def compute_final_error(self):
if self.model=='NMF':
V_string='*V_NMF.npy'
U_string='*U_NMF.npy'
if self.model=='SparsePCA':
V_string='*V_sPCA'
U_string='*U_sPCA'
for filename_V in glob.glob(os.path.join(self.save_path, V_string)):
for filename_U in glob.glob(os.path.join(self.save_path, U_string)):
if filename_V[:-10]==filename_U[:-10]:
U=np.load(filename_U)
V=np.load(filename_V)
data = io.loadmat(self.data_path+'/'+filename_V[43:78]+'.mat')
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
X=subtract_spont(spont,resp)
#print(X.shape)
if self.model=='SparsePCA':
X=stats.zscore(X,axis=0)
if self.model=='NMF':
X-=X.min(axis=0)
residuals_squared=np.mean((X-([email protected]).T)*(X-([email protected]).T))
U_V=([email protected]).T
#plt.hist(U_V, range=(-10,10))
#plt.show()
#plt.hist(X.flatten(),range=(-10,10))
plt.plot(range(0,100),X[:100,0])
plt.plot(range(0,100),U_V[:100,0])
plt.legend(('X','U_V'))
plt.show()
print(residuals_squared)
print('corrcoef',np.corrcoef(X[:,0],U_V[:,0]))
def NMF_regul_exps_fit(self):
self.model = 'NMF_regularization_experiments'
alphas = [0.01, 0.1, 1, 10, 100]
powers = [-2, -1, 0, 1, 2]
ind_dict = {0.01: 0, 0.1: 1, 1: 3, 10: 4, 100: 5}
for filename in self.mat_file_lst:
data = io.loadmat(self.data_path + filename)
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
X = subtract_spont(spont, resp)
X -= X.min(axis=0)
for alpha in alphas:
model = NMF(n_components=self.nr_of_components,
init='nndsvd',
random_state=7,
alpha=alpha,
l1_ratio=1.0)
start = time.time()
V = model.fit_transform(X)
end = time.time()
time_ = end - start
print(end - start)
U = model.components_
np.save(
self.save_path + filename + '_' + str(ind_dict[alpha]) +
'_U_NMF_reg_exps.npy', U)
np.save(
self.save_path + filename + '_' + str(ind_dict[alpha]) +
'_V_NMF_reg_exps.npy', V)
def variance_explained_across_neurons(self, U, V):
'''
From sklearn:
The coefficient R^2 is defined as (1 - u/v), where u is the residual sum of squares
((y_true - y_pred) ** 2).sum() and v is the total sum of squares
((y_true - y_true.mean()) ** 2).sum().
'''
#Fetch the original data and convert it into the same form as what goes into the
#matrix factorization model
data = io.loadmat(self.data_path + self.mouse_filename)
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
X = subtract_spont(spont, resp).T
X = zscore(X.T).T
u = []
v = []
approx = U @ V.T
for j in range(X.shape[0]):
u_j = ((X[j, :] - approx[j, :])**2).sum()
v_j = ((X[j, :] - np.mean(X[j, :]))**2).sum()
u.append(u_j)
v.append(v_j)
u = np.array(u)
v = np.array(v)
plt.plot(-np.divide(u, v) + 1)
plt.title('Variance explained across neurons')
plt.show()
print('Total variance explained, averaged over neurons is:',
(1 - np.mean(u) / np.mean(v)))
def knn(self):
if self.model=='SparsePCA':
model_string='*V_sPCA.npy'
if self.model=='EnsemblePursuit':
model_string='*_V_ep.npy'
if self.model=='NMF':
model_string='*_V_NMF.npy'
if self.model=='PCA':
model_string='*_V_pca.npy'
if self.model=='LDA':
model_string='*_V_lda.npy'
if self.model=='all':
#self.save_path=self.data_path
model_string='*.mat'
columns=['Experiment','accuracy']
acc_df=pd.DataFrame(columns=columns)
print(self.save_path)
for filename in glob.glob(os.path.join(self.save_path, model_string)):
if self.model=='all':
data = io.loadmat(filename)
resp = data['stim'][0]['resp'][0]
spont =data['stim'][0]['spont'][0]
