add mushroom

demo/mushroom/README

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+example of UCI dataset
+http://archive.ics.uci.edu/ml/datasets/Mushroom

demo/mushroom/agaricus-lepiota.fmap

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+     1. cap-shape:                bell=b,conical=c,convex=x,flat=f,knobbed=k,sunken=s
+     2. cap-surface:              fibrous=f,grooves=g,scaly=y,smooth=s
+     3. cap-color:                brown=n,buff=b,cinnamon=c,gray=g,green=r,pink=p,purple=u,red=e,white=w,yellow=y
+     4. bruises?:                 bruises=t,no=f
+     5. odor:                     almond=a,anise=l,creosote=c,fishy=y,foul=f,
+                                  musty=m,none=n,pungent=p,spicy=s
+     6. gill-attachment:          attached=a,descending=d,free=f,notched=n
+     7. gill-spacing:             close=c,crowded=w,distant=d
+     8. gill-size:                broad=b,narrow=n
+     9. gill-color:               black=k,brown=n,buff=b,chocolate=h,gray=g,
+                                  green=r,orange=o,pink=p,purple=u,red=e,
+                                  white=w,yellow=y
+    10. stalk-shape:              enlarging=e,tapering=t
+    11. stalk-root:               bulbous=b,club=c,cup=u,equal=e,
+                                  rhizomorphs=z,rooted=r,missing=?
+    12. stalk-surface-above-ring: fibrous=f,scaly=y,silky=k,smooth=s
+    13. stalk-surface-below-ring: fibrous=f,scaly=y,silky=k,smooth=s
+    14. stalk-color-above-ring:   brown=n,buff=b,cinnamon=c,gray=g,orange=o,
+                                  pink=p,red=e,white=w,yellow=y
+    15. stalk-color-below-ring:   brown=n,buff=b,cinnamon=c,gray=g,orange=o,
+                                  pink=p,red=e,white=w,yellow=y
+    16. veil-type:                partial=p,universal=u
+    17. veil-color:               brown=n,orange=o,white=w,yellow=y
+    18. ring-number:              none=n,one=o,two=t
+    19. ring-type:                cobwebby=c,evanescent=e,flaring=f,large=l,
+                                  none=n,pendant=p,sheathing=s,zone=z
+    20. spore-print-color:        black=k,brown=n,buff=b,chocolate=h,green=r,
+                                  orange=o,purple=u,white=w,yellow=y
+    21. population:               abundant=a,clustered=c,numerous=n,
+                                  scattered=s,several=v,solitary=y
+    22. habitat:                  grasses=g,leaves=l,meadows=m,paths=p,
+                                  urban=u,waste=w,woods=d

