def init_dnc(self):
if not os.path.isfile("Data/sequence_width.txt"):
self.read_data() # To set the sequence width
else:
self.sequence_width = pickle.load(open("Data/sequence_width.txt",'rb')) # To set the sequence width
self.machine = DNC_Module(self.sequence_width, self.sequence_width, self.controller_size, self.controller_layers, self.num_read_heads, self.num_write_heads, self.memory_N, self.memory_M)
self.machine.cuda() # Enabling GPU
class task_babi():
def __init__(self):
self.name = "bAbI_task_GPU"
self.controller_size = 128
self.controller_layers = 1
self.num_read_heads = 1
self.num_write_heads = 1
self.sequence_width = -1 # Length of each word
self.sequence_len = -1 # Word length of each story
self.memory_N = 128
self.memory_M = 128
self.num_batches = -1
self.num_epoch = 1
self.batch_size = 10
self.adam_lr = 1e-4
self.adam_betas = (0.9, 0.999)
self.adam_eps = 1e-8
self.machine = None
self.loss = None
self.optimizer = None
self.ind_to_word = None
self.data_dir = "Data/bAbI/en-10k" # Data directory
def get_task_name(self):
return self.name
def init_dnc(self):
if not os.path.isfile("Data/sequence_width.txt"):
self.read_data() # To set the sequence width
else:
self.sequence_width = pickle.load(open("Data/sequence_width.txt",'rb')) # To set the sequence width
self.machine = DNC_Module(self.sequence_width, self.sequence_width, self.controller_size, self.controller_layers, self.num_read_heads, self.num_write_heads, self.memory_N, self.memory_M)
self.machine.cuda() # Enabling GPU
def init_loss(self):
self.loss = nn.CrossEntropyLoss(reduction = 'none').cuda() # Cross Entropy Loss -> Sigmoid Activation + Cross Entropy Loss
def init_optimizer(self):
self.optimizer = optim.Adam(self.machine.parameters(), lr = self.adam_lr, betas = self.adam_betas, eps = self.adam_eps)
def calc_loss(self, Y_pred, Y, mask):
# Y: dim -> (sequence_len x batch_size)
# Y_pred: dim -> (sequence_len x batch_size x sequence_width)
# mask: dim -> (sequence_len x batch_size)
loss_vec = torch.empty(Y.shape, dtype=torch.float32).cuda()
for i in range(Y_pred.shape[0]):
loss_vec[i, :] = self.loss(Y_pred[i], Y[i])
return torch.sum(loss_vec*mask)/torch.sum(mask)
def calc_cost(self, Y_pred, Y, mask): # Calculates % Cost
# Y: dim -> (sequence_len x batch_size)
# Y_pred: dim -> (sequence_len x batch_size x sequence_width)
# mask: dim -> (sequence_len x batch_size)
Y_pred, Y, mask = Y_pred.cpu(), Y.cpu(), mask.cpu()
return torch.sum(((F.softmax(Y_pred, dim=2).max(2)[1]) == Y).type(torch.long)*mask.type(torch.long)).item(), torch.sum(mask).item()
def print_word(self, word_vec): # Prints the word from word vector
# "word_vect" dimension : (1 x sequence_width)
idx = np.argmax(word_vec, axis = 1)
word = self.ind_to_word[idx]
print(word + "\n")
def to_one_hot(self, story): # Converts a vector into one hot form
out_token = []
I = np.eye(self.sequence_width)
for idx in story:
out_token.append(I[int(idx)])
if len(out_token)>self.sequence_len:
self.sequence_len = len(out_token)
return out_token
def padding_labels(self, stories): # Making separate funcion to pad labels because, labels will not be in one-hot vector form due to the requirements of PyTorch Cross Entropy Loss Function
padded_stories = []
for story in stories:
if len(story)<self.sequence_len:
li = [1 for i in range(self.sequence_len - len(story))]
story.extend(li)
padded_stories.append(np.asarray(story, dtype = np.long))
return padded_stories
def padding(self, stories): # Pads padding element to make all the stories of equal length
padded_stories = []
for story in stories:
if len(story)<self.sequence_len:
li = self.to_one_hot(np.ones(self.sequence_len - len(story)))
story.extend(li)
padded_stories.append(np.asarray(story, dtype = np.float32))
return padded_stories
def flatten_if_list(self, l): # Merges all the list within a list with the outer list elements. Example: [you', '?', ['-']] -> ['you', '?', '-']
newl = []
for elem in l:
if isinstance(elem, list): # Checking whether the element is 'list' or not
newl.extend(elem) # input.extend(li_2) method appends all the elements of 'li_2' list into 'input' list
else:
newl.append(elem)
return newl
def structure_data(self, x, y): # Prepares data for bAbI task
# Preparing Data
keys = list(x.keys())
random.shuffle(keys) # Randomly Shuffling the key list
inp_story = []
out_story = []
for key in keys:
inp_story.extend(x[key])
out_story.extend(y[key])
story_idx = list(range(0, len(inp_story)))
random.shuffle(story_idx)
# Here I am breaking stories into different files because A single list can't store all the stories
num_batch = int(len(story_idx)/self.batch_size)
self.num_batches = num_batch
counter = 1
# Out Data
x_out = []
y_out = []
mask_inp = [] # Will be used for making the mask to make "non amswer" output words from DNC irrelevent
for i in story_idx:
if num_batch <= 0:
break
x_out.append(self.to_one_hot(inp_story[i]))
y_out.append(out_story[i])
mask_inp.append(inp_story[i]) # Appending input story For making the mask
if counter % self.batch_size == 0:
# Resetting Counter
counter = 0
# Padding
x_out_array = torch.tensor(np.asarray(self.padding(x_out)).swapaxes(0, 1)) # Converting from (batch_size x story_length x word size) to (story_length x batch_size x word size)
y_out_array = torch.tensor(np.asarray(self.padding_labels(y_out)).swapaxes(0, 1), dtype=torch.long) # Converting from (batch_size x story_length x word size) to (story_length x batch_size x word size)
m_inp_array = torch.tensor(np.asarray(self.padding_labels(mask_inp)).swapaxes(0, 1), dtype=torch.long) # Converting from (batch_size x story_length x word size) to (story_length x batch_size x word size)
# Renewing List and updating batch number
x_out = []
y_out = []
mask_inp = []
num_batch -= 1
yield (self.num_batches - num_batch), x_out_array, y_out_array, (m_inp_array == 0).float()
counter += 1
def read_data(self): # Reading and Cleaning data from the file
storage_file = "Data/cleaned_data_bAbI_" + self.data_dir.split('/')[2] +".txt"
if not os.path.isfile(storage_file):
output_symbol = "-" # Indicates an expectation of output to the DNC
newstory_delimiter = " NEWSTORY " # To separate stories
pad_symbol = "*" # Padding symbol
file_paths = []
word_to_ind = {output_symbol: 0, pad_symbol: 1} # Dictionary to store indices of all the word in the bAbI dataset. Predefined symbols already stored
all_input_stories = {}
all_output_stories = {}
# Making list of all the files in the data directory
for f in os.listdir(self.data_dir):
f_path = os.path.join(self.data_dir, f)
if os.path.isfile(f_path):
file_paths.append(f_path)
# Processing the text files
for file_path in file_paths:
# print(file_path)
# Cleaning the text
file = open(file_path).read().lower()
file = re.sub("\n1 ", newstory_delimiter, file) # Adding a delimeter between two stories
file = re.sub(r"\d+|\n|\t", " ", file) # Removing all numbers, newlines and tabs
file = re.sub("([?.])", r" \1", file) # Adding a space before all punctuations
stories = file.split(newstory_delimiter) # Splitting whole text into the stories
input_stories = [] # Stores the stories into the index form, where each word has unique index
output_stories = []
# Tokenizing the text
for i, story in enumerate(stories):
input_tokens = story.split() # Input stories are meant for inputting to the DNC
output_tokens = story.split() # Output stories works as labels
for i, token in enumerate(input_tokens): # This when encountered "?", replaces answers with "-" sign in the input for the SNC
if token == "?":
output_tokens[i + 1] = output_tokens[i + 1].split(",")
input_tokens[i + 1] = [output_symbol for _ in range(len(output_tokens[i + 1]))]
input_tokens = self.flatten_if_list(input_tokens)
output_tokens = self.flatten_if_list(output_tokens)
# Calculating index of all the words
for token in output_tokens:
if token not in word_to_ind:
word_to_ind[token] = len(word_to_ind)
input_stories.append([word_to_ind[elem] for elem in input_tokens]) # Storing each story into a list of word indices form
output_stories.append([word_to_ind[elem] for elem in output_tokens])
all_input_stories[file_path] = input_stories # Storing all the stories for each file
all_output_stories[file_path] = output_stories
# Dumping all the cleaned data into a file
pickle.dump((word_to_ind, all_input_stories, all_output_stories),open(storage_file,'wb'))
pickle.dump(len(word_to_ind),open("Data/sequence_width.txt",'wb'))
self.sequence_width = len(word_to_ind) # Vector length of one hot vector
else:
word_to_ind, all_input_stories, all_output_stories = pickle.load(open(storage_file,'rb'))
return word_to_ind, all_input_stories, all_output_stories
def get_training_data(self): # Data directory
word_to_ind, all_input_stories, all_output_stories = self.read_data()
self.ind_to_word = {ind: word for word, ind in word_to_ind.items()} # Reverse Index to Word dictionary to show final output
# Separating Test and Train Data
x_train_stories = {k: v for k, v in all_input_stories.items() if k[-9:] == "train.txt"}
y_train_stories = {k: v for k, v in all_output_stories.items() if k[-9:] == "train.txt"}
return self.structure_data(x_train_stories, y_train_stories) # dim: x_train, y_train -> A list of (sequence_len x sequence_width) sized stories
def get_test_data(self): # Sample data for Testing # Data directory
_, all_input_stories, all_output_stories = self.read_data()
# Separating Test and Train Data
x_test_stories = {k: v for k, v in all_input_stories.items() if k[-8:] == "test.txt"}
y_test_stories = {k: v for k, v in all_output_stories.items() if k[-8:] == "test.txt"}
return self.structure_data(x_test_stories, y_test_stories) # dim: x_test, y_test -> A list of (sequence_len x sequence_width) sized stories
def test_model(self): # Testing the model
correct = 0
total = 0
print("\n")
for batch_num, X, Y, mask in self.get_test_data():
self.machine.initialization(self.batch_size) # Initializing states
Y_out = torch.zeros(X.shape)
# Feeding the DNC network all the data first and then predicting output
# by giving zero vector as input and previous read states and hidden vector
# and thus training vector this way to give outputs matching the labels
X, Y, mask = X.cuda(), Y.cuda(), mask.cuda() # Sending to CUDA device
embeddings = self.machine.backward_prediction(X) # Creating embeddings from data for backward calculation
temp_size = X.shape[0]
for i in range(temp_size):
Y_out[i, :, :], _ = self.machine(X[i], embeddings[temp_size-i-1])
corr, tot = self.calc_cost(Y_out, Y, mask)
correct += corr
total += tot
print("Test Example " + str(batch_num) + "/" + str(self.num_batches) + " processed, Batch Accuracy: " + str((float(corr)/float(tot))*100.0) + " %")
accuracy = (float(correct)/float(total))*100.0
print("\nOverall Accuracy: " + str(accuracy) + " %")
return accuracy # in %
def clip_grads(self): # Clipping gradients for stability
"""Gradient clipping to the range [10, 10]."""
