MCMC samplers for Bayesian estimation in Python, including Metropolis-Hastings, NUTS, and Slice

Mat Leonard

Last update: Dec 25, 2022

Related tags

Deep Learning sampyl

Overview

Sampyl

May 29, 2018: version 0.3

Sampyl is a package for sampling from probability distributions using MCMC methods. Similar to PyMC3 using theano to compute gradients, Sampyl uses autograd to compute gradients. However, you are free to write your own gradient functions, autograd is not necessary. This project was started as a way to use MCMC samplers by defining models purely with Python and numpy.

Sampyl includes these samplers currently:

Metropolis-Hastings
Hamiltonian
NUTS
Slice

For each sampler, you pass in a function that calculates the log probability of the distribution you wish to sample from. For the Hamiltonian and NUTS samplers, gradient log probability functions are also required. If autograd is installed, the gradients are calculated automatically. Otherwise, the samplers accept gradient log-p functions which can be used whether autograd is installed or not.

It is still under active development with more features coming soon!

Dependencies

Works for Python 2 or 3.

Currently, numpy and scipy are the only dependencies. To use the automatic gradient log-P capabilities, you will need to install autograd.

Installation

Unfortunately, there was a name collision, so use this to install from PyPI:

pip install sampyl-mcmc

Documentation

You can find the documentation at http://mcleonard.github.io/sampyl/. It is a work in progress, of course, but we'll cover all the important bits soon enough.

Tests

Tests are written for use with pytest, in the tests folder.

License

MIT

Comments

Add ability of logp to return both log posterior and its gradient

There are situations where we have access to an analytic form of both the log posterior and its gradient. It is beneficial to use this, as autograd might not work (e.g. compiled code), or it's just wasteful to calculate both logp and its partial derivatives separately. Methods like e.g. fmin_l_bfgs_b allow one to provide a function that returns both the cost function and its gradient, or a function that only returns the cost function (with the gradient in their case calculated by finite differences).

opened by jgomezdans 11
discrete_uniform broken by autograd 1.1.3

Hi, thanks for the interesting library!

I was playing with the German Tank Problem example, and initially had trouble getting it to work - it would throw "TypeError: data type not understood" while computing the logp.

This turns out to only be a problem when using autograd 1.1.3 - the previous version 1.1.2 works fine. It happens because autograd now wraps numpy.int_ as a new function, which breaks the integral type check in discrete_uniform: if x.dtype != np.int_: because it is not checking against the real np.int_.

Currently it appears that discrete_uniform is only used by the tank example.

I am inclined to think that if autograd is going to wrap np.int_ then it should also make it work transparently in the numpy type hierarchy, but I don't know enough about numpy internals to know how that might be done.

A possible workaround is to replace the check with if x.dtype.kind in "iu":. I guess another is to use the unwrapped numpy to get access to numpy.int_, although it might be confusing to have two references to numpy which are not safely interchangeable.

opened by gbarta 2
Sampling in parallel

There needs to be functionality to run multiple chains in parallel. This can be used for convergence testing and for increasing the samples per second you get.

opened by mcleonard 2
Bump mistune from 0.7 to 2.0.3
Bumps mistune from 0.7 to 2.0.3.

Release notes

Sourced from mistune's releases.

Version 2.0.2

Fix escape_url via lepture/mistune#295

Version 2.0.1

Fix XSS for image link syntax.

Version 2.0.0

First release of Mistune v2.

Version 2.0.0 RC1

In this release, we have a Security Fix for harmful links.

Version 2.0.0 Alpha 1

This is the first release of v2. An alpha version for users to have a preview of the new mistune.

Version 0.8.4

Support an escaped pipe char in a table cell. #150

Fix ordered and unordered list. #152

Fix spaces between = in HTML tags

Add max_recursive_depth for list and blockquote.

Fix fences code block.

Changelog

Sourced from mistune's changelog.

Changelog

Here is the full history of mistune v2.

Version 2.0.4

Released on Jul 15, 2022 Fix url plugin in <a> tag Fix * formatting
Version 2.0.3

Released on Jun 27, 2022

Fix table plugin

Security fix for CVE-2022-34749

Version 2.0.2

Released on Jan 14, 2022 Fix escape_url
Version 2.0.1

Released on Dec 30, 2021

XSS fix for image link syntax.

