def main():
print "starting debugging:"
SPLIT_POINTER = -1
from expenv import MultiSplitSet
from helper import Options
# select dataset
#multi_split_set = MultiSplitSet.get(387)
#multi_split_set = MultiSplitSet.get(407)
multi_split_set = MultiSplitSet.get(399)
#dataset_name = multi_split_set.description
# create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeRBFKernel" #"WeightedDegreeStringKernel"#"PolyKernel"
param.wdk_degree = 2
param.cost = 1.0
param.transform = 0.2
param.base_similarity = 1.0
param.taxonomy = multi_split_set.taxonomy
param.id = 666
flags= {}
#flags["boosting"] = "ones"
#flags["boosting"] = "L1"
flags["boosting"] = "L2"
#flags["boosting"] = "L2_reg"
flags["signum"] = False
flags["normalize_cost"] = True
flags["all_positions"] = False
flags["wdk_rbf_on"] = False
param.flags = flags
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(434)
# flags
flags = {}
flags["normalize_cost"] = False
flags["epsilon"] = 1.0
#0.005
flags["kernel_cache"] = 200
flags["use_bias"] = False
# arts params
flags["svm_type"] = "liblineardual"
flags["degree"] = 24
flags["degree_spectrum"] = 4
flags["shifts"] = 0 #32
flags["center_offset"] = 70
flags["train_factor"] = 1
#create mock param object by freezable struct
param = Options()
param.kernel = "Promoter"
param.cost = 1.0
param.transform = 1.0
param.id = 666
param.flags = flags
param.taxonomy = multi_split_set.taxonomy
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = -1
from expenv import MultiSplitSet
from helper import Options
# select dataset
#multi_split_set = MultiSplitSet.get(387)
#multi_split_set = MultiSplitSet.get(407)
multi_split_set = MultiSplitSet.get(399)
#dataset_name = multi_split_set.description
# create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"#"PolyKernel"
param.wdk_degree = 2
param.cost = 1.0
param.transform = 0.2
param.base_similarity = 1
param.taxonomy = multi_split_set.taxonomy
param.id = 666
flags= {}
#flags["boosting"] = "ones"
flags["boosting"] = "L1"
#flags["boosting"] = "L2"
#flags["boosting"] = "L2_reg"
flags["signum"] = False
flags["normalize_cost"] = True
flags["all_positions"] = False
flags["wdk_rbf_on"] = False
param.flags = flags
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
# select dataset
multi_split_set = MultiSplitSet.get(384)
# flags
flags = {}
flags["normalize_cost"] = False
#flags["epsilon"] = 0.005
flags["kernel_cache"] = 200
flags["use_bias"] = False
# arts params
#flags["svm_type"] = "liblineardual"
flags["degree"] = 24
flags["local"] = False
flags["mem"] = "6G"
flags["maxNumThreads"] = 1
#create mock param object by freezable struct
param = Options()
#param.kernel = "GaussianKernel"
param.kernel = "PolyKernel"
param.sigma = 3.0
param.cost = 10.0
param.transform = 1.0
param.id = 666
param.flags = flags
param.taxonomy = multi_split_set.taxonomy.data
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(432)
# flags
flags = {}
flags["normalize_cost"] = False
#flags["epsilon"] = 0.005
flags["kernel_cache"] = 200
flags["use_bias"] = False
# arts params
flags["svm_type"] = "liblineardual"
flags["degree"] = 24
flags["degree_spectrum"] = 4
flags["shifts"] = 0 #32
flags["center_offset"] = 70
flags["train_factor"] = 1
flags["local"] = False
flags["mem"] = "6G"
flags["maxNumThreads"] = 1
#create mock param object by freezable struct
param = Options()
param.kernel = "Promoter"
param.cost = 1.0
param.transform = 1.0
param.id = 666
param.flags = flags
param.taxonomy = multi_split_set.taxonomy.data
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = -1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(399)
#dataset_name = multi_split_set.description
flags = {}
flags["normalize_cost"] = False
flags["epsilon"] = 0.05
flags["cache_size"] = 7
#flags["solver_type"] = "ST_DIRECT" #ST_CPLEX #ST_GLPK) #ST_DIRECT) #ST_NEWTON)
flags["normalize_trace"] = True
flags["interleaved"] = True