parameters = list(filter(lambda p: p.grad is not None, self.machine.parameters()))
for p in parameters:
p.grad.data.clamp_(-10, 10)
def train_model(self):
# Here, the model is optimized using Cross Entropy Loss, however, it is evaluated using Number of error bits in predction and actual labels (cost)
loss_list = []
seq_length = []
save_batch = 500
last_batch = 0
for j in range(self.num_epoch):
for batch_num, X, Y, mask in self.get_training_data():
self.optimizer.zero_grad() # Making old gradients zero before calculating the fresh ones
self.machine.initialization(self.batch_size) # Initializing states
Y_out = torch.zeros(X.shape).cuda()
# Feeding the DNC network all the data first and then predicting output
# by giving zero vector as input and previous read states and hidden vector
# and thus training vector this way to give outputs matching the labels
X, Y, mask = X.cuda(), Y.cuda(), mask.cuda() # Sending to CUDA device
embeddings = self.machine.backward_prediction(X) # Creating embeddings from data for backward calculation
temp_size = X.shape[0]
for i in range(temp_size):
Y_out[i, :, :], _ = self.machine(X[i], embeddings[temp_size-i-1]) # Passing Embeddings from backwards
loss = self.calc_loss(Y_out, Y, mask)
loss.backward()
self.clip_grads()
self.optimizer.step()
loss_list += [loss.item()]
seq_length += [Y.shape[0]]
if (batch_num % save_batch) == 0:
self.save_model(j, batch_num)
last_batch = batch_num
print("Epoch: " + str(j) + "/" + str(self.num_epoch) + ", Batch: " + str(batch_num) + "/" + str(self.num_batches) + ", Loss: " + str(loss.item()))
self.save_model(j, last_batch)
def save_model(self, curr_epoch, curr_batch):
# Here 'start_epoch' and 'start_batch' params below are the 'epoch' and 'batch' number from which to start training after next model loading
# Note: It is recommended to start from the 'start_epoch' and not 'start_epoch' + 'start_batch', because batches are formed randomly
if not os.path.exists("Saved_Models/" + self.name):
os.mkdir("Saved_Models/" + self.name)
state_dic = {'task_name': self.name, 'start_epoch': curr_epoch + 1, 'start_batch': curr_batch + 1, 'state_dict': self.machine.state_dict(), 'optimizer_dic' : self.optimizer.state_dict()}
filename = "Saved_Models/" + self.name + "/" + self.name + "_" + str(curr_epoch) + "_" + str(curr_batch) + "_saved_model.pth.tar"
torch.save(state_dic, filename)
def load_model(self, option, epoch, batch):
path = "Saved_Models/" + self.name + "/" + self.name + "_" + str(epoch) + "_" + str(batch) + "_saved_model.pth.tar"
if option == 1: # Loading for training
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.optimizer.load_state_dict(checkpoint['optimizer_dic'])
else: # Loading for testing
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.machine.eval()
def init_dnc(self):
self.machine = DNC_Module(self.num_inputs, self.num_outputs,
self.controller_size, self.controller_layers,
self.num_read_heads, self.num_write_heads,
self.memory_N, self.memory_M)
self.machine.cuda() # Enabling GPU
class task_NER():
def __init__(self):
self.name = "NER_task_bio"
# Controller Params
self.controller_size = 128
self.controller_layers = 1
# Head Params
self.num_read_heads = 1
self.num_write_heads = 1
# Processor Params
self.num_inputs = 200 # Length of Embeddings
self.num_outputs = 7 # Class size
# Memory Params
self.memory_N = 128
self.memory_M = 128
# Training Params
self.num_batches = -1
self.save_batch = 5 # Saving model after every save_batch number of batches
self.batch_size = 10
self.num_epoch = 4
# Optimizer Params
self.adam_lr = 1e-4
self.adam_betas = (0.9, 0.999)
self.adam_eps = 1e-8
# Handles
self.machine = None
self.loss = None
self.optimizer = None
# Class Dictionaries
self.labelDict = None # Label Dictionary - Labels to Index
self.reverseDict = None # Inverse Label Dictionary - Index to Labels
# File Paths
self.concept_path_train = "/home/entity_extraction/Projects/data/train_data/concept" # Path to train concept files
self.text_path_train = "/home/entity_extraction/Projects/data/train_data/txt" # Path to train text summaries
self.concept_path_test = "/home/entity_extraction/Projects/data/test_data/concept" # Path to test concept files
self.text_path_test = "/home/entity_extraction/Projects/data/test_data/txt" # Path to test text summaries
self.save_path = "/home/entity_extraction/Projects/data/cleaned_files" # Save path
self.embed_dic_path = "/home/entity_extraction/Projects/data/embeddings/bio_embedding_dictionary.dat" # Word2Vec embeddings Dictionary path
self.random_vec = "/home/entity_extraction/Projects/data/embeddings/random_vec.dat" # Path to random embedding (Used to create new vectors)
self.model_path = "/home/entity_extraction/Projects/code/saved_models/" # Stores Trained Models
# Miscellaneous
self.padding_symbol = np.full((self.num_inputs),
0.01) # Padding symbol embedding
def get_task_name(self):
return self.name
def init_dnc(self):
self.machine = DNC_Module(self.num_inputs, self.num_outputs,
self.controller_size, self.controller_layers,
self.num_read_heads, self.num_write_heads,
self.memory_N, self.memory_M)
self.machine.cuda() # Enabling GPU
def init_loss(self):
self.loss = nn.CrossEntropyLoss(reduction='mean').cuda(
) # Cross Entropy Loss -> Softmax Activation + Cross Entropy Loss
def init_optimizer(self):
self.optimizer = optim.Adam(self.machine.parameters(),
lr=self.adam_lr,
betas=self.adam_betas,
eps=self.adam_eps)
def calc_loss(self, Y_pred, Y):
# Y: dim -> (sequence_len x batch_size)
# Y_pred: dim -> (sequence_len x batch_size x num_outputs)
loss_vec = torch.empty(Y.shape[0], dtype=torch.float32).cuda()
for i in range(Y_pred.shape[0]):
loss_vec[i] = self.loss(Y_pred[i], Y[i])
return torch.mean(loss_vec)
def calc_cost(self, Y_pred, Y): # Calculates % Cost
# Y: dim -> (sequence_len x batch_size)
# Y_pred: dim -> (sequence_len x batch_size x sequence_width)
'''
Note:
1). For considering an prediction to be True Positive, prediction must match completely with labels entity (not partially). Else it is False Negative.
