pybaum provides tools to work with pytrees which is a concept burrowed from JAX.

Last update: May 11, 2022

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Deep Learning pybaum

Overview

pybaum

https://readthedocs.org/projects/pybaum/badge/?version=latest

https://img.shields.io/github/workflow/status/OpenSourceEconomics/pybaum/main/main

Installation

pybaum is available on PyPI and Anaconda.org. Install it with

$ pip install pybaum

# or

$ conda install -c conda-forge pybaum

About

pybaum provides tools to work with pytrees which is a concept burrowed from JAX.

What is a pytree?

In pybaum, we use the term pytree to refer to a tree-like structure built out of container-like Python objects. Classes are considered container-like if they are in the pytree registry, which by default includes lists, tuples, and dicts. That is:

Any object whose type is not in the pytree container registry is considered a leaf pytree.
Any object whose type is in the pytree container registry, and which contains pytrees, is considered a pytree.

For each entry in the pytree container registry, a container-like type is registered with a pair of functions that specify how to convert an instance of the container type to a (children, metadata) pair and how to convert such a pair back to an instance of the container type. Using these functions, pybaum can canonicalize any tree of registered container objects into tuples.

Example pytrees:

[1, "a", object()]  # 3 leaves

(1, (2, 3), ())  # 3 leaves

[1, {"k1": 2, "k2": (3, 4)}, 5]  # 5 leaves

pybaum can be extended to consider other container types as pytrees.

Comments

Fix for new jax version.

Problem

The type of a jax array has changed in jax version 0.4.1 and thus pybaum would not work with this jax version.

Solution

Handle jax arrays explicitly in get_type, as we are currently already doing for namedtuples.

opened by janosg 1
[pre-commit.ci] pre-commit autoupdate
updates:

github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0

github.com/asottile/reorder_python_imports: v3.1.0 → v3.9.0

github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0

github.com/psf/black: 22.3.0 → 22.12.0

github.com/PyCQA/flake8: 4.0.1 → 6.0.0

github.com/PyCQA/doc8: 0.11.2 → v1.0.0

github.com/mgedmin/check-manifest: 0.48 → 0.49

github.com/PyCQA/doc8: 0.11.2 → v1.0.0

github.com/asottile/setup-cfg-fmt: v1.20.1 → v2.2.0

github.com/codespell-project/codespell: v2.1.0 → v2.2.2

github.com/asottile/pyupgrade: v2.34.0 → v3.3.1
opened by pre-commit-ci[bot] 1
[pre-commit.ci] pre-commit autoupdate
updates:

github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0

github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0

github.com/PyCQA/doc8: 0.11.1 → 0.11.2

github.com/PyCQA/doc8: 0.11.1 → 0.11.2

github.com/asottile/pyupgrade: v2.32.1 → v2.34.0
opened by pre-commit-ci[bot] 1
[pre-commit.ci] pre-commit autoupdate
updates:

github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.2.0

github.com/asottile/reorder_python_imports: v2.7.1 → v3.1.0

github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.2.0

github.com/psf/black: 22.1.0 → 22.3.0

github.com/PyCQA/doc8: 0.10.1 → 0.11.1

github.com/mgedmin/check-manifest: 0.47 → 0.48

github.com/PyCQA/doc8: 0.10.1 → 0.11.1

github.com/asottile/setup-cfg-fmt: v1.20.0 → v1.20.1

github.com/asottile/pyupgrade: v2.31.0 → v2.32.1
opened by pre-commit-ci[bot] 1
Align default containers with jax
Currently we have only list, dict and tuple as default pytree containers.

Jax also has:

[x] None

[x] collections.namedtuple and typing.NamedTuple

[x] collections.OrderedDict
opened by janosg 1
[pre-commit.ci] pre-commit autoupdate
updates:

github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0

github.com/asottile/reorder_python_imports: v2.6.0 → v2.7.1

github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0

github.com/asottile/blacken-docs: v1.12.0 → v1.12.1

github.com/psf/black: 21.12b0 → 22.1.0
opened by pre-commit-ci[bot] 1
Additional option for flattening pandas DataFrames
Currently the user can decide between two ways of treating DataFrames

Only the entries in a fixed set of columns appears in the flat list of leaves

All entries appear in the flat list of leaves.

In estimagic a third mode would be very practical that automatically switches between the two cases above. If all columns from the specified subset are present, only those columns are considered. If None of the columns is present, all entries are considered.

