def main(args):
paramsfn = args[0]
exec(open(paramsfn,'r').read())
pdfpages = PdfPages('%s.pdf' % (outputlog))
output_test,input_test = load_data(testdatafilename)
if doscale:
maxinput,mininput = read_scale_data(scaledatafilename)
input_test = (input_test-mininput)/(maxinput-mininput)
if choose_specific_features:
for specific_selected_choice in specific_selected_features:
inputfiltered_test = input_test[:,specific_selected_choice]
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()
posclass = posclass[0]
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(output_test,[list(x) for x in inputfiltered_test],m)
ACC,confusionmatrix = mygrid.evaluations_classify(output_test, [x[0] for x in pred_values],posclass,optbias)
db = array([[output_test[i],pred_values[i][0]] for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test)-neg;
if neg != 0 and pos != 0:
auc,topacc,optbias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,[],True,pdfpages,'Test ROC curve')
print 'Test optimized accuracy = %g' % (ACC)
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[0],confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[1],confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(predictionslog,'w')
for label in pred_labels:
print >> fout, label
fout.close()
if outputlog != '':
fout = open(outputlog,'a')
print >> fout, '========================='
print >> fout, specific_selected_choice
print >> fout, ACC,auc
fout.close()
else:
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()
posclass = posclass[0]
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(output_test,[list(x) for x in input_test],m)
ACC,confusionmatrix = mygrid.evaluations_classify(output_test, [x[0] for x in pred_values],posclass,optbias)
db = array([[output_test[i],pred_values[i][0]] for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test)-neg;
if neg != 0 and pos != 0:
auc,topacc,optbias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,[],True,pdfpages,'Test ROC curve')
print 'Test optimized accuracy = %g' % (ACC)
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[0],confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[1],confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(testdatafilename + '_predictions.dat','w')
for label in pred_labels:
print >> fout, label
fout.close()
if outputlog != '':
fout = open(outputlog,'a')
print >> fout, '========================='
print >> fout, ACC
fout.close()
pdfpages.close()
def main(args):
paramsfn = args[0]
exec(open(paramsfn, 'r').read())
pdfpages = PdfPages('%s.pdf' % (outputlog))
output_test, input_test = load_data(testdatafilename)
if doscale:
maxinput, mininput = read_scale_data(scaledatafilename)
input_test = (input_test - mininput) / (maxinput - mininput)
if choose_specific_features:
for specific_selected_choice in specific_selected_features:
inputfiltered_test = input_test[:, specific_selected_choice]
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()
posclass = posclass[0]
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(
output_test, [list(x) for x in inputfiltered_test], m)
ACC, confusionmatrix = mygrid.evaluations_classify(
output_test, [x[0] for x in pred_values], posclass, optbias)
db = array([[output_test[i], pred_values[i][0]]
for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test) - neg
if neg != 0 and pos != 0:
auc, topacc, optbias, top_tps_bias, top_fps = mygrid.calc_AUC(
db, neg, pos, posclass, [], True, pdfpages,
'Test ROC curve')
print 'Test optimized accuracy = %g' % (ACC)
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],
m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[0], confusionmatrix[0, 0], confusionmatrix[0,
1],
pos) #confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[1], confusionmatrix[1, 0], confusionmatrix[1,
1],
neg) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (
confusionmatrix[0, 0] + confusionmatrix[1, 0],