2). For considering a prediction to be False Positive, it must be full entity (BIII) and not completely match the label entity.
'''
# Stores correct class labels for each entity type
class_bag = {}
class_bag['problem'] = 0 # Total labels
class_bag['test'] = 0 # Total labels
class_bag['treatment'] = 0 # Total labels
class_bag['problem_cor'] = 0 # Correctly classified labels
class_bag['test_cor'] = 0 # Correctly classified labels
class_bag['treatment_cor'] = 0 # Correctly classified labels
class_bag['problem_fp'] = 0 # False positive classified labels
class_bag['test_fp'] = 0 # False positive classified labels
class_bag['treatment_fp'] = 0 # False positive classified labels
pred_class = np.transpose(F.softmax(
Y_pred, dim=2).max(2)[1].numpy()).reshape(
-1) # Predicted class. dim -> (sequence_len*batch_size)
Y = np.transpose(Y.numpy()).reshape(
-1) # Converting to NumPy Array and linearizing
cor_pred = (Y == pred_class).astype(
np.int
) # Comparing Prediction and Labels to find correct predictions
class_bag['word_pred_acc'] = np.divide(
np.sum(cor_pred), cor_pred.size
) * 100.0 # % Accuracy of Correctly Predicted Words (Not Entities)
# Getting the beginning index of all the entities
beg_idx = list(np.where(np.in1d(Y, [0, 2, 4]))[0])
# Getting the end index of all the entities (All the Index previous of 'Other'/'Begin' and not equal to 'Other')
target = np.where(np.in1d(Y, [0, 2, 4, 6]))[0] - 1
if target[0] == -1:
target = target[1:]
end_idx = list(target[np.where(Y[target] != 6)[0]])
if Y[-1] != 6:
end_idx.append(Y.size - 1)
assert len(beg_idx) == len(end_idx) # Sanity Check
class_bag['total'] = len(beg_idx) # Total number of Entities
# Counting Entities
sum_vec = np.cumsum(
cor_pred) # Calculates cumulative summation of predicted vector
for b, e in zip(beg_idx, end_idx):
idx_range = e - b + 1 # Entity span
sum_range = sum_vec[e] - sum_vec[
b] + 1 # Count of entity elements which are predicted correctly
lab = self.reverseDict[Y[b]][
2:] # Extracting entity type (Problem, Test or Treatment)
class_bag[
lab] = class_bag[lab] + 1 # Getting count of each entities
if sum_range == idx_range: # +1 if entity is classified correctly
class_bag[lab + '_cor'] = class_bag[lab + '_cor'] + 1
# Detecting False Positives
# Getting the beginning index of all the entities in Predicted Results
beg_idx_p = list(np.where(np.in1d(pred_class, [0, 2, 4]))[0])
for b in beg_idx_p:
if cor_pred[b] == 0:
lab = self.reverseDict[pred_class[b]][2:]
class_bag[lab + '_fp'] = class_bag[lab + '_fp'] + 1
return class_bag
def print_word(self,
token_class): # Prints the Class name from Class number
word = self.reverseDict[token_class]
print(word + "\n")
def clip_grads(self): # Clipping gradients for stability
"""Gradient clipping to the range [10, 10]."""
parameters = list(
filter(lambda p: p.grad is not None, self.machine.parameters()))
for p in parameters:
p.grad.data.clamp_(-10, 10)
def initialize_labels(
self
): # Initializing label dictionaries for Labels->IDX and IDX->Labels
self.labelDict = {} # Label Dictionary - Labels to Index
self.reverseDict = {} # Inverse Label Dictionary - Index to Labels
# Using BIEOS labelling scheme
self.labelDict['b-problem'] = 0 # Problem - Beginning
self.labelDict['i-problem'] = 1 # Problem - Inside
self.labelDict['b-test'] = 2 # Test - Beginning
self.labelDict['i-test'] = 3 # Test - Inside
self.labelDict['b-treatment'] = 4 # Treatment - Beginning
self.labelDict['i-treatment'] = 5 # Treatment - Inside
self.labelDict['o'] = 6 # Outside Token
# Making Inverse Label Dictionary
for k in self.labelDict.keys():
self.reverseDict[self.labelDict[k]] = k
# Saving the diictionaries into a file
self.save_data([self.labelDict, self.reverseDict],
os.path.join(self.save_path, "label_dicts_bio.dat"))
def parse_concepts(
self, file_path
): # Parses the concept file to extract concepts and labels
conceptList = [] # Stores all the Concept in the File
f = open(file_path) # Opening and reading a concept file
content = f.readlines() # Reading all the lines in the concept file
f.close() # Closing the concept file
for x in content: # Reading each line in the concept file
dic = {}
# Cleaning and extracting the entities, labels and their positions in the corresponding medical summaries
x = re.sub('\n', ' ', x)
x = re.sub(r'\ +', ' ', x)
x = x.strip().split('||')
temp1, label = x[0].split(' '), x[1].split('=')[1][1:-1]
temp1[0] = temp1[0][3:]
temp1[-3] = temp1[-3][0:-1]
entity = temp1[0:-2]
if len(entity) >= 1:
lab = ['i'] * len(entity)
lab[0] = 'b'
lab = [l + "-" + label for l in lab]
else:
print("Data in File: " + file_path +
", not in expected format..")
exit()
noLab = [self.labelDict[l] for l in lab]
sLine, sCol = int(temp1[-2].split(":")[0]), int(
temp1[-2].split(":")[1])
eLine, eCol = int(temp1[-1].split(":")[0]), int(
temp1[-1].split(":")[1])
'''
# Printing the information
print("------------------------------------------------------------")
print("Entity: " + str(entity))
print("Entity Label: " + label)
print("Labels - BIO form: " + str(lab))
print("Labels Index: " + str(noLab))
print("Start Line: " + str(sLine) + ", Start Column: " + str(sCol))
print("End Line: " + str(eLine) + ", End Column: " + str(eCol))
print("------------------------------------------------------------")
'''
# Storing the information as a dictionary
dic['entity'] = entity # Entity Name (In the form of list of words)
dic['label'] = label # Common Label
dic['BIO_labels'] = lab # List of BIO labels for each word
dic['label_index'] = noLab # Labels in the index form
dic['start_line'] = sLine # Start line of the concept in the corresponding text summaries
dic['start_word_no'] = sCol # Starting word number of the concept in the corresponding start line
dic['end_line'] = eLine # End line of the concept in the corresponding text summaries
dic['end_word_no'] = eCol # Ending word number of the concept in the corresponding end line
# Appending the concept dictionary to the list
conceptList.append(dic)
return conceptList # Returning the all the concepts in the current file in the form of dictionary list
def parse_summary(self, file_path): # Parses the Text summaries
file_lines = [] # Stores the lins of files in the list form
tags = [
] # Stores corresponding labels for each word in the file (Default label: 'o' [Outside])
default_label = len(
self.labelDict
) - 1 # default_label is "7" (Corresponding to 'Other' entity)
# counter = 1 # Temporary variable used during print
f = open(file_path) # Opening and reading a concept file
content = f.readlines() # Reading all the lines in the concept file
f.close()
for x in content:
x = re.sub('\n', ' ', x)
x = re.sub(r'\ +', ' ', x)
file_lines.append(
x.strip().split(" ")
) # Spliting the lines into word list and Appending each of them in the file list
tags.append(
[default_label] * len(file_lines[-1])
) # Assigining the default_label to all the words in a line
'''
# Printing the information
print("------------------------------------------------------------")
print("File Lines No: " + str(counter))
print(file_lines[-1])
print("\nCorresponding labels:")
print(tags[-1])
print("------------------------------------------------------------")
counter += 1
'''
assert len(tags[-1]) == len(
file_lines[-1]
), "Line length is not matching labels length..." # Sanity Check
return file_lines, tags
def modify_labels(
self, conceptList, tags
): # Modifies the default labels of each word in text files with the true labels from the concept files
for e in conceptList: # Iterating over all the dictionary elements in the Concept List
if e['start_line'] == e[
