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https://github.com/ogeagla/closyr

A symbolic regression tool written in Clojure
https://github.com/ogeagla/closyr

clojure computer-algebra genetic-algorithms genetic-programming symbolic-ai symbolic-math symbolic-regression

Last synced: about 1 month ago
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A symbolic regression tool written in Clojure

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README 

          
# closyr



[![Clojure CI](https://github.com/ogeagla/closyr/actions/workflows/clojure.yml/badge.svg?branch=master)](https://github.com/ogeagla/closyr/actions/workflows/clojure.yml)



![icon_v5_qtr.png](resources%2Ficons%2Ficon_v5_qtr.png)



A Symbolic Regression tool to search for symbolic expressions which minimize residuals to an objective, written in Clojure.



![gui_evolution_sample_Peek 2024-02-14 08-21.gif](screenshots%2Fgui_evolution_sample_Peek%202024-02-14%2008-21.gif)



Warning: This is experimental software, with an unstable API. Expect breaking changes prior to a major release.



- Draw an objective function, select a built-in dataset, or provide a CSV

- Select number of points, iterations

- See progress 

  - Chart of best fitting function

  - Chart of loss over time

  - A selectable text version of the function



## Installation



Run the application from binary, download a release JAR and see the Usage section below.  

This project is not yet available in a JAR repository (though I'd use Clojars if enough requests).



Or, you can run the app from source, using Clojure development tools (`leiningen`) in this project:



    $ lein deps/repl/run/uberjar...



## Usage



Use the application via GUI or in the terminal. 



There are 4 ways to run the application.  See next section for details about the options you can provide when running the app.



### Run the provided realase JAR



Requirements: Java



    $ java -jar closyr-0.1.0-SNAPSHOT-standalone.jar ...options here...



### Lein Run



Requirements: Java, Leiningen



    $ lein run



Or headless (just in the terminal), where you can specify options and input data:



    $ lein run -t -p 25 -i 5 -x 0,1,2,3,4,5,6 -y 1,2,30,4,5,6,10



Which is the same as:



    $ lein run --headless --population 1000 --iterations 200 --xs 0,1,2,3,4,5,6 --ys 1,2,30,4,5,6,10 



###  In Clojure REPL



Requirements: Java, Leiningen (I will provide a deps file if enough interest)



    (require '[closyr.symbolic-regression :as symreg]) 

    (symreg/run-app-with-gui)



### Build and run JAR



Requirements: Java, Leiningen



    $ lein uberjar

    $ java -jar target/uberjar/closyr-0.1.0-standalone.jar



You can also provide the same command-line options to `java` command, like:



    $ java -jar target/uberjar/closyr-0.1.0-standalone.jar -t -p 25 -i 5 -x 0,1,2,3,4,5,6 -y 1,2,30,4,5,6,10



## Options

| Short, Long Option      | Required?       | Example | Default | Description                                                                                                                   |

|-------------------------|-----------------|---------|---------|-------------------------------------------------------------------------------------------------------------------------------|

| `-t`,`--headless`       | no              | `-t`    | `false` | run without GUI, in terminal only                                                                                             |     

| `-c`,`--use-flamechart` | no              | `-c`    | `false` | run with flamecharts, run then visit http://localhost:54321/flames.svg                                                        |     

| `-p`,`--population`     | no              | `100`   | `20`    | size of population which will evolve; the number of functions we create and modify                                            |    

| `-i`,`--iterations`     | no              | `50`    | `10`    | number of iterations to run for                                                                                               |    

| `-l`,`--max-leafs`      | no              | `40`    | `40`    | max number of AST tree leafs in candidate functions                                                                           |    

| `-x`,`--xs`             | no, unless `ys` | `1,3,4` | random  | the xs for the points in the dataset to fit against; if provided, must also provide `ys` and be the same count                | 

| `-y`,`--ys`             | no, unless `xs` | `2,4,8` | random  | the ys for the points in the dataset to fit against; if provided, must also provide `xs` and be the same count                |    

| `-f`,`--infile`         | no              | `f.csv` |         | A CSV file. Contains either 2 columns without titles in first row, or has columns `x` and `y` to be used as objective dataset |  



## Example Screenshots



On successful application start, you can start an run a search.  You might see something like this when done:



![gui_done_2024-02-12_08-44.png](screenshots%2Fgui_done_2024-02-12_08-44.png)



An example of using the GUI:



![gui_usage_clip_Peek 2024-02-12 09-03.gif](screenshots%2Fgui_usage_clip_Peek%202024-02-12%2009-03.gif)



## Tests



    $ lein test



Coverage looks like this if you run `lein cloverage`:



![test_coverage_2024-02-16_16-39.png](screenshots%2Ftest_coverage_2024-02-16_16-39.png)



## How It Works



- We use Genetic Algorithms to allow candidate functions of best fit to compete.

- They compete on a computed score on the input data, and we use the sum of residuals to generate the score.

- Evolution consists of mutation and crossover. 

- Mutations act on the function's AST and modify branches, leafs, or the whole tree.  Operations like `+0.1`, `*x`, `/Sin(x)` are applied to functions.

- Crossovers combine two functions' ASTs at a random point, and combine using various operators like `+`, and `*`.



## Roadmap



- [x] CLI options accept a CSV file (GUI already supports this)

- [ ] More tests

- [ ] Use something like ProGuard to shrink the JAR for releases 

  - https://www.guardsquare.com/manual/configuration/examples

  - https://stackoverflow.com/questions/12281365/obfuscating-clojure-uberjars-with-proguard

  - https://github.com/eiffelqiu/obfuscate-clojure-project-demo/tree/master

- [ ] A different frontend.  The current Java Swing frontend does the job, but it's not easy to maintain and it's hard to make look better.

- [ ] Can this be a follow-up to this issue, asking for a symbolic regression tool on the JVM? https://github.com/axkr/symja_android_library/issues/850

- [ ] When I created this and my other symbolic regression tools, I didn't know about the formal field of symbolic regression.  I've since found some great libraries that I should review and apply the lessons to this project: https://github.com/MilesCranmer/PySR



## Credits



- This project would not have been possible without the symbolic math library `Symja` (https://github.com/axkr/symja_android_library), which has been great to use and I consider it to be like a `MathJs` (https://github.com/josdejong/mathjs) on the JVM.



## Contribute



I accept PRs, please open an issue to discuss beforehand to make sure we are in alignment. Thanks!



## License



Copyright © 2024 Octavian Geagla



This program and the accompanying materials are made available under the

terms of the Eclipse Public License 2.0 which is available at

http://www.eclipse.org/legal/epl-2.0.



This Source Code may also be made available under the following Secondary

Licenses when the conditions for such availability set forth in the Eclipse

Public License, v. 2.0 are satisfied: GNU General Public License as published by

the Free Software Foundation, either version 2 of the License, or (at your

option) any later version, with the GNU Classpath Exception which is available

at https://www.gnu.org/software/classpath/license.html.



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```