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How to use prepare_sequence method in molecule

Best Python code snippet using molecule_python

lstm_pos.py

Source:lstm_pos.py

...3import torch.nn as nn4import torch.nn.functional as F5import torch.optim as optim6torch.manual_seed(1)7def prepare_sequence(seq, to_ix):8    idxs = [to_ix[w] for w in seq]9    return torch.tensor(idxs, dtype=torch.long)10training_data = [11    # Tags are: DET - determiner; NN - noun; V - verb12    # For example, the word "The" is a determiner13    ("The dog ate the apple".split(), ["DET", "NN", "V", "DET", "NN"]),14    ("Everybody read that book".split(), ["NN", "V", "DET", "NN"])15]16word_to_ix = {}17char_to_ix = {}18# For each words-list (sentence) and tags-list in each tuple of training_data19for sent, _ in training_data:20    for word in sent:21        if word not in word_to_ix:  # word has not been assigned an index yet22            word_to_ix[word] = len(word_to_ix)  # Assign each word with a unique index23        for char in word:24            if char not in char_to_ix:25                char_to_ix[char] = len(char_to_ix)26print(word_to_ix)27# {'The': 0, 'dog': 1, 'ate': 2, 'the': 3, 'apple': 4, 'Everybody': 5, 'read': 6, 'that': 7, 'book': 8}28print(char_to_ix)29# {'T': 0, 'h': 1, 'e': 2, 'd': 3, 'o': 4, 'g': 5, 'a': 6, 't': 7, 'p': 8, 'l': 9, 'E': 10, 'v': 11, 'r': 12, 'y': 13, 'b': 14, 'k': 15}30tag_to_ix = {"DET": 0, "NN": 1, "V": 2}31EMBEDDING_DIM_WORD = 632HIDDEN_DIM_WORD = 633EMBEDDING_DIM_CHAR = 334HIDDEN_DIM_CHAR = 335class LSTMTagger(nn.Module):36    def __init__(self, embedding_dim_word, hidden_dim_word, embedding_dim_char, hidden_dim_char, vocab_size_word, vocab_size_char, tagset_size):37        super(LSTMTagger, self).__init__()38        self.word_embeddings = nn.Embedding(vocab_size_word, embedding_dim_word)39        self.char_embeddings = nn.Embedding(vocab_size_char, embedding_dim_char)40        self.hidden_dim_word = hidden_dim_word41        self.hidden_dim_char = hidden_dim_char42        # The LSTM takes word embeddings as inputs, and outputs hidden states43        # with dimensionality hidden_dim.44        self.lstm_char = nn.LSTM(embedding_dim_char, hidden_dim_char)45        self.lstm_word = nn.LSTM(embedding_dim_word+embedding_dim_char, hidden_dim_word)46        # The linear layer that maps from hidden state space to tag space47        self.hidden2tag = nn.Linear(hidden_dim_word, tagset_size)48        self.hidden_word = self.init_hidden(self.hidden_dim_word)49        self.hidden_char = self.init_hidden(self.hidden_dim_char)50    def init_hidden(self, size):51        return (torch.zeros(1,1,size), torch.zeros(1,1,size))52    def forward(self, word_sequence, char_sequence):53        word_embeds = self.word_embeddings(word_sequence)54        char_embeds = self.char_embeddings(char_sequence)55        56        #print(char_embeds.view(len(char_sequence), 1, -1))57        lstm_char_out, self.hidden_char = self.lstm_char(char_embeds.view(len(char_sequence), 1, -1), self.hidden_char)58        concat = torch.cat([word_embeds.view(1,1,-1), lstm_char_out[-1].view(1,1,-1)], dim=2)59        lstm_word_out, self.hidden_word = self.lstm_word(concat, self.hidden_word)60        61        tag_space = self.hidden2tag(lstm_word_out.view(1, -1))62        tag_scores = F.log_softmax(tag_space, dim=1)63        64        return tag_scores65model = LSTMTagger(EMBEDDING_DIM_WORD, HIDDEN_DIM_WORD, EMBEDDING_DIM_CHAR, HIDDEN_DIM_CHAR, len(word_to_ix), len(char_to_ix), len(tag_to_ix))66loss_function = nn.NLLLoss()67optimizer = optim.SGD(model.parameters(), lr=0.1)68with torch.no_grad():69    for word in training_data[0][0]:70        word_sequence = prepare_sequence([word], word_to_ix)71        print(word_sequence)72        char_sequence = prepare_sequence(word, char_to_ix)73        print(char_sequence)74        tag_scores = model(word_sequence, char_sequence)75        print(tag_scores, tag_scores.argmax(dim=1))76for epoch in range(300):77    for sentence, tags in training_data:78        model.zero_grad()79        # word hidden init by sentence80        model.hidden_word = model.init_hidden(model.hidden_dim_word)81        for index, word in enumerate(sentence):82            # char hidden init by word83            model.hidden_char = model.init_hidden(model.hidden_dim_char)84            word_sequence = prepare_sequence([word], word_to_ix)85            char_sequence = prepare_sequence(word, char_to_ix)86            targets = prepare_sequence([tags[index]], tag_to_ix)87            tag_scores = model(word_sequence, char_sequence)88            loss = loss_function(tag_scores, targets)89            loss.backward(retain_graph=True)90        optimizer.step()91with torch.no_grad():92    for word in training_data[0][0]:93        word_sequence = prepare_sequence([word], word_to_ix)94        char_sequence = prepare_sequence(word, char_to_ix)95        tag_scores = model(word_sequence, char_sequence)...

