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https://github.com/MilesCranmer/PySR
High-Performance Symbolic Regression in Python and Julia
https://github.com/MilesCranmer/PySR
algorithm automl data-science distributed-systems equation-discovery evolutionary-algorithms explainable-ai genetic-algorithm interpretable-ml julia machine-learning python scikit-learn symbolic symbolic-regression
Last synced: about 1 month ago
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High-Performance Symbolic Regression in Python and Julia
- Host: GitHub
- URL: https://github.com/MilesCranmer/PySR
- Owner: MilesCranmer
- License: apache-2.0
- Created: 2020-09-14T11:16:09.000Z (about 4 years ago)
- Default Branch: master
- Last Pushed: 2024-10-08T00:14:31.000Z (2 months ago)
- Last Synced: 2024-10-29T15:17:19.911Z (about 1 month ago)
- Topics: algorithm, automl, data-science, distributed-systems, equation-discovery, evolutionary-algorithms, explainable-ai, genetic-algorithm, interpretable-ml, julia, machine-learning, python, scikit-learn, symbolic, symbolic-regression
- Language: Python
- Homepage: https://astroautomata.com/PySR
- Size: 4.88 MB
- Stars: 2,386
- Watchers: 32
- Forks: 214
- Open Issues: 88
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.md
Awesome Lists containing this project
- awesome-sciml - MilesCranmer/PySR: Simple, fast, and parallelized symbolic regression in Python/Julia via regularized evolution and simulated annealing
README
[//]: # (Logo:)
PySR searches for symbolic expressions which optimize a particular objective.
https://github.com/MilesCranmer/PySR/assets/7593028/c8511a49-b408-488f-8f18-b1749078268f
# PySR: High-Performance Symbolic Regression in Python and Julia
| **Docs** | **Forums** | **Paper** | **colab demo** |
|:---:|:---:|:---:|:---:|
|[](https://astroautomata.com/PySR/)|[](https://github.com/MilesCranmer/PySR/discussions)|[](https://arxiv.org/abs/2305.01582)|[](https://colab.research.google.com/github/MilesCranmer/PySR/blob/master/examples/pysr_demo.ipynb)|
| **pip** | **conda** | **Stats** |
| :---: | :---: | :---: |
|[](https://badge.fury.io/py/pysr)|[](https://anaconda.org/conda-forge/pysr)|
pip: [](https://pypi.org/project/pysr/)
conda: [](https://anaconda.org/conda-forge/pysr)|
If you find PySR useful, please cite the paper [arXiv:2305.01582](https://arxiv.org/abs/2305.01582).
If you've finished a project with PySR, please submit a PR to showcase your work on the [research showcase page](https://astroautomata.com/PySR/papers)!
**Contents**:
- [Why PySR?](#why-pysr)
- [Installation](#installation)
- [Quickstart](#quickstart)
- [→ Documentation](https://astroautomata.com/PySR)
- [Contributors](#contributors-)
### Test status
| **Linux** | **Windows** | **macOS** |
|---|---|---|
|[](https://github.com/MilesCranmer/PySR/actions/workflows/CI.yml)|[](https://github.com/MilesCranmer/PySR/actions/workflows/CI_Windows.yml)|[](https://github.com/MilesCranmer/PySR/actions/workflows/CI_mac.yml)|
| **Docker** | **Conda** | **Coverage** |
|[](https://github.com/MilesCranmer/PySR/actions/workflows/CI_docker.yml)|[](https://github.com/MilesCranmer/PySR/actions/workflows/CI_conda_forge.yml)|[](https://coveralls.io/github/MilesCranmer/PySR)|
## Why PySR?
PySR is an open-source tool for *Symbolic Regression*: a machine learning
task where the goal is to find an interpretable symbolic expression that optimizes some objective.
Over a period of several years, PySR has been engineered from the ground up
to be (1) as high-performance as possible,
(2) as configurable as possible, and (3) easy to use.
PySR is developed alongside the Julia library [SymbolicRegression.jl](https://github.com/MilesCranmer/SymbolicRegression.jl),
which forms the powerful search engine of PySR.
The details of these algorithms are described in the [PySR paper](https://arxiv.org/abs/2305.01582).
Symbolic regression works best on low-dimensional datasets, but
one can also extend these approaches to higher-dimensional
spaces by using "*Symbolic Distillation*" of Neural Networks, as explained in
[2006.11287](https://arxiv.org/abs/2006.11287), where we apply
it to N-body problems. Here, one essentially uses
symbolic regression to convert a neural net
to an analytic equation. Thus, these tools simultaneously present
an explicit and powerful way to interpret deep neural networks.
## Installation
### Pip
You can install PySR with pip:
```bash
pip install pysr
```
Julia dependencies will be installed at first import.
