def main():
cfg = Config()
data_dir = '../../data'
train = pd.read_csv(os.path.join(data_dir, 'train_features.csv'))
targets = pd.read_csv(os.path.join(data_dir, 'train_targets_scored.csv'))
drug = pd.read_csv(os.path.join(data_dir, 'train_drug.csv'))
test = pd.read_csv(os.path.join(data_dir, 'test_features.csv'))
submission = pd.read_csv(os.path.join(data_dir, 'sample_submission.csv'))
train = process_data_cp(train)
test = process_data_cp(test)
ff = make_folds(drug=drug,
folds=cfg.folds,
random_state=cfg.seed,
stratify=True,
scored=targets)
train['fold'] = ff.fold.values
targets['fold'] = ff.fold.values
set_trace()
# initialize
oof = np.zeros((len(train), targets.shape[1] - 2))
dna = np.random.uniform(0, 1, (cfg.population, 875))**2.0
cvs = np.zeros((cfg.population))
def cv(config, context, folds=5, repeat=2, save=False):
# TODO: too much overloading on folds here
if isinstance(folds, int):
folds = make_folds(context.data.index, folds, repeat)
scores = []
for train, test in folds:
context.train_index = train
preds, x, y = predict(config, context, test)
actuals = y.reindex(test)
config.update_reporters_with_predictions(context, x, actuals, preds)
scores.append(config.metric.score(actuals,
preds))
scores = np.array(scores)
#if save:
#dataset.save_models([(scores, copy.copy(config))])
return scores
def cv(config,
context,
folds=5,
repeat=2,
print_results=False,
predict_method=None,
predict_update_column=None):
# TODO: too much overloading on folds here
if isinstance(folds, int):
folds = make_folds(context.data.index, folds, repeat)
#else:
#folds.set_context(config, context)
scores = {get_metric_name(m): [] for m in config.metrics}
# we are overwriting indices, so make a copy
ctx = context.copy()
i = 0
folds = list(folds)
k = len(folds) / repeat
for train, test in folds:
print "\nCross-Validation fold %d/%d round %d/%d" % (i % k + 1, k,
i / k + 1, repeat)
i += 1
ctx.train_index = train
ctx.test_index = test
fold_scores, result = evaluate(config, ctx, test, predict_method,
predict_update_column)
context.latest_result = result
for metric_, s in fold_scores.items():
scores[metric_].append(s)
if print_results:
for metric_, s in scores.items():
print "%s: %s" % (metric_, pprint_scores(s))
result = {'config': config, 'scores': scores}
# report results
t = PrettyTable(["Reporter", "Report"])
t.hrules = ALL
t.align["Reporter"] = "l"
t.align["Report"] = "l"
for reporter in config.reporters:
t.add_row([reporter.__class__.__name__, reporter.report()])
reporter.reset()
print t
return result
def cv(config, context, folds=5, repeat=2, print_results=False):
# TODO: too much overloading on folds here
if isinstance(folds, int):
folds = make_folds(context.data.index, folds, repeat)
scores = dict([(m.name, []) for m in config.metrics])
# we are overwriting indices, so make a copy
ctx = context.copy()
for train, test in folds:
ctx.train_index = train
preds, x, y = predict(config, ctx, test)
actuals = y.reindex(test)
config.update_reporters_with_predictions(ctx, x, actuals, preds)
for metric in config.metrics:
scores[metric.name].append(metric.score(actuals, preds))
#if save:
#dataset.save_models([(scores, copy.copy(config))])
if print_results:
print "\n" + str(config)
print_scores(scores)
return scores
def cv(config, context, folds=5, repeat=2, print_results=False):
# TODO: too much overloading on folds here
if isinstance(folds, int):
folds = make_folds(context.data.index, folds, repeat)
else:
folds.set_context(config, context)
scores = {m.name: [] for m in config.metrics}
# we are overwriting indices, so make a copy
ctx = context.copy()
i = 0
folds = list(folds)
k = len(folds)/repeat
for train, test in folds:
print "\nCross-Validation fold %d/%d round %d/%d" % (i % k + 1, k, i/k + 1, repeat)
i += 1
ctx.train_index = train
ctx.test_index = test
preds, x, y = predict(config, ctx, test)
actuals = y.reindex(test)
config.update_reporters_with_predictions(ctx, x, actuals, preds)
for metric in config.metrics:
scores[metric.name].append(
metric.score(actuals,preds))
result = {'config':config, 'scores':scores}
# report results
t = PrettyTable(["Reporter", "Report"])
t.hrules = ALL
t.align["Reporter"] = "l"
t.align["Report"] = "l"
for reporter in config.reporters:
