Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/WassimTenachi/PhySO

Physical Symbolic Optimization
https://github.com/WassimTenachi/PhySO

deep-learning equation-discovery machine-learning physics python reinforcement-learning symbolic-regression

Last synced: 14 days ago
JSON representation

Physical Symbolic Optimization

Awesome Lists containing this project

README 

        
# $\Phi$-SO : Physical Symbolic Optimization

![logo](https://raw.githubusercontent.com/WassimTenachi/PhySO/main/docs/assets/logo_dark.png)

Physical symbolic optimization ( $\Phi$-SO ) - A symbolic optimization package built for physics.



[![GitHub Repo stars](https://img.shields.io/github/stars/WassimTenachi/PhySO?style=social)](https://github.com/WassimTenachi/PhySO)

[![Documentation Status](https://readthedocs.org/projects/physo/badge/?version=latest)](https://physo.readthedocs.io/en/latest/?badge=latest)

[![Coverage Status](https://coveralls.io/repos/github/WassimTenachi/PhySO/badge.svg?branch=main)](https://coveralls.io/github/WassimTenachi/PhySO?branch=main)

[![Twitter Follow](https://img.shields.io/twitter/follow/WassimTenachi?style=social)](https://twitter.com/WassimTenachi)

[![Paper](https://img.shields.io/badge/arXiv-2303.03192-b31b1b)](https://arxiv.org/abs/2303.03192)

[![Paper](https://img.shields.io/badge/arXiv-2312.01816-b31b1b)](https://arxiv.org/abs/2312.01816)



Source code: [WassimTenachi/PhySO](https://github.com/WassimTenachi/PhySO)\

Documentation: [physo.readthedocs.io](https://physo.readthedocs.io/en/latest/)



## Highlights



$\Phi$-SO's symbolic regression module uses deep reinforcement learning to infer analytical physical laws that fit data points, searching in the space of functional forms.  



`physo` is able to leverage:



* Physical units constraints, reducing the search space with dimensional analysis ([[Tenachi et al 2023]](https://arxiv.org/abs/2303.03192))



* Class constraints, searching for a single analytical functional form that accurately fits multiple datasets - each governed by its own (possibly) unique set of fitting parameters ([[Tenachi et al 2024]](https://arxiv.org/abs/2312.01816))



$\Phi$-SO recovering the equation for a damped harmonic oscillator:



https://github.com/WassimTenachi/PhySO/assets/63928316/655b0eea-70ba-4975-8a80-00553a6e2786



Performances on the standard Feynman benchmark from [SRBench](https://github.com/cavalab/srbench/tree/master)) comprising 120 expressions from the Feynman Lectures on Physics against popular SR packages.



$\Phi$-SO achieves state-of-the-art performance in the presence of noise (exceeding 0.1%) and shows robust performances even in the presence of substantial (10%) noise:



![feynman_results](https://github.com/WassimTenachi/PhySO/assets/63928316/bbb051a2-2737-40ca-bfbf-ed185c48aa71)



# Installation



The package has been tested on:

- Linux

- OSX (ARM & Intel)

- Windows



## Install procedure



### Virtual environment



To install the package it is recommended to first create a conda virtual environment:

```

conda create -n PhySO python=3.8

```

And activate it:

```

conda activate PhySO

```

### Downloading



`physo` can be downloaded using git:

```

git clone https://github.com/WassimTenachi/PhySO

```



Or by direct downloading a zip of the repository: [here](https://github.com/WassimTenachi/PhySO/zipball/master)



### Dependencies

From the repository root:



Installing dependencies :

```

conda install --file requirements.txt

```



In order to simplify the installation process, since its first version, `physo` has been updated to have minimal very standard dependencies.



---



**NOTE** : `physo` supports CUDA but it should be noted that since the bottleneck of the code is free constant optimization, using CUDA (even on a very high-end GPU) does not improve performances over a CPU and can actually hinder performances.



---



### Installing PhySO



Installing `physo` to the environment (from the repository root):

```

python -m pip install -e .

```



### Testing install



Import test:

```

python3

>>> import physo

```

This should result in `physo` being successfully imported.