'end_line']: # Checking whether concept is spanning over a single line or multiple line in the summary
tags[e['start_line'] - 1][e['start_word_no']:e['end_word_no'] +
1] = e['label_index'][:]
else:
start = e['start_line']
end = e['end_line']
beg = 0
for i in range(
start, end + 1
): # Distributing labels over multiple lines in the text summaries
if i == start:
tags[i - 1][e['start_word_no']:] = e['label_index'][
0:len(tags[i - 1]) - e['start_word_no']]
beg = len(tags[i - 1]) - e['start_word_no']
elif i == end:
tags[i - 1][0:e['end_word_no'] +
1] = e['label_index'][beg:]
else:
tags[i - 1][:] = e['label_index'][beg:beg +
len(tags[i - 1])]
beg = beg + len(tags[i - 1])
return tags
def print_data(self, file, file_lines, tags): # Prints the given data
counter = 1
print("\n************ Printing details of the file: " + file +
" ************\n")
for x in file_lines:
print(
"------------------------------------------------------------")
print("File Lines No: " + str(counter))
print(x)
print("\nCorresponding labels:")
print([self.reverseDict[i] for i in tags[counter - 1]])
print("\nCorresponding Label Indices:")
print(tags[counter - 1])
print(
"------------------------------------------------------------")
counter += 1
def save_data(self, obj_list,
s_path): # Saves the file into the binary file using Pickle
# Note: The 'obj_list' must be a list and none other than that
pickle.dump(tuple(obj_list), open(s_path, 'wb'))
def acquire_data(
self, task
): # Read all the concept files to get concepts and labels, proces them and save them
data = {
} # Dictionary to store all the data objects (conceptList, file_lines, tags) each indexed by file name
if task == 'train': # Determining the task type to assign the data path accordingly
t_path = self.text_path_train
c_path = self.concept_path_train
else:
t_path = self.text_path_test
c_path = self.concept_path_test
for f in os.listdir(t_path):
f1 = f.split('.')[0] + ".con"
if os.path.isfile(os.path.join(c_path, f1)):
conceptList = self.parse_concepts(
os.path.join(c_path, f1)
) # Parsing concepts and labels from the corresponding concept file
file_lines, tags = self.parse_summary(
os.path.join(t_path, f)
) # Parses the document summaries to get the written notes
tags = self.modify_labels(
conceptList, tags
) # Modifies he default labels to each word with the true labels from the concept files
data[f1] = [conceptList, file_lines,
tags] # Storing each object in dictionary
# self.print_data(f, file_lines, tags) # Printing the details
return data
def structure_data(
self, data_dict): # Structures the data in proper trainable form
final_line_list = [
] # Stores words of all the files in separate sub-lists
final_tag_list = [
] # Stores tags of all the files in separate sub-lists
for k in data_dict.keys(
): # Extracting data from each pre-processed file in dictionary
file_lines = data_dict[k][1] # Extracting story
tags = data_dict[k][2] # Extracting corresponding labels
# Creating empty lists
temp1 = []
temp2 = []
# Merging all the lines in file into a single list. Same for corresponding labels
for i in range(len(file_lines)):
temp1.extend(file_lines[i])
temp2.extend(tags[i])
assert len(temp1) == len(
temp2
), "Word length not matching Label length for story in " + str(
k) # Sanity Check
final_line_list.append(temp1)
final_tag_list.append(temp2)
assert len(final_line_list) == len(
final_tag_list
), "Number of stories not matching number of labels list" # Sanity Check
return final_line_list, final_tag_list
def padding(
self, line_list, tag_list
): # Pads stories with padding symbol to make them of same length
diff = 0
max_len = 0
outside_class = len(
self.labelDict) - 1 # Classifying padding symbol as "outside" term
# Calculating Max Summary Length
for i in range(len(line_list)):
if len(line_list[i]) > max_len:
max_len = len(line_list[i])
for i in range(len(line_list)):
diff = max_len - len(line_list[i])
line_list[i].extend([self.padding_symbol] * diff)
tag_list[i].extend([outside_class] * diff)
assert (len(line_list[i]) == max_len) and (len(
line_list[i]) == len(
tag_list[i])), "Padding unsuccessful" # Sanity check
return np.asarray(line_list), np.asarray(
tag_list
) # Making NumPy array of size (batch_size x story_length x word size) and (batch_size x story_length x 1) respectively
def embed_input(self, line_list): # Converts words to vector embeddings
final_list = [] # Stores embedded words
summary = None # Temp variable
word = None # Temp variable
temp = None # Temp variable
embed_dic = pickle.load(
open(self.embed_dic_path,
'rb')) # Loading word2vec dictionary using Pickle
r_embed = pickle.load(open(self.random_vec,
'rb')) # Loading Random embedding
for i in range(len(line_list)): # Iterating over all the summaries
summary = line_list[i]
final_list.append([]) # Reserving space for curent summary
for j in range(len(summary)):
word = summary[j].lower()
if word in embed_dic: # Checking for existence of word in dictionary
final_list[-1].append(embed_dic[word])
else:
temp = r_embed[:] # Copying the values of the list
random.shuffle(
temp
) # Randomly shuffling the word embedding to make it unique
temp = np.asarray(
temp, dtype=np.float32) # Converting to NumPy array
final_list[-1].append(temp)
return final_list
def prepare_data(self, task='train'): # Preparing all the data necessary
line_list, tag_list = None, None
'''
line_list is the list of rows, where each row is a list of all the words in a medical summary
Similar is the case for tag_list, except, it stores labels for each words
'''
if not os.path.exists(self.save_path):
os.mkdir(
self.save_path
) # Creating a new directory if it does not exist else reading previously saved data
if not os.path.exists(
os.path.join(self.save_path, "label_dicts_bio.dat")):
self.initialize_labels() # Initialize label to index dictionaries
else:
self.labelDict, self.reverseDict = pickle.load(
open(os.path.join(self.save_path, "label_dicts_bio.dat"),
'rb')) # Loading Label dictionaries
if not os.path.exists(
os.path.join(self.save_path,
"object_dict_bio_" + str(task) + ".dat")):
data_dict = self.acquire_data(task) # Read data from file
line_list, tag_list = self.structure_data(
data_dict) # Structures the data into proper form
line_list = self.embed_input(
line_list) # Embeds input data (words) into embeddings
self.save_data([line_list, tag_list],
os.path.join(
self.save_path,
"object_dict_bio_" + str(task) + ".dat"))
else:
line_list, tag_list = pickle.load(
open(
os.path.join(self.save_path,
"object_dict_bio_" + str(task) + ".dat"),
'rb')) # Loading Data dictionary
return line_list, tag_list
def get_data(self, task='train'):
line_list, tag_list = self.prepare_data(task)
# Shuffling stories
story_idx = list(range(0, len(line_list)))
random.shuffle(story_idx)
num_batch = int(len(story_idx) / self.batch_size)
self.num_batches = num_batch
# Out Data
x_out = []
y_out = []
counter = 1
for i in story_idx:
if num_batch <= 0:
break
x_out.append(line_list[i])
y_out.append(tag_list[i])
if counter % self.batch_size == 0:
counter = 0
# Padding and converting labels to one hot vectors
x_out_pad, y_out_pad = self.padding(x_out, y_out)
x_out_array = torch.tensor(
x_out_pad.swapaxes(0, 1), dtype=torch.float32
) # Converting from (batch_size x story_length x word size) to (story_length x batch_size x word size)
y_out_array = torch.tensor(
y_out_pad.swapaxes(0, 1), dtype=torch.long
) # Converting from (batch_size x story_length x 1) to (story_length x batch_size x 1)
x_out = []
y_out = []
num_batch -= 1
yield (self.num_batches - num_batch), x_out_array, y_out_array
counter += 1
def train_model(self):