If this sounds too special, we can also only add it in estimagic.
opened by janosg 1
Add basic documentation
To-Do

[x] Add all functions that can be directly imported from pybaum to an API Documentation

[ ] Write some text about the rationale behind pybaum

[ ] Explain deviations from JAX

[ ] Add examples

enhancement good first issue
opened by janosg 0
Test against JAX
To-Do

[ ] Write sample_tree function that creates a random pytree based on some high level information

[ ] Create random pytrees and test against JAX

[ ] Test current example pytrees against JAX

Note

Need to find a way of not installing JAX on windows in tox.
enhancement good first issue
opened by janosg 0
Improve treedef
Problem

The JAX treedef contains more information. Therefore, their tree_unflatten function does not need an is_leaf argument. The same way we could make the registry argument unnecessary.

This is not just more convenient. It reduces error potential because the unflattening will automatically use the same options as the flattening.

To-Do

[ ] Come up with better Treedef (namedtuple or Class) and implement it

[ ] Adjust interface of tree_unflatten.

enhancement
opened by janosg 1
Improve error checking
To-Do

[ ] Add explicit error handling to tree_equal

[ ] Check for typos in options and types in get_registry and suggest improvements with fuzzywuzzy

[ ] Look for more places where we need better error handling

enhancement
opened by janosg 0

Releases(v0.1.3)

v0.1.3(Dec 16, 2022)
#22 Improves the type check for jax arrays and enables support for Jax 0.4.1 or newer.

Source code(tar.gz)
Source code(zip)
v0.1.2(Jun 15, 2022)
Add JAX array support to pybaum. By @timmens and @janosg in #18 and #20

Source code(tar.gz)
Source code(zip)
v0.1.1(Feb 19, 2022)
What's Changed

Add a section about the API to the docs. by @tobiasraabe in https://github.com/OpenSourceEconomics/pybaum/pull/12

Add default arguments to tree_just_flatten. by @tobiasraabe in https://github.com/OpenSourceEconomics/pybaum/pull/10

Implement tree_yield and tree_just_yield. by @tobiasraabe in https://github.com/OpenSourceEconomics/pybaum/pull/11

Add badges and a short description to the readme. by @tobiasraabe in https://github.com/OpenSourceEconomics/pybaum/pull/13

Full Changelog: https://github.com/OpenSourceEconomics/pybaum/compare/v0.1.0...v0.1.1
Source code(tar.gz)
Source code(zip)
v0.1.0(Jan 28, 2022)

Source code(tar.gz)
Source code(zip)

Owner

Open Source Economics

A platform for transdisciplinary collaboration in the development, analysis, and application of computational economic models.

GitHub Repository https://pybaum.readthedocs.io

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pybaum provides tools to work with pytrees which is a concept burrowed from JAX.

Related tags

Overview

pybaum

Installation

About

Comments

Problem

Solution

To-Do

To-Do

Note

Problem

To-Do

To-Do

Releases(v0.1.3)

v0.1.3(Dec 16, 2022)

v0.1.2(Jun 15, 2022)

v0.1.1(Feb 19, 2022)

What's Changed

v0.1.0(Jan 28, 2022)

Owner

Open Source Economics

Using LSTM to detect spoofing attacks in an Air-Ground network

Code for Neural-GIF: Neural Generalized Implicit Functions for Animating People in Clothing(ICCV21)

PyTorch-Multi-Style-Transfer - Neural Style and MSG-Net

Research on controller area network Intrusion Detection Systems

Explaining Hyperparameter Optimization via PDPs

Patient-Survival - Using Python, I developed a Machine Learning model using classification techniques such as Random Forest and SVM classifiers to predict a patient's survival status that have undergone breast cancer surgery.

LeViT a Vision Transformer in ConvNet's Clothing for Faster Inference

Official Implementation of SWAGAN: A Style-based Wavelet-driven Generative Model

A Pytorch loader for MVTecAD dataset.

Position detection system of mobile robot in the warehouse enviroment

dataset for ECCV 2020 "Motion Capture from Internet Videos"

Code for Overinterpretation paper Overinterpretation reveals image classification model pathologies

Code for the paper One Thing One Click: A Self-Training Approach for Weakly Supervised 3D Semantic Segmentation, CVPR 2021.

PyTorch implementation of MuseMorphose, a Transformer-based model for music style transfer.

Blender Python - Node-based multi-line text and image flowchart

Ladder Variational Autoencoders (LVAE) in PyTorch

Official repository for the paper F, B, Alpha Matting

An open-source, low-cost, image-based weed detection device for fallow scenarios.

Trafffic prediction analysis using hybrid models - Machine Learning

CVAT is free, online, interactive video and image annotation tool for computer vision