StochasticForceInference 2.0.0__py3-none-any.whl

stochasticforceinference-2.0.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: StochasticForceInference
+Version: 2.0.0
+Summary: Stochastic Force Inference for Langevin SDEs
+Author-email: Pierre Ronceray <pierre.ronceray@univ-amu.fr>
+License: MIT
+Project-URL: Homepage, https://github.com/ronceray/StochasticForceInference
+Project-URL: Documentation, https://sfi.readthedocs.io
+Project-URL: Repository, https://github.com/ronceray/StochasticForceInference
+Project-URL: Issues, https://github.com/ronceray/StochasticForceInference/issues
+Project-URL: Changelog, https://github.com/ronceray/StochasticForceInference/blob/main/CHANGELOG.md
+Keywords: stochastic force inference,Langevin dynamics,stochastic differential equations,diffusion,inference,sparse model selection,active matter,biophysics,JAX
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: jax>=0.10
+Requires-Dist: jaxlib
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: pyyaml
+Requires-Dist: equinox>=0.12
+Requires-Dist: opt-einsum
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx-gallery; extra == "docs"
+Requires-Dist: sphinxcontrib-video; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid; extra == "docs"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pyright; extra == "dev"
+Requires-Dist: StochasticForceInference[docs]; extra == "dev"
+Provides-Extra: io
+Requires-Dist: pyarrow>=14; extra == "io"
+Requires-Dist: h5py>=3.9; extra == "io"
+Requires-Dist: pandas>=2.0; extra == "io"
+Requires-Dist: PyYAML>=6.0; extra == "io"
+Dynamic: license-file
+
+# Stochastic Force Inference (SFI)
+
+**Infer force and diffusion fields from stochastic trajectory data.**
+
+SFI is a JAX-based Python package for learning the drift (force) and diffusion
+of Langevin stochastic differential equations from time-series observations.
+It handles both overdamped and underdamped dynamics, supports interacting
+particles and spatially-extended (SPDE) systems, and provides built-in
+diagnostics, sparse model selection, and bootstrapped validation.
+
+> **Designed for experimental data.**  SFI is built for real experimental
+> trajectories (tracked particles, cells, organisms, …) where *no dynamical
+> model pre-exists*.  Two first-class estimator families share one API:
+> fast closed-form **linear estimators** that require no initial guess, and
+> **parametric estimators** that model measurement noise and finite sampling
+> explicitly — robust where real data is hard.  The PASTIS information
+> criterion rigorously identifies which terms the data actually supports.
+> Synthetic examples in the gallery serve as runnable demonstrations.
+
+## Key features
+
+- **Two estimator families** — closed-form linear estimators
+  (`infer_force_linear`, seconds even on large datasets) and parametric
+  estimators (`infer_force` / `infer_diffusion`: noise-aware likelihood
+  fit, robust to localization error and coarse sampling, accepts
+  nonlinear models such as neural-network drifts).
+- **Overdamped & underdamped inference** — works with position-only data;
+  velocities are reconstructed automatically for underdamped systems.
+- **Composable state functions** — build force/diffusion models from
+  monomials, custom basis functions, pair interactions, or arbitrary
+  parametric families, all with automatic differentiation via JAX.
+- **Sparse model selection** — Pareto-front beam search with AIC / BIC /
+  PASTIS information criteria.
+- **Simulation** — simulate Langevin SDEs (Euler–Maruyama) from the same
+  model objects used for inference.
+- **Trajectory toolkit** — mask-aware increments, synthetic degradation
+  (noise, downsampling, data loss, motion blur), streaming for large
+  datasets, I/O (CSV / Parquet / HDF5).
+- **Diagnostics** — compare inferred fields to exact models, compute
+  normalized errors, generate bootstrapped trajectories.
+
+## Installation
+
+```bash
+pip install StochasticForceInference
+```
+
+For development (editable install with test/doc dependencies):
+
+```bash
+git clone https://github.com/ronceray/StochasticForceInference.git
+cd StochasticForceInference
+pip install -e ".[dev,io]"
+```
+
+> **Note:** SFI requires Python ≥ 3.11 and JAX ≥ 0.10.
+
+## Quick start
+
+For **experimental data**, load your trajectories and infer directly:
+
+```python
+import numpy as np
+from SFI import OverdampedLangevinInference, TrajectoryCollection
+from SFI.bases import monomials_up_to
