_PROBLEM CoEPrA-2006_Classification_001

_GROUP_NAME Matt Segall

_GROUP_MEMBERS
Joelle Gola
Olga Obrezanova 
Matt Segall

_ADDRESS
Inpharmatica
127 Cambridge Science Park
Milton Road, Cambridge, CB4 0GD, UK
tel. +44(0)1223 706177
e-mail: o.obrezanova@inpharmatica.co.uk

_MODELING_PROCEDURE
1.Calculated one additional descriptor - Molecular weight. 
(for example, see http://www.expasy.org/tools/protparam.html)

2. Descriptor pre-selection. 
  Descriptors with low standard deviation, low occurence and highly 
  correlated were filtered out. 
  Excluded descriptors
- with standard deviation <  5.0E-04
- with occurence < 0.5%
- with correlation coefficient >= 0.9 (only one of a pair left). 

After filtering 1864 descriptors remained. 
 
3. Modelling technique. 
Decision Tree using C4.5 algorithm.
Gain ratio criterion is used to select descriptors.
Stopping rules used:  minimum number of cases on a tree leaf is  2,
upper limit for relative frequency of majority class on a node = 0.9.
 
4. Validation.
Cross-Validation procedure (5 groups) was used to obtain an estimate 
for the misclassification rate on unseen set.

5. Final model and statistics.
Calibration set: 89 cases, 1864 descriptors.

 Decision tree on calibration set:

 |Desc_02030 <= 0.8, 
 | |Desc_05258 <= 1.5, 
 | | |Desc_01704 <= 1.33, 
 | | | |Desc_00717 <= -34.5, class=-1  (3/0) 
 | | | |Desc_00717 >  -34.5, class=1  (44/3) 
 | | |Desc_01704 >  1.33, class=-1  (4/0) 
 | |Desc_05258 >  1.5, class=-1  (6/0) 
 |Desc_02030 >  0.8, class=-1  (32/3) 


  Total number of cases=89. 
  Number of misclassified cases=6.  Misclassification error = 6.74157%.
  Confusion matrix:
  Class -1  Class +1    <-- predicted 
  -------   --------   
       42         3    | Class -1
        3        41    | Class +1
  
  Kappa statistic: 0.865152
  Mutual Information: 0.643711. 
  Estimated misclassification rate on unseen set is 31.46% 
  (obtained by cross-validation).

_PREDICTION
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