diff --git a/mlpp_lib/models.py b/mlpp_lib/models.py index 5dd09e9..e756b8b 100644 --- a/mlpp_lib/models.py +++ b/mlpp_lib/models.py @@ -1,6 +1,8 @@ -import tensorflow as tf +import logging from typing import Optional, Union, Any +import numpy as np +import tensorflow as tf from tensorflow.keras.layers import ( Add, Dense, @@ -8,14 +10,11 @@ BatchNormalization, Activation, ) - from tensorflow.keras import Model, initializers from mlpp_lib.physical_layers import * from mlpp_lib.probabilistic_layers import * -import numpy as np - try: import tcn # type: ignore except ImportError: @@ -24,6 +23,10 @@ TCN_IMPORTED = True +_LOGGER = logging.getLogger(__name__) + + +@tf.keras.utils.register_keras_serializable() class MonteCarloDropout(Dropout): def call(self, inputs): return super().call(inputs, training=True) @@ -32,15 +35,22 @@ def call(self, inputs): def _build_fcn_block( inputs, hidden_layers, + batchnorm, activations, dropout, mc_dropout, skip_connection, idx=0, ): + if mc_dropout and dropout is None: + _LOGGER.warning("dropout=None, hence I will ignore mc_dropout=True") + x = inputs for i, units in enumerate(hidden_layers): - x = Dense(units, activation=activations[i], name=f"dense_{idx}_{i}")(x) + x = Dense(units, name=f"dense_{idx}_{i}")(x) + if batchnorm: + x = BatchNormalization()(x) + x = Activation(activations[i])(x) if i < len(dropout) and 0.0 < dropout[i] < 1.0: if mc_dropout: x = MonteCarloDropout(dropout[i], name=f"mc_dropout_{idx}_{i}")(x) @@ -82,6 +92,7 @@ def fully_connected_network( input_shape: tuple[int], output_size: int, hidden_layers: list, + batchnorm: bool = False, activations: Optional[Union[str, list[str]]] = "relu", dropout: Optional[Union[float, list[float]]] = None, mc_dropout: bool = False, @@ -101,6 +112,8 @@ def fully_connected_network( hidden_layers: list[int] List that is used to define the fully connected block. Each element creates a Dense layer with the corresponding units. + batchnorm: bool + Use batch normalization. Default is False. activations: str or list[str] (Optional) Activation function(s) for the Dense layer(s). See https://keras.io/api/layers/activations/#relu-function. If a string is passed, the same activation is used for all layers. Default is `relu`. @@ -150,6 +163,7 @@ def fully_connected_network( x = _build_fcn_block( inputs, hidden_layers, + batchnorm, activations, dropout, mc_dropout, @@ -165,6 +179,7 @@ def fully_connected_multibranch_network( input_shape: tuple[int], output_size: int, hidden_layers: list, + batchnorm: bool = False, activations: Optional[Union[str, list[str]]] = "relu", dropout: Optional[Union[float, list[float]]] = None, mc_dropout: bool = False, @@ -184,6 +199,8 @@ def fully_connected_multibranch_network( hidden_layers: list[int] List that is used to define the fully connected block. Each element creates a Dense layer with the corresponding units. + batchnorm: bool + Use batch normalization. Default is False. activations: str or list[str] (Optional) Activation function(s) for the Dense layer(s). See https://keras.io/api/layers/activations/#relu-function. If a string is passed, the same activation is used for all layers. Default is `relu`. @@ -242,6 +259,7 @@ def fully_connected_multibranch_network( x = _build_fcn_block( inputs, hidden_layers, + batchnorm, activations, dropout, mc_dropout, @@ -263,6 +281,7 @@ def deep_cross_network( input_shape: tuple[int], output_size: int, hidden_layers: list, + batchnorm: bool = True, activations: Optional[Union[str, list[str]]] = "relu", dropout: Optional[Union[float, list[float]]] = None, mc_dropout: bool = False, @@ -282,6 +301,8 @@ def deep_cross_network( hidden_layers: list[int] List that is used to define the fully connected block. Each element creates a Dense layer with the corresponding units. + batchnorm: bool + Use batch normalization. Default is True. activations: str or list[str] (Optional) Activation function(s) for the Dense layer(s). See https://keras.io/api/layers/activations/#relu-function. If a string is passed, the same activation is used for all layers. Default is `relu`. @@ -338,16 +359,15 @@ def deep_cross_network( # deep part deep = inputs - for i, u in enumerate(hidden_layers): - deep = Dense(u)(deep) - deep = BatchNormalization()(deep) - deep = Activation(activations[i])(deep) - if i < len(dropout) and 0.0 < dropout[i] < 1.0: - if mc_dropout: - deep = MonteCarloDropout(dropout[i])(deep) - else: - deep = Dropout(dropout[i])(deep) - # deep = tf.keras.Model(inputs=inputs, outputs=deep, name="deepblock") + deep = _build_fcn_block( + deep, + hidden_layers, + batchnorm, + activations, + dropout, + mc_dropout, + skip_connection=False, + ) # merge merge = tf.keras.layers.Concatenate()([cross, deep]) diff --git a/poetry.lock b/poetry.lock index 8b6664e..493574f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,16 +2,36 @@ [[package]] name = "absl-py" -version = "1.4.0" +version = "2.0.0" description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "absl-py-1.4.0.tar.gz", hash = "sha256:d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d"}, - {file = "absl_py-1.4.0-py3-none-any.whl", hash = "sha256:0d3fe606adfa4f7db64792dd4c7aee4ee0c38ab75dfd353b7a83ed3e957fcb47"}, + {file = "absl-py-2.0.0.tar.gz", hash = "sha256:d9690211c5fcfefcdd1a45470ac2b5c5acd45241c3af71eed96bc5441746c0d5"}, + {file = "absl_py-2.0.0-py3-none-any.whl", hash = "sha256:9a28abb62774ae4e8edbe2dd4c49ffcd45a6a848952a5eccc6a49f3f0fc1e2f3"}, ] +[[package]] +name = "alembic" +version = "1.12.1" +description = "A database migration tool for SQLAlchemy." +category = "dev" +optional = false +python-versions = ">=3.7" +files = [ + {file = "alembic-1.12.1-py3-none-any.whl", hash = "sha256:47d52e3dfb03666ed945becb723d6482e52190917fdb47071440cfdba05d92cb"}, + {file = "alembic-1.12.1.tar.gz", hash = "sha256:bca5877e9678b454706347bc10b97cb7d67f300320fa5c3a94423e8266e2823f"}, +] + +[package.dependencies] +Mako = "*" +SQLAlchemy = ">=1.3.0" +typing-extensions = ">=4" + +[package.extras] +tz = ["python-dateutil"] + [[package]] name = "asciitree" version = "0.3.3" @@ -75,113 +95,140 @@ d = ["aiohttp (>=3.7.4)"] jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] uvloop = ["uvloop (>=0.15.2)"] +[[package]] +name = "blinker" +version = "1.7.0" +description = "Fast, simple object-to-object and broadcast signaling" +category = "dev" +optional = false +python-versions = ">=3.8" +files = [ + {file = "blinker-1.7.0-py3-none-any.whl", hash = "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9"}, + {file = "blinker-1.7.0.tar.gz", hash = "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"}, +] + [[package]] name = "cachetools" -version = "5.3.1" +version = "5.3.2" description = "Extensible memoizing collections and decorators" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "cachetools-5.3.1-py3-none-any.whl", hash = "sha256:95ef631eeaea14ba2e36f06437f36463aac3a096799e876ee55e5cdccb102590"}, - {file = "cachetools-5.3.1.tar.gz", hash = "sha256:dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b"}, + {file = "cachetools-5.3.2-py3-none-any.whl", hash = "sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1"}, + {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"}, ] [[package]] name = "certifi" -version = "2023.7.22" +version = "2023.11.17" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, - {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, + {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"}, + {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"}, ] [[package]] name = "charset-normalizer" -version = "3.2.0" +version = "3.3.2" description = "The Real First Universal Charset Detector. 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-[tool.poetry.dev-dependencies] +[tool.poetry.group.dev.dependencies] tensorflow = "~2.12.1" pytest = "^7" black = "^22.1.0" +mlflow = "^2.8.1" [build-system] requires = ["poetry-core>=1.0.8"] diff --git a/tests/test_save_model.py b/tests/test_save_model.py index a9f0a06..bbfb9b3 100644 --- a/tests/test_save_model.py +++ b/tests/test_save_model.py @@ -9,7 +9,7 @@ from mlpp_lib import models from mlpp_lib import losses, metrics from mlpp_lib import probabilistic_layers -from mlpp_lib.utils import get_loss, get_metric +from mlpp_lib.utils import get_loss, get_metric, get_optimizer def _belongs_here(obj, module): @@ -63,7 +63,11 @@ def test_save_model(save_format, loss, prob_layer, tmp_path): save_traces = False model = models.fully_connected_network( - (5,), 2, hidden_layers=[3], probabilistic_layer=prob_layer + (5,), + 2, + hidden_layers=[3], + probabilistic_layer=prob_layer, + mc_dropout=True, ) assert isinstance(model.from_config(model.get_config()), Functional) loss = get_loss(loss) @@ -104,3 +108,31 @@ def test_save_model(save_format, loss, prob_layer, tmp_path): model = tf.keras.saving.load_model(tmp_path, compile=False) assert isinstance(model, Functional) np.testing.assert_allclose(model(input_arr).mean(), outputs) + + +def test_save_model_mlflow(tmp_path): + """Test model save/load""" + pytest.importorskip("mlflow") + + import mlflow + + mlflow_uri = f"file://{tmp_path.absolute()}/mlruns" + mlflow.set_tracking_uri(mlflow_uri) + + model = models.fully_connected_network( + (5,), 2, hidden_layers=[3, 3], dropout=0.5, mc_dropout=True + ) + optimizer = get_optimizer("Adam") + model.compile(optimizer=optimizer, loss=None, metrics=None) + custom_objects = tf.keras.layers.serialize(model) + + model_info = mlflow.tensorflow.log_model( + model, + "model_save", + custom_objects=custom_objects, + keras_model_kwargs={"save_format": "h5"}, + ) + + tf.keras.backend.clear_session() + model = mlflow.tensorflow.load_model(model_info.model_uri) + assert isinstance(model, Functional)