X=subtract_spont(spont,resp)
V=stats.zscore(X)
else:
print(filename)
V=np.load(filename)
#if self.model='PCA':
print(V.shape)
#print(self.data_path+'/'+filename[43:78]+'.mat')
istim_path=filename[len(self.save_path):len(self.save_path)+len(self.mat_file_lst[0])]
print(istim_path)
istim=sio.loadmat(self.data_path+istim_path)['stim']['istim'][0][0].astype(np.int32)
istim -= 1 # get out of MATLAB convention
istim = istim[:,0]
nimg = istim.max() # these are blank stims (exclude them)
V = V[istim<nimg, :]
istim = istim[istim<nimg]
x_train,x_test,y_train,y_test=test_train_split(V,istim)
acc=evaluate_model_torch(x_train,x_test)
acc_df=acc_df.append({'Experiment':filename[len(self.save_path):],'accuracy':acc},ignore_index=True)
pd.options.display.max_colwidth = 300
print(acc_df)
print(acc_df.describe())
return acc_df
def fit_model(self):
data = io.loadmat(self.data_path + self.mouse_filename)
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
if self.model == 'EnsemblePursuit_numpy':
X = subtract_spont(spont, resp).T
options_dict = {'seed_neuron_av_nr': 100, 'min_assembly_size': 8}
ep_np = EnsemblePursuitNumpyFast(n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_np.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
if self.save == True:
np.save(self.save_path + filename + '_V_ep_numpy.npy', V)
np.save(self.save_path + filename + '_U_ep_numpy.npy', U)
return U, V
def sort_by_variance_explained(self):
X_path='/home/maria/Documents/EnsemblePursuit/models/natimg2800_M170717_MP034_2017-09-11.mat'
if self.model=='EnsemblePursuit':
U_path='/home/maria/Documents/EnsemblePursuit/SAND9/experiments/natimg2800_M170717_MP034_2017-09-11.mat_U_ep.npy'
V_path='/home/maria/Documents/EnsemblePursuit/SAND9/experiments/natimg2800_M170717_MP034_2017-09-11.mat_V_ep.npy'
if self.model=='SparsePCA':
U_path='/home/maria/Documents/EnsemblePursuit/NIPS/natimg2800_M170717_MP034_2017-09-11.mat_0.9_150_U_sPCA.npy'
V_path='/home/maria/Documents/EnsemblePursuit/NIPS/natimg2800_M170717_MP034_2017-09-11.mat_0.9_150_V_sPCA.npy'
if self.model=='NMF':
V_path='/home/maria/Documents/EnsemblePursuit/NIPS/natimg2800_M170717_MP034_2017-09-11.mat_0_150_V_NMF.npy'
U_path='/home/maria/Documents/EnsemblePursuit/NIPS/natimg2800_M170717_MP034_2017-09-11.mat_0_150_U_NMF.npy'
if self.model=='LDA':
V_path='/home/maria/Documents/EnsemblePursuit/NIPS/natimg2800_M170717_MP034_2017-09-11.mat_150_V_lda.npy'
U_path='/home/maria/Documents/EnsemblePursuit/NIPS/natimg2800_M170717_MP034_2017-09-11.mat_150_U_lda.npy'
data = io.loadmat(X_path)
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
X=subtract_spont(spont,resp)
if self.model=='EnsemblePursuit':
X=stats.zscore(X,axis=0)
if self.model=='SparsePCA':
X=stats.zscore(X,axis=0)
if self.model=='NMF':
X-=X.min(axis=0)
if self.model=='LDA':
X-=X.min(axis=0)
V=np.load(V_path)
U=np.load(U_path).T
print(V.shape)
print(U.shape)
var_lst=[]
for j in range(0,150):
var=np.mean((X-(U[j,:].reshape(10103,1)@V[:,j].reshape(1,5880)).T)*(X-(U[j,:].reshape(10103,1)@V[:,j].reshape(1,5880)).T))
#var=(np.sum(U[:,j])**2)#*np.var(V[:,j])
#print(U[:,j])
var_lst.append(var)
sortd=np.argsort(var_lst)
return var_lst, sortd
def fit_model(self):
for filename in self.mat_file_lst:
print(filename)
data = io.loadmat(self.data_path + filename)
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
