def test_sda(sda, test_names, base, window_size=1, algo='viterbi'): test_reader = ICHISeqDataReader(test_names) test_set_x, test_set_y = test_reader.read_all() n_test_patients = len(test_names) for test_patient in xrange(n_test_patients): #get data divided on sequences with respect to labels test_set_x, test_set_y = test_reader.read_next_doc() test_x_array = test_set_x.get_value() n_test_times = test_x_array.shape[0] - window_size + 1 test_visible_after_sda = numpy.array([sda.get_da_output( test_x_array[time: time+window_size]).ravel() for time in xrange(n_test_times)]).ravel() new_test_visible, new_test_hidden = change_data_for_one_patient( hiddens_patient=test_set_y.eval(), visibles_patient=test_visible_after_sda, window_size=sda.da_layers_output_size, base_for_labels=base ) patient_error = get_error_on_patient( model=sda.hmmLayer, visible_set=new_test_visible, hidden_set=new_test_hidden, algo=algo ) print(patient_error, ' error for patient ' + str(test_patient)) gc.collect()
def train_SdA(datasets, train_names, output_folder, base_folder, window_size, corruption_levels, pretraining_epochs, base, pretrain_lr=0): """ Demonstrates how to train and test a stochastic denoising autoencoder. This is demonstrated on ICHI. :type pretraining_epochs: int :param pretraining_epochs: number of epoch to do pretraining :type n_iter: int :param n_iter: maximal number of iterations ot run the optimizer :type datasets: array :param datasets: [train_set, valid_set, test_set] :type output_folder: string :param output_folder: folder for costand error graphics with results """ # split the datasets (train_set_x, train_set_y) = datasets[0] (valid_set_x, valid_set_y) = datasets[1] (test_set_x, test_set_y) = datasets[2] # compute number of examples given in training set n_in = window_size*3 # number of input units n_out = 7 # number of output units # numpy random generator # start-snippet-3 numpy_rng = numpy.random.RandomState(89677) print '... building the model' # construct the stacked denoising autoencoder class sda = SdA( numpy_rng=numpy_rng, n_ins=n_in, hidden_layers_sizes=[window_size*2, window_size], n_outs=n_out ) # end-snippet-3 start-snippet-4 ######################### # PRETRAINING THE MODEL # ######################### start_time = timeit.default_timer() pretrained_sda = pretrain_sda_sgd(sda=sda, train_names=train_names, window_size=window_size, pretraining_epochs=pretraining_epochs, pretrain_lr=pretrain_lr, corruption_levels=corruption_levels) ''' pretrained_sda = pretrain_sda_cg(sda=sda, train_set_x=train_set_x, window_size=window_size, pretraining_epochs=pretraining_epochs, corruption_levels=corruption_levels) ''' end_time = timeit.default_timer() for i in xrange(sda.n_layers): print(i, 'i pretrained') visualize_pretraining(train_cost=pretrained_sda.dA_layers[i].train_cost_array, window_size=window_size, learning_rate=0, corruption_level=corruption_levels[i], n_hidden=sda.dA_layers[i].n_hidden, da_layer=i, datasets_folder=output_folder, base_folder=base_folder) print >> sys.stderr, ('The pretraining code for file ' + os.path.split(__file__)[1] + ' ran for %.2fm' % ((end_time - start_time) / 60.)) # end-snippet-4 ######################## # FINETUNING THE MODEL # ######################## #create matrices for params of HMM layer train_data_names = ['p10a','p011','p013','p014','p020','p022','p040', 'p045','p048','p09b','p023','p035','p038', 'p09a','p033'] n_train_patients=len(train_data_names) n_visible=pow(base, sda.da_layers_output_size) n_hidden=n_out train_reader = ICHISeqDataReader(train_data_names) pi_values = numpy.zeros((n_hidden,)) a_values = numpy.zeros((n_hidden, n_hidden)) b_values = numpy.zeros((n_hidden, n_visible)) array_from_hidden = numpy.zeros((n_hidden,)) for train_patient in xrange(n_train_patients): #get data divided on sequences with respect to labels train_set_x, train_set_y = train_reader.read_next_doc() train_x_array = train_set_x.get_value() n_train_times = train_x_array.shape[0] - window_size + 1 train_visible_after_sda = numpy.array([sda.get_da_output( train_x_array[time: time+window_size]).ravel() for time in xrange(n_train_times)]).ravel() new_train_visible, new_train_hidden = change_data_for_one_patient( hiddens_patient=train_set_y.eval(), visibles_patient=train_visible_after_sda, window_size=sda.da_layers_output_size, base_for_labels=base ) pi_values, a_values, b_values, array_from_hidden = update_params_on_patient( pi_values=pi_values, a_values=a_values, b_values=b_values, array_from_hidden=array_from_hidden, hiddens_patient=new_train_hidden, visibles_patient=new_train_visible, n_hidden=n_hidden ) gc.collect() pi_values, a_values, b_values = finish_training( pi_values=pi_values, a_values=a_values, b_values=b_values, array_from_hidden=array_from_hidden, n_hidden=n_hidden, n_patients=n_train_patients ) hmm_model = hmm.MultinomialHMM( n_components=n_hidden, startprob=pi_values, transmat=a_values ) hmm_model.n_symbols=n_visible hmm_model.emissionprob_=b_values gc.collect() print('MultinomialHMM created') sda.set_hmm_layer( hmm_model=hmm_model ) return sda