confusionmatrix[0, 1] + confusionmatrix[1, 1], pos + neg
) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(predictionslog, 'w')
for label in pred_labels:
print >> fout, label
fout.close()
if outputlog != '':
fout = open(outputlog, 'a')
print >> fout, '========================='
print >> fout, specific_selected_choice
print >> fout, ACC, auc
fout.close()
else:
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()
posclass = posclass[0]
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(
output_test, [list(x) for x in input_test], m)
ACC, confusionmatrix = mygrid.evaluations_classify(
output_test, [x[0] for x in pred_values], posclass, optbias)
db = array([[output_test[i], pred_values[i][0]]
for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test) - neg
if neg != 0 and pos != 0:
auc, topacc, optbias, top_tps_bias, top_fps = mygrid.calc_AUC(
db, neg, pos, posclass, [], True, pdfpages, 'Test ROC curve')
print 'Test optimized accuracy = %g' % (ACC)
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],
m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[0], confusionmatrix[0, 0], confusionmatrix[0, 1],
pos) #confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[1], confusionmatrix[1, 0], confusionmatrix[1, 1],
neg) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (
confusionmatrix[0, 0] + confusionmatrix[1, 0],
confusionmatrix[0, 1] + confusionmatrix[1, 1], pos + neg
) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(testdatafilename + '_predictions.dat', 'w')
for label in pred_labels:
print >> fout, label
fout.close()
if outputlog != '':
fout = open(outputlog, 'a')
print >> fout, '========================='
print >> fout, ACC
fout.close()
pdfpages.close()
def main(args):
paramsfn = args[0]
exec(open(paramsfn, 'r').read())
pdfpages = PdfPages('%s.pdf' % (outputlog))
output_test, input_test, fieldnames = load_data(testdatafilename)
if binarizeoutput:
output_test = [1 if x > boundary else -1 for x in output_test]
if doscale:
maxinput, mininput = read_scale_data(scaledatafilename)
input_test = (input_test - mininput) / (maxinput - mininput)
if donormalize:
means, stds = read_meansigma(normalizationfilename)
input_test = (input_test - means) / stds
if choose_specific_features:
for specific_selected_choice in specific_selected_features:
inputfiltered_test = input_test[:, specific_selected_choice]
if dopca:
coeffs, means = read_pcacoeffs(pcacoefffilename)
temp = (inputfiltered_test - means).T
inputfiltered_test = dot(coeffs.T, temp).T
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()[0]
negclass = m.get_labels()[1]
print posclass
print negclass
# print len(output_test)
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(
output_test, [list(x) for x in inputfiltered_test], m,
'-b %d' % (int(useprob)))
pred_labels = [
posclass if pred_values[i][0] > optbias else negclass
for i in xrange(len(output_test))
]
# print len(pred_labels)
ACC, PHI, confusionmatrix = mygrid.evaluations_classify(
output_test, [x[0] for x in pred_values], posclass, optbias)
db = array([[output_test[i], pred_values[i][0]]
for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test) - neg
if neg != 0 and pos != 0:
auc, topacc, optaccbias, topphi, optphibias, top_tps_bias, top_fps = mygrid.calc_AUC(
db, neg, pos, posclass, useprob, [], True, pdfpages,
'Test ROC curve', optbias)
numpred_pos = confusionmatrix[0, 0] + confusionmatrix[1, 0]
numpred_neg = confusionmatrix[0, 1] + confusionmatrix[1, 1]
N = pos + neg
probchance = (numpred_pos * pos + numpred_neg * neg) * 1.0 / (N *
N)
kappa = (ACC / 100.0 - probchance) * 1.0 / (1 - probchance)
print 'Test optimized Phi statistic = %g' % (PHI)
print 'Test optimized accuracy = %g' % (ACC / 100.0)
print 'Test optimized kappa = %g' % (kappa)
if pos == 0 or neg == 0:
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (nan, nan,
nan)