+
+# Load your tracked data (positions: T×d array, dt: time step)
+positions = np.load("my_experiment.npz")["positions"]  # shape (T, d)
+coll = TrajectoryCollection.from_arrays(X=positions, dt=0.01)
+
+# Infer using a polynomial basis — no model needed
+B = monomials_up_to(order=3, dim=2, rank="vector")
+inf = OverdampedLangevinInference(coll)
+inf.compute_diffusion_constant()
+inf.infer_force_linear(B)
+inf.sparsify_force(criterion="PASTIS")  # optional: find the minimal model
+inf.print_report()
+
+# Noisy or coarsely-sampled recordings? Use the parametric estimator
+# instead: inf.infer_force(B) — it models the measurement noise natively.
+```
+
+For a **synthetic example** (useful for validation):
+
+```python
+import jax.numpy as jnp
+from jax import random
+
+from SFI import OverdampedLangevinInference
+from SFI.bases import X, monomials_up_to
+from SFI.langevin import OverdampedProcess
+
+# 1. Build a force model (Ornstein–Uhlenbeck: F = -k x) and simulate a trajectory.
+#    X(dim) is the identity basis x ↦ x; theta_F holds its coefficient, so F(x) = -x.
+proc = OverdampedProcess(F=X(dim=2), D=jnp.eye(2) * 0.5, theta_F=jnp.array([-1.0]))
+proc.initialize(jnp.zeros(2))
+coll = proc.simulate(dt=0.01, Nsteps=10_000, key=random.PRNGKey(0))
+
+# 2. Infer from the trajectory using a generic polynomial basis
+B = monomials_up_to(order=2, dim=2, rank="vector")
+inf = OverdampedLangevinInference(coll)
+inf.compute_diffusion_constant()
+inf.infer_force_linear(B)
+inf.compute_force_error()
+
+# 3. Inspect results and validate against the known model
+inf.print_report()
+inf.compare_to_exact(model_exact=proc)
+```
+
+## Documentation
+
+Full documentation is available at
+[sfi.readthedocs.io](https://sfi.readthedocs.io), including:
+
+- **[Tutorial](https://sfi.readthedocs.io/en/latest/gallery/ou_demo.html)** — end-to-end walkthrough
+- **[Examples gallery](https://sfi.readthedocs.io/en/latest/gallery/index.html)** — worked examples covering sparsity, multi-particle, and SPDE inference
+- **[Model building](https://sfi.readthedocs.io/en/latest/statefunc/user_guide.html)** — composable state functions
+- **[Trajectory handling](https://sfi.readthedocs.io/en/latest/trajectory/user_guide.html)** — data ingestion, masking, degradation
+- **[Running inference](https://sfi.readthedocs.io/en/latest/inference/user_guide.html)** — estimator choice, overdamped/underdamped engines
+- **[API reference](https://sfi.readthedocs.io/en/latest/api_frontend.html)** — full autodoc
+
+## Package structure
+
+| Subpackage       | Purpose                                              |
+| ---------------- | ---------------------------------------------------- |
+| `SFI.statefunc`  | Composable state functions: `Basis`, `PSF`, `SF`     |
+| `SFI.inference`  | Overdamped & underdamped inference engines            |
+| `SFI.trajectory` | `TrajectoryCollection` / `TrajectoryDataset`          |
+| `SFI.langevin`   | Langevin simulators (`OverdampedProcess`, …)          |
+| `SFI.bases`      | Ready-made basis builders (monomials, constants, …)  |
+| `SFI.integrate`  | Time-averaging integration engine                    |
+| `SFI.utils`      | Math helpers, formatting, plotting                   |
+
+For contributors and AI coding agents: see [`AGENTS.md`](https://github.com/ronceray/StochasticForceInference/blob/main/AGENTS.md) for
+the canonical imports table, task playbooks, and "do not re-implement"
+guidance.
+
+## Citation
+
+If you use SFI in your research, please cite:
+
+> Frishman, A. & Ronceray, P., *Learning force fields from stochastic
+> trajectories*, Physical Review X (2020).
+> [DOI: 10.1103/PhysRevX.10.021009](https://doi.org/10.1103/PhysRevX.10.021009)
+
+## License
+
+MIT — see [LICENSE](https://github.com/ronceray/StochasticForceInference/blob/main/LICENSE) for details.

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+stochasticforceinference-2.0.0.dist-info/licenses/LICENSE,sha256=25o1rLAxoVqogpI7QHgadeoXNC7OnN_JMTf9BixSK-k,1077
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stochasticforceinference-2.0.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

stochasticforceinference-2.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020-2026 Pierre Ronceray
+
+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
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

stochasticforceinference-2.0.0.dist-info/top_level.txt

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+SFI