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An Error when Calling torch.sparse.sum and .to_dense(): Could not run 'aten::to_dense' with arguments from the 'CPU' backend

I met a problem when calling torch.sparse.sum(). The original code is as follows:
class RGCN_Layer(nn.Module):
""" A Relation GCN module operated on documents graphs. """
def __init__(self, in_dim, mem_dim, num_layers, relation_cnt=8):
super().__init__()
self.layers = num_layers
self.device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
self.mem_dim = mem_dim
self.relation_cnt = relation_cnt
self.in_dim = in_dim
self.dropout = 0.2
# self.in_drop = nn.Dropout(self.dropout)
self.gcn_drop = nn.Dropout(self.dropout)
# gcn layer
self.W_0 = nn.ModuleList()
self.W_r = nn.ModuleList()
# for i in range(self.relation_cnt):
for i in range(relation_cnt):
self.W_r.append(nn.ModuleList())
for layer in range(self.layers):
input_dim = self.in_dim if layer == 0 else self.mem_dim
self.W_0.append(nn.Linear(input_dim, self.mem_dim).to(self.device))
for W in self.W_r:
W.append(nn.Linear(input_dim, self.mem_dim).to(self.device))
def forward(self, nodes, adj):
"""
:param nodes: batch_size * num_event * num_event
:param adj: batch_size * 8 * num_event * num_event
:return:
"""
# gcn_inputs = self.in_drop(nodes)
gcn_inputs = nodes
maskss = []
denomss = []
for batch in range(adj.shape[0]):
masks = []
denoms = []
for i in range(self.relation_cnt):
denom = torch.sparse.sum(adj[batch, i], dim=1).to_dense()
t_g = denom + torch.sparse.sum(adj[batch, i], dim=0).to_dense()
mask = t_g.eq(0)
denoms.append(denom.unsqueeze(1))
masks.append(mask)
denoms = torch.sum(torch.stack(denoms), 0)
denoms = denoms + 1
masks = sum(masks)
maskss.append(masks)
denomss.append(denoms)
denomss = torch.stack(denomss) # 40 * 61 * 1
# sparse rgcn layer
for l in range(self.layers):
gAxWs = []
for j in range(self.relation_cnt):
gAxW = []
bxW = self.W_r[j][l](gcn_inputs)
for batch in range(adj.shape[0]):
xW = bxW[batch] # 255 * 25
AxW = torch.sparse.mm(adj[batch][j], xW) # 255, 25
# AxW = AxW/ denomss[batch][j] # 255, 25
gAxW.append(AxW)
gAxW = torch.stack(gAxW)
gAxWs.append(gAxW)
gAxWs = torch.stack(gAxWs, dim=1)
# print("denomss", denomss.shape)
# print((torch.sum(gAxWs, 1) + self.W_0[l](gcn_inputs)).shape)
gAxWs = F.relu((torch.sum(gAxWs, 1) + self.W_0[l](gcn_inputs)) / denomss) # self loop
gcn_inputs = self.gcn_drop(gAxWs) if l < self.layers - 1 else gAxWs
return gcn_inputs, maskss
However, when executing to the line denom = torch.sparse.sum(adj[batch, i], dim=1).to_dense(), an error occurred as follows:
RuntimeError: Could not run 'aten::to_dense' with arguments from the 'CPU' backend. 'aten::to_dense' is only available for these backends: [MkldnnCPU, SparseCPU, BackendSelect, Named, AutogradOther, AutogradCPU, AutogradCUDA, AutogradXLA, AutogradPrivateUse1, AutogradPrivateUse2, AutogradPrivateUse3, Tracer, Autocast, Batched, VmapMode].
The error told me that the code cannot be executed on the CPU platform; however, I noticed the CUDA is also not listed in the supported list. In addition, after checking the library, the execution on CPU and CUDA might be supported. Could someone help me to deal with this problem? Thanks!