else:
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (
confusionmatrix[0, 0] / pos, confusionmatrix[1, 0] / neg,
confusionmatrix[0, 0] /
(confusionmatrix[0, 0] + confusionmatrix[1, 0]))
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],
m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[0], confusionmatrix[0, 0], confusionmatrix[0,
1],
pos) #confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[1], confusionmatrix[1, 0], confusionmatrix[1,
1],
neg) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (
confusionmatrix[0, 0] + confusionmatrix[1, 0],
confusionmatrix[0, 1] + confusionmatrix[1, 1], pos + neg
) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(predictionslog, 'w')
for ind in xrange(len(pred_values)):
groundtruth = output_test[ind]
label = pred_labels[ind]
value = pred_values[ind][0]
print >> fout, groundtruth, label, value,
oneinputrow = input_test[ind, :]
for j in xrange(len(oneinputrow)):
print >> fout, '%d:%f' % (j + 1, oneinputrow[j]),
print >> fout
fout.close()
if outputlog != '':
fout = open(outputlog, 'a')
print >> fout, '========================='
print >> fout, 'SPECIFIC FIELDS:'
print >> fout, specific_selected_choice
for i in specific_selected_choice:
print >> fout, fieldnames[i],
print >> fout
if neg != 0 and pos != 0:
print >> fout, 'test: ACC=%g,AUC=%g' % (ACC, auc)
fout.close()
else:
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()
posclass = posclass[0]
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(
output_test, [list(x) for x in input_test], m,
'-b %d' % (int(useprob)))
ACC, PHI, confusionmatrix = mygrid.evaluations_classify(
output_test, [x[0] for x in pred_values], posclass, optbias)
db = array([[output_test[i], pred_values[i][0]]
for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test) - neg
if neg != 0 and pos != 0:
auc, topacc, optaccbias, topphi, optphibias, top_tps_bias, top_fps = mygrid.calc_AUC(
db, neg, pos, posclass, useprob, [], True, pdfpages,
'Test ROC curve', optbias)
numpred_pos = confusionmatrix[0, 0] + confusionmatrix[1, 0]
numpred_neg = confusionmatrix[0, 1] + confusionmatrix[1, 1]
N = pos + neg
probchance = (numpred_pos * pos + numpred_neg * neg) * 1.0 / (N * N)
testkappa = (ACC - probchance) * 1.0 / (1 - probchance)
print 'Test optimized Phi statistic = %g' % (PHI)
print 'Test optimized accuracy = %g' % (ACC)
print 'Test optimized kappa = %g' % (kappa)
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (
confusionmatrix[0, 0] / pos, confusionmatrix[1, 0] / neg,
confusionmatrix[0, 0] /
(confusionmatrix[0, 0] + confusionmatrix[1, 0]))
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],
m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[0], confusionmatrix[0, 0], confusionmatrix[0, 1],
pos) #confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (
m.get_labels()[1], confusionmatrix[1, 0], confusionmatrix[1, 1],
neg) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (
confusionmatrix[0, 0] + confusionmatrix[1, 0],
confusionmatrix[0, 1] + confusionmatrix[1, 1], pos + neg
) #confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(testdatafilename + '_predictions.dat', 'w')
for labelind in xrange(len(pred_labels)):
print >> fout, output_test[labelind], pred_labels[
labelind], pred_values[labelind][0]
fout.close()
if outputlog != '':
fout = open(outputlog, 'a')
print >> fout, '========================='
print >> fout, ACC
fout.close()
pdfpages.close()
def main(args):
paramsfn = args[0]
exec(open(paramsfn,'r').read())
if len(args) > 1:
gammarange = [float(args[1])]
crange = [float(args[2])]
output,input,fieldnames,fold_inds = load_data(datafilename,use_specific_fold_inds)
sep_validation = False
if separate_validation_set != '':
output_valid,input_valid,fieldnames,fold_inds_valid = load_data(separate_validation_set,use_specific_fold_inds)
sep_validation = True
fold_start = [-1]
if sep_validation:
