_PROBLEM CoEPrA-2006_Classification_004

_GROUP_NAME Hendrik Blockeel

_GROUP_MEMBERS
Joaquin Vanschoren
Leander Schietgat
Elisa Fromont
Jan Ramon
Hendrik Blockeel
Kurt De Grave
Luc Dehaspe
Walter Luyten

_ADDRESS
Dept. of Computer Science, Katholieke Universiteit Leuven
Celestijnenlaan 200A, 3001 Leuven, Belgium

_MODELING_PROCEDURE

1) construction of different views on the data

As data representation is known to have an important impact on
learning results, we have constructed different views on the
same data set.

View 1 is the raw data, with 643 descriptors for each amino acid.

View 2 contains information on "frequent subsequences at specific
positions" in the peptide sequences.  Patterns of length 1, 2 and 3
with a minimum frequency of 5% (i.e., occurring in at least 5% of
all examples) were mined using the Warmr algorithm [Dehaspe99].
An example of such a pattern is (7,V,T), which means that VT is
occurring at positions 7 and 8 in the peptide sequence. These frequent
patterns were mined in the calibration and prediction set together.
Then, every example was checked against all the frequent patterns:
1 was written if the pattern was occurring in the example, 0 otherwise.

After consulting a domain expert, we decided to make a variant of this
first view (called ``view2_inter'') that looks for alternating
patterns in the peptide sequence. Apparently the interactions between
alternating amino acids are sometimes more important, since their
side-chains are directed in the same direction. An example of such a
pattern is (4,P,P,T), which means that a P is occurring at position 4,
a second P at position 6, and a T at position 8. The corresponding
view was constructed in the same way.

These two variants of the first view were also combined in a single
view (called ``view2_combined'').

View 3 (called ``view3_names'' in our results) focused on different properties
of amino acids. Instead of using the given (unknown) descriptors, we
used some of the most popular amino acid properties (i.e. size,
charge, polarity, hydrophobicity) and converted for each of the 9
amino acids a row with all of its properties.

View 4 is similar to View 2 but contains information on occurrence of
subsequences independent of the position.  For a pattern (P,F)
for example, it doesn't matter where this pattern occurs in the
sequence. The same strategy was applied for alternating patterns and
also a combined view was constructed (these views are ``view4'',
``view4_inter'' and ``view4_combined'').

These views contain complementary information, in the sense that for instance
a condition "the subsequence PPT occurs somewhere in the peptide"
would be very complex to express using any view but View 4, whereas
"the 5th amino acid has a positive charge" can be expressed using View 3 but
not using View 4, etc.

We therefore constructed some combinations. A first combination (called
``cl4_view2_view1_combined'') merges the 5787 descriptors
of the calibration data with the frequent patterns of view2_combined.
A second combination (called ``cl4_view2_view3_combined'') merges the
information of view3 and view2_combined.

2) construction of the predictive model

The following procedure was followed:

1. the different views on the data were constructed, for calibration as well as
test set

2. 62 different algorithms encoded in the WEKA data mining tool were trained
with their default parameters using 10-fold cross-validation on the
different views. However, to enhance stacking performance (see point 5) we used 
the confidence values of the predictions of these algorithms instead of their class 
predictions.

3. Because the class distribution was heavily skewed, we resampled each of our datasets
to correct this. We then repeated the procedure of step 2, evaluating the predictions on
the original datasets.

4. We also tried different parameter settings for three of the algorithms:
J48 -> confidence value
Logistic -> ridge parameter
SMO -> Complexity value, exponent for polynomial kernels and gamma for RBF kernels.

5. One of the best of these models was RandomForest
(with default parameters) on 
the resampled view2_inter dataset. This model was then
used to predict the target values of the test set.

_PREDICTION
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