the function torch.sparse.sum returns a dense tensor if you sum over all of the sparse dimensions. And since you're slicing the adjacency matrix first and then summing, you're calling the method .to_dense() on a dense tensor.
torch.arange(10).to_dense() # will give same error

Transformer PyTorch Error- ValueError: too many values to unpack (expected 2)

I am having issues getting my model to run. I am not sure which model to use in the translate_sentence function, I have tried model.transformer, model.encoder_de, etc. It is based off of the Transformer class and the forward() function I believe but I am getting a type error. These are the directions:
As in the forward(self, src, tgt) function of the
TransformerModel class, you need to create the appropriate
mask and encode the source sentence (just once).
You also need to create the appropriate mask and encode the
output sentence for sequential predictions. Unlike the source,
for every iteration, you need to re-encode the previous output and
pass both the source sentence and previous output into the
Transformer.
from torch.nn import Transformer
class TransformerModel(nn.Module):
def __init__(self, ntoken_in, ntoken_out, ninp, nhead, npf_dim, nlayers, src_pad_idx, trg_pad_idx, dropout=0.5):
super(TransformerModel, self).__init__()
# --------------- param -----------------
# ntoken_in: the idx of the input word after tokenization
# ntoken_out: the idx of the input word w.r.t. the tokenization
# ninp: the number of expected features in the encoder/decoder inputs
# nhead: the number of multiAttention heads
# npf_dim: the dimension of the feedforward layer
# src_pad_idx: the token for padding in source language
# trg_pad_idx: the token for padding in target language
# ----------------------------------------
self.model_type = 'Transformer'
self.pos_encoder = PositionalEncoding(ninp, dropout)
self.transformer = Transformer(d_model=ninp, nhead=nhead, num_encoder_layers=nlayers, num_decoder_layers=nlayers,
dim_feedforward=npf_dim, dropout=dropout, activation='relu')
self.encoder_en = nn.Embedding(ntoken_in, ninp) # tok_embedding for input
self.encoder_de = nn.Embedding(ntoken_out, ninp) # tok_embedding for output
self.ninp = ninp
self.decoder = nn.Linear(ninp, ntoken_out)
self.src_pad_idx = src_pad_idx
self.tgt_pad_idx = trg_pad_idx
self.init_weights()
def _generate_src_key_mask(self, src):
# for key_padding_mask in transformer
# the positions with the value of True will be ignored while the position
# with the value of False will be unchanged. We mask all padding words.
# The output dim is b*s
src_mask = (src == self.src_pad_idx)
return src_mask.T
def _generate_tgt_mask(self, tgt, sz):
# Beside key_padding_mask in transformer, the output or teacher input
# should be masked sequentially to prevent the model get any information
# from the future words it is going to predict
tgt_key_mask = tgt == self.tgt_pad_idx
# We provide FloatTensor attn_mask. It will be added to the attention weight.
mask = (torch.triu(torch.ones(sz, sz)) == 1).transpose(0, 1)
attn_mask = mask.float().masked_fill(mask == 0, float('-inf')).masked_fill(mask == 1, float(0.0)).to(tgt.device)
return attn_mask, tgt_key_mask.T
def init_weights(self):
initrange = 0.1
self.encoder_en.weight.data.uniform_(-initrange, initrange)
self.encoder_de.weight.data.uniform_(-initrange, initrange)
self.decoder.bias.data.zero_()
self.decoder.weight.data.uniform_(-initrange, initrange)
def forward(self, src, tgt):
# src
src_key_mask = self._generate_src_key_mask(src)