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"
param.wdk_degree = 1
param.cost = 1
param.transform = 1 #2.0
param.taxonomy = multi_split_set.taxonomy
param.id = 666
param.flags = flags
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
from task_similarities import fetch_gammas
# select dataset
multi_split_set = MultiSplitSet.get(317)
#multi_split_set = MultiSplitSet.get(374)
#multi_split_set = MultiSplitSet.get(2)
dataset_name = multi_split_set.description
transform = 1.0
base = 1.0
similarity_matrix = fetch_gammas(transform, base, dataset_name)
#create mock taxonomy object by freezable struct
taxonomy = Options()
taxonomy.data = similarity_matrix
taxonomy.description = dataset_name
taxonomy.freeze()
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"
param.wdk_degree = 1
param.cost = 1.0
param.transform = 1.0
param.taxonomy = taxonomy
param.id = 666
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
create_plot_inner(param, data_train, data_eval)
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(379)
dataset_name = multi_split_set.description
print "dataset_name", dataset_name
#create mock taxonomy object by freezable struct
#taxonomy = Options()
#taxonomy.data = taxonomy_graph.data
#taxonomy.description = dataset_name
#taxonomy.freeze()
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"
param.wdk_degree = 1
param.cost = 1.0
param.transform = 2.0
param.taxonomy = multi_split_set.taxonomy
param.id = 666
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train hierarchical xval
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf();
def training_for_sigma(sigma):
print "starting debugging:"
from expenv import MultiSplitSet
# select dataset
multi_split_set = MultiSplitSet.get(393)
SPLIT_POINTER = 1
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel" #"WeightedDegreeRBFKernel" # #
param.wdk_degree = 2
param.cost = 1.0
param.transform = 1.0
param.id = 666
param.base_similarity = sigma
param.degree = 2
param.flags = {}
param.flags["wdk_rbf_on"] = False
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
return assessment.auROC
def main():
print "starting debugging:"
SPLIT_POINTER = -1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(399)
#dataset_name = multi_split_set.description
flags = {}
flags["normalize_cost"] = False
flags["epsilon"] = 0.05
flags["cache_size"] = 7
#flags["solver_type"] = "ST_DIRECT" #ST_CPLEX #ST_GLPK) #ST_DIRECT) #ST_NEWTON)
flags["normalize_trace"] = True
flags["interleaved"] = True
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"
param.wdk_degree = 1
param.cost = 1
param.transform = 1 #2.0
param.taxonomy = multi_split_set.taxonomy
param.id = 666
param.flags = flags
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(379)
dataset_name = multi_split_set.description
print "dataset_name", dataset_name
#create mock taxonomy object by freezable struct
#taxonomy = Options()
#taxonomy.data = taxonomy_graph.data
#taxonomy.description = dataset_name
#taxonomy.freeze()
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"
param.wdk_degree = 1
param.cost = 1.0
param.transform = 2.0
param.taxonomy = multi_split_set.taxonomy
param.id = 666
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train hierarchical xval
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = -1
from expenv import MultiSplitSet
from helper import Options
# select dataset
#multi_split_set = MultiSplitSet.get(387)
multi_split_set = MultiSplitSet.get(386)
#dataset_name = multi_split_set.description
# create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"#"PolyKernel"
param.wdk_degree = 1
param.cost = 100
param.transform = 2 #2.0
param.taxonomy = multi_split_set.taxonomy
param.id = 666
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(399)
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeRBFKernel" #"WeightedDegreeStringKernel"# #