# Here, the model is optimized using Cross Entropy Loss.
loss_list = []
seq_length = []
last_batch = 0
# self.load_model(1, 99, 13) # Loading Pre-Trained model to train further
for j in range(self.num_epoch):
for batch_num, X, Y in self.get_data(task='train'):
self.optimizer.zero_grad(
) # Making old gradients zero before calculating the fresh ones
self.machine.initialization(
self.batch_size) # Initializing states
Y_out = torch.empty(
(X.shape[0], X.shape[1], self.num_outputs),
dtype=torch.float32).cuda(
) # dim: (seq_len x batch_size x num_output)
# Feeding the DNC network all the data first and then predicting output
X, Y = X.cuda(), Y.cuda()
embeddings = self.machine.backward_prediction(
X
) # Creating embeddings from data for backward calculation
temp_size = X.shape[0]
for i in range(temp_size):
Y_out[i, :, :], _ = self.machine(
X[i],
embeddings[temp_size - i -
1]) # Passing Embeddings from backwards
loss = self.calc_loss(Y_out, Y)
loss.backward()
self.clip_grads()
self.optimizer.step()
class_bag = self.calc_cost(Y_out.cpu(), Y.cpu())
corr = class_bag['problem_cor'] + class_bag[
'test_cor'] + class_bag['treatment_cor']
tot = class_bag['total']
loss_list += [loss.item()]
seq_length += [Y.shape[0]]
if (batch_num % self.save_batch) == 0:
self.save_model(j, batch_num)
last_batch = batch_num
print("Epoch: " + str(j) + "/" + str(self.num_epoch) + ", Batch: " + str(batch_num) + "/" + str(self.num_batches) + ", Loss: {0:.2f}, ".format(loss.item()) + \
"Batch Accuracy (Entity Prediction): {0:.2f} %, ".format((float(corr)/float(tot))*100.0) + "Batch Accuracy (Word Prediction): {0:.2f} %".format(class_bag['word_pred_acc']))
self.save_model(j, last_batch)
def test_model(self): # Testing the model
correct = 0
total = 0
result_dict = {}
result_dict['total_problem'] = 0 # Total labels in data
result_dict['total_test'] = 0 # Total labels in data
result_dict['total_treatment'] = 0 # Total labels in data
result_dict['correct_problem'] = 0 # Correctly classified labels
result_dict['correct_test'] = 0 # Correctly classified labels
result_dict['correct_treatment'] = 0 # Correctly classified labels
result_dict['false_positive_problem'] = 0 # False Positive labels
result_dict['false_positive_test'] = 0 # False Positive labels
result_dict['false_positive_treatment'] = 0 # False Positive labels
print("\n")
for batch_num, X, Y in self.get_data(task='test'):
self.machine.initialization(self.batch_size) # Initializing states
Y_out = torch.empty((X.shape[0], X.shape[1], self.num_outputs),
dtype=torch.float32).cuda(
) # dim: (seq_len x batch_size x num_output)
# Feeding the DNC network all the data first and then predicting output
# by giving zero vector as input and previous read states and hidden vector
# and thus training vector this way to give outputs matching the labels
X = X.cuda()
embeddings = self.machine.backward_prediction(
X) # Creating embeddings from data for backward calculation
temp_size = X.shape[0]
for i in range(temp_size):
Y_out[i, :, :], _ = self.machine(X[i],
embeddings[temp_size - i - 1])
class_bag = self.calc_cost(Y_out.cpu(), Y)
corr = class_bag['problem_cor'] + class_bag[
'test_cor'] + class_bag['treatment_cor']
tot = class_bag['total']
result_dict['total_problem'] = result_dict[
'total_problem'] + class_bag['problem']
result_dict[
'total_test'] = result_dict['total_test'] + class_bag['test']
result_dict['total_treatment'] = result_dict[
'total_treatment'] + class_bag['treatment']
result_dict['correct_problem'] = result_dict[
'correct_problem'] + class_bag['problem_cor']
result_dict['correct_test'] = result_dict[
'correct_test'] + class_bag['test_cor']
result_dict['correct_treatment'] = result_dict[
'correct_treatment'] + class_bag['treatment_cor']
result_dict['false_positive_problem'] = result_dict[
'false_positive_problem'] + class_bag['problem_fp']
result_dict['false_positive_test'] = result_dict[
'false_positive_test'] + class_bag['test_fp']
result_dict['false_positive_treatment'] = result_dict[
'false_positive_treatment'] + class_bag['treatment_fp']
correct += corr
total += tot
print("Test Example " + str(batch_num) + "/" +
str(self.num_batches) +
" processed, Batch Accuracy: {0:.2f} %, ".format(
(float(corr) / float(tot)) * 100.0) +
"Batch Accuracy (Word Prediction): {0:.2f} %".format(
class_bag['word_pred_acc']))
result_dict['accuracy'] = (float(correct) / float(total)) * 100.0
result_dict = self.calc_metrics(result_dict)
print("\nOverall Entity Prediction Accuracy: {0:.2f} %".format(
result_dict['accuracy']))
return result_dict
def calc_metrics(self, result_dict): # Calculates Certain Metrices
precision_p = float(result_dict['correct_problem']) / float(
result_dict['correct_problem'] +
result_dict['false_positive_problem']) # Problem Precision
recall_p = float(result_dict['correct_problem']) / float(
result_dict['total_problem']) # Problem Recall
precision_ts = float(result_dict['correct_test']) / float(
result_dict['correct_test'] +
result_dict['false_positive_test']) # Test Precision
recall_ts = float(result_dict['correct_test']) / float(
result_dict['total_test']) # Test Recall
precision_tr = float(result_dict['correct_treatment']) / float(
result_dict['correct_treatment'] +
result_dict['false_positive_treatment']) # Treatment Precision
recall_tr = float(result_dict['correct_treatment']) / float(
result_dict['total_treatment']) # Treatment Recall
f_score_p = 2 * precision_p * recall_p / (precision_p + recall_p
) # Problem F1 Score
f_score_ts = 2 * precision_ts * recall_ts / (precision_ts + recall_ts
) # Test F1 Score
f_score_tr = 2 * precision_tr * recall_tr / (precision_tr + recall_tr
) # Treatment F1 Score
result_dict['problem_precision'] = precision_p
result_dict['problem_recall'] = recall_p
result_dict['problem_f1'] = f_score_p
result_dict['test_precision'] = precision_ts
result_dict['test_recall'] = recall_ts
result_dict['test_f1'] = f_score_ts
result_dict['treatment_precision'] = precision_tr
result_dict['treatment_recall'] = recall_tr
result_dict['treatment_f1'] = f_score_tr
result_dict['macro_average_f1'] = (f_score_p + f_score_ts + f_score_tr
) / 3.0 # Macro Average F1 Score
# Micro Average F1 Score
correct_sum = result_dict['correct_problem'] + result_dict[
'correct_test'] + result_dict['correct_treatment']
fp_sum = result_dict['false_positive_problem'] + result_dict[
'false_positive_test'] + result_dict['false_positive_treatment']
total_sum = result_dict['total_problem'] + result_dict[
'total_test'] + result_dict['total_treatment']
precision_avg = float(correct_sum) / float(correct_sum + fp_sum)
recall_avg = float(correct_sum) / float(total_sum)
result_dict['micro_average_f1'] = 2 * precision_avg * recall_avg / (
precision_avg + recall_avg)
return result_dict
def save_model(self, curr_epoch, curr_batch):
# Here 'start_epoch' and 'start_batch' params below are the 'epoch' and 'batch' number from which to start training after next model loading
# Note: It is recommended to start from the 'start_epoch' and not 'start_epoch' + 'start_batch', because batches are formed randomly
if not os.path.exists(os.path.join(self.model_path, self.name)):
os.mkdir(os.path.join(self.model_path, self.name))
state_dic = {
'task_name': self.name,
'start_epoch': curr_epoch + 1,
'start_batch': curr_batch + 1,
'state_dict': self.machine.state_dict(),
'optimizer_dic': self.optimizer.state_dict()
}
filename = self.model_path + self.name + "/" + self.name + "_" + str(
curr_epoch) + "_" + str(curr_batch) + "_saved_model.pth.tar"
torch.save(state_dic, filename)
def load_model(self, option, epoch, batch):
path = self.model_path + self.name + "/" + self.name + "_" + str(
epoch) + "_" + str(batch) + "_saved_model.pth.tar"
if option == 1: # Loading for training
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.optimizer.load_state_dict(checkpoint['optimizer_dic'])
else: # Loading for testing
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.machine.eval()
def init_dnc(self):
self.machine = DNC_Module(self.sequence_width + 1, self.sequence_width, self.controller_size, self.controller_layers, self.num_read_heads, self.num_write_heads, self.memory_N, self.memory_M)
self.machine.cuda()
class task_copy():
def __init__(self):
self.name = "copy_task_GPU"
self.controller_size = 100
self.controller_layers = 1
self.num_read_heads = 2
self.num_write_heads = 1
self.sequence_width = 8
self.sequence_min_len = 5
self.sequence_max_len = 20 # Default: 20
self.memory_N = 128
self.memory_M = 20
self.num_batches = 10000
self.batch_size = 1
self.rmsprop_lr = 1e-4
self.rmsprop_momentum = 0.9
self.rmsprop_alpha = 0.95
self.machine = None
self.loss = None
self.optimizer = None
def get_task_name(self):
return self.name
def _data_maker(self, num_batches, batch_size, seq_width, min_len, max_len): # Generates data for copy task
# The input data vector will be of size (num_data_rows x batch_size x num_data_columns)
#
# 1 1 1 0 1 | 1 1 0 1 0 | 1 1 1 0 1 | 1 0 1 1 1
# 0 0 1 0 1 | 0 1 0 1 1 | 0 1 0 0 1 | 0 0 1 1 0
# 0 1 1 0 1 | 1 1 0 0 0 | 1 0 1 0 1 | 0 0 1 1 0
#
# Above is the example of data. num_data_rows = 3, num_data_columns = 5, batch_size = 4
#
# At a time we will give each row strip to the NTM for prediction as shown below. Therefore input size for one interaction will be (batch_size x num_data_columns)
#
# 1 1 1 0 1 | 1 1 0 1 0 | 1 1 1 0 1 | 1 0 1 1 1
for batch_num in range(num_batches+1):
