args = parser.parse_args()
results_dir = args.results_dir
log_dir = make_and_get_dir(results_dir, 'log')
fitting_dir = make_and_get_dir(results_dir, 'model_fitting')
mv_fitting_dir = make_and_get_dir(fitting_dir, 'multi_view')
model_sel_dir = make_and_get_dir(results_dir, 'model_selection')
# bd_sel_dir = make_and_get_dir(model_sel_dir, 'bd_mvmm')
# log_sel_dir = make_and_get_dir(model_sel_dir, 'log_pen_mvmm')
bd_sel_dir = make_and_get_dir(model_sel_dir)
log_sel_dir = make_and_get_dir(model_sel_dir)
opt_diag_dir = make_and_get_dir(results_dir, 'opt_diagnostics')
res_writer = ResultsWriter(os.path.join(log_dir, 'mvmm_model_selection.txt'),
delete_if_exists=True)
res_writer.write('user_bd_mvmm_best_idx: {}'.
format(args.user_bd_mvmm_best_idx))
res_writer.write('user_log_pen_mvmm_best_idx: {}'.
format(args.user_log_pen_mvmm_best_idx))
res_writer.write('select_metric: {}'.format(args.select_metric))
# data = load(os.path.join(save_dir, 'multi_view_fit_data'))
#############
# load data #
#############
mvmm_results = load_fitted_mvmms(fitting_dir)
action='store_true',
default=False,
help='Dont run cat gmm.')
parser = add_parsers(parser, to_add=[general_opt_parser, base_gmm_parser])
parser = bayes_parser(parser)
args = parser.parse_args()
bayes_submit(args)
args = format_mini_experiment(args)
results_dir = args.results_dir
log_dir = make_and_get_dir(results_dir, 'log')
fitting_dir = make_and_get_dir(results_dir, 'model_fitting', 'single_view')
res_writer = ResultsWriter(join(log_dir, 'single_view_fitting.txt'),
delete_if_exists=True)
res_writer.write(args)
run_start_time = time()
n_views = len(args.fpaths)
#############
# load data #
#############
view_data, dataset_names, sample_names, feat_names = \
load_data(*args.fpaths)
for v in range(n_views):
# # 'rank_sel_kws': {'rotate': True},
# 'max_rank': 500}
# else:
# rank_sel_kws = {'n_components': 'rmt_threshold',
# 'rank_sel_kws': {'thresh_method': 'dg'}}
# rank_sel_kws = {'n_components': 'bai_ng_bic',
# 'rank_sel_kws': {'who': 1},
# 'max_rank': 400
# }
for k in data.keys():
res_writer = ResultsWriter(fpath=join(diagnostics_dir,
'{}_log.txt'.format(k)),
delete_if_exists=True)
res_writer.write(k)
res_writer.write('shape {}'.format(data[k].shape))
rank_sel_kws = {'n_components': 'rmt_threshold',
'rank_sel_kws': {'thresh_method': 'dg'}}
pca = PCA(**rank_sel_kws)
start_time = time()
pca.fit(data[k].values)
runtime = time() - start_time
res_writer.write("computed pca took {:1.2f} seconds".format(runtime))
res_writer.write('Estimated n components {}'.format(pca.n_components_))
spect_pen_parser
])
parser = bayes_parser(parser)
args = parser.parse_args()
args = format_mini_experiment(args)
args.job_name = args.sim_name
bayes_submit(args)
if args.sim_name is None:
args.sim_name = 'meow'
save_dir = make_and_get_dir(Paths().results_dir, 'single', args.sim_name)
res_writer = ResultsWriter(os.path.join(save_dir, 'results.txt'),
delete_if_exists=True)
res_writer.write('\n\n\n Input args')
res_writer.write(args)
rng = check_random_state(args.metaseed)
to_exclude = []
# if args.exclude_sp_mvmm:
to_exclude.append('sp_mvmm')
if args.exclude_bd_mvmm:
to_exclude.append('bd_mvmm')
if args.exclude_log_pen_mvmm:
to_exclude.append('log_pen_mvmm')
inches = 8
def run_sim(models,
data_dist,
Pi,
view_params,
n_samples_tr,
data_seed,
n_samples_tst=2000,
zero_thresh=0,
reg_covar_mult=1e-2,
mc_index=None,
to_exclude=None,
log_fpath=None):
"""
Parameters
----------
models
data_dist: callable(n_samples, seed)
Function to generate data.
n_samples_tr: int
Number of training samples.
data_seed: int
Seed for sampling train/test observations.
n_samples_tst: int
Number of samples to get for test data.