src = self.encoder_en(src) * math.sqrt(self.ninp) # use a learned encoder put stoi index to a feature space s*b --> s*b*e
src = self.pos_encoder(src) # add the pos feature toward feature space
# tgt
tgt_mask, tgt_key_mask = self._generate_tgt_mask(tgt, tgt.size(0))
tgt = self.encoder_de(tgt) * math.sqrt(self.ninp)
tgt = self.pos_encoder(tgt)
output = self.transformer(src, tgt, tgt_mask=tgt_mask,
src_key_padding_mask = src_key_mask,
tgt_key_padding_mask = tgt_key_mask)
output = self.decoder(output)
return output
class PositionalEncoding(nn.Module):
# The positional encoding as described in the paper
# https://arxiv.org/pdf/1706.03762.pdf
def __init__(self, d_model, dropout=0.1, max_len=5000):
super(PositionalEncoding, self).__init__()
self.dropout = nn.Dropout(p=dropout)
pe = torch.zeros(max_len, d_model)
position = torch.arange(0, max_len, dtype=torch.float).unsqueeze(1)
div_term = torch.exp(torch.arange(0, d_model, 2).float() * (-math.log(10000.0) / d_model))
pe[:, 0::2] = torch.sin(position * div_term)
pe[:, 1::2] = torch.cos(position * div_term)
pe = pe.unsqueeze(0).transpose(0, 1)
self.register_buffer('pe', pe)
def forward(self, x):
x = x + self.pe[:x.size(0), :]
return self.dropout(x)
# Here we intialize our model
INPUT_DIM = len(SRC.vocab)
OUTPUT_DIM = len(TRG.vocab)
print(INPUT_DIM, OUTPUT_DIM)
HID_DIM = 256
N_LAYERS = 3
N_HEADS = 8
N_PF_DIM = 512
DROPOUT = 0.1
SRC_PAD_IDX = SRC.vocab.stoi[SRC.pad_token]
TRG_PAD_IDX = TRG.vocab.stoi[TRG.pad_token]
model =TransformerModel(ntoken_in = INPUT_DIM, ntoken_out=OUTPUT_DIM, ninp=HID_DIM,
nhead=N_HEADS, npf_dim=N_PF_DIM, nlayers=N_LAYERS,
src_pad_idx=SRC_PAD_IDX, trg_pad_idx=TRG_PAD_IDX, dropout=DROPOUT).to(device)
def count_parameters(model: nn.Module):
return sum(p.numel() for p in model.parameters() if p.requires_grad)
print(f'The model has {count_parameters(model):,} trainable parameters')
def initialize_weights(m):
if hasattr(m, 'weight') and m.weight.dim() > 1:
nn.init.xavier_uniform_(m.weight.data)
model.apply(initialize_weights)
----------
def translate_sentence(sentence, src_field, trg_field, model, device, max_len = 50):
model.eval()
if isinstance(sentence, str):
nlp = spacy.load('de')
tokens = [token.text.lower() for token in nlp(sentence)]
else:
tokens = [token.lower() for token in sentence]
#tokens = [src_field.init_token] + tokens + [src_field.eos_token]
src_indexes = [src_field.vocab.stoi[token] for token in tokens]
src_tensor = torch.LongTensor(src_indexes).unsqueeze(1).to(device)
with torch.no_grad():
#model.?
hidden, cell = model.encoder_en(src_tensor)
# create a list to hold the output sentence, initialized with an <sos> token
trg_indexes = [trg_field.vocab.stoi[trg_field.init_token]]
for i in range(max_len):
trg_tensor = torch.LongTensor(trg_indexes).unsqueeze(1).to(device)
with torch.no_grad():
#model.?
output, hidden, cell = model.encoder_de(trg_tensor, hidden, cell)
pred_token = output.argmax(1).item()
trg_indexes.append(pred_token)
if pred_token == trg_field.vocab.stoi[trg_field.eos_token]:
break
trg_tokens = [trg_field.vocab.itos[i] for i in trg_indexes]
return trg_tokens[1:]
----------
#getting error here
example_idx = 18
src = vars(train_data.examples[example_idx])['src']
trg = vars(train_data.examples[example_idx])['trg']
print(f'src = {src}')
print(f'trg = {trg}')
translation = translate_sentence(src, TRG, SRC, model, device)
print(f'predicted trg = {translation}')

Adding layers and bidirectionality to custom LSTM cell in pytorch

I use a very custom LSTM-cell inspired by http://mlexplained.com/2019/02/15/building-an-lstm-from-scratch-in-pytorch-lstms-in-depth-part-1/.