param.wdk_degree = 1
param.cost = 1.0
param.transform = 1.0
param.sigma = 1.0
param.id = 666
param.base_similarity = 1
param.degree = 2
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = -1
from expenv import MultiSplitSet
from helper import Options
# select dataset
#multi_split_set = MultiSplitSet.get(387)
multi_split_set = MultiSplitSet.get(386)
#dataset_name = multi_split_set.description
# create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel"#"PolyKernel"
param.wdk_degree = 1
param.cost = 1
param.transform = 2 #2.0
param.taxonomy = multi_split_set.taxonomy
param.id = 666
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(384)
# flags
flags = {}
flags["normalize_cost"] = False
flags["kernel_cache"] = 1000
flags["use_bias"] = False
#flags["debug"] = False
#create mock param object by freezable struct
param = Options()
param.kernel = "PolyKernel"
param.cost = 100.0
param.id = 1
param.flags = flags
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def training_for_sigma(sigma):
print "starting debugging:"
from expenv import MultiSplitSet
# select dataset
multi_split_set = MultiSplitSet.get(393)
SPLIT_POINTER = 1
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeStringKernel" #"WeightedDegreeRBFKernel" # #
param.wdk_degree = 2
param.cost = 1.0
param.transform = 1.0
param.id = 666
param.base_similarity = sigma
param.degree = 2
param.flags = {}
param.flags["wdk_rbf_on"] = False
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
return assessment.auROC
def main():
print "starting debugging:"
SPLIT_POINTER = 1
from expenv import MultiSplitSet
from helper import Options
# select dataset
multi_split_set = MultiSplitSet.get(399)
#create mock param object by freezable struct
param = Options()
param.kernel = "WeightedDegreeRBFKernel" #"WeightedDegreeStringKernel"# #
param.wdk_degree = 1
param.cost = 1.0
param.transform = 1.0
param.sigma = 1.0
param.id = 666
param.base_similarity = 1
param.degree = 2
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
# train
mymethod = Method(param)
mymethod.train(data_train)
print "training done"
assessment = mymethod.evaluate(data_eval)
print assessment
assessment.destroySelf()
def run_multi_example(dataset_idx, mymethod, comment):
"""
sets up and runs experiment
"""
#######################################
# fix parameters
#######################################
flags= {}
# general
flags["normalize_cost"] = True #False
flags["epsilon"] = 0.03
flags["cache_size"] = 500
# Boosting
#flags["boosting"] = "ones"
#flags["boosting"] = "L1"
#flags["boosting"] = "L2"
flags["boosting"] = "L2_reg"
#flags["use_all_nodes"] = False
flags["signum"] = False
#flags["all_positions"] = True
# MKL
#flags["solver_type"] = "ST_DIRECT" #ST_CPLEX #ST_GLPK) #ST_DIRECT) #ST_NEWTON)
#flags["normalize_trace"] = True
#flags["interleaved"] = True
#flags["mkl_q"] = 0
#WDK_RBF
flags["wdk_rbf_on"] = False
# define parameter search space [float(numpy.power(10, 3.58))] #
costs = [float(c) for c in numpy.exp(numpy.linspace(numpy.log(1000), numpy.log(100000), 8))]
#costs = [float(c) for c in numpy.exp(numpy.linspace(numpy.log(float(numpy.power(10, 3))), numpy.log(10000), 4))]
#costs = [float(c) for c in numpy.exp(numpy.linspace(numpy.log(0.01), numpy.log(1000), 8))]
#[float(c) for c in numpy.exp(numpy.linspace(numpy.log(10), numpy.log(2000), 10))]
costs.reverse()
degrees = [1,2,3,4,5] #[1, 5, 10, 15, 20, 22]
#print "WARNING: Degree is ONE"
base_similarities = [200] #[float(c) for c in numpy.exp(numpy.linspace(numpy.log(1), numpy.log(1000), 8))]
#base_similarities = [float(c) for c in numpy.linspace(1, 5000, 6)] #[1]
#transform_params = [float(c) for c in numpy.linspace(1, 10000, 6)] #[1] #1.5, 2.0, 2.5, 3.0] #, 3.5, 4.0, 4.5, 5.0]
#transform_params = [float(c) for c in numpy.linspace(0.01, 0.99, 6)]
transform_params = [0.99]
generation_parameters = locals()