# All batches have the same sequence length
seq_len = random.randint(min_len, max_len)
seq = np.random.binomial(1, 0.5, (seq_len, batch_size, seq_width)) # Here, seq_len = num_data_rows and seq_width = num_data_columns
seq = torch.from_numpy(seq)
# The input includes an additional channel used for the delimiter
inp = torch.zeros(seq_len + 1, batch_size, seq_width + 1)
inp[:seq_len, :, :seq_width] = seq
inp[seq_len, :, seq_width] = 1.0 # delimiter in our control channel
outp = seq.clone()
yield batch_num+1, inp.float(), outp.float()
def init_dnc(self):
self.machine = DNC_Module(self.sequence_width + 1, self.sequence_width, self.controller_size, self.controller_layers, self.num_read_heads, self.num_write_heads, self.memory_N, self.memory_M)
self.machine.cuda()
def init_loss(self):
self.loss = nn.BCEWithLogitsLoss().cuda() # Binary Cross Entropy Loss -> Sigmoid Activation + Cross Entropy Loss
def init_optimizer(self):
self.optimizer = optim.RMSprop(self.machine.parameters(), momentum = self.rmsprop_momentum, alpha = self.rmsprop_alpha, lr = self.rmsprop_lr)
def calc_loss(self, Y_pred, Y):
return self.loss(Y_pred, Y)
def get_sample_data(self): # Sample data for Testing
batch_size = 1
seq_len = random.randint(self.sequence_min_len, self.sequence_max_len)
seq = np.random.binomial(1, 0.5, (seq_len, batch_size, self.sequence_width)) # Here, seq_len = num_data_rows and seq_width = num_data_columns
seq = torch.from_numpy(seq)
# The input includes an additional channel used for the delimiter
inp = torch.zeros(seq_len + 1, batch_size, self.sequence_width + 1)
inp[:seq_len, :, :self.sequence_width] = seq
inp[seq_len, :, self.sequence_width] = 1.0 # delimiter in our control channel
outp = seq.clone()
return inp.float().cuda(), outp.float().cuda()
def calc_cost(self, Y_out, Y, batch_size):
y_out_binarized = torch.sigmoid(Y_out.cpu()).clone().data
y_out_binarized.apply_(lambda x: 0 if x < 0.5 else 1)
cost = torch.sum(torch.abs(y_out_binarized - Y.cpu().data))
return cost.item()/batch_size
def get_training_data(self):
return self._data_maker(self.num_batches, self.batch_size, self.sequence_width, self.sequence_min_len, self.sequence_max_len)
def test_model(self):
self.machine.initialization(self.batch_size) # Initializing states
X, Y = self.get_sample_data()
X, Y = X.cuda(), Y.cuda()
Y_out = torch.zeros(Y.shape).cuda()
# Feeding the DNC network all the data first and then predicting output
# by giving zero vector as input and previous read states and hidden vector
# and thus training vector this way to give outputs matching the labels
for i in range(X.shape[0]):
self.machine(X[i])
for i in range(Y.shape[0]):
Y_out[i, :, :], _ = self.machine()
loss = self.calc_loss(Y_out, Y)
cost = self.calc_cost(Y_out, Y, self.batch_size) # The cost is the number of error bits per sequence
print("\n\nTest Data - Loss: " + str(loss.cpu().item()) + ", Cost: " + str(cost))
X.squeeze(1)
Y.squeeze(1)
Y_out = torch.sigmoid(Y_out.cpu().squeeze(1))
print("\n------Input---------\n")
print(X.cpu().data)
print("\n------Labels---------\n")
print(Y.cpu().data)
print("\n------Output---------")
print((Y_out.data).apply_(lambda x: 0 if x < 0.5 else 1))
print("\n")
return loss.cpu().item(), cost, X.cpu(), Y.cpu(), Y_out
def clip_grads(self): # Clipping gradients for stability
"""Gradient clipping to the range [10, 10]."""
parameters = list(filter(lambda p: p.grad is not None, self.machine.parameters()))
for p in parameters:
p.grad.data.clamp_(-10, 10)
def train_model(self):
# Here, the model is optimized using BCE Loss, however, it is evaluated using Number of error bits in predction and actual labels (cost)
loss_list = []
cost_list = []
seq_length = []
if (self.num_batches/10) > 0:
model_save_interval = (self.num_batches/10)
else:
model_save_interval = 1
for batch_num, X, Y in self.get_training_data():
if batch_num>self.num_batches:
break
self.optimizer.zero_grad() # Making old gradients zero before calculating the fresh ones
self.machine.initialization(self.batch_size) # Initializing states
X, Y = X.cuda(), Y.cuda()
Y_out = torch.zeros(Y.shape).cuda()
# Feeding the NTM network all the data first and then predicting output
# by giving zero vector as input and previous read states and hidden vector
# and thus training vector this way to give outputs matching the labels
for i in range(X.shape[0]):
self.machine(X[i])
for i in range(Y.shape[0]):
Y_out[i, :, :], _ = self.machine()
loss = self.calc_loss(Y_out, Y)
loss.backward()
self.clip_grads()
self.optimizer.step()
# The cost is the number of error bits per sequence
cost = self.calc_cost(Y_out, Y, self.batch_size)
loss_list += [loss.item()]
cost_list += [cost]
seq_length += [Y.shape[0]]
if batch_num % model_save_interval == 0:
self.save_model(batch_num)
print("Batch: " + str(batch_num) + "/" + str(self.num_batches) + ", Loss: " + str(loss.item()) + ", Cost: " + str(cost) + ", Sequence Length: " + str(Y.shape[0]))
def save_model(self, curr_epoch):
if not os.path.exists("Saved_Models/" + self.name):
os.mkdir("Saved_Models/" + self.name)
state_dic = {'task_name': self.name, 'start_epoch': curr_epoch + 1, 'state_dict': self.machine.state_dict(), 'optimizer_dic' : self.optimizer.state_dict()}
filename = "Saved_Models/" + self.name + "/" + self.name + "_" + str(curr_epoch) + "_saved_model.pth.tar"
torch.save(state_dic, filename)
def load_model(self, option, epoch):
path = "Saved_Models/" + self.name + "/" + self.name + "_" + str(epoch) + "_saved_model.pth.tar"
if option == 1: # Loading for training
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.optimizer.load_state_dict(checkpoint['optimizer_dic'])
else: # Loading for testing
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.machine.eval()
class task_NER():
def __init__(self):
self.name = "NER_task_bieos"
# Controller Params
self.controller_size = 128
self.controller_layers = 1
# Head Params
self.num_read_heads = 2
self.num_write_heads = 2
# Processor Params
self.num_inputs = 200 # Length of Embeddings
self.num_outputs = 13 # Class size
# Memory Params
self.memory_N = 128
self.memory_M = 128
# Training Params
self.num_batches = -1
self.save_batch = 500 # Saving model after every save_batch number of batches
self.batch_size = 10
self.num_epoch = 1
# Optimizer Params
self.adam_lr = 1e-4
self.adam_betas = (0.9, 0.999)
self.adam_eps = 1e-8
# Handles
self.machine = None
self.loss = None
self.optimizer = None
# Class Dictionaries
self.labelDict = None # Label Dictionary - Labels to Index
self.reverseDict = None # Inverse Label Dictionary - Index to Labels
# File Paths
self.concept_path_train = "/media/ramkabir/PC Data/ASU Data/Semester 3/BMNLP/Projects/medical_data/train_data/concept" # Path to train concept files
self.text_path_train = "/media/ramkabir/PC Data/ASU Data/Semester 3/BMNLP/Projects/medical_data/train_data/txt" # Path to train text summaries
self.concept_path_test = "/media/ramkabir/PC Data/ASU Data/Semester 3/BMNLP/Projects/medical_data/test_data/concept" # Path to test concept files
self.text_path_test = "/media/ramkabir/PC Data/ASU Data/Semester 3/BMNLP/Projects/medical_data/test_data/txt" # Path to test text summaries
self.save_path = "/media/ramkabir/PC Data/ASU Data/Semester 3/BMNLP/Projects/medical_data/cleaned_files" # Save path
self.embed_dic_path = "/media/ramkabir/PC Data/ASU Data/Semester 3/BMNLP/Projects/medical_data/embeddings/bio_embedding_dictionary.dat" # Word2Vec embeddings Dictionary path
self.random_vec = "/media/ramkabir/PC Data/ASU Data/Semester 3/BMNLP/Projects/medical_data/embeddings/random_vec.dat" # Path to random embedding (Used to create new vectors)
# Miscellaneous
self.padding_symbol = np.full((self.num_inputs),
0.01) # Padding symbol embedding
def get_task_name(self):
return self.name
def init_dnc(self):
self.machine = DNC_Module(self.num_inputs, self.num_outputs,
self.controller_size, self.controller_layers,
self.num_read_heads, self.num_write_heads,
self.memory_N, self.memory_M)
self.machine.cuda()
def init_loss(self):
self.loss = nn.CrossEntropyLoss(reduction='mean').cuda(
) # Cross Entropy Loss -> Softmax Activation + Cross Entropy Loss
def init_optimizer(self):
self.optimizer = optim.Adam(self.machine.parameters(),
lr=self.adam_lr,
betas=self.adam_betas,
eps=self.adam_eps)
def calc_loss(self, Y_pred, Y):
# Y: dim -> (sequence_len x batch_size)
# Y_pred: dim -> (sequence_len x batch_size x num_outputs)
loss_vec = torch.empty(Y.shape[0], dtype=torch.float32).cuda()
for i in range(Y_pred.shape[0]):
loss_vec[i] = self.loss(Y_pred[i], Y[i])
return torch.mean(loss_vec)
def calc_cost(
self, Y_pred, Y
): # Calculates % Cost # Needs rework. Consider whole entity instead of words
# Y: dim -> (sequence_len x batch_size)
# Y_pred: dim -> (sequence_len x batch_size x sequence_width)
return torch.sum(((F.softmax(Y_pred, dim=2).max(2)[1]) == Y).type(
torch.long)).item(), Y.shape[0] * Y.shape[1]
def print_word(self,
token_class): # Prints the Class name from Class number
word = self.reverseDict[token_class]
print(word + "\n")
def clip_grads(self): # Clipping gradients for stability
"""Gradient clipping to the range [10, 10]."""