demo/mushroom/agaricus-lepiota.names

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+1. Title: Mushroom Database
+
+2. Sources: 
+    (a) Mushroom records drawn from The Audubon Society Field Guide to North
+        American Mushrooms (1981). G. H. Lincoff (Pres.), New York: Alfred
+        A. Knopf
+    (b) Donor: Jeff Schlimmer (Jeffrey.Schlimmer@a.gp.cs.cmu.edu)
+    (c) Date: 27 April 1987
+
+3. Past Usage:
+    1. Schlimmer,J.S. (1987). Concept Acquisition Through Representational
+       Adjustment (Technical Report 87-19).  Doctoral disseration, Department
+       of Information and Computer Science, University of California, Irvine.
+       --- STAGGER: asymptoted to 95% classification accuracy after reviewing
+           1000 instances.
+    2. Iba,W., Wogulis,J., & Langley,P. (1988).  Trading off Simplicity
+       and Coverage in Incremental Concept Learning. In Proceedings of 
+       the 5th International Conference on Machine Learning, 73-79.
+       Ann Arbor, Michigan: Morgan Kaufmann.  
+       -- approximately the same results with their HILLARY algorithm    
+    3. In the following references a set of rules (given below) were
+	learned for this data set which may serve as a point of
+	comparison for other researchers.
+
+	Duch W, Adamczak R, Grabczewski K (1996) Extraction of logical rules
+	from training data using backpropagation networks, in: Proc. of the
+	The 1st Online Workshop on Soft Computing, 19-30.Aug.1996, pp. 25-30,
+	available on-line at: http://www.bioele.nuee.nagoya-u.ac.jp/wsc1/
+
+	Duch W, Adamczak R, Grabczewski K, Ishikawa M, Ueda H, Extraction of
+	crisp logical rules using constrained backpropagation networks -
+	comparison of two new approaches, in: Proc. of the European Symposium
+	on Artificial Neural Networks (ESANN'97), Bruge, Belgium 16-18.4.1997,
+	pp. xx-xx
+
+	Wlodzislaw Duch, Department of Computer Methods, Nicholas Copernicus
+	University, 87-100 Torun, Grudziadzka 5, Poland
+	e-mail: duch@phys.uni.torun.pl
+	WWW     http://www.phys.uni.torun.pl/kmk/
+	
+	Date: Mon, 17 Feb 1997 13:47:40 +0100
+	From: Wlodzislaw Duch <duch@phys.uni.torun.pl>
+	Organization: Dept. of Computer Methods, UMK
+
+	I have attached a file containing logical rules for mushrooms.
+	It should be helpful for other people since only in the last year I
+	have seen about 10 papers analyzing this dataset and obtaining quite
+	complex rules. We will try to contribute other results later.
+
+	With best regards, Wlodek Duch
+	________________________________________________________________
+
+	Logical rules for the mushroom data sets.
+
+	Logical rules given below seem to be the simplest possible for the
+	mushroom dataset and therefore should be treated as benchmark results.
+
+	Disjunctive rules for poisonous mushrooms, from most general
+	to most specific:
+
+	P_1) odor=NOT(almond.OR.anise.OR.none)
+	     120 poisonous cases missed, 98.52% accuracy
+
+	P_2) spore-print-color=green
+	     48 cases missed, 99.41% accuracy
+         
+	P_3) odor=none.AND.stalk-surface-below-ring=scaly.AND.
+	          (stalk-color-above-ring=NOT.brown) 
+	     8 cases missed, 99.90% accuracy
+         
+	P_4) habitat=leaves.AND.cap-color=white
+	         100% accuracy     
+
+	Rule P_4) may also be
+
+	P_4') population=clustered.AND.cap_color=white
+
+	These rule involve 6 attributes (out of 22). Rules for edible
+	mushrooms are obtained as negation of the rules given above, for
+	example the rule:
+
+	odor=(almond.OR.anise.OR.none).AND.spore-print-color=NOT.green
+
+	gives 48 errors, or 99.41% accuracy on the whole dataset.
+
+	Several slightly more complex variations on these rules exist,
+	involving other attributes, such as gill_size, gill_spacing,
+	stalk_surface_above_ring, but the rules given above are the simplest
+	we have found.
+
+
+4. Relevant Information:
+    This data set includes descriptions of hypothetical samples
+    corresponding to 23 species of gilled mushrooms in the Agaricus and
+    Lepiota Family (pp. 500-525).  Each species is identified as
+    definitely edible, definitely poisonous, or of unknown edibility and
+    not recommended.  This latter class was combined with the poisonous
+    one.  The Guide clearly states that there is no simple rule for
+    determining the edibility of a mushroom; no rule like ``leaflets
+    three, let it be'' for Poisonous Oak and Ivy.
+
+5. Number of Instances: 8124
+
+6. Number of Attributes: 22 (all nominally valued)
+
+7. Attribute Information: (classes: edible=e, poisonous=p)
+     1. cap-shape:                bell=b,conical=c,convex=x,flat=f,
+                                  knobbed=k,sunken=s
+     2. cap-surface:              fibrous=f,grooves=g,scaly=y,smooth=s
+     3. cap-color:                brown=n,buff=b,cinnamon=c,gray=g,green=r,
+                                  pink=p,purple=u,red=e,white=w,yellow=y
+     4. bruises?:                 bruises=t,no=f
+     5. odor:                     almond=a,anise=l,creosote=c,fishy=y,foul=f,
+                                  musty=m,none=n,pungent=p,spicy=s
+     6. gill-attachment:          attached=a,descending=d,free=f,notched=n
+     7. gill-spacing:             close=c,crowded=w,distant=d
+     8. gill-size:                broad=b,narrow=n
+     9. gill-color:               black=k,brown=n,buff=b,chocolate=h,gray=g,
+                                  green=r,orange=o,pink=p,purple=u,red=e,
+                                  white=w,yellow=y
+    10. stalk-shape:              enlarging=e,tapering=t
+    11. stalk-root:               bulbous=b,club=c,cup=u,equal=e,
+                                  rhizomorphs=z,rooted=r,missing=?
+    12. stalk-surface-above-ring: fibrous=f,scaly=y,silky=k,smooth=s
+    13. stalk-surface-below-ring: fibrous=f,scaly=y,silky=k,smooth=s
+    14. stalk-color-above-ring:   brown=n,buff=b,cinnamon=c,gray=g,orange=o,
+                                  pink=p,red=e,white=w,yellow=y
+    15. stalk-color-below-ring:   brown=n,buff=b,cinnamon=c,gray=g,orange=o,
+                                  pink=p,red=e,white=w,yellow=y
+    16. veil-type:                partial=p,universal=u
+    17. veil-color:               brown=n,orange=o,white=w,yellow=y
+    18. ring-number:              none=n,one=o,two=t
+    19. ring-type:                cobwebby=c,evanescent=e,flaring=f,large=l,
+                                  none=n,pendant=p,sheathing=s,zone=z
+    20. spore-print-color:        black=k,brown=n,buff=b,chocolate=h,green=r,
+                                  orange=o,purple=u,white=w,yellow=y
+    21. population:               abundant=a,clustered=c,numerous=n,
+                                  scattered=s,several=v,solitary=y
+    22. habitat:                  grasses=g,leaves=l,meadows=m,paths=p,
+                                  urban=u,waste=w,woods=d
+
+8. Missing Attribute Values: 2480 of them (denoted by "?"), all for
+   attribute #11.
+
+9. Class Distribution: 
+    --    edible: 4208 (51.8%)
+    -- poisonous: 3916 (48.2%)
+    --     total: 8124 instances

