33 research outputs found
AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models
Ordinary differential equation models facilitate the understanding of
cellular signal transduction and other biological processes. However, for large
and comprehensive models, the computational cost of simulating or calibrating
can be limiting. AMICI is a modular toolbox implemented in C++/Python/MATLAB
that provides efficient simulation and sensitivity analysis routines tailored
for scalable, gradient-based parameter estimation and uncertainty
quantification.
AMICI is published under the permissive BSD-3-Clause license with source code
publicly available on https://github.com/AMICI-dev/AMICI. Citeable releases are
archived on Zenodo
pyPESTO: A modular and scalable tool for parameter estimation for dynamic models
Mechanistic models are important tools to describe and understand biological
processes. However, they typically rely on unknown parameters, the estimation
of which can be challenging for large and complex systems. We present pyPESTO,
a modular framework for systematic parameter estimation, with scalable
algorithms for optimization and uncertainty quantification. While tailored to
ordinary differential equation problems, pyPESTO is broadly applicable to
black-box parameter estimation problems. Besides own implementations, it
provides a unified interface to various popular simulation and inference
methods. pyPESTO is implemented in Python, open-source under a 3-Clause BSD
license. Code and documentation are available on GitHub
(https://github.com/icb-dcm/pypesto)
PEtab -- interoperable specification of parameter estimation problems in systems biology
Reproducibility and reusability of the results of data-based modeling studies
are essential. Yet, there has been -- so far -- no broadly supported format for
the specification of parameter estimation problems in systems biology. Here, we
introduce PEtab, a format which facilitates the specification of parameter
estimation problems using Systems Biology Markup Language (SBML) models and a
set of tab-separated value files describing the observation model and
experimental data as well as parameters to be estimated. We already implemented
PEtab support into eight well-established model simulation and parameter
estimation toolboxes with hundreds of users in total. We provide a Python
library for validation and modification of a PEtab problem and currently 20
example parameter estimation problems based on recent studies. Specifications
of PEtab, the PEtab Python library, as well as links to examples, and all
supporting software tools are available at https://github.com/PEtab-dev/PEtab,
a snapshot is available at https://doi.org/10.5281/zenodo.3732958. All original
content is available under permissive licenses
Informative and adaptive distances and summary statistics in sequential approximate Bayesian computation.
Calibrating model parameters on heterogeneous data can be challenging and inefficient. This holds especially for likelihood-free methods such as approximate Bayesian computation (ABC), which rely on the comparison of relevant features in simulated and observed data and are popular for otherwise intractable problems. To address this problem, methods have been developed to scale-normalize data, and to derive informative low-dimensional summary statistics using inverse regression models of parameters on data. However, while approaches only correcting for scale can be inefficient on partly uninformative data, the use of summary statistics can lead to information loss and relies on the accuracy of employed methods. In this work, we first show that the combination of adaptive scale normalization with regression-based summary statistics is advantageous on heterogeneous parameter scales. Second, we present an approach employing regression models not to transform data, but to inform sensitivity weights quantifying data informativeness. Third, we discuss problems for regression models under non-identifiability, and present a solution using target augmentation. We demonstrate improved accuracy and efficiency of the presented approach on various problems, in particular robustness and wide applicability of the sensitivity weights. Our findings demonstrate the potential of the adaptive approach. The developed algorithms have been made available in the open-source Python toolbox pyABC
ICB-DCM/PEtab v0.0.0a11
PEtab - a tsv-based data format for parameter estimation problems in systems biolog
ICB-DCM/pyABC: Release 0.12.14
<p>Visualization:</p>
<ul>
<li>Selected plotly versions of matplotlib visualizations</li>
</ul>
<p>General:</p>
<ul>
<li>Added functionality to evaluate the model using boundary values of parameter</li>
</ul>
FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes
<p>Supplementary Data to the publication "FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes", Alamoudi et al. 2023.</p>
AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models
<p><strong>Deprecations</strong></p>
<ul>
<li>Moved PEtab-related functionality from <code>amici.petab_*</code> to the
petab-subpackage <code>amici.petab.*</code>. The old public functions are still
available but will be removed in a future release.
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2205, https://github.com/AMICI-dev/AMICI/pull/2211, https://github.com/AMICI-dev/AMICI/pull/2252</li>
</ul>
<p><strong>Features</strong></p>
<ul>
<li>Handle events occurring at fixed timepoints without root-finding.
This avoids event-after-reinitialization errors in many cases a brings a
slight performance improvement.
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2227</li>
<li>Added <code>PetabProblem</code> class for handling PEtab-defined simulation conditions,
making it easier to perform customized operations based on PEtab-defined
simulation conditions.
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2255</li>
<li>code-gen: Simplified <code>switch</code> statements, leading to reduced file sizes and
faster compilation for certain models.
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2240</li>
<li>Made <code>Model</code> and <code>ModelPtr</code> deepcopyable
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2247</li>
<li>Made <code>Solver</code> and <code>SolverPtr</code> deepcopyable
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2245</li>
<li>Added a debugging helper <code>get_model_for_preeq</code> for debugging simulation
issues during pre-equilibration.
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2250</li>
<li>Added <code>SwigPtrView</code> fields to <code>dir()</code> outputs
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2244</li>
<li>Use proper labels for in plotting functions if IDs are available in
<code>ReturnData</code>.
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2249</li>
<li>Added <code>ExpData::clear_observations</code> to set all measurements/sigmas to NaN
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2258</li>
</ul>
<p><strong>Fixes</strong></p>
<ul>
<li>Fixed AMICI hiding all warnings. Previously, importing <code>amici</code> resulted
in all warnings being hidden in the rest of the program.
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2243</li>
<li>CMake: Fixed model debug builds
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2222</li>
<li>Fixed CMake potentially using incorrect Python library for building model
extension
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2220</li>
<li>CMake: fixed cxx flag check
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2225</li>
<li>Fixed potential out-of-bounds read in <code>Model::checkFinite</code> for
matlab-imported models
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2232</li>
<li>Fixed piecewise/Heaviside handling
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2234</li>
<li>Deterministic order of event assignments
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2242</li>
<li>Proper error message in case of unsupported state-dependent sigmas
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2239</li>
<li>Fixed swig shadow warning + other linting issues
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2261</li>
<li>Fixed <code>SwigPtrView.__getattr__</code>
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2259</li>
<li><code>simulate_petab</code>: Avoid warning when simulating with default parameters
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2265</li>
</ul>
<p><strong>Documentation</strong></p>
<ul>
<li>Updated Python package installation instructions for Arch Linux
by @willov in https://github.com/AMICI-dev/AMICI/pull/2212</li>
<li>Updated <code>ExpData</code> documentation
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2254</li>
<li>Documented simulation starting time <code>t0</code>
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2263</li>
<li>Updated PEtab example
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2255</li>
</ul>
<p>...</p>
<p><strong>Full Changelog</strong>: https://github.com/AMICI-dev/AMICI/compare/v0.20.0...v0.21.0</p>If you use this software, please cite both the article from preferred-citation and the software itself