parameters = list(
filter(lambda p: p.grad is not None, self.machine.parameters()))
for p in parameters:
p.grad.data.clamp_(-10, 10)
def initialize_labels(
self
): # Initializing label dictionaries for Labels->IDX and IDX->Labels
self.labelDict = {} # Label Dictionary - Labels to Index
self.reverseDict = {} # Inverse Label Dictionary - Index to Labels
# Using BIEOS labelling scheme
self.labelDict['b-problem'] = 0 # Problem - Beginning
self.labelDict['i-problem'] = 1 # Problem - Inside
self.labelDict['e-problem'] = 2 # Problem - End
self.labelDict['s-problem'] = 3 # Problem - Single
self.labelDict['b-test'] = 4 # Test - Beginning
self.labelDict['i-test'] = 5 # Test - Inside
self.labelDict['e-test'] = 6 # Test - End
self.labelDict['s-test'] = 7 # Test - Single
self.labelDict['b-treatment'] = 8 # Treatment - Beginning
self.labelDict['i-treatment'] = 9 # Treatment - Inside
self.labelDict['e-treatment'] = 10 # Treatment - End
self.labelDict['s-treatment'] = 11 # Treatment - Single
self.labelDict['o'] = 12 # Outside Token
# Making Inverse Label Dictionary
for k in self.labelDict.keys():
self.reverseDict[self.labelDict[k]] = k
# Saving the diictionaries into a file
self.save_data([self.labelDict, self.reverseDict],
os.path.join(self.save_path, "label_dicts_bieos.dat"))
def parse_concepts(
self, file_path
): # Parses the concept file to extract concepts and labels
conceptList = [] # Stores all the Concept in the File
f = open(file_path) # Opening and reading a concept file
content = f.readlines() # Reading all the lines in the concept file
f.close() # Closing the concept file
for x in content: # Reading each line in the concept file
dic = {}
# Cleaning and extracting the entities, labels and their positions in the corresponding medical summaries
x = re.sub('\n', ' ', x)
x = re.sub(r'\ +', ' ', x)
x = x.strip().split('||')
temp1, label = x[0].split(' '), x[1].split('=')[1][1:-1]
temp1[0] = temp1[0][3:]
temp1[-3] = temp1[-3][0:-1]
entity = temp1[0:-2]
if len(entity) > 1:
lab = ['i'] * len(entity)
lab[0] = 'b'
lab[-1] = 'e'
lab = [l + "-" + label for l in lab]
elif len(entity) == 1:
lab = ["s" + "-" + label]
else:
print("Data in File: " + file_path +
", not in expected format..")
exit()
noLab = [self.labelDict[l] for l in lab]
sLine, sCol = int(temp1[-2].split(":")[0]), int(
temp1[-2].split(":")[1])
eLine, eCol = int(temp1[-1].split(":")[0]), int(
temp1[-1].split(":")[1])
'''
# Printing the information
print("------------------------------------------------------------")
print("Entity: " + str(entity))
print("Entity Label: " + label)
print("Labels - BIEOS form: " + str(lab))
print("Labels Index: " + str(noLab))
print("Start Line: " + str(sLine) + ", Start Column: " + str(sCol))
print("End Line: " + str(eLine) + ", End Column: " + str(eCol))
print("------------------------------------------------------------")
'''
# Storing the information as a dictionary
dic['entity'] = entity # Entity Name (In the form of list of words)
dic['label'] = label # Common Label
dic['BIEOS_labels'] = lab # List of BIEOS labels for each word
dic['label_index'] = noLab # Labels in the index form
dic['start_line'] = sLine # Start line of the concept in the corresponding text summaries
dic['start_word_no'] = sCol # Starting word number of the concept in the corresponding start line
dic['end_line'] = eLine # End line of the concept in the corresponding text summaries
dic['end_word_no'] = eCol # Ending word number of the concept in the corresponding end line
# Appending the concept dictionary to the list
conceptList.append(dic)
return conceptList # Returning the all the concepts in the current file in the form of dictionary list
def parse_summary(self, file_path): # Parses the Text summaries
file_lines = [] # Stores the lins of files in the list form
tags = [
] # Stores corresponding labels for each word in the file (Default label: 'o' [Outside])
default_label = len(
self.labelDict
) - 1 # default_label is "12" (Corresponding to 'Other' entity)
# counter = 1 # Temporary variable used during print
f = open(file_path) # Opening and reading a concept file
content = f.readlines() # Reading all the lines in the concept file
f.close()
for x in content:
x = re.sub('\n', ' ', x)
x = re.sub(r'\ +', ' ', x)
file_lines.append(
x.strip().split(" ")
) # Spliting the lines into word list and Appending each of them in the file list
tags.append(
[default_label] * len(file_lines[-1])
) # Assigining the default_label to all the words in a line
'''
# Printing the information
print("------------------------------------------------------------")
print("File Lines No: " + str(counter))
print(file_lines[-1])
print("\nCorresponding labels:")
print(tags[-1])
print("------------------------------------------------------------")
counter += 1
'''
assert len(tags[-1]) == len(
file_lines[-1]
), "Line length is not matching labels length..." # Sanity Check
return file_lines, tags
def modify_labels(
self, conceptList, tags
): # Modifies the default labels of each word in text files with the true labels from the concept files
for e in conceptList: # Iterating over all the dictionary elements in the Concept List
if e['start_line'] == e[
'end_line']: # Checking whether concept is spanning over a single line or multiple line in the summary
tags[e['start_line'] - 1][e['start_word_no']:e['end_word_no'] +
1] = e['label_index'][:]
else:
start = e['start_line']
end = e['end_line']
beg = 0
for i in range(
start, end + 1
): # Distributing labels over multiple lines in the text summaries
if i == start:
tags[i - 1][e['start_word_no']:] = e['label_index'][
0:len(tags[i - 1]) - e['start_word_no']]
beg = len(tags[i - 1]) - e['start_word_no']
elif i == end:
tags[i - 1][0:e['end_word_no'] +
1] = e['label_index'][beg:]
else:
tags[i - 1][:] = e['label_index'][beg:beg +
len(tags[i - 1])]
beg = beg + len(tags[i - 1])
return tags
def print_data(self, file, file_lines, tags): # Prints the given data
counter = 1
print("\n************ Printing details of the file: " + file +
" ************\n")
for x in file_lines:
print(
"------------------------------------------------------------")
print("File Lines No: " + str(counter))
print(x)
print("\nCorresponding labels:")
print([self.reverseDict[i] for i in tags[counter - 1]])
print("\nCorresponding Label Indices:")
print(tags[counter - 1])
print(
"------------------------------------------------------------")
counter += 1
def save_data(self, obj_list,
s_path): # Saves the file into the binary file using Pickle
# Note: The 'obj_list' must be a list and none other than that
pickle.dump(tuple(obj_list), open(s_path, 'wb'))
def acquire_data(
self, task
): # Read all the concept files to get concepts and labels, proces them and save them
data = {
} # Dictionary to store all the data objects (conceptList, file_lines, tags) each indexed by file name
if task == 'train': # Determining the task type to assign the data path accordingly
t_path = self.text_path_train
c_path = self.concept_path_train
else:
t_path = self.text_path_test
c_path = self.concept_path_test
for f in os.listdir(t_path):
f1 = f.split('.')[0] + ".con"
if os.path.isfile(os.path.join(c_path, f1)):
conceptList = self.parse_concepts(
os.path.join(c_path, f1)
) # Parsing concepts and labels from the corresponding concept file
file_lines, tags = self.parse_summary(
os.path.join(t_path, f)
) # Parses the document summaries to get the written notes
tags = self.modify_labels(
conceptList, tags
) # Modifies he default labels to each word with the true labels from the concept files
data[f1] = [conceptList, file_lines,
tags] # Storing each object in dictionary
# self.print_data(f, file_lines, tags) # Printing the details
return data
def structure_data(
self, data_dict): # Structures the data in proper trainable form
final_line_list = [
] # Stores words of all the files in separate sub-lists
final_tag_list = [
] # Stores tags of all the files in separate sub-lists
for k in data_dict.keys(
): # Extracting data from each pre-processed file in dictionary
file_lines = data_dict[k][1] # Extracting story
tags = data_dict[k][2] # Extracting corresponding labels
# Creating empty lists
temp1 = []
temp2 = []
# Merging all the lines in file into a single list. Same for corresponding labels
for i in range(len(file_lines)):
temp1.extend(file_lines[i])
temp2.extend(tags[i])
assert len(temp1) == len(
temp2