fold_start_valid = [-1]
if use_specific_fold_inds:
unique_fold_ids = unique(fold_inds)
row_inds = []
outputcopy = []
inputcopy = zeros([size(input,0),size(input,1)],dtype='float64')
fold_start = [0]
curind = 0
for ind in unique_fold_ids:
row_inds = [i for i in xrange(len(fold_inds)) if fold_inds[i] == ind]
inputcopy[curind:curind+len(row_inds),:] = input[row_inds,:]
outputcopy.extend([output[i] for i in row_inds])
curind += len(row_inds)
fold_start.append(fold_start[-1]+len(row_inds))
input = inputcopy
output = outputcopy
nf = len(fold_start)-1
if sep_validation:
unique_fold_ids_valid = unique(fold_inds_valid)
row_inds = []
outputcopy = []
inputcopy = zeros([size(input_valid,0),size(input_valid,1)],dtype='float64')
fold_start_valid = [0]
curind = 0
for ind in unique_fold_ids_valid:
row_inds = [i for i in xrange(len(fold_inds_valid)) if fold_inds_valid[i] == ind]
inputcopy[curind:curind+len(row_inds),:] = input_valid[row_inds,:]
outputcopy.extend([output_valid[i] for i in row_inds])
curind += len(row_inds)
fold_start_valid.append(fold_start_valid[-1]+len(row_inds))
input_valid = inputcopy
output_valid = outputcopy
nf = len(fold_start_valid)-1
if binarizeoutput:
output,boundary = binarize_output(output,binary_threshold,binary_boundary_type)
if testdatafilename != '':
output_test,input_test,fieldnames,fold_inds_test = load_data(testdatafilename,False)
if binarizeoutput:
output_test = [1 if x > boundary else -1 for x in output_test]
if doscale:
maxinput = input.max(0);
mininput = input.min(0);
input = (input-mininput)/(maxinput-mininput)
if testdatafilename != '':
input_test = (input_test-mininput)/(maxinput-mininput)
if savemodel:
save_scale_data(datafilename+'_scales.dat',maxinput,mininput)
if sep_validation:
input_valid = (input_valid-mininput)/(maxinput-mininput)
if donormalize:
means = input.mean(0)
stds = sqrt(input.var(0))
input = (input-means)/stds
if testdatafilename != '':
input_test = (input_test-means)/stds
if savemodel:
save_zscore_data(datafilename+'_meansstdevs.dat',means,stds)
if sep_validation:
input_valid = (input_valid-means)/stds
if numcpus == 'auto':
p = Pool()
else:
p = Pool(numcpus)
if choose_specific_features:
if choose_specific_features_increasing:
specific_selected_features = [specific_selected_features[:i] for i in xrange(2,len(specific_selected_features),2)]
for specific_selected_choice in specific_selected_features:
inputfiltered = input[:,specific_selected_choice]
if sep_validation:
inputfiltered_valid = input_valid[:,specific_selected_choice]
if dopca:
coeff,temp,latent = princomp(inputfiltered)
if savemodel:
save_pca_coeffs(datafilename+'_pcacoeffs.dat',coeff,mean(inputfiltered.T,axis=1))
inputfiltered = temp
if sep_validation:
return
with Timer():
if sep_validation:
if use_specific_fold_inds:
results = mygrid.grid_classify_sepvalid (crange,gammarange,output,[list(x) for x in inputfiltered],output_valid,[list(x) for x in inputfiltered_valid],nf,useprob,timeout,p,fold_start,fold_start_valid)
else:
results = mygrid.grid_classify_sepvalid (crange,gammarange,output,[list(x) for x in inputfiltered],output_valid,[list(x) for x in inputfiltered_valid],nf,useprob,timeout,p)
else:
if use_specific_fold_inds:
results = mygrid.grid_classify (crange,gammarange,output,[list(x) for x in inputfiltered],nf,useprob,timeout,p,fold_start)
else:
results = mygrid.grid_classify (crange,gammarange,output,[list(x) for x in inputfiltered],nf,useprob,timeout,p)
param = svm.svm_parameter('-c %g -g %g -b %d' % (results[-2],results[-1],int(useprob)))
prob = svm.svm_problem(output, [list(x) for x in inputfiltered])
fold_start_p = (c_int *len(fold_start))()
for i in xrange(len(fold_start)):
fold_start_p[i] = fold_start[i]
if posclass == 'auto':
posclass = output[0]
if sep_validation:
prob_valid = svm.svm_problem(output_valid, [list(x) for x in inputfiltered_valid])
testlength = prob_valid.l