Unit tests:



Running all unit tests except parallel mode ones (from the repository root):

```

python -m unittest discover -p "*UnitTest.py"

```

This should result in all tests being successfully passed.



Running all unit tests (from the repository root):

```

python -m unittest discover -p "*Test.py"

```

This  should take 5-15 min depending on your system (as if you have a lot of CPU cores, it will take longer to make the efficiency curves).



## Uninstalling

Uninstalling the package.

```

conda deactivate

conda env remove -n PhySO

```

## Getting started (SR)



In this tutorial, we show how to use `physo` to perform Symbolic Regression (SR).

The reference notebook for this tutorial can be found here: [sr_quick_start.ipynb](https://github.com/WassimTenachi/PhySO/blob/main/demos/sr_quick_start.ipynb).



### Setup



Importing the necessary libraries:

```

# External packages

import numpy as np

import matplotlib.pyplot as plt

import torch

```



Importing `physo`:

```

# Internal code import

import physo

import physo.learn.monitoring as monitoring

```



It is recommended to fix the seed for reproducibility:

```

# Seed

seed = 0

np.random.seed(seed)

torch.manual_seed(seed)

```



### Making synthetic datasets



Making a toy synthetic dataset:

```

# Making toy synthetic data

z = np.random.uniform(-10, 10, 50)

v = np.random.uniform(-10, 10, 50)

X = np.stack((z, v), axis=0)

y = 1.234*9.807*z + 1.234*v**2

```

It should be noted that free constants search starts around 1. by default. Therefore when using default hyperparameters, normalizing the data around an order of magnitude of 1 is strongly recommended.



---



__DA side notes__:  

$\Phi$-SO can exploit DA (dimensional analysis) to make SR more efficient.  

On can consider the physical units of $X=(z,v)$, $z$ being a length of dimension $L^{1}, T^{0}, M^{0}$, v a velocity of dimension $L^{1}, T^{-1}, M^{0}$, $y=E$ if an energy of dimension $L^{2}, T^{-2}, M^{1}$.

If you are not working on a physics problem and all your variables/constants are dimensionless, do not specify any of the `xx_units` arguments (or specify them as `[0,0]` for all variables/constants) and `physo` will perform a dimensionless symbolic regression task.  



---



Datasets plot:

```

n_dim = X.shape[0]

fig, ax = plt.subplots(n_dim, 1, figsize=(10,5))

for i in range (n_dim):

    curr_ax = ax if n_dim==1 else ax[i]

    curr_ax.plot(X[i], y, 'k.',)

    curr_ax.set_xlabel("X[%i]"%(i))

    curr_ax.set_ylabel("y")

plt.show()

```



### SR configuration



It should be noted that SR capabilities of `physo` are heavily dependent on hyperparameters, it is therefore recommended to tune hyperparameters to your own specific problem for doing science.  

Summary of currently available hyperparameters presets configurations:



|  Config    |            Recommended usecases                           |    Speed    |   Effectiveness   |                           Notes                                |

|:----------:|:---------------------------------------------------------:|:-----------:|:-----------------:|:--------------------------------------------------------------:|

| `config0`  | Demos                                                     |     ★★★     |          ★        | Light and fast config.                                         |

| `config1`  | SR with DA $^*$ ;  Class SR with DA $^*$                    |       ★     |        ★★★        | Config used for Feynman Benchmark and MW streams Benchmark.    |

| `config2`  | SR ; Class SR                                             |      ★★     |         ★★        | Config used for Class Benchmark.                               |



$^*$ DA = Dimensional Analysis



Users are encouraged to edit configurations (they can be found in: [physo/config/](https://github.com/WassimTenachi/PhySO/tree/main/physo/config)).  

By default, `config0` is used, however it is recommended to follow the upper recommendations for doing science.



---

__DA side notes__:   

1. During the first tens of iterations, the neural network is typically still learning the rules of dimensional analysis, resulting in most candidates being discarded and not learned on, effectively resulting in a much smaller batch size (typically 10x smaller), thus making the evaluation process much less computationally expensive. It is therefore recommended to compensate this behavior by using a higher batch size configuration which helps provide the neural network sufficient learning information.  