"""
res_writer = ResultsWriter(log_fpath, delete_if_exists=True)
res_writer.write("Beginning simulation at {}".format(get_current_time))
overall_start_time = time()
seeds = get_seeds(random_state=data_seed, n_seeds=2)
# sample data
X_tr, Y_tr = data_dist(n_samples=n_samples_tr, random_state=seeds[0])
X_tst, Y_tst = data_dist(n_samples=n_samples_tst, random_state=seeds[1])
n_views = len(X_tr)
Pi_empirical = get_empirical_pi(Y_tr, Pi.shape, scale='counts')
runtimes = {}
if to_exclude is None:
to_exclude = []
for m in to_exclude:
assert m in ['bd_mvmm', 'sp_mvmm', 'log_pen_mvmm']
#############################
# covariance regularization #
#############################
n_views = len(X_tr)
reg_covar = {}
# set cov reg for each view
for v in range(n_views):
reg = default_cov_regularization(X=X_tr[v], mult=reg_covar_mult)
models['view_gmms'][v].base_estimator.set_params(reg_covar=reg)
models['full_mvmm'].base_view_models[v].set_params(reg_covar=reg)
models['bd_mvmm'].base_estimator.base_start.base_view_models[v].\
set_params(reg_covar=reg)
models['bd_mvmm'].base_estimator.base_final.base_view_models[v].\
set_params(reg_covar=reg)
models['log_pen_mvmm'].base_estimator.base_start.base_view_models[v].\
set_params(reg_covar=reg)
models['log_pen_mvmm'].base_estimator.base_start.base_view_models[v].\
set_params(reg_covar=reg)
models['sp_mvmm'].base_mvmm_0.base_view_models[v].\
set_params(reg_covar=reg)
models['sp_mvmm'].base_wbd_mvmm.base_view_models[v].\
set_params(reg_covar=reg)
# print and save
reg_covar[v] = reg
res_writer.write(
"\nCovarinace regularization for view {} is {}".format(v, reg))
stds = X_tr[v].std(axis=0)
res_writer.write("Smallest variance: {}".format(stds.min()**2))
res_writer.write("Largest variance: {}".format(stds.max()**2))
# for cat GMM
reg = default_cov_regularization(X=np.hstack(X_tr), mult=reg_covar_mult)
models['cat_gmm'].base_estimator.set_params(reg_covar=reg)
reg_covar['cat_gmm'] = reg
##############
# fit models #
##############
# get classification resuls
clf_results = {}
start_time = time()
clf_results['cat'] = clf_fit_and_score(clone(models['clf']),
X_tr=np.hstack(X_tr),
y_tr=view_labs_to_overall(Y_tr),
X_tst=np.hstack(X_tst),
y_tst=view_labs_to_overall(Y_tst))
runtimes['cat'] = time() - start_time
for v in range(n_views):
start_time = time()
clf_results['view_{}'.format(v)] =\
clf_fit_and_score(clone(models['clf']),
X_tr=X_tr[v],
y_tr=Y_tr[:, v],
X_tst=X_tst[v],
y_tst=Y_tst[:, v])
runtimes['clf_view_{}'.format(v)] = time() - start_time
# fit clustering
simplefilter('ignore', ConvergenceWarning)
results_df = pd.DataFrame()
sim_stub = {'mc_index': mc_index, 'n_samples': n_samples_tr}
dists_cat = pairwise_distances(X=np.hstack(X_tr))
dists_views = [pairwise_distances(X=X_tr[v]) for v in range(n_views)]
kws = {
'sim_stub': sim_stub,
'X_tr': X_tr,
'Y_tr': Y_tr,
'X_tst': X_tst,
'Y_tst': Y_tst,
'Pi_true': Pi,
'view_params_true': view_params,
'zero_thresh': zero_thresh,
}
###########
# cat-GMM #
###########
# print('start fitting cat-GMM at {}'.
# format(datetime.now().strftime("%d/%m/%Y %H:%M:%S")))
start_time = time()
models['cat_gmm'].fit(np.hstack(X_tr))
runtimes['cat_gmm'] = time() - start_time
res_writer.write('fitting grid search cat-GMM took {:1.2f} seconds'.format(
runtimes['cat_gmm']))
