vpop-calibration 2.2.8__py3-none-any.whl

vpop_calibration-2.2.8.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: vpop-calibration
+Version: 2.2.8
+Summary: 
+License-File: LICENSE
+Author: Paul Lemarre
+Author-email: paul.lemarre@novainsilico.ai
+Requires-Python: >=3.12,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: gpytorch (>=1.14.2,<2.0.0)
+Requires-Dist: matplotlib (>=3.10.7,<4.0.0)
+Requires-Dist: numpy (>=2.3.4,<3.0.0)
+Requires-Dist: pandas (>=2.3.3,<3.0.0)
+Requires-Dist: plotly (>=6.4.0,<7.0.0)
+Requires-Dist: scipy (>=1.16.3,<2.0.0)
+Requires-Dist: torch
+Requires-Dist: tqdm (>=4.67.1,<5.0.0)
+Requires-Dist: uuid (>=1.30,<2.0)
+Description-Content-Type: text/markdown
+
+# Vpop calibration
+
+## Description
+
+A set of Python tools to allow for virtual population calibration, using a non-linear mixed effects (NLME) model approach, combined with surrogate models in order to speed up the simulation of QSP models.
+
+### Currently available features
+
+- Surrogate modeling using gaussian processes, implemented using [GPyTorch](https://github.com/cornellius-gp/gpytorch)
+- Synthetic data generation using ODE models. The current implementation uses [scipy.integrate.solve_ivp](https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.solve_ivp.html), parallelized with [multiprocessing](https://docs.python.org/3/library/multiprocessing.html)
+- Non-linear mixed effect models:
+  - Log-distributed parameters
+  - Additive or multiplicative error model
+  - Covariates handling
+  - Known individual patient descriptors (i.e. covariates with no effect on other descriptors outside of the structural model)
+- SAEM: see the [dedicated doc](./docs/saem_implementation.md) for more details
+
+## Getting started
+
+- [Tutorial](./examples/saem_gp_model.ipynb): this notebook demonstrates step-by-step how to create and train a surrogate model, using a reference ODE model and a GP surrogate model. It then showcases how to optimize the surrogate model on synthetic data using SAEM
+- Other available examples:
+  - [Data generation using Sobol sequences](./examples/generate_data_ranges.ipynb)
+  - [Data generation using a reference NLME model](./examples/generate_data_nlme.ipynb)
+  - [Training and exporting a GP using synthetic data](./examples/train_gp.ipynb)
+  - [Running SAEM on a reference ODE model](./examples/saem_ode_model.ipynb). Note: the current implementation is notably under-optimized for running SAEM directly on an ODE structural model. This is implemented for testing purposes mostly
+  - [Training a GP with a deep kernel](./examples/train_deep_kernel.ipynb)
+
+## Support
+
+For any issue or comments, please reach out to paul.lemarre@novainsilico.ai, or feel free to open an issue in the repo directly.
+
+## Authors and acknowledgment
+
+- Paul Lemarre
+- Eléonore Dravet
+- Adeline Leclerq-Sampson
+
+## Roadmap
+
+- NLME:
+  - Support additional error models (additive-multiplicative, power, etc...)
+  - Support additional covariate models (categorical covariates)
+  - Add residual diagnostic methods (weighted residuals computation and visualization)
+- Structural models:
+  - Integrate with SBML models (Roadrunner)
+- Surrogate models:
+  - Support additional surrogate models in PyTorch
+- Optimizer:
+  - Add SVGP for surrogate model optimization
+
+## References
+
+- [Delyon et al. 99](https://doi.org/10.1214/aos/1018031103): Bernard Delyon. Marc Lavielle. Eric Moulines. "Convergence of a stochastic approximation version of the EM algorithm." Ann. Statist. 27 (1) 94 - 128, February 1999. https://doi.org/10.1214/aos/1018031103
+- [Grenier et al. 2018](https://doi.org/10.1007/s40314-016-0337-5): Grenier, E., Helbert, C., Louvet, V. et al. Population parametrization of costly black box models using iterations between SAEM algorithm and kriging. Comp. Appl. Math. 37, 161–173 (2018). https://doi.org/10.1007/s40314-016-0337-5
+

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vpop_calibration-2.2.8.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2024 Nova
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+SOFTWARE.