fold_start_p_valid = (c_int *len(fold_start_valid))()
for i in xrange(len(fold_start_valid)):
fold_start_p_valid[i] = fold_start_valid[i]
else:
testlength = prob.l
target = (c_double * testlength)()
#[maxauc,maxoptacc,maxphi,minfpfnration,maxf1,optbias,optc,optgamma]
if sep_validation:
libsvm.svm_cross_validation_sepsets(prob, prob_valid,fold_start_p, fold_start_p_valid,param, nf, target)
else:
libsvm.svm_cross_validation(prob, fold_start_p, param, nf, target)
if sep_validation:
ys = prob_valid.y[:testlength]
else:
ys = prob.y[:prob.l]
db = array([[ys[i],target[i]] for i in range(testlength)])
neg = len([x for x in ys if x != posclass])
pos = testlength-neg;
if len(specific_selected_features) == 1 or True:
pdfpages = PdfPages('%s_train.pdf' % (outputlog))
# auc,topacc,optaccbias,topphi,optphibias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,useprob,[],True,pdfpages,'Optimal Cross-Validation ROC curve')
topacc,topphi,minfpfnratio,topf1,auc,optbias = mygrid.optimize_results(db,neg,pos,posclass,'F1')
print [topacc,results[1]]
print [topphi,results[2]]
print [topf1,results[4]]
print [auc,results[0]]
pdfpages.close()
# print target
if sep_validation:
ACC,PHI,confusionmatrix = mygrid.evaluations_classify(output_valid,target,posclass,results[-3])
else:
ACC,PHI,confusionmatrix = mygrid.evaluations_classify(output,target,posclass,results[-3])
if posclass == 1:
negclass = 0;
else:
negclass = 1;
numpred_pos = confusionmatrix[0,0]+confusionmatrix[1,0]
numpred_neg = confusionmatrix[0,1]+confusionmatrix[1,1]
N = pos+neg
probchance = (numpred_pos*pos+numpred_neg*neg)*1.0/(N*N)
kappa = (topacc-probchance)*1.0/(1-probchance);
print 'Train optimized accuracy = %g' % (topacc)
print 'Train optimized Phi statistic = %g' % (topphi)
print 'Train optimized kappa = %g' % (kappa)
print 'Train optimized F1 score = %f' % (topf1)
print 'Train optimized TP/RECALL = %g, FP = %g, PRECISION = %g' % (confusionmatrix[0,0]/pos,confusionmatrix[1,0]/neg,confusionmatrix[0,0]/(confusionmatrix[0,0]+confusionmatrix[1,0]))
print '================================'
print '|| ||%6d |%6d | ||' % (posclass,negclass)
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (posclass,confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (negclass,confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
else:
auc,topacc,optaccbias,topphi,optphibias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,useprob,[],False,0,'Optimal Cross-Validation ROC curve')
print 'Optimal gamma = %g\nOptimal c = %g\nOptimal Bias = %g' % (results[-1],results[-2],results[-3])
print 'Top CV results: AUC = %g, OPTIMIZED ACC = %g, OPTIMIZED PHI = %g' % (auc,topacc,topphi)
if outputlog != '':
fout = open(outputlog,'a')
print >> fout, '========================='
print >> fout, datafilename
print >> fout, doscale, donormalize, dopca, '(scale/norm/pca)'
print >> fout, crange[0],crange[-1], gammarange[0], gammarange[-1], '(cs,gammas)'
print >> fout, use_specific_fold_inds, nf, '(use specific folds, numfold)'
print >> fout, 'SPECIFIC FIELDS:'
print >> fout, specific_selected_choice
if fieldnames != []:
for i in specific_selected_choice:
print >> fout, fieldnames[i],
print >> fout
print >> fout, 'train: '
print >> fout, ' AUC=%g,ACC=%g,kappa=%g,phi=%g,f1=%g (g=%g,c=%g,bias=%g)' % (auc,topacc,kappa,topphi,topf1,results[-1],results[-2],results[-3])
print >> fout, ' ||%3d||%6g |%6g |%6g ||' % (posclass,confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print >> fout, ' ||%3d||%6g |%6g |%6g ||' % (negclass,confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
fout.close()
if outputpredictions:
fout = open(predictionslog,'w')
if sep_validation:
for ind in xrange(len(output_valid)):
label = output_valid[ind]
value = target[ind]
oneinputrow = input_valid[ind,:]
print >> fout, value, label,
for j in xrange(len(oneinputrow)):
print >> fout, '%d:%f' % (j+1,oneinputrow[j]),