if self.model == 'EnsemblePursuit_numpy':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_np = EnsemblePursuitNumpy(n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_np.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_numpy.npy', V)
np.save(self.save_path + filename + '_U_ep_numpy.npy', U)
np.save(self.save_path + filename + '_timing_ep_numpy.npy', tm)
if self.model == 'EnsemblePursuit_pytorch':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitPyTorch(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_pytorch.npy', V)
np.save(self.save_path + filename + '_U_ep_pytorch.npy', U)
np.save(self.save_path + filename + '_timing_ep_pytorch.npy',
tm)
if self.model == 'EnsemblePursuit_adaptive':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitPyTorch(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_adaptive.npy', V)
np.save(self.save_path + filename + '_U_ep_adaptive.npy', U)
if self.model == 'SparsePCA':
X = subtract_spont(spont, resp)
X = zscore(X)
sPCA = SparsePCA(n_components=self.nr_of_components,
random_state=7,
max_iter=100,
n_jobs=-1,
verbose=1)
start = time.time()
model = sPCA.fit(X)
end = time.time()
elapsed_time = end - start
U = model.components_
V = sPCA.transform(X)
np.save(self.save_path + filename + '_U_sPCA.npy', U)
np.save(self.save_path + filename + '_V_sPCA.npy', V)
np.save(self.save_path + filename + '_time_sPCA.npy',
elapsed_time)
if self.model == 'ICA':
X = subtract_spont(spont, resp)
X = zscore(X)
ICA = FastICA(n_components=self.nr_of_components,
random_state=7)
start = time.time()
V = ICA.fit_transform(X)
end = time.time()
elapsed_time = end - start
U = ICA.components_
np.save(self.save_path + filename + '_U_ICA.npy', U)
np.save(self.save_path + filename + '_V_ICA.npy', V)
np.save(self.save_path + filename + '_time_ICA.npy',
elapsed_time)
def fit_model(self):
for filename in self.mat_file_lst:
print(filename)
data = io.loadmat(self.data_path + filename)
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
if self.model == 'EnsemblePursuit_numpy':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_np = EnsemblePursuitNumpy(n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_np.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_numpy.npy', V)
np.save(self.save_path + filename + '_U_ep_numpy.npy', U)
np.save(self.save_path + filename + '_timing_ep_numpy.npy', tm)
if self.model == 'EnsemblePursuit_pytorch':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitPyTorch(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_pytorch.npy', V)
np.save(self.save_path + filename + '_U_ep_pytorch.npy', U)
np.save(self.save_path + filename + '_timing_ep_pytorch.npy',
tm)
if self.model == 'EnsemblePursuit_numpy_fast':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_np = EnsemblePursuitNumpyFast(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_np.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_numpy_fast.npy', V)
np.save(self.save_path + filename + '_U_ep_numpy_fast.npy', U)
np.save(
self.save_path + filename + '_timing_ep_numpy_fast.npy',
tm)
if self.model == 'EnsemblePursuit_pytorch_fast':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitPyTorchFast(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_pytorch_fast.npy',
V)
np.save(self.save_path + filename + '_U_ep_pytorch_fast.npy',
U)
np.save(
self.save_path + filename + '_timing_ep_pytorch_fast.npy',
tm)