#######################################
# create experiment
#######################################
# select dataset
multi_split_set = MultiSplitSet.get(dataset_idx)
dataset_name = multi_split_set.description
print "method:", mymethod
print "dataset:", dataset_name
print "multi split set id:", dataset_idx
experiment_description = dataset_name + " (" + mymethod + ") " + comment
# allow different features/kernel types
feature_type = multi_split_set.feature_type
if feature_type == "string":
kernel_type = "WeightedDegreeStringKernel"
else:
kernel_type = "PolyKernel"
kernel_type = "WeightedDegreeRBFKernel"
# create experiment
experiment = MultiSourceExperiment(split_set = multi_split_set,
description = experiment_description,
method_name = mymethod,
meta_data = generation_parameters)
print "experiment id:", experiment.id
#######################################
# create runs
#######################################
if multi_split_set.taxonomy==None:
print "WARNING: NO taxonomy set, generating one for dataset " + dataset_name
taxonomy = dataset_to_hierarchy(dataset_name)
else:
taxonomy = multi_split_set.taxonomy
for cost in costs:
for degree in degrees:
for base in base_similarities:
for transform in transform_params:
param = ParameterMultiSvm(cost=cost,
wdk_degree=degree,
base_similarity=base,
transform=transform,
taxonomy=taxonomy,
kernel=kernel_type,
flags=flags)
print param
Method(module_name=mymethod, param=param, experiment=experiment)
# skip model selection if we only have one model
if len(experiment.methods) > 1:
# create evaluation runs based on splits and methods
run_ids = [run.id for run in experiment.create_eval_runs()]
# execute runs
execute_runs(run_ids)
# finally perform model selection and retrain
select_best_and_test(experiment, target)
#experiment.select_best_method(target)
return experiment.id
def main():
print "starting debugging:"
from expenv import MultiSplitSet
from helper import Options
from task_similarities import dataset_to_hierarchy
# select dataset
#multi_split_set = MultiSplitSet.get(317)
multi_split_set = MultiSplitSet.get(432)
#multi_split_set = MultiSplitSet.get(2) #small splicing
#multi_split_set = MultiSplitSet.get(377) #medium splicing
dataset_name = multi_split_set.description
# flags
flags = {}
flags["normalize_cost"] = False
flags["epsilon"] = 1.0
#0.005
flags["kernel_cache"] = 1000
flags["use_bias"] = False
# arts params
flags["svm_type"] = "liblineardual"
flags["degree"] = 24
flags["degree_spectrum"] = 4
flags["shifts"] = 0 #32
flags["train_factor"] = 1
flags["center_offset"] = 70
flags["center_pos"] = 500
#create mock param object by freezable struct
param = Options()
param.kernel = "Promoter"
param.cost = 1.0
param.transform = 1.0
param.id = 666
param.flags = flags
param.taxonomy = multi_split_set.taxonomy
param.freeze()
data_train = multi_split_set.get_train_data(SPLIT_POINTER)
data_eval = multi_split_set.get_eval_data(SPLIT_POINTER)
(perf_xval, final_pred, best_idx_cost) = create_plot_inner(param, data_train, data_eval)
perf_regular = create_plot_regular(param, data_train, data_eval)
# plot performances
import pylab
if TARGET_PARAM=="both":
#X,Y = pylab.meshgrid(range(len(RANGE)), range(len(RANGE)))
cmap = pylab.cm.get_cmap('jet', 20) # 10 discrete colors
pylab.contourf(RANGE, RANGE, perf_xval, cmap=cmap)
#im = pylab.imshow(perf_xval, cmap=cmap, interpolation='bilinear')
pylab.axis('on')
pylab.colorbar()
pylab.title("mss:" + str(multi_split_set.id) + ", task:" + TARGET_TASK + " , param:" + TARGET_PARAM + ", split:" + str(SPLIT_POINTER))
pylab.show()
else:
pylab.semilogx(RANGE, perf_regular, "g-o")
pylab.semilogx(RANGE, perf_xval, "b-o")
#pylab.semilogx([a*0.66 for a in RANGE], perf_xval, "b-o")
#pylab.plot(numpy.array(perf_regular) - numpy.array(perf_xval), "y-o")
#pylab.plot([best_idx_cost], [final_pred], "r+")
pylab.axhline(y=final_pred, color="r")