I use it to look at intermediate gating values. My question is, how would I expand this class to have an option for adding more layers and for adding bidirectionality? Should it be wrapped in a new class or added in the present one?
class Dim(IntEnum):
batch = 0
seq = 1
class simpleLSTM(nn.Module):
def __init__(self, input_sz: int, hidden_sz: int):
super().__init__()
self.input_size = input_sz
self.hidden_size = hidden_sz
# input gate
self.W_ii = Parameter(torch.Tensor(input_sz, hidden_sz))
self.W_hi = Parameter(torch.Tensor(hidden_sz, hidden_sz))
self.b_i = Parameter(torch.Tensor(hidden_sz))
# forget gate
self.W_if = Parameter(torch.Tensor(input_sz, hidden_sz))
self.W_hf = Parameter(torch.Tensor(hidden_sz, hidden_sz))
self.b_f = Parameter(torch.Tensor(hidden_sz))
# ???
self.W_ig = Parameter(torch.Tensor(input_sz, hidden_sz))
self.W_hg = Parameter(torch.Tensor(hidden_sz, hidden_sz))
self.b_g = Parameter(torch.Tensor(hidden_sz))
# output gate
self.W_io = Parameter(torch.Tensor(input_sz, hidden_sz))
self.W_ho = Parameter(torch.Tensor(hidden_sz, hidden_sz))
self.b_o = Parameter(torch.Tensor(hidden_sz))
self.init_weights()
self.out = nn.Linear(hidden_sz, len(TRG.vocab))
def init_weights(self):
for p in self.parameters():
if p.data.ndimension() >= 2:
nn.init.xavier_uniform_(p.data)
else:
nn.init.zeros_(p.data)
def forward(self, x, init_states=None ):
"""Assumes x is of shape (batch, sequence, feature)"""
seq_sz, bs, = x.size()
hidden_seq = []
prediction = []
if init_states is None:
h_t, c_t = torch.zeros(self.hidden_size).to(x.device), torch.zeros(self.hidden_size).to(x.device)
else:
h_t, c_t = init_states
for t in range(seq_sz): # iterate over the time steps
x_t = x[t, :].float()
#LOOK HERE!!!
i_t = torch.sigmoid(x_t # self.W_ii + h_t # self.W_hi + self.b_i)
f_t = torch.sigmoid(x_t # self.W_if + h_t # self.W_hf + self.b_f)
g_t = torch.tanh(x_t # self.W_ig + h_t # self.W_hg + self.b_g)
o_t = torch.sigmoid(x_t # self.W_io + h_t # self.W_ho + self.b_o)
c_t = f_t * c_t + i_t * g_t
h_t = o_t * torch.tanh(c_t)
hidden_seq.append(h_t.unsqueeze(Dim.batch))
pred_t = self.out(h_t.unsqueeze(Dim.batch))
#pred_t = F.softmax(pred_t)
prediction.append(pred_t)
hidden_seq = torch.cat(hidden_seq, dim=Dim.batch)
prediction = torch.cat(prediction, dim=Dim.batch)
# reshape from shape (sequence, batch, feature) to (batch, sequence, feature)
hidden_seq = hidden_seq.transpose(Dim.batch, Dim.seq).contiguous()
prediction = prediction.transpose(Dim.batch, Dim.seq).contiguous()
return prediction, hidden_seq, (h_t, c_t)
I call it and train using the following as an example.
lstm = simpleLSTM(1, 100)
hidden_size = lstm.hidden_size
optimizer = optim.Adam(lstm.parameters())
h_0, c_0 = (torch.zeros(hidden_size, requires_grad=True),
torch.zeros(hidden_size, requires_grad=True))
grads = []
h_t, c_t = h_0, c_0
N_EPOCHS = 10
for epoch in range(N_EPOCHS):
epoch_loss = 0
for i, batch in enumerate(train):
optimizer.zero_grad()
src, src_len = batch.src
trg = batch.trg
trg = trg.view(-1)
predict, output, hidden_states = lstm(src)
predict = predict.t().unsqueeze(1)
predict= predict.view(-1, predict.shape[-1])
loss = criterion(predict,trg)
loss.backward()
optimizer.step()
epoch_loss += loss.item()
print(epoch_loss)

The easiest would be to create another module (say Bidirectional) and pass any cell you want to it.
Implementation itself is quite easy to do. Notice that I'm using concat operation for joining bi-directional output, you may want to specify other modes like summation etc.