if self.model == 'EnsemblePursuit_reg':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitRegressionInit(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_pytorch_reg.npy', V)
np.save(self.save_path + filename + '_U_ep_pytorch_reg.npy', U)
np.save(
self.save_path + filename + '_timing_ep_pytorch_reg.npy',
tm)
if self.model == 'EnsemblePursuit_var':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitVarianceInit(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_pytorch_var.npy', V)
np.save(self.save_path + filename + '_U_ep_pytorch_var.npy', U)
np.save(
self.save_path + filename + '_timing_ep_pytorch_var.npy',
tm)
if self.model == 'EnsemblePursuit_thresh':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitThresholdInit(
n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_pytorch_thresh.npy',
V)
np.save(self.save_path + filename + '_U_ep_pytorch_thresh.npy',
U)
np.save(
self.save_path + filename +
'_timing_ep_pytorch_thresh.npy', tm)
if self.model == 'EnsemblePursuit_tfidf':
X = subtract_spont(spont, resp).T
options_dict = {
'seed_neuron_av_nr': 100,
'min_assembly_size': 8
}
ep_pt = EnsemblePursuitTFIDF(n_ensembles=self.nr_of_components,
lambd=self.lambd_,
options_dict=options_dict)
start = time.time()
U, V = ep_pt.fit_transform(X)
end = time.time()
tm = end - start
print('Time', tm)
np.save(self.save_path + filename + '_V_ep_pytorch_tfidf.npy',
V)
np.save(self.save_path + filename + '_U_ep_pytorch_tfidf.npy',
U)
np.save(
self.save_path + filename + '_timing_ep_pytorch_tfidf.npy',
tm)
def fit_model(self):
#for filename in glob.glob(os.path.join(self.data_path, '*MP034_2017-09-11.mat')):
#for filename in glob.glob(os.path.join(self.data_path, '*.mat')):
#self.mat_file_lst=[#'natimg2800_M170717_MP034_2017-09-11.mat',#'natimg2800_M160825_MP027_2016-12-14.mat',
#'natimg2800_M161025_MP030_2017-05-29.mat'#,
#'natimg2800_M170604_MP031_2017-06-28.mat','natimg2800_M170714_MP032_2017-09-14.mat','natimg2800_M170714_MP032_2017-08-07.mat','natimg2800_M170717_MP033_2017-08-20.mat'
#]
for filename in self.mat_file_lst:
print(filename)
data = io.loadmat(self.data_path+filename)
resp = data['stim'][0]['resp'][0]
spont =data['stim'][0]['spont'][0]
if self.model=='EnsemblePursuit':
X=subtract_spont(spont,resp)
for lambd_ in self.lambdas:
neuron_init_dict={'method':'top_k_corr','parameters':{'n_av_neurons':100,'n_of_neurons':1,'min_assembly_size':8}}
print(str(neuron_init_dict['parameters']['n_av_neurons']))
ep=EnsemblePursuitPyTorch()
start=time.time()
U_V,nr_of_neurons,U,V, cost_lst,seed_neurons,ensemble_neuron_lst=ep.fit_transform(X,lambd_,self.nr_of_components,neuron_init_dict)
end=time.time()
tm=end-start
print('Time', tm)
#np.save(self.save_path+filename[45:85]+'_n_av_n_'+str(neuron_init_dict['parameters']['n_av_neurons'])+'_'+str(lambd_)+'_'+str(self.nr_of_components)+'_V_ep.npy',V)
np.save(self.save_path+filename+'_V_ep.npy',V)
np.save(self.save_path+filename+'_U_ep.npy',U)
np.save(self.save_path+filename+'_ensemble_pursuit_lst_ep.npy',ensemble_neuron_lst)
np.save(self.save_path+filename+'_seed_neurons_ep.npy', seed_neurons)
np.save(self.save_path+filename+'_time_ep.npy', tm)
#np.save(self.save_path+filename[45:85]+'_n_av_n_'+str(neuron_init_dict['parameters']['n_av_neurons'])+'_'+str(lambd_)+'_'+str(self.nr_of_components)+'_U_ep.npy',U)
#np.save(self.save_path+filename[45:85]+'_n_av_n_'+str(neuron_init_dict['parameters']['n_av_neurons'])+'_'+str(lambd_)+'_'+str(self.nr_of_components)+'_cost_ep.npy',cost_lst)
