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I didn't change any parameters, but the weights and model dimensions don't match

ValueError: Shape mismatch in layer #2 (named Embedding-Token) for weight Embedding-Token/embeddings:0. Weight expects shape (3138, 256). Received saved weight with shape (3138, 128)

type: [1]
label: [1]
(1837498,)
(1837498,)
(1837498,)
Traceback (most recent call last):
File "00_cadd_create_vcf_sequence_data_multi_thread.py", line 548, in
y_label=1
File "00_cadd_create_vcf_sequence_data_multi_thread.py", line 437, in process_raw_text
batch_no=slice_index)
File "00_cadd_create_vcf_sequence_data_multi_thread.py", line 162, in create_tfrecord_with_sequence
'alt_type': tf.train.Feature(int64_list=tf.train.Int64List(value=list(type))),
TypeError: 'numpy.int64' object is not iterable

Hello,

When I ran the model “02_cadd_classification_transformer_tfrecord.py” for CADD data, I used the following data and ran into error messages: can’t parse serialized example. Can you provide help? I would like to apply this process to predict pathogenic effects of somatic variants. Or can you provide revised codes and an example data?

train_slice_files = [
'/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_5_slice_100000_100000_train.tfrecord','/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_5_slice_200000_200000_train.tfrecord'
]
valid_slice_files = [
'/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_5_slice_100000_100000_valid.tfrecord' ]
test_slice_files = [
'/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_5_slice_100000_100000_test.tfrecord' ]

        train_total_size =180000
        valid_total_size = 5000
        test_total_size = 5000

I ran into the following errors:

Train on 175 steps, validate on 2 steps
Epoch 1/100
2021-10-25 21:11:09.434153: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
2021-10-25 21:11:09.434270: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
Traceback (most recent call last):
File "02_cadd_classification_transformer_tfrecord.py", line 278, in
verbose=1)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training.py", line 727, in fit
2021-10-25 21:11:09.434995: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.435078: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
2021-10-25 21:11:09.435134: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
2021-10-25 21:11:09.435209: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.435261: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
use_multiprocessing=use_multiprocessing)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_arrays.py", line 675, in fit
2021-10-25 21:11:09.435613: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.435697: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
steps_name='steps_per_epoch')
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_arrays.py", line 300, in model_iteration
2021-10-25 21:11:09.436015: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
batch_outs = f(actual_inputs)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/backend.py", line 3476, in call
2021-10-25 21:11:09.436259: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
2021-10-25 21:11:09.436336: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
run_metadata=self.run_metadata)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/client/session.py", line 1472, in call
2021-10-25 21:11:09.437045: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.437105: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.437173: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
2021-10-25 21:11:09.437225: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
run_metadata_ptr)
tensorflow.python.framework.errors_impl.InvalidArgumentError: {{function_node __inference_Dataset_map_single_example_parser_1272}} Key: alt_seq. Can't parse serialized Example.
[[{{node ParseSingleExample/ParseSingleExample}}]]
[[IteratorGetNext]]
2021-10-25 21:11:09.452867: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
2021-10-25 21:11:09.452934: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.

The following have been reloaded with a version change:

1. gcc/7.2.0 => gcc/7.1.0

Using TensorFlow backend.
WARNING:tensorflow:There is non-GPU devices in tf.distribute.Strategy, not using nccl allreduce.
WARNING:tensorflow:From ../bgi/bert4keras/models.py:179: The name tf.keras.initializers.TruncatedNormal is deprecated. Please use tf.compat.v1.keras.initializers.TruncatedNormal instead.

WARNING:tensorflow:From /risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/initializers.py:94: calling TruncatedNormal.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version.
Instructions for updating:
Call initializer instance with the dtype argument instead of passing it to the constructor
WARNING:tensorflow:From /risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/ops/resource_variable_ops.py:1630: calling BaseResourceVariable.init (from tensorflow.python.ops.resource_variable_ops) with constraint is deprecated and will be removed in a future version.
Instructions for updating:
If using Keras pass *_constraint arguments to layers.
WARNING:tensorflow:From /risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/ops/math_grad.py:1424: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.where in 2.0, which has the same broadcast rule as np.where
Traceback (most recent call last):
File "02_train_gene_transformer_lm_hg_bert4keras_tfrecord.py", line 339, in
verbose=1
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training.py", line 727, in fit
use_multiprocessing=use_multiprocessing)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_distributed.py", line 685, in fit
steps_name='steps_per_epoch')
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_arrays.py", line 300, in model_iteration
batch_outs = f(actual_inputs)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/backend.py", line 3476, in call
run_metadata=self.run_metadata)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/client/session.py", line 1472, in call
run_metadata_ptr)
tensorflow.python.framework.errors_impl.InvalidArgumentError: {{function_node __inference_Dataset_map_parse_function_2564}} Key: sequence. Can't parse serialized Example.
[[{{node ParseSingleExample/ParseSingleExample}}]]
[[MultiDeviceIteratorGetNextFromShard]]
[[RemoteCall]]
[[IteratorGetNext]]