---



Logging and visualisation setup:

```

save_path_training_curves = 'demo_curves.png'

save_path_log             = 'demo.log'



run_logger     = lambda : monitoring.RunLogger(save_path = save_path_log,

                                                do_save = True)



run_visualiser = lambda : monitoring.RunVisualiser (epoch_refresh_rate = 1,

                                           save_path = save_path_training_curves,

                                           do_show   = False,

                                           do_prints = True,

                                           do_save   = True, )

```



### Running SR



Given variables data $(x_0,..., x_n)$ (here $(z, v)$ ), the root variable $y$ (here $E$) as well as free and fixed constants, you can run an SR task to recover $f$ via the following command.



---



__DA side notes__:    

Here we are allowing the use of a fixed constant $1$ of dimension $L^{0}, T^{0}, M^{0}$ (ie dimensionless) and free constants $m$ of dimension $L^{0}, T^{0}, M^{1}$ and $g$ of dimension $L^{1}, T^{-2}, M^{0}$.  

It should be noted that here the units vector are of size 3 (eg: `[1, 0, 0]`) as in this example the variables have units dependent on length, time and mass only.

However, units vectors can be of any size $\leq 7$ as long as it is consistent across X, y and constants, allowing the user to express any units (dependent on length, time, mass, temperature, electric current, amount of light, or amount of matter). 

In addition, dimensional analysis can be performed regardless of the order in which units are given, allowing the user to use any convention ([length, mass, time] or [mass, time, length] etc.) as long as it is consistent across X,y and constants.  



---



```

# Running SR task

expression, logs = physo.SR(X, y,

                            # Giving names of variables (for display purposes)

                            X_names = [ "z"       , "v"        ],

                            # Associated physical units (ignore or pass zeroes if irrelevant)

                            X_units = [ [1, 0, 0] , [1, -1, 0] ],

                            # Giving name of root variable (for display purposes)

                            y_name  = "E",

                            y_units = [2, -2, 1],

                            # Fixed constants

                            fixed_consts       = [ 1.      ],

                            fixed_consts_units = [ [0,0,0] ],

                            # Free constants names (for display purposes)

                            free_consts_names = [ "m"       , "g"        ],

                            free_consts_units = [ [0, 0, 1] , [1, -2, 0] ],

                            # Symbolic operations that can be used to make f

                            op_names = ["mul", "add", "sub", "div", "inv", "n2", "sqrt", "neg", "exp", "log", "sin", "cos"],

                            get_run_logger     = run_logger,

                            get_run_visualiser = run_visualiser,

                            # Run config

                            run_config = physo.config.config0.config0,

                            # Parallel mode (only available when running from python scripts, not notebooks)

                            parallel_mode = False,

                            # Number of iterations

                            epochs = 20

)

```



### Inspecting the best expression found



__Getting best expression:__



The best expression found (in accuracy) is returned in the `expression` variable:

```

best_expr = expression

print(best_expr.get_infix_pretty())

```

```

>>> 

                     2           

    -g⋅m⋅z + -v⋅v⋅sin (1.0)⋅1.0⋅m

```



It can also be loaded later on from log files:

```

import physo

from physo.benchmark.utils import symbolic_utils as su

import sympy



# Loading pareto front expressions

pareto_expressions = physo.read_pareto_pkl("demo_curves_pareto.pkl")

# Most accurate expression is the last in the Pareto front:

best_expr = pareto_expressions[-1]

print(best_expr.get_infix_pretty())

```



__Display:__



The expression can be converted into...  

A sympy expression:



```

best_expr.get_infix_sympy()

```

```

>>> -g*m*z - v*v*sin(1.0)**2*1.0*m

```



A sympy expression (with evaluated free constants values):



```

best_expr.get_infix_sympy(evaluate_consts=True)[0]

```



```

>>> 1.74275713004454*v**2*sin(1.0)**2 + 12.1018380702846*z

```



A latex string:



```

best_expr.get_infix_latex()

```



```

>>> '\\frac{m \\left(- 1000000000000000 g z - 708073418273571 v^{2}\\right)}{1000000000000000}'

```



A latex string (with evaluated free constants values):

```

sympy.latex(best_expr.get_infix_sympy(evaluate_consts=True))