### Conda
Similarly, with conda:
```bash
conda install -c conda-forge pysr
```
### Docker
You can also use the `Dockerfile` to install PySR in a docker container
1. Clone this repo.
2. Within the repo's directory, build the docker container:
```bash
docker build -t pysr .
```
3. You can then start the container with an IPython execution with:
```bash
docker run -it --rm pysr ipython
```
For more details, see the [docker section](#docker).
### Apptainer
If you are using PySR on a cluster where you do not have root access,
you can use [Apptainer](https://apptainer.org/) to build a container
instead of Docker. The `Apptainer.def` file is analogous to the `Dockerfile`,
and can be built with:
```bash
apptainer build --notest pysr.sif Apptainer.def
```
and launched with
```bash
apptainer run pysr.sif
```
### Troubleshooting
One issue you might run into can result in a hard crash at import with
a message like "`GLIBCXX_...` not found". This is due to another one of the Python dependencies
loading an incorrect `libstdc++` library. To fix this, you should modify your
`LD_LIBRARY_PATH` variable to reference the Julia libraries. For example, if the Julia
version of `libstdc++.so` is located in `$HOME/.julia/juliaup/julia-1.10.0+0.x64.linux.gnu/lib/julia/`
(which likely differs on your system!), you could add:
```
export LD_LIBRARY_PATH=$HOME/.julia/juliaup/julia-1.10.0+0.x64.linux.gnu/lib/julia/:$LD_LIBRARY_PATH
```
to your `.bashrc` or `.zshrc` file.
## Quickstart
You might wish to try the interactive tutorial [here](https://colab.research.google.com/github/MilesCranmer/PySR/blob/master/examples/pysr_demo.ipynb), which uses the notebook in `examples/pysr_demo.ipynb`.
In practice, I highly recommend using IPython rather than Jupyter, as the printing is much nicer.
Below is a quick demo here which you can paste into a Python runtime.
First, let's import numpy to generate some test data:
```python
import numpy as np
X = 2 * np.random.randn(100, 5)
y = 2.5382 * np.cos(X[:, 3]) + X[:, 0] ** 2 - 0.5
```
We have created a dataset with 100 datapoints, with 5 features each.
The relation we wish to model is $2.5382 \cos(x_3) + x_0^2 - 0.5$.
Now, let's create a PySR model and train it.
PySR's main interface is in the style of scikit-learn:
```python
from pysr import PySRRegressor
model = PySRRegressor(
niterations=40, # < Increase me for better results
binary_operators=["+", "*"],
unary_operators=[
"cos",
"exp",
"sin",
"inv(x) = 1/x",
# ^ Custom operator (julia syntax)
],
extra_sympy_mappings={"inv": lambda x: 1 / x},
# ^ Define operator for SymPy as well
elementwise_loss="loss(prediction, target) = (prediction - target)^2",
# ^ Custom loss function (julia syntax)
)
```
This will set up the model for 40 iterations of the search code, which contains hundreds of thousands of mutations and equation evaluations.
Let's train this model on our dataset:
```python
model.fit(X, y)
```
Internally, this launches a Julia process which will do a multithreaded search for equations to fit the dataset.
Equations will be printed during training, and once you are satisfied, you may
quit early by hitting 'q' and then \.
After the model has been fit, you can run `model.predict(X)`
to see the predictions on a given dataset using the automatically-selected expression,
or, for example, `model.predict(X, 3)` to see the predictions of the 3rd equation.
You may run:
```python
print(model)
```
to print the learned equations:
```python
PySRRegressor.equations_ = [
pick score equation loss complexity
0 0.000000 4.4324794 42.354317 1
1 1.255691 (x0 * x0) 3.437307 3
2 0.011629 ((x0 * x0) + -0.28087974) 3.358285 5
3 0.897855 ((x0 * x0) + cos(x3)) 1.368308 6
4 0.857018 ((x0 * x0) + (cos(x3) * 2.4566472)) 0.246483 8
5 >>>> inf (((cos(x3) + -0.19699033) * 2.5382123) + (x0 *... 0.000000 10
]
```
This arrow in the `pick` column indicates which equation is currently selected by your
`model_selection` strategy for prediction.
(You may change `model_selection` after `.fit(X, y)` as well.)
`model.equations_` is a pandas DataFrame containing all equations, including callable format
(`lambda_format`),
SymPy format (`sympy_format` - which you can also get with `model.sympy()`), and even JAX and PyTorch format
(both of which are differentiable - which you can get with `model.jax()` and `model.pytorch()`).
Note that `PySRRegressor` stores the state of the last search, and will restart from where you left off the next time you call `.fit()`, assuming you have set `warm_start=True`.