t.add_row([reporter.__class__.__name__, reporter.report()])
reporter.reset()
print t
#if save:
#dataset.save_models([(scores, copy.copy(config))])
if print_results:
print "\n" + str(config)
print_scores(scores)
return result
def cv(config, context, folds=5, repeat=2, print_results=False):
# TODO: too much overloading on folds here
if isinstance(folds, int):
folds = make_folds(context.data.index, folds, repeat)
scores = dict([(m.name, []) for m in config.metrics])
# we are overwriting indices, so make a copy
ctx = context.copy()
for train, test in folds:
ctx.train_index = train
preds, x, y = predict(config, ctx, test)
actuals = y.reindex(test)
config.update_reporters_with_predictions(ctx, x, actuals, preds)
for metric in config.metrics:
scores[metric.name].append(
metric.score(actuals,preds))
#if save:
#dataset.save_models([(scores, copy.copy(config))])
if print_results:
print "\n" + str(config)
print_scores(scores)
return scores
def cv(config, context, folds=5, repeat=2, print_results=False,
predict_method=None, predict_update_column=None):
# TODO: too much overloading on folds here
if isinstance(folds, int):
folds = make_folds(context.data.index, folds, repeat)
#else:
#folds.set_context(config, context)
scores = {get_metric_name(m): [] for m in config.metrics}
# we are overwriting indices, so make a copy
ctx = context.copy()
i = 0
folds = list(folds)
k = len(folds)/repeat
for train, test in folds:
print "\nCross-Validation fold %d/%d round %d/%d" % (i % k + 1, k, i/k + 1, repeat)
i += 1
ctx.train_index = train
ctx.test_index = test
fold_scores, result = evaluate(config, ctx, test, predict_method, predict_update_column)
context.latest_result = result
for metric_, s in fold_scores.items():
scores[metric_].append(s)
if print_results:
for metric_, s in scores.items():
print "%s: %s" % (metric_, pprint_scores(s))
result = {'config':config, 'scores':scores}
# report results
t = PrettyTable(["Reporter", "Report"])
t.hrules = ALL
t.align["Reporter"] = "l"
t.align["Report"] = "l"
for reporter in config.reporters:
t.add_row([reporter.__class__.__name__, reporter.report()])
reporter.reset()
print t
return result
def cv_predictiveness(data,
S,
measure,
pred_func,
V=5,
stratified=True,
na_rm=False,
type="regression",
ensemble=False,
run_cv=False):
"""
Compute a cross-validated measure of predictiveness based on the data
and the chosen measure
@param data: dataset
@param S: the covariates to fit
@param measure: measure of predictiveness
@param pred_func: function that fits to the data
@param V: the number of CV folds
@param stratified: should the folds be stratified?
@param na_rm: should we do a complete-case analysis (True) or not (False)
@param type: is this regression (use predict) or classification (use predict_proba)?
@param ensemble: is this an ensemble (True) or not (False)?
@return cross-validated measure of predictiveness, along with preds and ics
"""
import numpy as np
from compute_ic import compute_ic
import utils as uts
from data_generator import Dataset
## if na_rm = True, do a complete-case analysis
if na_rm:
xs = data.x_train[:, S]
cc = np.sum(np.isnan(xs), axis=1) == 0
newdata = Dataset(x_train=data.x_train[cc, :],
y_train=data.y_train[cc])
else:
cc = np.repeat(True, data.x_train.shape[0])
newdata = data
## set up CV folds
folds = uts.make_folds(newdata, V, stratified=stratified)
## do CV
preds = np.empty((data.y_train.shape[0], ))
preds.fill(np.nan)
ics = np.empty((data.y_train.shape[0], ))
ics.fill(np.nan)
# preds = np.empty((newdata.y_train.shape[0],))
vs = np.empty((V, ))
# ics = np.empty((newdata.y_train.shape[0],))
cc_cond = np.flatnonzero(cc)
for v in range(V):
fold_cond = np.flatnonzero(folds == v)
x_train, y_train = newdata.x_train[folds != v, :], newdata.y_train[
folds != v]
x_test, y_test = newdata.x_train[folds == v, :], newdata.y_train[folds
== v]
pred_func.fit(x_train[:, S], np.ravel(y_train))
if ensemble:
preds_v = np.mean(pred_func.transform(x_test[:, S]))
else:
if type == "classification":
preds_v = pred_func.predict_proba(x_test[:, S])[:, 1]
else:
preds_v = pred_func.predict(x_test[:, S])
preds[cc_cond[fold_cond]] = preds_v
vs[v] = measure(y_test, preds_v)
ics[cc_cond[fold_cond]] = compute_ic(y_test, preds_v, measure.__name__)
return np.mean(vs), preds, ics, folds