```



```

>>> '\\mathtt{\\text{[1.74275713004454*v**2*sin(1.0)**2 + 12.1018380702846*z]}}'

```



__Getting free constant values:__



```

best_expr.free_consts

```

```

>>> FreeConstantsTable

     -> Class consts (['g' 'm']) : (1, 2)

     -> Spe consts   ([]) : (1, 0, 1)

```



```

best_expr.free_consts.class_values

```

```

>>> tensor([[ 6.9441, -1.7428]], dtype=torch.float64)

```



### Checking exact symbolic recovery



```

# To sympy

best_expr = best_expr.get_infix_sympy(evaluate_consts=True)



best_expr = best_expr[0]



# Printing best expression simplified and with rounded constants

print("best_expr : ", su.clean_sympy_expr(best_expr, round_decimal = 4))



# Target expression was:

target_expr = sympy.parse_expr("1.234*9.807*z + 1.234*v**2")

print("target_expr : ", su.clean_sympy_expr(target_expr, round_decimal = 4))



# Check equivalence

print("\nChecking equivalence:")

is_equivalent, log = su.compare_expression(

                        trial_expr  = best_expr,

                        target_expr = target_expr,

                        handle_trigo            = True,

                        prevent_zero_frac       = True,

                        prevent_inf_equivalence = True,

                        verbose                 = True,

)

print("Is equivalent:", is_equivalent)

```



```

>>> best_expr :  1.234*v**2 + 12.1018*z

    target_expr :  1.234*v**2 + 12.1018*z

    

    Checking equivalence:

      -> Assessing if 1.234*v**2 + 12.101838*z (target) is equivalent to 1.74275713004454*v**2*sin(1.0)**2 + 12.1018380702846*z (trial)

       -> Simplified expression : 1.23*v**2 + 12.1*z

       -> Symbolic error        : 0

       -> Symbolic fraction     : 1

       -> Trigo symbolic error        : 0

       -> Trigo symbolic fraction     : 1

       -> Equivalent : True

    Is equivalent: True

```



# Documentation



Further documentation can be found at [physo.readthedocs.io](https://physo.readthedocs.io/en/latest/).



Quick start guide for __Symbolic Regression__ : [HERE](https://physo.readthedocs.io/en/latest/r_sr.html#getting-started-sr)  



Quick start guide for __Class Symbolic Regression__ : [HERE](https://physo.readthedocs.io/en/latest/r_class_sr.html#getting-started-class-sr)  



# Citing this work

 

Symbolic Regression with reinforcement learning & dimensional analysis



```

@ARTICLE{PhySO_RL_DA,

       author = {{Tenachi}, Wassim and {Ibata}, Rodrigo and {Diakogiannis}, Foivos I.},

        title = "{Deep Symbolic Regression for Physics Guided by Units Constraints: Toward the Automated Discovery of Physical Laws}",

      journal = {ApJ},

         year = 2023,

        month = dec,

       volume = {959},

       number = {2},

          eid = {99},

        pages = {99},

          doi = {10.3847/1538-4357/ad014c},

archivePrefix = {arXiv},

       eprint = {2303.03192},

 primaryClass = {astro-ph.IM},

       adsurl = {https://ui.adsabs.harvard.edu/abs/2023ApJ...959...99T},

      adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}

```



Class Symbolic Regression

```

@ARTICLE{PhySO_ClassSR,

       author = {{Tenachi}, Wassim and {Ibata}, Rodrigo and {Fran{\c{c}}ois}, Thibaut L. and {Diakogiannis}, Foivos I.},

        title = "{Class Symbolic Regression: Gotta Fit 'Em All}",

      journal = {arXiv e-prints},

     keywords = {Computer Science - Machine Learning, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics},

         year = 2023,

        month = dec,

          eid = {arXiv:2312.01816},

        pages = {arXiv:2312.01816},

          doi = {10.48550/arXiv.2312.01816},

archivePrefix = {arXiv},

       eprint = {2312.01816},

 primaryClass = {cs.LG},

       adsurl = {https://ui.adsabs.harvard.edu/abs/2023arXiv231201816T},

      adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}

```