Please read the comments in the code below, you may have to change it appropriately.
import torch
class Bidirectional(torch.nn.Module):
def __init__(self, cell):
super().__init__()
self.cell = cell
def __call__(self, x, init_states=None):
prediction, hidden_seq, (h_t, c_t) = self.cell(x, init_states)
backward_prediction, backward_hidden_seq, (
backward_h_t,
backward_c_t,
# Assuming sequence is first dimension, otherwise change 0 appropriately
# Reverses sequences so the LSTM cell acts on the reversed sequence
) = self.cell(torch.flip(x, (0,)), init_states)
return (
# Assuming you transpose so it has (batch, seq, features) dimensionality
torch.cat((prediction, backward_prediction), 2),
torch.cat((hidden_seq, backward_hidden_seq), 2),
# Assuming it has (batch, features) dimensionality
torch.cat((h_t, backward_ht), 1),
torch.cat((c_t, backward_ct), 1),
)
When it comes to multiple layers you could do something similiar in principle:
import torch
class Multilayer(torch.nn.Module):
def __init__(self, *cells):
super().__init__()
self.cells = torch.nn.ModuleList(cells)
def __call__(self, x, init_states=None):
inputs = x
for cell in self.cells:
prediction, hidden_seq, (h_t, c_t) = cell(inputs, init_states)
inputs = hidden_seq
return prediction, hidden_seq, (h_t, c_t)
Please note you have to pass created cell objects into Multilayer e.g.:
# For three layers of LSTM, each needs features to be set up correctly
multilayer_LSTM = Multilayer(LSTM(), LSTM(), LSTM())
You may also pass classes instead of instances into constructor and create those inside Multilayer (so hidden_size matches automatically), but those ideas should get you started.

The node 'Merge/MergeSummary' has inputs from different frames: what does it mean?

trying to merge all my summaries, I have an error saying that the inputs of Merge/MergeSummary comes from different frames. So, first of all: what is a frame? Could you please point me somewhere in the TF documentation about such stuff? -- of course, I googled a bit but could find almost nothing. How can I fix this issue? Below the code to reproduce the error. Thanks in advance.
import numpy as np
import tensorflow as tf
tf.reset_default_graph()
tf.set_random_seed(23)
BATCH = 2
LENGTH = 4
SIZE = 5
ATT_SIZE = 3
NUM_QUERIES = 2
def linear(inputs, output_size, use_bias=True, activation_fn=None):
"""Linear projection."""
input_shape = inputs.get_shape().as_list()
input_size = input_shape[-1]
output_shape = input_shape[:-1] + [output_size]
if len(output_shape) > 2:
output_shape_tensor = tf.unstack(tf.shape(inputs))
output_shape_tensor[-1] = output_size
output_shape_tensor = tf.stack(output_shape_tensor)
inputs = tf.reshape(inputs, [-1, input_size])
kernel = tf.get_variable("kernel", [input_size, output_size])
output = tf.matmul(inputs, kernel)
if use_bias:
output = output + tf.get_variable('bias', [output_size])
if len(output_shape) > 2:
output = tf.reshape(output, output_shape_tensor)
output.set_shape(output_shape) # pylint: disable=I0011,E1101
if activation_fn is not None:
return activation_fn(output)
return output
class Attention(object):
"""Attention mechanism implementation."""
def __init__(self, attention_states, attention_size):
"""Initializes a new instance of the Attention class."""
self._states = attention_states
self._attention_size = attention_size
self._batch = tf.shape(self._states)[0]
self._length = tf.shape(self._states)[1]
self._size = self._states.get_shape()[2].value
self._features = None
def _init_features(self):
states = tf.reshape(
self._states, [self._batch, self._length, 1, self._size])
weights = tf.get_variable(
"kernel", [1, 1, self._size, self._attention_size])
self._features = tf.nn.conv2d(states, weights, [1, 1, 1, 1], "SAME")
def get_weights(self, query, scope=None):
"""Reurns the attention weights for the given query."""
