale Classification Domains Jaume Bacardit Natalio Krasnogor {jqb,nxk}@cs.nott.ac.uk University of Nottingham
  • 2. Outline • Motivation and objectives • Framework: The BioHEL GBML system • Improving the Attribute List Knowledge Representation • Experimental design • Results and discussion • Conclusions and further work
  • 3. Motivation • We live in times of a great “data deluge” • Many different disciplines and industries generate vast amounts of data • Large scale can mean – Many records, many dimensions, many classes, … • Our work is focused on representations that – Can deal with large attribute spaces – Are efficient, as this can make a big difference when dealing with really large datasets
  • 4. The Attribute List knowledge representation (ALKR) • This representation was recently proposed [Bacardit et al., 09] to achieve these aims • This representation exploits a very frequent situation – In high-dimensionality domains it is usual that each rule only uses a very small subset of the attributes • Example of a rule for predicting a Bioinformatics dataset [Bacardit and Krasnogor, 2009] • Att Leu-2 ∈ [-0.51,7] and Glu ∈ [0.19,8] and Asp+1 ∈ [-5.01,2.67] and Met+1∈ [-3.98,10] and Pro+2 ∈ [-7,-4.02] and Pro+3 ∈ [-7,-1.89] and Trp+3 ∈ [-8,13] and Glu+4 ∈ [0.70,5.52] and Lys+4 ∈ [-0.43,4.94]  alpha • Only 9 attributes out of 300 were actually in the rule – Can we get rid of the 291 irrelevant attributes?
  • 5. The Attribute List knowledge representation • Thus, if we can get rid of the irrelevant attributes – The representation will be more efficient, avoiding the waste of cycles dealing with irrelevant data – Exploration will be more focused, as the chromosomes will only contain data that matters • This representation automatically identifies the relevant attributes in the domain for each rule • It was tested on several small datasets and a couple of large protein datasets, showing good performance
  • 6. Objectives of this work • We propose an efficient extension of the representation that can deal at the same time with continuous and discrete attributes – The original representation only dealt with continuous variables • We evaluate the representation using several large- scale domains – To assess its performance, and to identify where to improve it • We compare ALKR against other standard machine learning techniques
  • 7. The BioHEL GBML System • BIOinformatics-oriented Hiearchical Evolutionary Learning – BioHEL (Bacardit et al., 2007) • BioHEL is a GBML system that employs the Iterative Rule Learning (IRL) paradigm – First used in EC in Venturini’s SIA system (Venturini, 1993) – Widely used for both Fuzzy and non-fuzzy evolutionary learning • BioHEL inherits most of its components from GAssist [Bacardit, 04], a Pittsburgh GBML system
  • 8. Iterative Rule Learning • IRL has been used for many years in the ML community, with the name of separate-and-conquer
  • 9. Characteristics of BioHEL • A fitness function based on the Minimum-Description-Length (MDL) (Rissanen,1978) principle that tries to – Evolve accurate rules – Evolve high coverage rules – Evolve rules with low complexity, as general as possible • The Attribute List Knowledge representation – Representation designed to handle high-dimensionality domains • The ILAS windowing scheme – Efficiency enhancement method, not all training points are used for each fitness computation • An explicit default rule mechanism – Generating more compact rule sets • Ensembles for consensus prediction – Easy system to boost robustness
  • 10. Fitness function of BioHEL • Coverage term penalizes rules that do not cover a minimum percentage of examples • Choice of the coverage break is crucial for the proper performance of the system
  • 11. Improving the Attribute List Knowledge Representation • Mixed discrete-continuous representation – Intervalar represenation for continuous variables [Llora et al., 07] • If Att ∈ [ LB, UB] • 2 real-valued parameters, specifying the bounds – GABIL binary representation [De Jong & Spears, 91] for discrete variables • If Att takes value A or B • One bit for each possible value, indicating if value is included in the disjunction • If Att1∈ [0.2,0.5] and Att2 is (A or B)  Class 1 • {0.2,0.5|1,1,0|1}
  • 12. Improving the Attribute List Knowledge Representation • Each rule contains:
  • 13. Improving the Attribute List Knowledge Representation The match process is a crucial element in the performance of the system This code is run millions of times Do you think that this code is efficient? Look at the If