), "Word length not matching Label length for story in " + str(
k) # Sanity Check
final_line_list.append(temp1)
final_tag_list.append(temp2)
assert len(final_line_list) == len(
final_tag_list
), "Number of stories not matching number of labels list" # Sanity Check
return final_line_list, final_tag_list
def padding(
self, line_list, tag_list
): # Pads stories with padding symbol to make them of same length
diff = 0
max_len = 0
outside_class = len(
self.labelDict) - 1 # Classifying padding symbol as "outside" term
# Calculating Max Summary Length
for i in range(len(line_list)):
if len(line_list[i]) > max_len:
max_len = len(line_list[i])
for i in range(len(line_list)):
diff = max_len - len(line_list[i])
line_list[i].extend([self.padding_symbol] * diff)
tag_list[i].extend([outside_class] * diff)
assert (len(line_list[i]) == max_len) and (len(
line_list[i]) == len(
tag_list[i])), "Padding unsuccessful" # Sanity check
return np.asarray(line_list), np.asarray(
tag_list
) # Making NumPy array of size (batch_size x story_length x word size) and (batch_size x story_length x 1) respectively
def embed_input(self, line_list): # Converts words to vector embeddings
final_list = [] # Stores embedded words
summary = None # Temp variable
word = None # Temp variable
temp = None # Temp variable
embed_dic = pickle.load(
open(self.embed_dic_path,
'rb')) # Loading word2vec dictionary using Pickle
r_embed = pickle.load(open(self.random_vec,
'rb')) # Loading Random embedding
for i in range(len(line_list)): # Iterating over all the summaries
summary = line_list[i]
final_list.append([]) # Reserving space for curent summary
for j in range(len(summary)):
word = summary[j].lower()
if word in embed_dic: # Checking for existence of word in dictionary
final_list[-1].append(embed_dic[word])
else:
temp = r_embed[:] # Copying the values of the list
random.shuffle(
temp
) # Randomly shuffling the word embedding to make it unique
temp = np.asarray(
temp, dtype=np.float32) # Converting to NumPy array
final_list[-1].append(temp)
return final_list
def prepare_data(self, task='train'): # Preparing all the data necessary
line_list, tag_list = None, None
'''
line_list is the list of rows, where each row is a list of all the words in a medical summary
Similar is the case for tag_list, except, it stores labels for each words
'''
if not os.path.exists(self.save_path):
os.mkdir(
self.save_path
) # Creating a new directory if it does not exist else reading previously saved data
if not os.path.exists(
os.path.join(self.save_path, "label_dicts_bieos.dat")):
self.initialize_labels() # Initialize label to index dictionaries
else:
self.labelDict, self.reverseDict = pickle.load(
open(os.path.join(self.save_path, "label_dicts_bieos.dat"),
'rb')) # Loading Label dictionaries
if not os.path.exists(
os.path.join(self.save_path,
"object_dict_bieos_" + str(task) + ".dat")):
data_dict = self.acquire_data(task) # Read data from file
line_list, tag_list = self.structure_data(
data_dict) # Structures the data into proper form
line_list = self.embed_input(
line_list) # Embeds input data (words) into embeddings : Left
self.save_data([line_list, tag_list],
os.path.join(
self.save_path,
"object_dict_bieos_" + str(task) + ".dat"))
else:
line_list, tag_list = pickle.load(
open(
os.path.join(self.save_path,
"object_dict_bieos_" + str(task) + ".dat"),
'rb')) # Loading Data dictionary
return line_list, tag_list
def get_data(self, task='train'):
line_list, tag_list = self.prepare_data(task)
# Shuffling stories
story_idx = list(range(0, len(line_list)))
random.shuffle(story_idx)
num_batch = int(len(story_idx) / self.batch_size)
self.num_batches = num_batch
# Out Data
x_out = []
y_out = []
counter = 1
for i in story_idx:
if num_batch <= 0:
break
x_out.append(line_list[i])
y_out.append(tag_list[i])
if counter % self.batch_size == 0:
counter = 0
# Padding and converting labels to one hot vectors
x_out_pad, y_out_pad = self.padding(x_out, y_out)
x_out_array = torch.tensor(
x_out_pad.swapaxes(0, 1), dtype=torch.float32
) # Converting from (batch_size x story_length x word size) to (story_length x batch_size x word size)
y_out_array = torch.tensor(
y_out_pad.swapaxes(0, 1), dtype=torch.long
) # Converting from (batch_size x story_length x 1) to (story_length x batch_size x 1)
x_out = []
y_out = []
num_batch -= 1
yield (self.num_batches - num_batch), x_out_array, y_out_array
counter += 1
def train_model(self):
# Here, the model is optimized using Cross Entropy Loss, however, it is evaluated using Number of error bits in predction and actual labels (cost)
loss_list = []
seq_length = []
last_batch = 0
for j in range(self.num_epoch):
for batch_num, X, Y in self.get_data(task='train'):
self.optimizer.zero_grad(
) # Making old gradients zero before calculating the fresh ones
self.machine.initialization(
self.batch_size) # Initializing states
Y_out = torch.empty(
(X.shape[0], X.shape[1], self.num_outputs),
dtype=torch.float32).cuda(
) # dim: (seq_len x batch_size x num_output)
# Feeding the DNC network all the data first and then predicting output
# by giving zero vector as input and previous read states and hidden vector
# and thus training vector this way to give outputs matching the labels
X, Y = X.cuda(), Y.cuda()
embeddings = self.machine.backward_prediction(
X
) # Creating embeddings from data for backward calculation
temp_size = X.shape[0]
for i in range(temp_size):
Y_out[i, :, :], _ = self.machine(
X[i],
embeddings[temp_size - i -
1]) # Passing Embeddings from backwards
loss = self.calc_loss(Y_out, Y)
loss.backward()
self.clip_grads()
self.optimizer.step()
corr, tot = self.calc_cost(Y_out.cpu(), Y.cpu())
loss_list += [loss.item()]
seq_length += [Y.shape[0]]
if (batch_num % self.save_batch) == 0:
self.save_model(j, batch_num)
last_batch = batch_num
print("Epoch: " + str(j) + "/" + str(self.num_epoch) +
", Batch: " + str(batch_num) + "/" +
str(self.num_batches) + ", Loss: " + str(loss.item()) +
", Batch Accuracy: " +
str((float(corr) / float(tot)) * 100.0) + " %")
self.save_model(j, last_batch)
def test_model(self): # Testing the model
correct = 0
total = 0
print("\n")
for batch_num, X, Y in self.get_data(task='test'):
self.machine.initialization(self.batch_size) # Initializing states
Y_out = torch.empty((X.shape[0], X.shape[1], self.num_outputs),
dtype=torch.float32).cuda(
) # dim: (seq_len x batch_size x num_output)
# Feeding the DNC network all the data first and then predicting output
# by giving zero vector as input and previous read states and hidden vector
# and thus training vector this way to give outputs matching the labels
X = X.cuda()
embeddings = self.machine.backward_prediction(
X) # Creating embeddings from data for backward calculation
temp_size = X.shape[0]
for i in range(temp_size):
Y_out[i, :, :], _ = self.machine(X[i],
embeddings[temp_size - i - 1])
corr, tot = self.calc_cost(Y_out.cpu(), Y)
correct += corr
total += tot
print("Test Example " + str(batch_num) + "/" +
str(self.num_batches) + " processed, Batch Accuracy: " +
str((float(corr) / float(tot)) * 100.0) + " %")
accuracy = (float(correct) / float(total)) * 100.0
print("\nOverall Accuracy: " + str(accuracy) + " %")
return accuracy # in %
def save_model(self, curr_epoch, curr_batch):
# Here 'start_epoch' and 'start_batch' params below are the 'epoch' and 'batch' number from which to start training after next model loading
# Note: It is recommended to start from the 'start_epoch' and not 'start_epoch' + 'start_batch', because batches are formed randomly
if not os.path.exists("Saved_Models/" + self.name):
os.mkdir("Saved_Models/" + self.name)
state_dic = {
'task_name': self.name,
'start_epoch': curr_epoch + 1,
'start_batch': curr_batch + 1,
'state_dict': self.machine.state_dict(),
'optimizer_dic': self.optimizer.state_dict()
}
filename = "Saved_Models/" + self.name + "/" + self.name + "_" + str(
curr_epoch) + "_" + str(curr_batch) + "_saved_model.pth.tar"
torch.save(state_dic, filename)
def load_model(self, option, epoch, batch):
path = "Saved_Models/" + self.name + "/" + self.name + "_" + str(
epoch) + "_" + str(batch) + "_saved_model.pth.tar"
if option == 1: # Loading for training
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.optimizer.load_state_dict(checkpoint['optimizer_dic'])
else: # Loading for testing
checkpoint = torch.load(path)
self.machine.load_state_dict(checkpoint['state_dict'])
self.machine.eval()