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Accenture / AmpliGraph

Python library for Representation Learning on Knowledge Graphs https://docs.ampligraph.org
Apache License 2.0
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ValueError: `generator` yielded an element of shape (3,) where an element of shape (?, 3) was expected. #255

Open millmi17 opened 3 years ago

millmi17 commented 3 years ago

I am getting the below error when using model.fit(X_train, early_stopping = False). To get X_train I loaded in a csv using the load_from_csv function which outputs below. I am new to github so if you need anything else to help try and fix it let me know array([['bill ', 'takes', 'calc'], ['bill ', 'is a ', 'person'], ['fred ', 'takes ', 'eng'], ['fred ', 'takes', 'chem'], ['chem ', 'located in ', 'pike'], ['pike ', 'is a ', 'building'], ['calc', 'located in ', 'smith'], ['calc ', 'is a ', 'building'], ['fred ', 'is a ', 'person']], dtype=object)

This was just a quick thing I put together to see if I could get this to work with ampligraph. I then use the below code to get the train test split. I follow the example code they had for complex E. The info is shown below

X_train, X_test = train_test_split_no_unseen(x, test_size=1) X_train[1] array(['bill ', 'takes', 'calc'], dtype=object)

model = ComplEx(batches_count=100, seed=0, epochs=1, k=150, eta=5, optimizer='adam', optimizer_params={'lr':1e-3}, loss='multiclass_nll', regularizer='LP', regularizer_params={'p':3, 'lambda':1e-5}, verbose=True)

tf.logging.set_verbosity(tf.logging.ERROR)

model.fit(X_train, early_stopping = False)

InvalidArgumentError Traceback (most recent call last) ~/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/client/session.py in _do_call(self, fn, args) 1364 try: -> 1365 return fn(args) 1366 except errors.OpError as e:

~/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/client/session.py in _run_fn(feed_dict, fetch_list, target_list, options, run_metadata) 1349 return self._call_tf_sessionrun(options, feed_dict, fetch_list, -> 1350 target_list, run_metadata) 1351

~/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/client/session.py in _call_tf_sessionrun(self, options, feed_dict, fetch_list, target_list, run_metadata) 1442 fetch_list, target_list, -> 1443 run_metadata) 1444

InvalidArgumentError: ValueError: generator yielded an element of shape (3,) where an element of shape (?, 3) was expected. Traceback (most recent call last):

File "/home/dataiku/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/ops/script_ops.py", line 235, in call ret = func(*args)

File "/home/dataiku/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/data/ops/dataset_ops.py", line 630, in generator_py_func "of shape %s was expected." % (ret_array.shape, expected_shape))

ValueError: generator yielded an element of shape (3,) where an element of shape (?, 3) was expected.

 [[{{node PyFunc}}]]
 [[IteratorGetNext]]

During handling of the above exception, another exception occurred:

InvalidArgumentError Traceback (most recent call last)

in 2 tf.logging.set_verbosity(tf.logging.ERROR) 3 ----> 4 model.fit(X_train, early_stopping = False) ~/dss/code-envs/python/kge/lib/python3.6/site-packages/ampligraph/latent_features/models/ComplEx.py in fit(self, X, early_stopping, early_stopping_params, focusE_numeric_edge_values, tensorboard_logs_path) 371 """ 372 super().fit(X, early_stopping, early_stopping_params, focusE_numeric_edge_values, --> 373 tensorboard_logs_path=tensorboard_logs_path) 374 375 def predict(self, X, from_idx=False): ~/dss/code-envs/python/kge/lib/python3.6/site-packages/ampligraph/latent_features/models/EmbeddingModel.py in fit(self, X, early_stopping, early_stopping_params, focusE_numeric_edge_values, tensorboard_logs_path) 1210 except BaseException as e: 1211 self._end_training() -> 1212 raise e 1213 1214 def set_filter_for_eval(self): ~/dss/code-envs/python/kge/lib/python3.6/site-packages/ampligraph/latent_features/models/EmbeddingModel.py in fit(self, X, early_stopping, early_stopping_params, focusE_numeric_edge_values, tensorboard_logs_path) 1155 self.sess_train.run(self.ent_emb)[:unique_entities.shape[0], :] 1156 else: -> 1157 loss_batch, _ = self.sess_train.run([loss, train], feed_dict=feed_dict) 1158 1159 if np.isnan(loss_batch) or np.isinf(loss_batch): ~/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/client/session.py in run(self, fetches, feed_dict, options, run_metadata) 954 try: 955 result = self._run(None, fetches, feed_dict, options_ptr, --> 956 run_metadata_ptr) 957 if run_metadata: 958 proto_data = tf_session.TF_GetBuffer(run_metadata_ptr) ~/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/client/session.py in _run(self, handle, fetches, feed_dict, options, run_metadata) 1178 if final_fetches or final_targets or (handle and feed_dict_tensor): 1179 results = self._do_run(handle, final_targets, final_fetches, -> 1180 feed_dict_tensor, options, run_metadata) 1181 else: 1182 results = [] ~/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/client/session.py in _do_run(self, handle, target_list, fetch_list, feed_dict, options, run_metadata) 1357 if handle is None: 1358 return self._do_call(_run_fn, feeds, fetches, targets, options, -> 1359 run_metadata) 1360 else: 1361 return self._do_call(_prun_fn, handle, feeds, fetches) ~/dss/code-envs/python/kge/lib64/python3.6/site-packages/tensorflow_core/python/client/session.py in _do_call(self, fn, *args) 1382 '\nsession_config.graph_options.rewrite_options.' 1383 'disable_meta_optimizer = True') -> 1384 raise type(e)(node_def, op, message) 1385 1386 def _extend_graph(self):
sumitpai commented 3 years ago

Thanks for reporting this bug. We had not handled the edge case gracefully. Here your training set size is much less than the batch count. So it treats each batch as size of 1. So we are getting this error. I will mark this as a bug. You can try with a smaller batch count - say 3 or 4