SciPy fixes and extensions

Last update: Jul 17, 2022

Related tags

Overview

scipyx

SciPy is large library used everywhere in scientific computing. That's why breaking backwards-compatibility comes as a significant cost and is almost always avoided, even if the API of some methods is arguably lacking. This package provides drop-in wrappers "fixing" those.

npx does the same for NumPy.

If you have a fix for a SciPy method that can't go upstream for some reason, feel free to PR here.

Krylov methods

import numpy as np
import scipy.sparse
import scipyx as spx

# create tridiagonal (-1, 2, -1) matrix
n = 100
data = -np.ones((3, n))
data[1] = 2.0
A = scipy.sparse.spdiags(data, [-1, 0, 1], n, n)
A = A.tocsr()
b = np.ones(n)


sol, info = spx.cg(A, b, tol=1.0e-10)
sol, info = spx.minres(A, b, tol=1.0e-10)
sol, info = spx.gmres(A, b, tol=1.0e-10)
sol, info = spx.bicg(A, b, tol=1.0e-10)
sol, info = spx.bicgstab(A, b, tol=1.0e-10)
sol, info = spx.cgs(A, b, tol=1.0e-10)
sol, info = spx.qmr(A, b, tol=1.0e-10)

sol is the solution of the linear system A @ x = b (or None if no convergence), and info contains some useful data, e.g., info.resnorms. The solution sol and all callback x have the shape of x0/b. The methods are wrappers around SciPy's iterative solvers.

Relevant issues:

inconsistent number of callback calls between cg, minres

Optimization

import scipyx as spx


def f(x):
    return (x ** 2 - 2) ** 2


x0 = 1.5
out = spx.minimize(f, x0)
print(out.x)

x0 = -3.2
x, _ = spx.leastsq(f, x0)
print(x)

In scipyx, all intermediate values x and the result from a minimization out.x will have the same shape as x0. (In SciPy, they always have shape (n,), no matter the input vector.)

Relevant issues:

optimization: let out.x have the same shape as x0

Root-finding

import scipyx as spx


def f(x):
    return x ** 2 - 2


a, b = spx.bisect(f, 0.0, 5.0, tol=1.0e-12)
a, b = spx.regula_falsi(f, 0.0, 5.0, tol=1.0e-12)

scipyx provides some basic nonlinear root-findings algorithms: bisection and regula falsi. They're not as fast-converging as other methods, but are very robust and work with almost any function.

License

This software is published under the BSD-3-Clause license.

Comments

Add ITP method?

I think the ITP method for root-finding would be a nice addition since it's unlikely to make it into scipy.

Reference

https://en.wikipedia.org/wiki/ITP_Method

opened by zoj613 3

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow

eXtreme Gradient Boosting Community | Documentation | Resources | Contributors | Release Notes XGBoost is an optimized distributed gradient boosting l

Distributed (Deep) Machine Learning Community

23.6k Dec 31, 2022

Python Library for learning (Structure and Parameter) and inference (Statistical and Causal) in Bayesian Networks.

pgmpy pgmpy is a python library for working with Probabilistic Graphical Models. Documentation and list of algorithms supported is at our official sit

2.2k Jan 3, 2023

High performance, easy-to-use, and scalable machine learning (ML) package, including linear model (LR), factorization machines (FM), and field-aware factorization machines (FFM) for Python and CLI interface.

What is xLearn? xLearn is a high performance, easy-to-use, and scalable machine learning package that contains linear model (LR), factorization machin

3k Jan 3, 2023

This repository is related to an Arabic tutorial, within the tutorial we discuss the common data structure and algorithms and their worst and best case for each, then implement the code using Python.

Data Structure and Algorithms with Python This repository is related to the Arabic tutorial here, within the tutorial we discuss the common data struc

33 Dec 2, 2022

20.6k Feb 13, 2021

2.8k Feb 12, 2021

BBB streaming without Xorg and Pulseaudio and Chromium and other nonsense (heavily WIP)

BBB Streamer NG? Makes a conference like this... ...streamable like this! I also recorded a small video showing the basic features: https://www.youtub

60 Oct 21, 2022

All the essential resources and template code needed to understand and practice data structures and algorithms in python with few small projects to demonstrate their practical application.

Data Structures and Algorithms Python INDEX 1. Resources - Books Data Structures - Reema Thareja competitiveCoding Big-O Cheat Sheet DAA Syllabus Inte

129 Dec 15, 2022

Implement face detection, and age and gender classification, and emotion classification.

YOLO Keras Face Detection Implement Face detection, and Age and Gender Classification, and Emotion Classification. (image from wider face dataset) Ove

10 Nov 14, 2022

SciPy fixes and extensions

Related tags

Overview

scipyx

Krylov methods

Optimization

Root-finding

License

You might also like...

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow

Python Library for learning (Structure and Parameter) and inference (Statistical and Causal) in Bayesian Networks.

High performance, easy-to-use, and scalable machine learning (ML) package, including linear model (LR), factorization machines (FM), and field-aware factorization machines (FFM) for Python and CLI interface.

This repository is related to an Arabic tutorial, within the tutorial we discuss the common data structure and algorithms and their worst and best case for each, then implement the code using Python.

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow

High performance, easy-to-use, and scalable machine learning (ML) package, including linear model (LR), factorization machines (FM), and field-aware factorization machines (FFM) for Python and CLI interface.

BBB streaming without Xorg and Pulseaudio and Chromium and other nonsense (heavily WIP)

All the essential resources and template code needed to understand and practice data structures and algorithms in python with few small projects to demonstrate their practical application.

Implement face detection, and age and gender classification, and emotion classification.

Comments

Add ITP method?

Reference

Releases(0.0.18)

0.0.18(Dec 9, 2021)

0.0.17(Oct 19, 2021)

0.0.16(Sep 2, 2021)

v0.0.15(May 1, 2021)

v0.0.14(Apr 30, 2021)

v0.0.13(Apr 28, 2021)

v0.0.12(Apr 28, 2021)

Owner

Nico Schlömer

PyTorch implementation of residual gated graph ConvNets, ICLR’18

An End-to-End Machine Learning Library to Optimize AUC (AUROC, AUPRC).

Securetar - A streaming wrapper around python tarfile and allow secure handling files and support encryption

A solution to ensure Crowd Management with Contactless and Safe systems.

Official repo of the paper "Surface Form Competition: Why the Highest Probability Answer Isn't Always Right"

Example repository for custom C++/CUDA operators for TorchScript

Official PyTorch implementation of U-GAT-IT: Unsupervised Generative Attentional Networks with Adaptive Layer-Instance Normalization for Image-to-Image Translation

Age and Gender prediction using Keras

GAN JAX - A toy project to generate images from GANs with JAX

PoolFormer: MetaFormer is Actually What You Need for Vision

Material related to the Principles of Cloud Computing course.

A fast and easy to use, moddable, Python based Minecraft server!

Can we learn gradients by Hamiltonian Neural Networks?

A motion detection system with RaspberryPi, OpenCV, Python

CVPR 2021 Challenge on Super-Resolution Space

Codes and Data Processing Files for our paper.

Implementation of the GVP-Transformer, which was used in the paper "Learning inverse folding from millions of predicted structures" for de novo protein design alongside Alphafold2

Finetune SSL models for MOS prediction

Consistency Regularization for Adversarial Robustness

Gems & Holiday Package Prediction