print >> fout
else:
for ind in xrange(len(output)):
label = output[ind]
value = target[ind]
oneinputrow = input[ind,:]
print >> fout, value, label,
for j in xrange(len(oneinputrow)):
print >> fout, '%d:%f' % (j+1,oneinputrow[j]),
print >> fout
fout.close()
del target
if savemodel:
param = ('-c %g -g %g -b %d' % (results[-2],results[-1],int(useprob)))
m = svm_train(output,[list(x) for x in inputfiltered],param)
svm_save_model(datafilename + '.model',m)
if testdatafilename != '':
inputfiltered_test = input_test[:,specific_selected_choice]
if dopca:
M = (inputfiltered_test-mean(inputfiltered_test.T,axis=1)).T # subtract the mean (along columns)
inputfiltered_test = dot(coeff.T,M).T # projection of the data in the new space
param = ('-c %g -g %g -b %d' % (results[-2],results[-1],int(useprob)))
m = svm_train(output,[list(x) for x in inputfiltered],param)
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(output_test,[list(x) for x in inputfiltered_test],m,'-b %d' % (int(useprob)))
ACC,PHI,confusionmatrix = mygrid.evaluations_classify(output_test, [x[0] for x in pred_values],posclass,results[-3])
db = array([[output_test[i],pred_values[i][0]] for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test)-neg
auctest = 0
if neg != 0 and pos != 0:
auctest,topacctest,optaccbias,topphitest,optphibias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,useprob,[],False,pdfpages,'Test ROC curve',results[-3])
numpred_pos = confusionmatrix[0,0]+confusionmatrix[1,0]
numpred_neg = confusionmatrix[0,1]+confusionmatrix[1,1]
N = pos+neg
probchance = (numpred_pos*pos+numpred_neg*neg)*1.0/(N*N)
testkappa = (ACC/100.0-probchance)*1.0/(1-probchance);
print 'Test optimized accuracy = %g' % (ACC)
print 'Test optimized Phi statistic = %g' % (PHI)
print 'Test optimized kappa = %g' % (testkappa)
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[0],confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[1],confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputlog != '':
fout = open(outputlog,'a')
print >> fout, 'test: '
print >> fout, ' ACC=%g,AUC=%g,kappa=%g,phi=%g' % (ACC,auctest,testkappa,PHI)
print >> fout, ' ||%3d||%6g |%6g |%6g ||' % (m.get_labels()[0],confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print >> fout, ' ||%3d||%6g |%6g |%6g ||' % (m.get_labels()[1],confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
fout.close()
else:
with Timer():
if use_specific_fold_inds:
results = mygrid.grid_classify (crange,gammarange,output,[list(x) for x in input],nf,useprob,timeout,p,fold_start)
else:
results = mygrid.grid_classify (crange,gammarange,output,[list(x) for x in input],nf,useprob,timeout,p)
param = svm.svm_parameter('-c %g -g %g -b %d' % (results[-2],results[-1],int(useprob)))
prob = svm.svm_problem(output, [list(x) for x in input])
target = (c_double * prob.l)()
fold_start_p = (c_int *len(fold_start))()
for i in xrange(len(fold_start)):
fold_start_p[i] = fold_start[i]
if posclass == 'auto':
posclass = output[0]
libsvm.svm_cross_validation(prob, fold_start_p, param, nf, target)
ys = prob.y[:prob.l]
db = [[ys[i],target[i]] for i in range(prob.l)]
db = array(db)
neg = len([x for x in ys if x != posclass])
pos = prob.l-neg;
pdfpages = PdfPages('%s_train.pdf' % (outputlog))
auc,topacc,optaccbias,topphi,optphibias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,useprob,[],True,pdfpages,'Optimal Cross-Validation ROC curve')
pdfpages.close()
ACC,PHI,confusionmatrix = mygrid.evaluations_classify(output, target,posclass,results[-3])
if posclass == 1:
negclass = 0;
else:
negclass = 1;
print 'Train optimized accuracy = %g' % (topacc)
print 'Train optimized phi statististic = %g' % (topphi)
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (confusionmatrix[0,0]/pos,confusionmatrix[1,0]/neg,confusionmatrix[0,0]/(confusionmatrix[0,0]+confusionmatrix[1,0]))
print '================================'