with tf.variable_scope(scope or "Attention"):
if self._features is None:
self._init_features()
else:
tf.get_variable_scope().reuse_variables()
vect = tf.get_variable("Vector", [self._attention_size])
with tf.variable_scope("Query"):
query_features = linear(query, self._attention_size, False)
query_features = tf.reshape(
query_features, [-1, 1, 1, self._attention_size])
activations = vect * tf.tanh(self._features + query_features)
activations = tf.reduce_sum(activations, [2, 3])
with tf.name_scope('summaries'):
tf.summary.histogram('histogram', activations)
return tf.nn.softmax(activations)
states = tf.placeholder(tf.float32, shape=[BATCH, None, SIZE]) # unknown length
queries = tf.placeholder(tf.float32, shape=[NUM_QUERIES, BATCH, ATT_SIZE])
attention = Attention(states, ATT_SIZE)
func = lambda x: attention.get_weights(x, "Softmax")
weights = tf.map_fn(func, queries)
for var in tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES):
name = var.name.replace(':', '_')
tf.summary.histogram(name, var)
summary_op = tf.summary.merge_all()
states_np = np.random.rand(BATCH, LENGTH, SIZE)
queries_np = np.random.rand(NUM_QUERIES, BATCH, ATT_SIZE)
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
weights_np, summary_str = sess.run([weights, summary_op], {states: states_np, queries: queries_np})
print weights_np

The error message was indeed not user friendly. It has been updated to
ValueError: Cannot use 'map/while/summaries/histogram' as input to 'Merge/MergeSummary' because 'map/while/summaries/histogram' is in a while loop. See info log for more details.
As the new message says, the problem is that you cannot produce summaries from inside of the while loop. The frame that the original message referred to is the "execution frame" of the while loop - all the state for each iteration of the while loop is kept in a frame.
In this case, the while_loop is created by tf.map_fn and the summary inside it is tf.summary.histogram('histogram', activations).
There are a couple of ways to deal with this. You can take the summary out of the get_weights, have the get_weights return activations as well, create the summary using the newly returned activations from tf.map_fn call.
Another approach, if NUM_QUERIES is constant and small, can be to statically unroll the loop instead of using tf.map_fn. Here is the code to do this:
# TOP PART OF THE CODE IS THE SAME
states = tf.placeholder(tf.float32, shape=[BATCH, None, SIZE]) # unknown length
queries = tf.placeholder(tf.float32, shape=[NUM_QUERIES, BATCH, ATT_SIZE])
attention = Attention(states, ATT_SIZE)
func = lambda x: attention.get_weights(x, "Softmax")
# NEW CODE BEGIN
split_queries = tf.split(queries, NUM_QUERIES)
weights = []
for query in split_queries:
weights.append(func(query))
# NEW CODE END
for var in tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES):
name = var.name.replace(':', '_')
tf.summary.histogram(name, var)
summary_op = tf.summary.merge_all()
states_np = np.random.rand(BATCH, LENGTH, SIZE)
queries_np = np.random.rand(NUM_QUERIES, BATCH, ATT_SIZE)
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
# NEW CODE BEGIN
results = sess.run(weights + [summary_op], {states: states_np, queries: queries_np})
weights_np, summary_str = results[:-1], results[-1]
# NEW CODE END
print weights_np

Tensorflow evaluate: Aborted (core dumped)

tl;dr: I input a word to my model, and am supposed to get a list of similar words and their associated measures of similarity back. I get an error: Aborted (core dumped).
My goal is to determine which words are similar to an input word, based on their feature vectors. I have model already trained. I load it and call two functions:
def main(argv=None):
model = NVDM(args)
sess_saver = tf.train.Saver()
sess = tf.Session()
init = tf.initialize_all_variables()
sess.run(init)
loaded = load_for_similar(sess, sess_saver) #my function
wm = word_match(sess, loaded[0], loaded[1], "bottle", loaded[2], loaded[3], topN=5)
My problem is that I can't print out the words which are similar and the associated similarity measure. I tried (in main):
sess.run(wm)
wm[0].eval(session=sess)
print(wm)
All of which gave me the error:
F tensorflow/core/kernels/strided_slice_op.cc:316] Check failed: tmp.CopyFrom(input.Slice(begin[0], end[0]), final_shape)
Aborted (core dumped)
This tells me I'm not running the session properly. What am I doing wrong?