task2.py

Source:task2.py

...15    for epoch in range(5):16      model.train()17      predictions = []18      for (words, tags) in zip(trainset["word"], trainset["tag"]):19         sentence_in = prepare_sequence(words, word_to_ix)20         targets = prepare_sequence(tags, labeldict)21         tags = tags.type(torch.FloatTensor)22         tags_pred = model(words)23         loss = F.binary_cross_entropy(tags)24         optimizer.zero_grad()25         loss.backward()26         optimizer.step()2728         predictions += list(tags_pred.detach().numpy())29    print("Epoch: %d, loss: %.5f" % (epoch+1, loss.item()))303132def test(model, test):33    test_losses = []34    model.eval()35    test_loss = 036    correct = 037    with torch.no_grad():38        for (data, target) in zip(test["word"], test["tag"]):39            for (word, tag) in zip(data, target):40                output = model(data)41                test_loss += F.nll_loss(output, target, size_average=False).item()42                pred = output.data.max(1, keepdim=True)[1]43                correct += pred.eq(target.data.view_as(pred)).sum()44    test_loss /= len(testloader.dataset)45    test_losses.append(test_loss)46    print('\nTest set: Avg. loss: {:.4f}, Accuracy: {}/{} ({:.0f}%)\n'.format(47    test_loss, correct, len(testloader.dataset),48    100. * correct / len(testloader.dataset)))4950word_to_ix = {}5152def word_index(data):53    for sentence in data:54        for word in sentence:55            if word not in word_to_ix:56                word_to_ix[word] = len(word_to_ix)57    return word_to_ix585960def encoding_labels(data):61    possible = set(data)62    possible_labels = list(possible)63    label_dict = {}64    for index, possible_label in enumerate(possible_labels):65        label_dict[possible_label] = index6667    return label_dict6869def prepare_sequence(seq, to_ix):70    idxs = [to_ix[w] for w in seq]71    return torch.tensor(idxs, dtype=torch.long)7273def encode_dataset(data):74    tokenizer = BertTokenizerFast.from_pretrained('bert-base-cased')75    encoded_data = tokenizer(data,76    padding=True,77    return_tensors='pt',)7879    input_ids = encoded_data["input_ids"]8081    model = BertModel.from_pretrained('bert-base-cased')82    return model8384def lstm_train(word_to_ix, labeldict, trainset, embedder):85    model_lstm = LSTM(6, len(word_to_ix), len(labeldict), embedder)86    loss_function = nn.NLLLoss()87    optimizer_lstm = optim.SGD(model_lstm.parameters(), lr=0.1)8889    for epoch in range(5):90        for (words, tags) in zip(trainset["word"], trainset["tag"]):9192                model_lstm.zero_grad()93                sentence_in = prepare_sequence(words, word_to_ix)94                targets = prepare_sequence(tags, labeldict)95                tag_scores = model_lstm(sentence_in)9697                loss = loss_function(tag_scores, targets)98                loss.backward()99                optimizer_lstm.step()100    with torch.no_grad():101        inputs = prepare_sequence(trainset["word"], word_to_ix)102        tag_scores = model_lstm(inputs)103104105if __name__ == '__main__':106    parser = argparse.ArgumentParser(description="Task 2")107    parser.add_argument("--output_dir", dest="output_dir", type=str, default=".")108109    args = parser.parse_args()110    dataset = load_dataset("loading_script.py")111    trainset = dataset["train"]112    testset = dataset["test"]113    trainloader = torch.utils.data.DataLoader(trainset,114                                          shuffle=False, num_workers=0)115    testloader = torch.utils.data.DataLoader(testset,
...