print '|| ||%6d |%6d | ||' % (posclass,negclass)
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (posclass,confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (negclass,confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(predictionslog,'w')
for ind in xrange(len(output)):
label = output[ind]
value = target[ind]
oneinputrow = input[ind,:]
print >> fout, value, label,
for j in xrange(len(oneinputrow)):
print >> fout, '%d:%f' % (j+1,oneinputrow[j]),
print >> fout
fout.close()
del target
print 'Optimal gamma = %g\nOptimal c = %g\nOptimal Bias = %g' % (results[-1],results[-2],optphibias)
print 'Top CV results: AUC = %g, OPTIMIZED ACC = %g, OPTIMIZED PHI = %g' % (auc,topacc,topphi)
if savemodel:
param = ('-c %g -g %g -b %d' % (results[-2],results[-1],int(useprob)))
m = svm_train(output,[list(x) for x in input],param)
svm_save_model(datafilename+'.model',m)
if testdatafilename != '':
param = ('-c %g -g %g -b %d' % (results[-2],results[-1],int(useprob)))
m = svm_train(output,[list(x) for x in input],param)
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(output_test,[list(x) for x in input_test],m,'-b %d' % (int(useprob)))
ACC,PHI,confusionmatrix = mygrid.evaluations_classify(output_test, [x[0] for x in pred_values],posclass,results[-3])
db = array([[output_test[i],pred_values[i][0]] for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test)-neg;
pdfpages = PdfPages('%s_test.pdf' % (outputlog))
auctest = 0
if neg != 0 and pos != 0:
auctest,topacctest,optaccbias,topphitest,optphibias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,useprob,[],True,pdfpages,'Test ROC curve',results[-3])
pdfpages.close()
print 'Test accuracy = %g' % (ACC)
print 'Test Phi statistic = %g' % (PHI)
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (confusionmatrix[0,0]/pos,confusionmatrix[1,0]/neg,confusionmatrix[0,0]/(confusionmatrix[0,0]+confusionmatrix[1,0]))
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[0],confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[1],confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputlog != '':
fout = open(outputlog,'a')
print >> fout, '========================='
print >> fout, fieldnames
print >> fout, 'train: AUC=%g,ACC=%g,PHI=%g (g=%g,c=%g,bias=%g)' % (auc,topacc,topphi,results[-1],results[-2],results[-3])
if testdatafilename != '':
print >> fout, 'test: ACC=%g,AUC=%g,PHI=%g' % (ACC,auctest,PHI)
fout.close()
def main(args):
paramsfn = args[0]
exec(open(paramsfn,'r').read())
pdfpages = PdfPages('%s.pdf' % (outputlog))
output_test,input_test,fieldnames = load_data(testdatafilename)
if binarizeoutput:
output_test = [1 if x > boundary else -1 for x in output_test]
if doscale:
maxinput,mininput = read_scale_data(scaledatafilename)
input_test = (input_test-mininput)/(maxinput-mininput)
if donormalize:
means,stds = read_meansigma(normalizationfilename)
input_test = (input_test-means)/stds
if choose_specific_features:
for specific_selected_choice in specific_selected_features:
inputfiltered_test = input_test[:,specific_selected_choice]
if dopca:
coeffs,means = read_pcacoeffs(pcacoefffilename)
temp = (inputfiltered_test-means).T
inputfiltered_test = dot(coeffs.T,temp).T
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()[0]
negclass = m.get_labels()[1]
print posclass
print negclass
# print len(output_test)
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(output_test,[list(x) for x in inputfiltered_test],m,'-b %d' % (int(useprob)))
pred_labels = [posclass if pred_values[i][0] > optbias else negclass for i in xrange(len(output_test))]
# print len(pred_labels)
ACC,PHI,confusionmatrix = mygrid.evaluations_classify(output_test, [x[0] for x in pred_values],posclass,optbias)
db = array([[output_test[i],pred_values[i][0]] for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test)-neg;
if neg != 0 and pos != 0:
auc,topacc,optaccbias,topphi,optphibias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,useprob,[],True,pdfpages,'Test ROC curve',optbias)
numpred_pos = confusionmatrix[0,0]+confusionmatrix[1,0]
numpred_neg = confusionmatrix[0,1]+confusionmatrix[1,1]
N = pos+neg
probchance = (numpred_pos*pos+numpred_neg*neg)*1.0/(N*N)
kappa = (ACC/100.0-probchance)*1.0/(1-probchance);
print 'Test optimized Phi statistic = %g' % (PHI)
print 'Test optimized accuracy = %g' % (ACC/100.0)
print 'Test optimized kappa = %g' % (kappa)
if pos == 0 or neg == 0:
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (nan,nan,nan)
else:
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (confusionmatrix[0,0]/pos,confusionmatrix[1,0]/neg,confusionmatrix[0,0]/(confusionmatrix[0,0]+confusionmatrix[1,0]))
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[0],confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[1],confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(predictionslog,'w')
for ind in xrange(len(pred_values)):
groundtruth = output_test[ind]
label = pred_labels[ind]
value = pred_values[ind][0]
print >> fout, groundtruth,label,value,
oneinputrow = input_test[ind,:]
for j in xrange(len(oneinputrow)):
print >> fout, '%d:%f' % (j+1,oneinputrow[j]),
print >> fout
fout.close()
if outputlog != '':
fout = open(outputlog,'a')
print >> fout, '========================='
print >> fout, 'SPECIFIC FIELDS:'
print >> fout, specific_selected_choice
for i in specific_selected_choice:
print >> fout, fieldnames[i],
print >> fout
if neg != 0 and pos != 0:
print >> fout, 'test: ACC=%g,AUC=%g' % (ACC,auc)
fout.close()
else:
m = svm_load_model(modelfilename)
if posclass == 'auto':
posclass = m.get_labels()
posclass = posclass[0]
pred_labels, (ACC, MSE, SCC), pred_values = svm_predict(output_test,[list(x) for x in input_test],m,'-b %d' % (int(useprob)))
ACC,PHI,confusionmatrix = mygrid.evaluations_classify(output_test, [x[0] for x in pred_values],posclass,optbias)
db = array([[output_test[i],pred_values[i][0]] for i in range(len(output_test))])
neg = len([x for x in output_test if x != posclass])
pos = len(output_test)-neg;
if neg != 0 and pos != 0:
auc,topacc,optaccbias,topphi,optphibias,top_tps_bias,top_fps = mygrid.calc_AUC(db,neg,pos,posclass,useprob,[],True,pdfpages,'Test ROC curve',optbias)
numpred_pos = confusionmatrix[0,0]+confusionmatrix[1,0]
numpred_neg = confusionmatrix[0,1]+confusionmatrix[1,1]
N = pos+neg
probchance = (numpred_pos*pos+numpred_neg*neg)*1.0/(N*N)
testkappa = (ACC-probchance)*1.0/(1-probchance);
print 'Test optimized Phi statistic = %g' % (PHI)
print 'Test optimized accuracy = %g' % (ACC)
print 'Test optimized kappa = %g' % (kappa)
print 'TP/RECALL = %g, FP = %g, PRECISION = %g' % (confusionmatrix[0,0]/pos,confusionmatrix[1,0]/neg,confusionmatrix[0,0]/(confusionmatrix[0,0]+confusionmatrix[1,0]))
print '================================'
print '|| ||%6d |%6d | ||' % (m.get_labels()[0],m.get_labels()[1])
print '================================'
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[0],confusionmatrix[0,0],confusionmatrix[0,1],pos)#confusionmatrix[0,0]+confusionmatrix[0,1])
print '||%3d||%6g |%6g |%6g ||' % (m.get_labels()[1],confusionmatrix[1,0],confusionmatrix[1,1],neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '||----------------------------||'
print '|| ||%6g |%6g |%6g ||' % (confusionmatrix[0,0]+confusionmatrix[1,0],confusionmatrix[0,1]+confusionmatrix[1,1],pos+neg)#confusionmatrix[1,0]+confusionmatrix[1,1])
print '================================'
if outputpredictions:
fout = open(testdatafilename + '_predictions.dat','w')
for labelind in xrange(len(pred_labels)):
print >> fout, output_test[labelind],pred_labels[labelind],pred_values[labelind][0]
fout.close()
if outputlog != '':
fout = open(outputlog,'a')
print >> fout, '========================='
print >> fout, ACC
fout.close()
pdfpages.close()