results_df = add_gs_results(results_df=results_df,
model=models['cat_gmm'],
model_name='gmm_cat',
dataset='full',
view='both',
X_tr_precomp_dists=dists_cat,
**kws)
#############
# View GMMs #
#############
# print('start fitting view marginal GMMs at {}'.
# format(datetime.now().strftime("%d/%m/%Y %H:%M:%S")))
for v in range(n_views):
start_time = time()
models['view_gmms'][v].fit(X_tr[v])
runtimes['gmm_view_{}'.format(v)] = time() - start_time
res_writer.write(
'fitting marginal view {} GMM took {:1.2f} seconds'.format(
v, runtimes['gmm_view_{}'.format(v)]))
# gmm fit on this view
results_df = add_gs_results(results_df=results_df,
model=models['view_gmms'][v],
model_name='marginal_view_{}'.format(v),
dataset='view',
view=v,
X_tr_precomp_dists=dists_views[v],
**kws)
#############
# Full MVMM #
#############
# print('start fitting full MVMM at {}'.
# format(datetime.now().strftime("%d/%m/%Y %H:%M:%S")))
start_time = time()
models['full_mvmm'].fit(X_tr)
runtimes['full_mvmm'] = time() - start_time
res_writer.write('fitting full mvmm took {:1.2f} seconds'.format(
runtimes['full_mvmm']))
results_df = add_gs_results(results_df=results_df,
model=models['full_mvmm'],
model_name='full_mvmm',
run_biptsp_on_full=True,
dataset='full',
view='both',
X_tr_precomp_dists=dists_cat,
**kws)
for v in range(n_views):
# add MVMM results for this view
results_df = add_gs_results(
results_df=results_df,
model=models['full_mvmm'],
model_name='full_mvmm',
dataset='view',
view=v,
X_tr_precomp_dists=dists_views[v], # TODO is this what we want
**kws)
################
# log pen MVMM #
################
if 'log_pen_mvmm' not in to_exclude:
# print('start fitting log pen grid search MVMM at {}'.
# format(datetime.now().strftime("%d/%m/%Y %H:%M:%S")))
start_time = time()
models['log_pen_mvmm'].fit(X_tr)
runtimes['log_pen_mvmm'] = time() - start_time
res_writer.write('fitting grid search for log pen'
'mvmm took {:1.2f} seconds'.format(
runtimes['log_pen_mvmm']))
results_df = add_gs_results(results_df=results_df,
model=models['log_pen_mvmm'],
model_name='log_pen_mvmm',
dataset='full',
view='both',
X_tr_precomp_dists=dists_cat,
**kws)
for v in range(n_views):
# add log pen MVMM results for this view
results_df = add_gs_results(
results_df=results_df,
model=models['log_pen_mvmm'],
model_name='log_pen_mvmm',
dataset='view',
view=v,
X_tr_precomp_dists=dists_views[
v], # TODO: is this what we want
**kws)
#######################
# block diagonal MVMM #
#######################
if 'bd_mvmm' not in to_exclude:
# print('start fitting block diag grid search MVMM at {}'.
# format(datetime.now().strftime("%d/%m/%Y %H:%M:%S")))
start_time = time()
models['bd_mvmm'].fit(X_tr)
runtimes['bd_mvmm'] = time() - start_time
res_writer.write('fitting grid search for block'
'diag mvmm took {:1.2f} seconds'.format(
runtimes['bd_mvmm']))
results_df = add_gs_results(results_df=results_df,
model=models['bd_mvmm'],
model_name='bd_mvmm',
dataset='full',
view='both',
X_tr_precomp_dists=dists_cat,
**kws)
for v in range(n_views):
# add bd MVMM results for this view
results_df = add_gs_results(
results_df=results_df,
model=models['bd_mvmm'],
model_name='bd_mvmm',
dataset='view',
view=v,
X_tr_precomp_dists=dists_views[
v], # TODO: is this what we want
**kws)
#########################
# spectral penalty MVMM #
#########################
if 'sp_mvmm' not in to_exclude:
# print('start fitting spectral penalty MVMM at {}'.
# format(datetime.now().strftime("%d/%m/%Y %H:%M:%S")))
start_time = time()
models['sp_mvmm'].fit(X_tr)
runtimes['sp_mvmm'] = time() - start_time
res_writer.write('fitting grid search for spect pen'
'mvmm took {:1.2f} seconds'.format(
runtimes['sp_mvmm']))
results_df = add_gs_results(results_df=results_df,
model=models['sp_mvmm'],
model_name='sp_mvmm',
dataset='full',
view='both',
X_tr_precomp_dists=dists_cat,
**kws)
for v in range(n_views):
# add sp MVMM results for this view
results_df = add_gs_results(
results_df=results_df,
model=models['sp_mvmm'],
model_name='sp_mvmm',
dataset='view',
view=v,
X_tr_precomp_dists=dists_views[
v], # TODO: is this what we want
**kws)
##########
# oracle #
##########
results_df = add_gs_results(
results_df,
model=models['oracle'],
model_name='oracle',
run_biptsp_on_full=False, # or true?