LSTM.py

Source:LSTM.py

...14print(out)15print(hidden)16# ----------- LSTMTagger ------------17print('-----------LSTMTagger------------')18def prepare_sequence(seq, to_ix):19    idxs = [to_ix[w] for w in seq]20    return torch.tensor(idxs, dtype=torch.long)21training_data = [22    ("The dog ate the apple".split(), ["DET", "NN", "V", "DET", "NN"]),23    ("Everybody read that book".split(), ["NN", "V", "DET", "NN"])24]25word_to_ix = {}26for sent, tag in training_data:27    for word in sent:28        if word not in word_to_ix:29            word_to_ix[word] = len(word_to_ix)30print(word_to_ix)31tag_to_ix = {'DET': 0, 'NN': 1, 'V': 2}32EMBEDDING_DIM = 633HIDDEN_DIM = 634class LSTMTagger(nn.Module):35    def __init__(self, embedding_dim, hidden_dim, vocab_size, target_size):36        super(LSTMTagger, self).__init__()37        self.hidden_dim = hidden_dim38        self.word_embedding = nn.Embedding(vocab_size, embedding_dim)39        self.lstm = nn.LSTM(embedding_dim, hidden_dim)40        self.hidden_dim2tag = nn.Linear(hidden_dim, target_size)41        self.hidden = self.init_hidden()42    def init_hidden(self):43        return (torch.zeros(1, 1, self.hidden_dim),44                (torch.zeros(1, 1, self.hidden_dim)))45    def forward(self, sentence):46        embeds = self.word_embedding(sentence)47        lstm_out, self.hidden = self.lstm(embeds.view(len(sentence), 1, -1),48                                          self.hidden)49        tag_space = self.hidden_dim2tag(lstm_out.view(len(sentence), -1))50        tag_scores = F.log_softmax(tag_space, dim=1)51        return tag_scores52model = LSTMTagger(EMBEDDING_DIM, HIDDEN_DIM, len(word_to_ix), len(tag_to_ix))53loss_function = nn.NLLLoss()54optimizer = optim.SGD(model.parameters(), lr=0.1)55with torch.no_grad():56    inputs = prepare_sequence(training_data[0][0], word_to_ix)57    tag_scores = model(inputs)58    print(tag_scores)59for epoch in range(300):60    for sentence, tags in training_data:61        model.zero_grad()62        model.hidden = model.init_hidden()63        sentence_in = prepare_sequence(sentence, word_to_ix)64        targets = prepare_sequence(tags, tag_to_ix)65        tag_scores = model(sentence_in)66        loss = loss_function(tag_scores, targets)67        loss.backward()68        optimizer.step()69with torch.no_grad():70    inputs = prepare_sequence(training_data[0][0], word_to_ix)71    tag_scores = model(inputs)72    print(tag_scores)73# ------------- Bi-LSTM CRF ---------------...

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