#np.save(self.save_path+filename[45:85]+'_n_av_n_'+str(neuron_init_dict['parameters']['n_av_neurons'])+'_'+str(lambd_)+'_'+str(self.nr_of_components)+'_n_neurons_ep.npy',nr_of_neurons)
#np.save(self.save_path+filename[45:85]+'_n_av_n_'+str(neuron_init_dict['parameters']['n_av_neurons'])+'_'+str(lambd_)+'_'+str(self.nr_of_components)+'_ensemble_neuron_lst.npy',ensemble_neuron_lst)
#np.save(self.save_path+filename[45:85]+'_n_av_n_'+str(neuron_init_dict['parameters']['n_av_neurons'])+'_'+str(lambd_)+'_'+str(self.nr_of_components)+'_time_ep.npy',tm)
#np.save(self.save_path+filename[45:85]+'_n_av_n_'+str(neuron_init_dict['parameters']['n_av_neurons'])+'_'+str(lambd_)+'_'+str(self.nr_of_components)+'_seed_neurons.npy',seed_neurons)
if self.model=='SparsePCA':
X=subtract_spont(spont,resp)
X=stats.zscore(X)
print(X.shape)
for alpha in self.alphas:
sPCA=SparsePCA(n_components=self.nr_of_components,alpha=alpha,random_state=7, max_iter=100, n_jobs=-1,verbose=1)
#X=X.T
start=time.time()
model=sPCA.fit(X)
end=time.time()
elapsed_time=end-start
U=model.components_
print('U',U.shape)
#errors=model.error_
V=sPCA.transform(X)
print('V',V.shape)
np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_U_sPCA.npy',U)
np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_V_sPCA.npy',V)
np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_time_sPCA.npy',elapsed_time)
#np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_errors_sPCA.npy',errors)
if self.model=='NMF':
X=subtract_spont(spont,resp)
X-=X.min(axis=0)
for alpha in self.alphas:
model = NMF(n_components=self.nr_of_components, init='nndsvd', random_state=7,alpha=alpha)
start=time.time()
V=model.fit_transform(X)
end=time.time()
time_=end-start
print(end-start)
U=model.components_
np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_U_NMF.npy',U)
np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_V_NMF.npy',V)
np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_time_NMF.npy',time_)
if self.model=='PCA':
X=subtract_spont(spont,resp)
X=stats.zscore(X)
pca=PCA(n_components=self.nr_of_components)
start=time.time()
V=pca.fit_transform(X)
U=pca.components_
end=time.time()
elapsed_time=end-start
#V=pca.components_
var=pca.explained_variance_
np.save(self.save_path+filename[45:85]+'_'+str(self.nr_of_components)+'_V_pca.npy',V)
np.save(self.save_path+filename[45:85]+'_'+str(self.nr_of_components)+'_time_pca.npy',elapsed_time)
np.save(self.save_path+filename[45:85]+'_'+str(self.nr_of_components)+'_var_pca.npy',var)
np.save(self.save_path+filename[45:85]+'_'+str(self.nr_of_components)+'_U_pca.npy',U)
if self.model=='LDA':
X=resp
X-=X.min(axis=0)
lda=LatentDirichletAllocation(n_components=self.nr_of_components, random_state=7)
start=time.time()
V=lda.fit_transform(X)
end=time.time()
elapsed_time=end-start
print('time',elapsed_time)
U=lda.components_
np.save(self.save_path+filename[45:85]+'_'+str(self.nr_of_components)+'_V_lda.npy',V)
np.save(self.save_path+filename[45:85]+'_'+str(self.nr_of_components)+'_U_lda.npy',U)
np.save(self.save_path+filename[45:85]+'_'+str(self.nr_of_components)+'_time_lda.npy',elapsed_time)
def fit_model(self):
#for filename in glob.glob(os.path.join(self.data_path, '*MP034_2017-09-11.mat')):
for filename in glob.glob(os.path.join(self.data_path, '*.mat')):
print(filename[45:85])