dataset='full',
view='both',
**kws)
# Some formatting
# ensure these columns are saved as integers
int_cols = [
'mc_index', 'best_tuning_idx', 'n_comp_est', 'n_comp_resid',
'n_comp_tot_est', 'n_samples', 'tune_idx'
]
results_df[int_cols] = results_df[int_cols].astype(int)
# block diagonal summary of Pi estimates
bd_summary = {}
if 'log_pen_mvmm' not in to_exclude:
_sim_stub = deepcopy(sim_stub)
_sim_stub.update({'model_name': 'log_pen_mvmm'})
bd_summary['log_pen_mvmm'] = \
get_bd_summary_for_gs(_sim_stub, models['log_pen_mvmm'],
zero_thresh=zero_thresh)
if 'bd_mvmm' not in to_exclude:
_sim_stub = deepcopy(sim_stub)
_sim_stub.update({'model_name': 'bd_mvmm'})
bd_summary['bd_mvmm'] = \
get_bd_summary_for_gs(_sim_stub, models['bd_mvmm'],
zero_thresh=zero_thresh)
if 'sp_mvmm' not in to_exclude:
_sim_stub = deepcopy(sim_stub)
_sim_stub.update({'model_name': 'sp_mvmm'})
bd_summary['sp_mvmm'] = \
get_bd_summary_for_gs(_sim_stub, models['sp_mvmm'],
zero_thresh=zero_thresh)
res_writer.write(
"Entire simulation took {:1.2f} seconds".format(time() -
overall_start_time))
tr_data = {'X_tr': X_tr, 'Y_tr': Y_tr}
return results_df, clf_results, models, bd_summary, Pi_empirical, tr_data,\
runtimes
assert feat_list in ['all', 'icluster'] or 'top' in feat_list
filter_kws = {
'tumor_sample_only': True,
'primary_tumor_only': True,
'keep_first_of_participant_multiples': True,
'ensure_participant_idx': True,
'verbose': True
}
raw_data_dir = TCGAPaths().raw_data_dir
pro_data_dir = make_and_get_dir(TCGAPaths().pro_data_dir, cancer_type)
feat_save_dir = make_and_get_dir(pro_data_dir, feat_list)
res_writer = ResultsWriter(join(feat_save_dir, 'log.txt'),
delete_if_exists=True)
res_writer.write(args)
fnames = {
'mi_rna':
'pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16.csv',
'rna': 'EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2-v2.geneExp.tsv',
'dna_meth':
'jhu-usc.edu_PANCAN_merged_HumanMethylation27_HumanMethylation450.betaValue_whitelisted.tsv',
'cp': 'all_data_by_genes_whitelisted.tsv'
}
start_time = time()
##################
bayes_submit(args)
args = format_mini_experiment(args)
# stub = 'mvmm_fitting_{}_{}'.format(args.n_comp_v0, args.n_comp_v1)
stub = 'mvmm_fitting'
for nc in args.n_view_comps:
stub += '_{}'.format(nc)
results_dir = args.results_dir
# results_dir = make_and_get_dir(args.top_dir, args.sim_name)
log_dir = make_and_get_dir(results_dir, 'log')
fitting_dir = make_and_get_dir(results_dir, 'model_fitting')
model_sel_dir = make_and_get_dir(results_dir, 'model_selection')
opt_diag_dir = make_and_get_dir(results_dir, 'opt_diagnostics')
res_writer = ResultsWriter(os.path.join(log_dir, '{}.txt'.format(stub)),
delete_if_exists=True)
res_writer.write(args)
run_start_time = time()
to_exclude = []
# if args.exclude_sp_mvmm:
# to_exclude.append('sp_mvmm')
if args.exclude_bd_mvmm:
to_exclude.append('bd_mvmm')
if args.exclude_log_pen_mvmm:
to_exclude.append('log_pen_mvmm')
#############
# load data #
parser.add_argument('--results_dir', default=None,
help='Directory to save results.')
args = parser.parse_args()
# sim_name = args.sim_name
results_dir = args.results_dir
log_dir = make_and_get_dir(results_dir, 'log')
fitting_dir = make_and_get_dir(results_dir, 'model_fitting')
sv_fitting_dir = make_and_get_dir(fitting_dir, 'single_view')
model_sel_dir = make_and_get_dir(results_dir, 'model_selection')
opt_diag_dir = make_and_get_dir(results_dir, 'opt_diagnostics')
res_writer = ResultsWriter(os.path.join(log_dir,
'single_view_model_selection.txt'),
delete_if_exists=True)
# data = load(os.path.join(save_dir, 'multi_view_fit_data'))
#############
# load data #
#############
metadata = load(os.path.join(sv_fitting_dir, 'single_view_fit_metadata'))
dataset_names = metadata['dataset_names']
# load models
fpaths = glob(join(sv_fitting_dir, 'fitted*'))
n_view_models = sum(('fitted_view' in os.path.basename(fpath))
for fpath in fpaths)