BioPy is a collection (in-progress) of biologically-inspired algorithms written in Python

Overview

BioPy

####Overview:

BioPy is a collection (in-progress) of biologically-inspired algorithms written in Python. Some of the algorithms included are more focused on artificial model's of biological computation, such as Hopfield Neural Networks, while others are inherently more biologically-focused, such as the basic genetic programming module included in this project. Use it for whatever you like, and please contribute back to the project by cleaning up code that is here or contributing new code for applications in biology that you may find interesting to program.

NOTE: The code is currently messy in some places. If you want to make a Pull Request by tidying up the code, that would certainly be merged. Since most of this was written while in the middle of our (jaredmichaelsmith and davpcunn) Graduate Bio-Inspired computation course, there are some places where the code has diverged into a dark chasm of non-pythonic mess, despite the algorithms still performing very well. Contributions in this area are much appreciated!

####Dependencies:

  • NumPy
  • SciPy
  • Scikit-Learn
  • Matplotlib

####Categories

Below you will find several categories of applications in this project.

#####Neural Networks:

  • Hopfield Neural Network
  • Back Propagation Neural Network

#####Genetic Programming:

  • Basic Genetic Computation Algorithm
    • Features:
      • "drag-n-drop" fitness functions
      • crossover and mutation of genes
      • learning ability for offspring of each generation

#####Self-Organization and Autonomous Agents

  • Particle Swarm Optimization
    • Features:
      • You can configure many of the parameters of the algorithm such as the velocity, acceleration, and number of initial particles, as well as several other parameters.
Owner
Jared M. Smith
Senior Director of Threat Intel @securityscorecard. Co-Founder/CTO of @uncat. CS PhD. Founder of @knxhx, @volhacks, @hackutk.
Jared M. Smith
MasTrade is a trading bot in baselines3,pytorch,gym

mastrade MasTrade is a trading bot in baselines3,pytorch,gym idea we have for example 1 btc and we buy a crypto with it with market option to trade in

Masoud Azizi 18 May 24, 2022
scikit-multimodallearn is a Python package implementing algorithms multimodal data.

scikit-multimodallearn is a Python package implementing algorithms multimodal data. It is compatible with scikit-learn, a popul

12 Jun 29, 2022
inding a method to objectively quantify skill versus chance in games, using reinforcement learning

Skill-vs-chance-games-analysis - Finding a method to objectively quantify skill versus chance in games, using reinforcement learning

Marcus Chiam 4 Nov 19, 2022
A collection of video resources for machine learning

Machine Learning Videos This is a collection of recorded talks at machine learning conferences, workshops, seminars, summer schools, and miscellaneous

Dustin Tran 1.5k Dec 29, 2022
[HELP REQUESTED] Generalized Additive Models in Python

pyGAM Generalized Additive Models in Python. Documentation Official pyGAM Documentation: Read the Docs Building interpretable models with Generalized

daniel servén 747 Jan 05, 2023
The MLOps is the process of continuous integration and continuous delivery of Machine Learning artifacts as a software product, keeping it inside a loop of Design, Model Development and Operations.

MLOps The MLOps is the process of continuous integration and continuous delivery of Machine Learning artifacts as a software product, keeping it insid

Maykon Schots 25 Nov 27, 2022
Machine learning model evaluation made easy: plots, tables, HTML reports, experiment tracking and Jupyter notebook analysis.

sklearn-evaluation Machine learning model evaluation made easy: plots, tables, HTML reports, experiment tracking, and Jupyter notebook analysis. Suppo

Eduardo Blancas 354 Dec 31, 2022
Dragonfly is an open source python library for scalable Bayesian optimisation.

Dragonfly is an open source python library for scalable Bayesian optimisation. Bayesian optimisation is used for optimising black-box functions whose

744 Jan 02, 2023
Price forecasting of SGB and IRFC Bonds and comparing there returns

Project_Bonds Project Title : Price forecasting of SGB and IRFC Bonds and comparing there returns. Introduction of the Project The 2008-09 global fina

Tishya S 1 Oct 28, 2021
TIANCHI Purchase Redemption Forecast Challenge

TIANCHI Purchase Redemption Forecast Challenge

Haorui HE 4 Aug 26, 2022
whylogs: A Data and Machine Learning Logging Standard

whylogs: A Data and Machine Learning Logging Standard whylogs is an open source standard for data and ML logging whylogs logging agent is the easiest

WhyLabs 2k Jan 06, 2023
A data preprocessing and feature engineering script for a machine learning pipeline is prepared.

FEATURE ENGINEERING Business Problem: A data preprocessing and feature engineering script for a machine learning pipeline needs to be prepared. It is

Pinar Oner 7 Dec 18, 2021
Magenta: Music and Art Generation with Machine Intelligence

Magenta is a research project exploring the role of machine learning in the process of creating art and music. Primarily this involves developing new

Magenta 18.1k Dec 30, 2022
A linear equation solver using gaussian elimination. Implemented for fun and learning/teaching.

A linear equation solver using gaussian elimination. Implemented for fun and learning/teaching. The solver will solve equations of the type: A can be

Sanjeet N. Dasharath 3 Feb 15, 2022
CyLP is a Python interface to COIN-OR’s Linear and mixed-integer program solvers (CLP, CBC, and CGL)

CyLP CyLP is a Python interface to COIN-OR’s Linear and mixed-integer program solvers (CLP, CBC, and CGL). CyLP’s unique feature is that you can use i

COIN-OR Foundation 161 Dec 14, 2022
OptaPy is an AI constraint solver for Python to optimize planning and scheduling problems.

OptaPy is an AI constraint solver for Python to optimize the Vehicle Routing Problem, Employee Rostering, Maintenance Scheduling, Task Assignment, School Timetabling, Cloud Optimization, Conference S

OptaPy 208 Dec 27, 2022
STUMPY is a powerful and scalable Python library for computing a Matrix Profile, which can be used for a variety of time series data mining tasks

STUMPY STUMPY is a powerful and scalable library that efficiently computes something called the matrix profile, which can be used for a variety of tim

TD Ameritrade 2.5k Jan 06, 2023
A GitHub action that suggests type annotations for Python using machine learning.

Typilus: Suggest Python Type Annotations A GitHub action that suggests type annotations for Python using machine learning. This action makes suggestio

40 Sep 18, 2022
pywFM is a Python wrapper for Steffen Rendle's factorization machines library libFM

pywFM pywFM is a Python wrapper for Steffen Rendle's libFM. libFM is a Factorization Machine library: Factorization machines (FM) are a generic approa

João Ferreira Loff 251 Sep 23, 2022