data = io.loadmat(filename)
resp = data['stim'][0]['resp'][0]
spont = data['stim'][0]['spont'][0]
if self.model == 'EnsemblePursuit':
X = subtract_spont(spont, resp)
for lambd_ in self.lambdas:
neuron_init_dict = {
'method': 'top_k_corr',
'parameters': {
'n_av_neurons': 100,
'n_of_neurons': 1,
'min_assembly_size': 8
}
}
print(str(neuron_init_dict['parameters']['n_av_neurons']))
ep = EnsemblePursuitPyTorch()
start = time.time()
U_V, nr_of_neurons, U, V, cost_lst, seed_neurons, ensemble_neuron_lst = ep.fit_transform(
X, lambd_, self.nr_of_components, neuron_init_dict)
end = time.time()
tm = end - start
print('Time', tm)
np.save(
self.save_path + filename[45:85] + '_n_av_n_' +
str(neuron_init_dict['parameters']['n_av_neurons']) +
'_' + str(lambd_) + '_' + str(self.nr_of_components) +
'_V_ep.npy', V)
np.save(
self.save_path + filename[45:85] + '_n_av_n_' +
str(neuron_init_dict['parameters']['n_av_neurons']) +
'_' + str(lambd_) + '_' + str(self.nr_of_components) +
'_U_ep.npy', U)
np.save(
self.save_path + filename[45:85] + '_n_av_n_' +
str(neuron_init_dict['parameters']['n_av_neurons']) +
'_' + str(lambd_) + '_' + str(self.nr_of_components) +
'_cost_ep.npy', cost_lst)
np.save(
self.save_path + filename[45:85] + '_n_av_n_' +
str(neuron_init_dict['parameters']['n_av_neurons']) +
'_' + str(lambd_) + '_' + str(self.nr_of_components) +
'_n_neurons_ep.npy', nr_of_neurons)
np.save(
self.save_path + filename[45:85] + '_n_av_n_' +
str(neuron_init_dict['parameters']['n_av_neurons']) +
'_' + str(lambd_) + '_' + str(self.nr_of_components) +
'_ensemble_neuron_lst.npy', ensemble_neuron_lst)
np.save(
self.save_path + filename[45:85] + '_n_av_n_' +
str(neuron_init_dict['parameters']['n_av_neurons']) +
'_' + str(lambd_) + '_' + str(self.nr_of_components) +
'_time_ep.npy', tm)
np.save(
self.save_path + filename[45:85] + '_n_av_n_' +
str(neuron_init_dict['parameters']['n_av_neurons']) +
'_' + str(lambd_) + '_' + str(self.nr_of_components) +
'_seed_neurons.npy', seed_neurons)
if self.model == 'SparsePCA':
X = subtract_spont(spont, resp)
X = stats.zscore(X)
print(X.shape)
for alpha in self.alphas:
sPCA = SparsePCA(n_components=self.nr_of_components,
alpha=alpha,
random_state=7,
max_iter=100,
n_jobs=-1,
verbose=1)
#X=X.T
start = time.time()
model = sPCA.fit(X)
end = time.time()
elapsed_time = end - start
U = model.components_
print('U', U.shape)
#errors=model.error_
V = sPCA.transform(X)
print('V', V.shape)
np.save(
self.save_path + filename[45:85] + '_' + str(alpha) +
'_' + str(self.nr_of_components) + '_U_sPCA.npy', U)
np.save(
self.save_path + filename[45:85] + '_' + str(alpha) +
'_' + str(self.nr_of_components) + '_V_sPCA.npy', V)
np.save(
self.save_path + filename[45:85] + '_' + str(alpha) +
'_' + str(self.nr_of_components) + '_time_sPCA.npy',
elapsed_time)
#np.save(self.save_path+filename[45:85]+'_'+str(alpha)+'_'+str(self.nr_of_components)+'_errors_sPCA.npy',errors)
if self.model == 'NMF':
X = subtract_spont(spont, resp)
X -= X.min(axis=0)
for alpha in self.alphas:
model = NMF(n_components=self.nr_of_components,
init='nndsvd',
random_state=7,
alpha=alpha)
V = model.fit_transform(X)
U = model.components_
np.save(
self.save_path + filename[45:85] + '_' + str(alpha) +
'_' + str(self.nr_of_components) + '_U_NMF.npy', U)
np.save(
self.save_path + filename[45:85] + '_' + str(alpha) +
'_' + str(self.nr_of_components) + '_V_NMF.npy', V)