This will cause problems if significant changes are made to the search parameters (like changing the operators). You can run `model.reset()` to reset the state.
You will notice that PySR will save two files:
`hall_of_fame...csv` and `hall_of_fame...pkl`.
The csv file is a list of equations and their losses, and the pkl file is a saved state of the model.
You may load the model from the `pkl` file with:
```python
model = PySRRegressor.from_file("hall_of_fame.2022-08-10_100832.281.pkl")
```
There are several other useful features such as denoising (e.g., `denoise=True`),
feature selection (e.g., `select_k_features=3`).
For examples of these and other features, see the [examples page](https://astroautomata.com/PySR/examples).
For a detailed look at more options, see the [options page](https://astroautomata.com/PySR/options).
You can also see the full API at [this page](https://astroautomata.com/PySR/api).
There are also tips for tuning PySR on [this page](https://astroautomata.com/PySR/tuning).
### Detailed Example
The following code makes use of as many PySR features as possible.
Note that is just a demonstration of features and you should not use this example as-is.
For details on what each parameter does, check out the [API page](https://astroautomata.com/PySR/api/).
```python
model = PySRRegressor(
procs=4,
populations=8,
# ^ 2 populations per core, so one is always running.
population_size=50,
# ^ Slightly larger populations, for greater diversity.
ncycles_per_iteration=500,
# ^ Generations between migrations.
niterations=10000000, # Run forever
early_stop_condition=(
"stop_if(loss, complexity) = loss < 1e-6 && complexity < 10"
# Stop early if we find a good and simple equation
),
timeout_in_seconds=60 * 60 * 24,
# ^ Alternatively, stop after 24 hours have passed.
maxsize=50,
# ^ Allow greater complexity.
maxdepth=10,
# ^ But, avoid deep nesting.
binary_operators=["*", "+", "-", "/"],
unary_operators=["square", "cube", "exp", "cos2(x)=cos(x)^2"],
constraints={
"/": (-1, 9),
"square": 9,
"cube": 9,
"exp": 9,
},
# ^ Limit the complexity within each argument.
# "inv": (-1, 9) states that the numerator has no constraint,
# but the denominator has a max complexity of 9.
# "exp": 9 simply states that `exp` can only have
# an expression of complexity 9 as input.
nested_constraints={
"square": {"square": 1, "cube": 1, "exp": 0},
"cube": {"square": 1, "cube": 1, "exp": 0},
"exp": {"square": 1, "cube": 1, "exp": 0},
},
# ^ Nesting constraints on operators. For example,
# "square(exp(x))" is not allowed, since "square": {"exp": 0}.
complexity_of_operators={"/": 2, "exp": 3},
# ^ Custom complexity of particular operators.
complexity_of_constants=2,
# ^ Punish constants more than variables
select_k_features=4,
# ^ Train on only the 4 most important features
progress=True,
# ^ Can set to false if printing to a file.
weight_randomize=0.1,
# ^ Randomize the tree much more frequently
cluster_manager=None,
# ^ Can be set to, e.g., "slurm", to run a slurm
# cluster. Just launch one script from the head node.
precision=64,
# ^ Higher precision calculations.
warm_start=True,
# ^ Start from where left off.
turbo=True,
# ^ Faster evaluation (experimental)
extra_sympy_mappings={"cos2": lambda x: sympy.cos(x)**2},
# extra_torch_mappings={sympy.cos: torch.cos},
# ^ Not needed as cos already defined, but this
# is how you define custom torch operators.
# extra_jax_mappings={sympy.cos: "jnp.cos"},
# ^ For JAX, one passes a string.
)
```
### Docker
You can also test out PySR in Docker, without
installing it locally, by running the following command in
the root directory of this repo:
```bash
docker build -t pysr .
```
This builds an image called `pysr` for your system's architecture,
which also contains IPython. You can select a specific version
of Python and Julia with:
```bash
docker build -t pysr --build-arg JLVERSION=1.10.0 --build-arg PYVERSION=3.11.6 .
```
You can then run with this dockerfile using:
```bash
docker run -it --rm -v "$PWD:/data" pysr ipython
```
which will link the current directory to the container's `/data` directory
and then launch ipython.
If you have issues building for your system's architecture,
you can emulate another architecture by including `--platform linux/amd64`,
before the `build` and `run` commands.
### Contributors ✨
We are eager to welcome new contributors! Check out our contributors [guide](https://github.com/MilesCranmer/PySR/blob/master/CONTRIBUTORS.md) for tips 🚀.
If you have an idea for a new feature, don't hesitate to share it on the [issues](https://github.com/MilesCranmer/PySR/issues) or [discussions](https://github.com/MilesCranmer/PySR/discussions) page.
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