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Fusion of Quality Evaluation Metrics and Convolutional Neural Network Representations for Accurate Peak Detection in LC-MS

License: BSD 3-Clause "New" or "Revised" License

Python 23.64% Jupyter Notebook 75.11% R 1.25%

dffroi's Issues

running demo failed, problem with custom metric classes

python example2.py

2024-06-13 20:43:24.736156: I external/local_tsl/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2024-06-13 20:43:24.747995: I external/local_tsl/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2024-06-13 20:43:24.836248: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-06-13 20:43:26.183936: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-06-13 20:43:27.885783: E external/local_xla/xla/stream_executor/cuda/cuda_driver.cc:282] failed call to cuInit: UNKNOWN ERROR (-1)
/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/optimizers/base_optimizer.py:33: UserWarning: Argument decay is no longer supported and will be ignored.
warnings.warn(
Traceback (most recent call last):
File "/share/home/jianglab/yuanmengyi/dffROI-main2/example2.py", line 19, in
dffROI_model = load_model(model_path, custom_objects={'BinaryAccuracy': tf.keras.metrics.BinaryAccuracy, 'TPR': TPR, 'FPR': FPR})
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/saving/saving_api.py", line 183, in load_model
return legacy_h5_format.load_model_from_hdf5(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/legacy/saving/legacy_h5_format.py", line 155, in load_model_from_hdf5
**saving_utils.compile_args_from_training_config(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/legacy/saving/saving_utils.py", line 151, in compile_args_from_training_config
metrics = _deserialize_nested_config(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/legacy/saving/saving_utils.py", line 210, in _deserialize_nested_config
_deserialize_nested_config(deserialize_fn, obj) for obj in config
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/legacy/saving/saving_utils.py", line 210, in _deserialize_nested_config
_deserialize_nested_config(deserialize_fn, obj) for obj in config
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/legacy/saving/saving_utils.py", line 202, in _deserialize_nested_config
return deserialize_fn(config)
^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/legacy/saving/saving_utils.py", line 226, in _deserialize_metric
return metrics_module.deserialize(metric_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/metrics/init.py", line 155, in deserialize
return serialization_lib.deserialize_keras_object(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/saving/serialization_lib.py", line 581, in deserialize_keras_object
return deserialize_keras_object(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/saving/serialization_lib.py", line 718, in deserialize_keras_object
instance = cls.from_config(inner_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/metrics/reduction_metrics.py", line 219, in from_config
return cls(**config)
^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/metrics/reduction_metrics.py", line 187, in init
super().init(name=name, dtype=dtype)
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/metrics/reduction_metrics.py", line 124, in init
self.total = self.add_variable(
^^^^^^^^^^^^^^^^^^
File "/share/home/jianglab/yuanmengyi/miniconda3/envs/R44/lib/python3.12/site-packages/keras/src/metrics/metric.py", line 190, in add_variable
with backend.name_scope(self.name.replace("/", ">"), caller=self):
^^^^^^^^^^^^^^^^^
AttributeError: type object 'TPR' has no attribute 'replace'

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