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

Last update: May 11, 2022

Related tags

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

A small library of 3D related utilities used in my research.

utils3D A small library of 3D related utilities used in my research. Installation Install via GitHub pip install git+https://github.com/Steve-Tod/util

8 May 20, 2022

Conflict-aware Inference of Python Compatible Runtime Environments with Domain Knowledge Graph, ICSE 2022

PyCRE Conflict-aware Inference of Python Compatible Runtime Environments with Domain Knowledge Graph, ICSE 2022 Dependencies This project is developed

[email protected]"> 7 May 06, 2022

Deep-Learning-Book-Chapter-Summaries - Attempting to make the Deep Learning Book easier to understand.

Deep-Learning-Book-Chapter-Summaries This repository provides a summary for each chapter of the Deep Learning book by Ian Goodfellow, Yoshua Bengio an

1k Dec 27, 2022

Makes patches from huge resolution .svs slide files using openslide

openslide_patcher Makes patches from huge resolution .svs slide files using openslide Example collage I made from outputs:

2 Dec 23, 2021

ESP32 python application to read data from a Tilt™ Hydrometer for homebrewing

TitlESP32 ESP32 MicroPython application to read and log data from a Tilt™ Hydrometer. Requirements A board with an ESP32 chip USB cable - USB A / micr

5 Dec 01, 2022

pytorch implementation of fast-neural-style

fast-neural-style 🌇 🚀 NOTICE: This codebase is no longer maintained, please use the codebase from pytorch examples repository available at pytorch/e

405 Dec 15, 2022

DeLag: Detecting Latency Degradation Patterns in Service-based Systems

DeLag: Detecting Latency Degradation Patterns in Service-based Systems Replication package of the work "DeLag: Detecting Latency Degradation Patterns

2 Mar 24, 2022

Implementing yolov4 target detection and tracking based on nao robot

6 Apr 19, 2022

This is a demo app to be used in the video streaming applications

MoViDNN: A Mobile Platform for Evaluating Video Quality Enhancement with Deep Neural Networks MoViDNN is an Android application that can be used to ev

7 Jul 21, 2022

🐦 Opytimizer is a Python library consisting of meta-heuristic optimization techniques.

Opytimizer: A Nature-Inspired Python Optimizer Welcome to Opytimizer. Did you ever reach a bottleneck in your computational experiments? Are you tired

546 Dec 31, 2022

Video Swin Transformer - PyTorch

Video-Swin-Transformer-Pytorch This repo is a simple usage of the official implementation "Video Swin Transformer". Introduction Video Swin Transforme

116 Dec 20, 2022

TensorFlow implementation of the paper "Hierarchical Attention Networks for Document Classification"

Hierarchical Attention Networks for Document Classification This is an implementation of the paper Hierarchical Attention Networks for Document Classi

83 Dec 05, 2022

Forecasting for knowable future events using Bayesian informative priors (forecasting with judgmental-adjustment).

What is judgyprophet? judgyprophet is a Bayesian forecasting algorithm based on Prophet, that enables forecasting while using information known by the

56 Oct 26, 2022

2D&3D human pose estimation

Human Pose Estimation Papers [CVPR 2016] - 201511 [IJCAI 2016] - 201602 Other Action Recognition with Joints-Pooled 3D Deep Convolutional Descriptors

133 Jan 02, 2023

CvT2DistilGPT2 is an encoder-to-decoder model that was developed for chest X-ray report generation.

CvT2DistilGPT2 Improving Chest X-Ray Report Generation by Leveraging Warm-Starting This repository houses the implementation of CvT2DistilGPT2 from [1

21 Dec 28, 2022

Beginner-friendly repository for Hacktober Fest 2021. Start your contribution to open source through baby steps. 💜

Hacktober Fest 2021 🎉 Open source is changing the world – one contribution at a time! 🎉 This repository is made for beginners who are unfamiliar wit

32 Dec 11, 2022

Repo for CVPR2021 paper "QPIC: Query-Based Pairwise Human-Object Interaction Detection with Image-Wide Contextual Information"

QPIC: Query-Based Pairwise Human-Object Interaction Detection with Image-Wide Contextual Information by Masato Tamura, Hiroki Ohashi, and Tomoaki Yosh

105 Dec 23, 2022

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

A small library of 3D related utilities used in my research.

Conflict-aware Inference of Python Compatible Runtime Environments with Domain Knowledge Graph, ICSE 2022

Deep-Learning-Book-Chapter-Summaries - Attempting to make the Deep Learning Book easier to understand.

Makes patches from huge resolution .svs slide files using openslide

ESP32 python application to read data from a Tilt™ Hydrometer for homebrewing

pytorch implementation of fast-neural-style

DeLag: Detecting Latency Degradation Patterns in Service-based Systems

Implementing yolov4 target detection and tracking based on nao robot

This is a demo app to be used in the video streaming applications

🐦 Opytimizer is a Python library consisting of meta-heuristic optimization techniques.

Video Swin Transformer - PyTorch

TensorFlow implementation of the paper "Hierarchical Attention Networks for Document Classification"

Forecasting for knowable future events using Bayesian informative priors (forecasting with judgmental-adjustment).

2D&3D human pose estimation

CvT2DistilGPT2 is an encoder-to-decoder model that was developed for chest X-ray report generation.

Beginner-friendly repository for Hacktober Fest 2021. Start your contribution to open source through baby steps. 💜

Repo for CVPR2021 paper "QPIC: Query-Based Pairwise Human-Object Interaction Detection with Image-Wide Contextual Information"

Cascaded Deep Video Deblurring Using Temporal Sharpness Prior and Non-local Spatial-Temporal Similarity

Equivariant Imaging: Learning Beyond the Range Space

Baseline inference Algorithm for the STOIC2021 challenge.