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HUST-NingKang-Lab / EXPERT

Transfer Learning-enabled context-aware microbial source tracking
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TypeError: Expected `trainable` argument to be a boolean, but got: {} #11

Open JiaLonghao1997 opened 1 year ago

JiaLonghao1997 commented 1 year ago

When we try to use EXPERT, we found a error about expected trainable argument in the transfering knowledge about disease (from the disease model) to the CRC model step. 

(expert) [jialh@head03 testwork]$ expert transfer -i SourceCM.h5 -l SourceLabels.h5 -t ontology.pkl -m disease_model -o CRC_model
2023-05-06 17:15:38.624934: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
Reordering labels and samples...
Total matched samples: 571
WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.Adam.
WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.Adam.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
2023-05-06 17:15:44.386039: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 73801728 exceeds 10% of free system memory.
2023-05-06 17:15:44.411676: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 73801728 exceeds 10% of free system memory.
2023-05-06 17:15:44.425247: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 73801728 exceeds 10% of free system memory.
2023-05-06 17:15:44.588591: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 73801728 exceeds 10% of free system memory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named "keras_metadata.pb" in the SavedModel directory.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
Traceback (most recent call last):
  File "/home1/jialh/anaconda3/envs/expert/bin/expert", line 8, in <module>
    sys.exit(main())
  File "/home1/jialh/anaconda3/envs/expert/lib/python3.8/site-packages/expert/CLI/main.py", line 41, in main
    transfer(cfg, args)
  File "/home1/jialh/anaconda3/envs/expert/lib/python3.8/site-packages/expert/CLI/main_transfer.py", line 62, in transfer
    base_model = Model(phylogeny=phylogeny, num_features=X.shape[1], restore_from=args.model)
  File "/home1/jialh/anaconda3/envs/expert/lib/python3.8/site-packages/expert/src/model.py", line 42, in __init__
    self.encoder = self.init_encoder_block(phylogeny)
  File "/home1/jialh/anaconda3/envs/expert/lib/python3.8/site-packages/expert/src/model.py", line 87, in init_encoder_block
    block.add(Encoder(phylogeny=phylogeny, name=None))
  File "/home1/jialh/anaconda3/envs/expert/lib/python3.8/site-packages/expert/src/model.py", line 210, in __init__
    super(Encoder, self).__init__(kwargs)
  File "/home1/jialh/anaconda3/envs/expert/lib/python3.8/site-packages/tensorflow/python/trackable/base.py", line 205, in _method_wrapper
    result = method(self, *args, **kwargs)
  File "/home1/jialh/anaconda3/envs/expert/lib/python3.8/site-packages/keras/engine/base_layer.py", line 353, in __init__
    raise TypeError(
TypeError: Expected `trainable` argument to be a boolean, but got: {}

If we try to suppress these error messages by commenting out the line, we got a terriable result as following:

,ROC-AUC,F-max
root:CRC (stage 0),0.0,
root:CRC (stage I),0.4432,0.45
root:CRC (stage II),0.5728,0.2581
root:CRC (stage III),0.4084,0.2286
root:CRC (stage IV),0.5278,0.5747

My python environment is:

(expert) [jialh@head03 testwork]$ conda list
# packages in environment at /home1/jialh/anaconda3/envs/expert:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
absl-py                   1.4.0                    pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
blosc2                    2.0.0                    pypi_0    pypi
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cachetools                5.3.0                    pypi_0    pypi
certifi                   2022.12.7                pypi_0    pypi
charset-normalizer        3.1.0                    pypi_0    pypi
contourpy                 1.0.7                    pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
cython                    0.29.34                  pypi_0    pypi
ete3                      3.1.3                    pypi_0    pypi
expert-mst                0.3                      pypi_0    pypi
flatbuffers               23.3.3                   pypi_0    pypi
fonttools                 4.39.3                   pypi_0    pypi
gast                      0.4.0                    pypi_0    pypi
google-auth               2.17.3                   pypi_0    pypi
google-auth-oauthlib      1.0.0                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
grpcio                    1.54.0                   pypi_0    pypi
h5py                      3.8.0                    pypi_0    pypi
idna                      3.4                      pypi_0    pypi
importlib-metadata        6.6.0                    pypi_0    pypi
importlib-resources       5.12.0                   pypi_0    pypi
jax                       0.4.8                    pypi_0    pypi
joblib                    1.2.0                    pypi_0    pypi
keras                     2.12.0                   pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libclang                  16.0.0                   pypi_0    pypi
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsqlite                 3.40.0               h753d276_1    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
living-tree               0.0.5                    pypi_0    pypi
markdown                  3.4.3                    pypi_0    pypi
markupsafe                2.1.2                    pypi_0    pypi
matplotlib                3.7.1                    pypi_0    pypi
ml-dtypes                 0.1.0                    pypi_0    pypi
msgpack                   1.0.5                    pypi_0    pypi
ncurses                   6.3                  h27087fc_1    conda-forge
numexpr                   2.8.4                    pypi_0    pypi
numpy                     1.23.5                   pypi_0    pypi
oauthlib                  3.2.2                    pypi_0    pypi
openssl                   3.1.0                hd590300_3    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 23.1                     pypi_0    pypi
pandas                    2.0.1                    pypi_0    pypi
pillow                    9.5.0                    pypi_0    pypi
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
protobuf                  4.22.3                   pypi_0    pypi
py-cpuinfo                9.0.0                    pypi_0    pypi
pyasn1                    0.5.0                    pypi_0    pypi
pyasn1-modules            0.3.0                    pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
python                    3.8.16          he550d4f_1_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
pytz                      2023.3                   pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
requests                  2.30.0                   pypi_0    pypi
requests-oauthlib         1.3.1                    pypi_0    pypi
rsa                       4.9                      pypi_0    pypi
scikit-learn              1.2.2                    pypi_0    pypi
scipy                     1.10.1                   pypi_0    pypi
seaborn                   0.12.2                   pypi_0    pypi
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0                   pypi_0    pypi
tables                    3.8.0                    pypi_0    pypi
tensorboard               2.12.3                   pypi_0    pypi
tensorboard-data-server   0.7.0                    pypi_0    pypi
tensorflow-cpu            2.12.0                   pypi_0    pypi
tensorflow-estimator      2.12.0                   pypi_0    pypi
tensorflow-io-gcs-filesystem 0.32.0                   pypi_0    pypi
termcolor                 2.3.0                    pypi_0    pypi
threadpoolctl             3.1.0                    pypi_0    pypi
tk                        8.6.12               h27826a3_0    conda-forge
tqdm                      4.65.0                   pypi_0    pypi
treelib                   1.5.5                    pypi_0    pypi
typing-extensions         4.5.0                    pypi_0    pypi
tzdata                    2023.3                   pypi_0    pypi
urllib3                   2.0.2                    pypi_0    pypi
werkzeug                  2.3.3                    pypi_0    pypi
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.14.1                   pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
SantiagoSanchezF commented 4 months ago

Same problem here