pylab.axvline(x=RANGE[best_idx_cost], color="r")
pylab.axvline(x=1.0, color="g")
pylab.ylabel(TARGET_MEASURE)
pylab.xlabel(TARGET_PARAM)
pylab.legend( ("outer", "inner xval"), loc="best")
pylab.title("mss:" + str(multi_split_set.id) + ", task:" + TARGET_TASK + " , degree:" + str(param.wdk_degree) + ", split:" + str(SPLIT_POINTER))
pylab.show()
def run_multi_example(dataset_idx, mymethod, comment):
"""
sets up and runs experiment
"""
#######################################
# fix parameters
#######################################
flags = {}
# general
flags["normalize_cost"] = True #False
flags["epsilon"] = 0.03
flags["cache_size"] = 500
# Boosting
#flags["boosting"] = "ones"
#flags["boosting"] = "L1"
#flags["boosting"] = "L2"
flags["boosting"] = "L2_reg"
#flags["use_all_nodes"] = False
flags["signum"] = False
#flags["all_positions"] = True
# MKL
#flags["solver_type"] = "ST_DIRECT" #ST_CPLEX #ST_GLPK) #ST_DIRECT) #ST_NEWTON)
#flags["normalize_trace"] = True
#flags["interleaved"] = True
#flags["mkl_q"] = 0
#WDK_RBF
flags["wdk_rbf_on"] = False
# define parameter search space [float(numpy.power(10, 3.58))] #
costs = [
float(c) for c in numpy.exp(
numpy.linspace(numpy.log(1000), numpy.log(100000), 8))
]
#costs = [float(c) for c in numpy.exp(numpy.linspace(numpy.log(float(numpy.power(10, 3))), numpy.log(10000), 4))]
#costs = [float(c) for c in numpy.exp(numpy.linspace(numpy.log(0.01), numpy.log(1000), 8))]
#[float(c) for c in numpy.exp(numpy.linspace(numpy.log(10), numpy.log(2000), 10))]
costs.reverse()
degrees = [1, 2, 3, 4, 5] #[1, 5, 10, 15, 20, 22]
#print "WARNING: Degree is ONE"
base_similarities = [
200
] #[float(c) for c in numpy.exp(numpy.linspace(numpy.log(1), numpy.log(1000), 8))]
#base_similarities = [float(c) for c in numpy.linspace(1, 5000, 6)] #[1]
#transform_params = [float(c) for c in numpy.linspace(1, 10000, 6)] #[1] #1.5, 2.0, 2.5, 3.0] #, 3.5, 4.0, 4.5, 5.0]
#transform_params = [float(c) for c in numpy.linspace(0.01, 0.99, 6)]
transform_params = [0.99]
generation_parameters = locals()
#######################################
# create experiment
#######################################
# select dataset
multi_split_set = MultiSplitSet.get(dataset_idx)
dataset_name = multi_split_set.description
print "method:", mymethod
print "dataset:", dataset_name
print "multi split set id:", dataset_idx
experiment_description = dataset_name + " (" + mymethod + ") " + comment
# allow different features/kernel types
feature_type = multi_split_set.feature_type
if feature_type == "string":
kernel_type = "WeightedDegreeStringKernel"
else:
kernel_type = "PolyKernel"
kernel_type = "WeightedDegreeRBFKernel"
# create experiment
experiment = MultiSourceExperiment(split_set=multi_split_set,
description=experiment_description,
method_name=mymethod,
meta_data=generation_parameters)
print "experiment id:", experiment.id
#######################################
# create runs
#######################################
if multi_split_set.taxonomy == None:
print "WARNING: NO taxonomy set, generating one for dataset " + dataset_name
taxonomy = dataset_to_hierarchy(dataset_name)
else:
taxonomy = multi_split_set.taxonomy
for cost in costs:
for degree in degrees:
for base in base_similarities:
for transform in transform_params:
param = ParameterMultiSvm(cost=cost,
wdk_degree=degree,
base_similarity=base,
transform=transform,
taxonomy=taxonomy,
kernel=kernel_type,
flags=flags)
print param
Method(module_name=mymethod,
param=param,
experiment=experiment)
# skip model selection if we only have one model
if len(experiment.methods) > 1:
# create evaluation runs based on splits and methods
run_ids = [run.id for run in experiment.create_eval_runs()]
# execute runs
execute_runs(run_ids)
# finally perform model selection and retrain
select_best_and_test(experiment, target)
#experiment.select_best_method(target)
return experiment.id
