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

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?