Details on the functions, just in case:
The function 'load_for_similar' restores the weights and bias of the decoder in my model (a variational autoencoder), and normalizes them. It also reverses the order of the keys and values in my vocabulary dictionary for later use:
def load_for_similar(sess, saver_obj):
saver_obj.restore(sess, "./CA_checkpoints/saved_model.ckpt")
vocab_file = '/path/to/vocab.pkl'
t1 = loader_object(vocab_file)
v1 = t1.get_vocab()
v1_rev = {k:v for v, k in v1.iteritems()}
decoder_mat = tf.get_collection(tf.GraphKeys.VARIABLES, scope='decoder')[0]
decoder_bias = tf.get_collection(tf.GraphKeys.VARIABLES, scope='decoder')[1]
return (find_norm(decoder_mat), find_norm(decoder_bias), v1, v1_rev)
To find similar words, I pass the normalized weight matrix and bias in to an new function, along with the feature vector of my word (vec):
def find_similar(sess, Weights, vec, bias):
dists = tf.add(tf.reduce_sum(tf.mul(Weights, vec)), bias)
best = argsort(sess, dists, reverse=True)
dist_sort = tf.nn.top_k(dists, k=dists.get_shape().as_list()[0], sorted=True).values
return dist_sort, best
Finally, I want to match the words that are closest to my supplied word, "bottle":
def word_match(sess, norm_mat , norm_bias, word_ , vocab, vocab_inverse , topN = 10):
idx = vocab[word_]
similarity_meas , indexes = find_similar(sess, norm_mat , norm_mat[idx], norm_bias)
words = tf.gather(vocab_inverse.keys(), indexes[:topN])
return (words, similarity_meas[:topN])
EDIT: in response to mrry's comment, here is the model (I hope this is what you wanted?). This code depends on utils.py, a separate utilities file. I will include that as well. Please note that this code is heavily based on Yishu Miao's and Sarath Nair's.
class NVDM(object):
""" Neural Variational Document Model -- BOW VAE.
"""
def __init__(self,
vocab_size=15000, #was 2000
n_hidden=500,
n_topic=50,
n_sample=1,
learning_rate=1e-5,
batch_size=100, #was 64
non_linearity=tf.nn.tanh):
self.vocab_size = vocab_size
self.n_hidden = n_hidden
self.n_topic = n_topic
self.n_sample = n_sample
self.non_linearity = non_linearity
self.learning_rate = learning_rate/batch_size #CA
self.batch_size = batch_size
self.x = tf.placeholder(tf.float32, [None, vocab_size], name='input')
self.mask = tf.placeholder(tf.float32, [None], name='mask') # mask paddings
# encoder
with tf.variable_scope('encoder'):
self.enc_vec = utils.mlp(self.x, [self.n_hidden, self.n_hidden])
self.mean = utils.linear(self.enc_vec, self.n_topic, scope='mean')
self.logsigm = utils.linear(self.enc_vec,
self.n_topic,
bias_start_zero=True,
matrix_start_zero=False,
scope='logsigm')
self.kld = -0.5 * tf.reduce_sum(1 - tf.square(self.mean) + 2 * self.logsigm - tf.exp(2 * self.logsigm), 1)
self.kld = self.mask*self.kld # mask paddings
with tf.variable_scope('decoder'):
if self.n_sample ==1: # single sample
p1 = tf.cast(tf.reduce_sum(self.mask), tf.int32) #needed for random normal generation
eps = tf.random_normal((p1, self.n_topic), 0, 1)
doc_vec = tf.mul(tf.exp(self.logsigm), eps) + self.mean
logits = tf.nn.log_softmax(utils.linear(doc_vec, self.vocab_size, scope='projection'))
self.recons_loss = -tf.reduce_sum(tf.mul(logits, self.x), 1)
# multiple samples
else:
eps = tf.random_normal((self.n_sample*batch_size, self.n_topic), 0, 1)
eps_list = tf.split(0, self.n_sample, eps)
recons_loss_list = []
for i in xrange(self.n_sample):
if i > 0: tf.get_variable_scope().reuse_variables()
curr_eps = eps_list[i]
doc_vec = tf.mul(tf.exp(self.logsigm), curr_eps) + self.mean
logits = tf.nn.log_softmax(utils.linear(doc_vec, self.vocab_size, scope='projection'))