demo/mushroom/mapfeat.py

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+#!/usr/bin/python
+import sys
+
+def loadfmap( fname ):
+    fmap = {}
+    nmap = {}
+    
+    for l in open( fname ):
+        arr = l.split()
+        if arr[0].find('.') != -1:            
+            idx = int( arr[0].strip('.') )
+            assert idx not in fmap        
+            fmap[ idx ] = {}
+            ftype = arr[1].strip(':')        
+            content = arr[2]
+        else:
+            content = arr[0]
+        for it in content.split(','):
+            if it.strip() == '':
+                continue
+            k , v = it.split('=')
+            fmap[ idx ][ v ] = len(nmap)
+            nmap[ len(nmap) ] = ftype+'='+k
+    return fmap, nmap
+
+def write_nmap( fo, nmap ):    
+    for i in xrange( len(nmap) ):
+        fo.write('%d\t%s\n' % (i, nmap[i]) )
+
+# start here
+fmap, nmap = loadfmap( 'agaricus-lepiota.fmap' )
+fo = open( 'featname.txt', 'w' )
+write_nmap( fo, nmap )
+fo.close()
+
+fo = open( 'agaricus.txt', 'w' ) 
+for l in open( 'agaricus-lepiota.data' ):
+    arr = l.split(',')
+    if arr[0] == 'p':
+        fo.write('1')
+    else:
+        assert arr[0] == 'e'
+        fo.write('0')
+    for i in xrange( 1,len(arr) ):
+        fo.write( ' %d:1' % fmap[i][arr[i].strip()] )
+    fo.write('\n')
+
+fo.close()
+
+ 

demo/mushroom/mknfold.py

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+#!/usr/bin/python
+import sys
+import random
+
+if len(sys.argv) < 2:
+    print 'Usage:<filename> <k> [nfold = 5]'
+    exit(0)
+
+random.seed( 10 )
+
+k = int( sys.argv[2] )
+if len(sys.argv) > 3:
+    nfold = int( sys.argv[3] )
+else:
+    nfold = 5
+
+fi = open( sys.argv[1], 'r' )
+ftr = open( sys.argv[1]+'.train', 'w' )
+fte = open( sys.argv[1]+'.test', 'w' )
+for l in fi:
+    if random.randint( 1 , nfold ) == k:
+        fte.write( l )
+    else:
+        ftr.write( l )
+
+fi.close()
+ftr.close()
+fte.close()
+

demo/mushroom/mushroom.conf

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+num_round=10
+
+save_period=0
+
+data = "agaricus.txt.train"
+eval[test] = "agaricus.txt.test"
+
+booster_type = 0
+loss_type = 1
+
+bst:num_feature=126
+bst:eta=1.0
+bst:gamma=1                
+bst:min_child_weight=1   
+bst:max_depth=3           
+                
+
+

demo/mushroom/runexp.sh

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+#!/bin/bash
+python mapfeat.py
+python mknfold.py agaricus.txt 1
+../../xgboost mushroom.conf