  • 14. Improving the Attribute List Knowledge Representation • Doing supervised learning allows us to exploit one trick – When we evaluate a rule, we test it against each example in the training set – Thus, we can precalculate two lists, of discrete and continuous attributes • The match process is performed separately for both kinds of attributes • Essentially, we have unrolled the loop
  • 15. Improving the Attribute List Knowledge Representation • Recombination remains unchanged – Simulated 1-point crossover to deal with the variable-length lists of attributes – Standard GA mutation – Two operators (specialize and generalize) add or remove attributes from the list with a given probability, hence exploring the space of the relevant attributes for this rule
  • 16. Experimental design • Seven datasets were used – They represent a broad range of characteristics in terms of instances, attributes, classes, type of attributes and class balance/unbalance
  • 17. Experimental design • First, ALKR was compared against BioHEL using its original representation (labelled orig) • Also, three standard machine learning techniques were used in the comparison: – C4.5 [Quinlan, 93] – Naive Bayes [John and Langley, 95] – LIBSVM [Chang & Lin, 01] • The default parameters of BioHEL were used, except for two of them: – The number of strata of the ILAS windowing scheme – The coverage breakpoint of BioHEL’s fitness function – These two parameters were strongly problem-dependant
  • 18. The traditional big table of results
  • 19. And one more (much larger) dataset • Protein Structure Prediction dataset (Solvent Accessibility - SA) with 270 attributes, 550K instances and 2 classes Method Accuracy Size solution #exp atts Run-time (h) BioHEL-orig 79.0±0.3 236.23±5.7 14.9±3.7 20.7±1.4 BioHEL-ALKR 79.2±0.3 243.23±5.2 8.4±2.7 14.8±1.0 BioHEL-naive 79.2±0.3 242.62±4.5 8.4±2.7 19.4±1.0 Run in a different C4.5 --- cluster Naïve Bayes 74.1±0.4 with more memory SVM 79.9±0.3 10 days and faster nodes
  • 20. ALKR vs Original BioHEL • Except for one dataset (and the difference is minor), ALKR always obtains better accuracy • Datasets where is ALKR is much better are those with larger number of attributes – ALKR is better at exploring the search space • ALKR generates more compact solutions, in #rules and, specially, in #attributes • Except for the ParMX domain (with a very small number of attributes), ALKR is always faster (72 times faster in the Germ dataset!)
  • 21. BioHEL vs other ML methods • The accuracy results were analyzed overall using a Friedman test for multiple comparisons • The test detected with a 97.77% confidence that there were significant differences in the performance of the compared methods • A post-hoc Holm test indicated that ALKR was significantly better than Naive Bayes with 95% confidence. • If we look at individual datasets, BioHEL is only outperformed largely in the wav and SA datasets by SVM • BioHEL’s advantage in the Germ dataset is specially large
  • 22. Where can we improve BioHEL? • ParMX is a synthetic dataset for which the optimal solution consists in 257 rules. BioHEL generated 402 rules • The rules were accurate but suboptimal • The coverage pressure introduced by the coverage breakpoint parameter was not appropiate for the whole learning process • BioHEL also had some problems in datasets with class unbalance (c-4)
  • 23. Conclusions • In this work we have – Extended the Attribute List Knowledge Representation of the BioHEL LCS to deal with mixed discrete-continuous domains in an efficient way – Assessed the performance of BioHEL using a broad range of large-scale scenarios – Compared BioHEL’s performance against other representations/learning techniques • The experiments have shown that BioHEL+ALKR is efficient, it generates compact and accurate solutions and it is competitive against other machine learning methods • We also identified several directions of improvement
  • 24. Future work • Identify the causes and address the issues that were observed in these experiments about BioHEL’s performance • Compare and combine ALKR against similar recent LCS work [Butz et al., 08] • Is possible to create a parameter-less BioHEL? • The development of theoretical models that can explain the behavior of both BioHEL and ALKR would – Made all of the above easier – Be an important milestone in the principled application of LCS to large-scale domains
  • 25. Questions?