recons_loss_list.append(-tf.reduce_sum(tf.mul(logits, self.x), 1))
self.recons_loss = tf.add_n(recons_loss_list) / self.n_sample
self.objective = self.recons_loss + self.kld
optimizer = tf.train.AdamOptimizer(learning_rate=self.learning_rate)
fullvars = tf.trainable_variables()
enc_vars = utils.variable_parser(fullvars, 'encoder')
dec_vars = utils.variable_parser(fullvars, 'decoder')
enc_grads = tf.gradients(self.objective, enc_vars)
dec_grads = tf.gradients(self.objective, dec_vars)
self.optim_enc = optimizer.apply_gradients(zip(enc_grads, enc_vars))
self.optim_dec = optimizer.apply_gradients(zip(dec_grads, dec_vars))
def minibatch_bow(it1, Instance1, n_samples, batch_size, used_ints = set()):
available = set(np.arange(n_samples)) - used_ints #
if len(available) < batch_size:
indices = np.array(list(available))
else:
indices = np.random.choice(tuple(available), batch_size, replace=False)
used = used_ints
mb = itemgetter(*indices)(it1)
batch_xs = Instance1._bag_of_words(mb, vocab_size=15000)
batch_flattened = np.ravel(batch_xs)
index_positions = np.where(batch_flattened > 0)[0]
return (batch_xs, index_positions, set(indices)) #batch_xs[0] is the bag of words; batch_xs[1] is the 0/1 word used/not;
def train(sess, model, train_file, vocab_file, saver_obj, training_epochs, alternate_epochs, batch_size):
Instance1 = testchunk_Nov23.testLoader(train_file, vocab_file)
data_set = Instance1.get_batch(batch_size) #get all minibatches of size 100
n_samples = Instance1.num_reviews()
train_batches = list(data_set) #this is an itertools.chain object
it1_train = list(itertools.chain(*train_batches)) #length is 732,356. This is all the reviews.atch_size
if len(it1_train) % batch_size != 0:
total_batch = int(len(it1_train)/batch_size) + 1
else:
total_batch = int(len(it1_train)/batch_size)
trainfilesave = "train_ELBO_and_perplexity_Dec1.txt"
#Training
train_time = time.time()
for epoch in range(training_epochs):
for switch in xrange(0, 2):
if switch == 0:
optim = model.optim_dec
print_mode = 'updating decoder'
else:
optim = model.optim_enc
print_mode = 'updating encoder'
with open(trainfilesave, 'w') as f:
for i in xrange(alternate_epochs):
loss_sum = 0.0
kld_sum = 0.0
word_count = 0
used_indices = set()
for idx_batch in range(total_batch): #train_batches:
mb = minibatch_bow(it1_train, Instance1, n_samples, batch_size, used_ints=used_indices)
print('minibatch', idx_batch)
used_indices.update(mb[2])
num_mb = np.ones(mb[0][0].shape[0])
input_feed = {model.x.name: mb[0][0], model.mask: num_mb}
_, (loss, kld) = sess.run((optim,[model.objective, model.kld]) , input_feed)
loss_sum += np.sum(loss)
And the utils.py file:
def linear(inputs,
output_size,
no_bias=False,
bias_start_zero=False,
matrix_start_zero=False,
scope=None):
"""Define a linear connection."""
with tf.variable_scope(scope or 'Linear'):
if matrix_start_zero:
matrix_initializer = tf.constant_initializer(0)
else:
matrix_initializer = None
if bias_start_zero:
bias_initializer = tf.constant_initializer(0)
else:
bias_initializer = None
input_size = inputs.get_shape()[1].value
matrix = tf.get_variable('Matrix', [input_size, output_size],
initializer=matrix_initializer)
bias_term = tf.get_variable('Bias', [output_size],
initializer=bias_initializer)
output = tf.matmul(inputs, matrix)
if not no_bias:
output = output + bias_term
return output
def mlp(inputs,
mlp_hidden=[],
mlp_nonlinearity=tf.nn.tanh,
scope=None):
"""Define an MLP."""
with tf.variable_scope(scope or 'Linear'):
mlp_layer = len(mlp_hidden)
res = inputs
for l in xrange(mlp_layer):
res = mlp_nonlinearity(linear(res, mlp_hidden[l], scope='l'+str(l)))
return res