This tool aims to create hybrid machine learning models using tensorflow and keras. In this context hybrid means, that the models consist of submodels that are connected in a feed forward graph. These submodels, called nodes are machine learning models themselves. We currently support neural networks, mechanistic models (formulas) and linear odes as nodes. It is possible to add more types of models. More can be found under "How to to implement new node types".
- tensorflow
- casadi
- numpy
- matlotlib
- tqdm
Install the requirements with:
pip install -r ./requirements.txt
We include several demos of varying complexity into the project.
Basic functionality of the Tool:
Models can be loaded by using the Project Module.
The behaviour of the models mimics the behaviour of tensorflow/keras models.
A simple demo can be found in simple_demo.py.
Here is an excerpt of simple_demo.py.
from HybridML import Project
# Create model from description
model_description_path = "simple_model.json"
model = Project.create_model(model_description_path)
# Train model with generated data
model.fit(X_train, y_train, validation_split=0.8, epochs=1)
# Evaluate model on test data
model.evaluate(X_test, y_test)
# Save model to file
model_path = model_description_path + ".h5"
model.save_to_file(model_path)
# Load model from file. The model description is needed to load the model.
loaded_model = Project.load_model(model_description_path, model_path)
# Predict both models and compare output
prediction = model.predict(X_test)
loaded_model_prediction = loaded_model.predict(X_test)
assert np.all(prediction - loaded_model_prediction < 1e-5)extrapolation_demo.py Contains a project with at hybrid model and a black box model. It demonstrates the project api and anecdotally shows the extrapolation capability of hybrid models.
theoph_demo.py This demo contains a complex model, that uses neural nets and mechanistic models to estimate parameters for an ode system. The model resembles a two compartiment model for drug concentration in the blood system. It makes use of the Theophylline dataset, that comes with the R language.
flux_demo.py, structured_flux_demo.py Similar type of model to the theophylline demo. Contains a more refined model for a use case that is closer to the industry.
HybridML can also be used with the project architecture. A project contains a name, one or multiple models and one or multiple datasources. A new model can be created by using:
import Project
project = Project.create(containing_dir, "project_name")Then a file of the name project_name.json is created in the containing directory.
There, new models and datasources can be added.
To open an already existing model the method Project.open(project_file_path) can be used, where project_file_path is the path to the formerly created project_name.json.
The project class has the ability to create and load all of its models at once, using the methods generate_models() and load_models().
Note, that it is not necessary to state the location of the model description or the saved model file, as both are handled by the project instance.
All models can be saved, using the save() method.
The data sources can be loaded, using load_data_sources(), where we again don't have to state the location of the data sources, because they are handled by the project instance.
The data sources can then be accessed via the data_sources propoerty, which is a list of data_sources.
The model creation process consists of the two phases parsing and building. In the parsing phase, the model description file is read and loaded into memory. In the building phase, the parsed model is then built. The two phases are independant from each other.
The model creation process is coordinated by the ModelCreator.
It has a NodeRegistry, which contains parsers and builders for all possible types of nodes, as well as all custom Tensorflow objects.
Furthermore, it has a ModelParser, which recieves the model-json.
The parsed output is then given to its ModelBuilder, which performs the final step of building the tensorflow model.
At first the simple parameters of the model, such as name, mse, loss, etc are parsed.
Then the network structure of the model is parsed by an instance of NetParser.
The parsing itself consists of two passes.
In the first pass, all nodes of the network are parsed by NodeParsers.
The resulting ParsedNodes are connected with NodeConnors, which are represented by variable names in the model-json.s
In the second pass the parser walks through the network and propagates the input and output sizes of each node thorugh the ParsedNodes and NodeConnectors.
In the first step, a NetworkBuilder is used to build the network.
The tensorflow/keras functional api is used to construct the network.
At first, Inputs are built, which represent the NodeConnectors, labelled as inputs in the model description.
Then the builder walks throught the network, building the nodes using NodeBuilders, and connecting them to their input tensors, and collecting all input and output tensors in a dictionary.
This parsed network is then used to build a model and an additional_outputs_model.
For each type of node there is an implementation of each of the three classes NodeBuilder, NodeParser, Node.
The parsers and builders select the correct implementation during the process.
More on that in How to implement new node types.
An example of the usage is the fluvoxamine use case. The goal is to fit a model that predicts the concentration of the drug fluvoxamine in the blood of a patient. The inputs of the model are a set of covariates of the patient (eg. weight, gender, ...), the initial dose and a time series. The output is a concentration for each time point. Input sizes: [covariates: (n_covariates), init_dose:(1), time_series:(n_time_steps)] Output Sizes: [(n_time_steps)]
The chosen model is a pharmacokinetic three-compartement model. The model estimates the k parameters and solves the ode-system. The k parameters are estimated, using a black box. The outputs of the blackbox are transposed and scaled to initial guesses.
The fluvoxamine use case can be found in flux_demo.py.
See model-json.md.
See create-nodes.md.
Our paper can be retrieved at https://doi.org/10.1016/j.compchemeng.2022.107736. If you use HybridML in your work, please cite our paper using the following citation.
@article{MERKELBACH2022107736,
title = {HybridML: Open source platform for hybrid modeling},
journal = {Computers & Chemical Engineering},
volume = {160},
pages = {107736},
year = {2022},
issn = {0098-1354},
doi = {https://doi.org/10.1016/j.compchemeng.2022.107736},
url = {https://www.sciencedirect.com/science/article/pii/S0098135422000771},
author = {Kilian Merkelbach and Artur M. Schweidtmann and Younes Müller and Patrick Schwoebel and Adel Mhamdi and Alexander Mitsos and Andreas Schuppert and Thomas Mrziglod and Sebastian Schneckener},
keywords = {Hybrid modeling, Machine learning, Modeling tools, Tensorflow, Python, Pharmacokinetics},
abstract = {Hybrid modelling, i.e., the combination of data-driven modelling with mechanistic model components, reduces the data demand and enables extrapolation of data-driven models. However, building, training and evaluation of hybrid models is cumbersome with current frameworks. We developed HybridML, an open-source modeling platform, in which hybrid models can be trained, i.e., combinations of artificial neural networks, arithmetic expressions, and differential equations. We employ TensorFlow for artificial neural network training and Casadi to integrate ordinary differential equations and provide gradients of differential model equations enabling continuous time representations. HybridML provides also a JSON interface for the model development. We apply HybridML to an industrial case study, in which the trained model is used to predict drug concentrations over time, based on physiological information about the patients. To demonstrate its versatility, we also present a nonlinear application, where HybridML is used to model the spread of the COVID-19 pandemic in German federal states based on the state’s socio-economic attributes.}
}
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