Version 2.0.0

Released on Dec 5, 2021 This is the first non-alpha release of mistune v2.
Version 2.0.0rc1

Released on Feb 16, 2021

Version 2.0.0a6

</tr></table>

... (truncated)

Commits

3f422f1 Version bump 2.0.3

a6d4321 Fix asteris emphasis regex CVE-2022-34749

5638e46 Merge pull request #307 from jieter/patch-1

0eba471 Fix typo in guide.rst

61e9337 Fix table plugin

76dec68 Add documentation for renderer heading when TOC enabled

799cd11 Version bump 2.0.2

babb0cf Merge pull request #295 from dairiki/bug.escape_url

fc2cd53 Make mistune.util.escape_url less aggressive

3e8d352 Version bump 2.0.1

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dependencies
opened by dependabot[bot] 1
Bump numpy from 1.9.2 to 1.21.0
Bumps numpy from 1.9.2 to 1.21.0.

Release notes

Sourced from numpy's releases.

v1.21.0

NumPy 1.21.0 Release Notes

The NumPy 1.21.0 release highlights are

continued SIMD work covering more functions and platforms,

initial work on the new dtype infrastructure and casting,

universal2 wheels for Python 3.8 and Python 3.9 on Mac,

improved documentation,

improved annotations,

new PCG64DXSM bitgenerator for random numbers.

In addition there are the usual large number of bug fixes and other improvements.

The Python versions supported for this release are 3.7-3.9. Official support for Python 3.10 will be added when it is released.

:warning: Warning: there are unresolved problems compiling NumPy 1.21.0 with gcc-11.1 .

Optimization level -O3 results in many wrong warnings when running the tests.

On some hardware NumPy will hang in an infinite loop.

New functions

Add PCG64DXSM BitGenerator

Uses of the PCG64 BitGenerator in a massively-parallel context have been shown to have statistical weaknesses that were not apparent at the first release in numpy 1.17. Most users will never observe this weakness and are safe to continue to use PCG64. We have introduced a new PCG64DXSM BitGenerator that will eventually become the new default BitGenerator implementation used by default_rng in future releases. PCG64DXSM solves the statistical weakness while preserving the performance and the features of PCG64.

See upgrading-pcg64 for more details.

(gh-18906)

Expired deprecations

The shape argument numpy.unravel_index cannot be passed as dims keyword argument anymore. (Was deprecated in NumPy 1.16.)

... (truncated)

Commits

b235f9e Merge pull request #19283 from charris/prepare-1.21.0-release

34aebc2 MAINT: Update 1.21.0-notes.rst

493b64b MAINT: Update 1.21.0-changelog.rst

07d7e72 MAINT: Remove accidentally created directory.

032fca5 Merge pull request #19280 from charris/backport-19277

7d25b81 BUG: Fix refcount leak in ResultType

fa5754e BUG: Add missing DECREF in new path

61127bb Merge pull request #19268 from charris/backport-19264

143d45f Merge pull request #19269 from charris/backport-19228

d80e473 BUG: Removed typing for == and != in dtypes

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dependencies
opened by dependabot[bot] 1
more robust int checking with numbers.Integral

This change together with the autograd change from @mattjj seem to fix https://github.com/mcleonard/sampyl/issues/14

It uses the numbers type hierarchy introduced in python 2.6 to check for integral types.

opened by gbarta 1
added slice sampler and simple example

Added a simple component-wise and random direction slice sampler that implements stepping out and doubling. See demo in examples/slice_sample.py.

I also modified the State class and added a class function fromvector(self, vec) and a static function init_fromvector(vec, state) that convert between numpy arrays and State objects.

opened by andymiller 1
Issue 12 combo logp

I added a model class that bundles together the logp and grad_logp functions. This makes it easier to write samplers because now you can just do self.model.logp(state) or self.model.grad(state). It also contains caches for logp and grad values. There are two different model classes. One expects separate functions, the other expects one function that returns the gradient also. When a logp function also returns the gradient, you can indicate this when initializing a sampler with grad_logp=True, the second model will be used, but the subsequent behavior is completely the same.

opened by mcleonard 0
Bump certifi from 14.5.14 to 2022.12.7
Bumps certifi from 14.5.14 to 2022.12.7.

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dependencies
opened by dependabot[bot] 0

Bump mistune from 0.7 to 0.8.1

Bumps mistune from 0.7 to 0.8.1.

Changelog

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Changelog

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Version 0.8.1


Released on Nov. 07, 2017

Security fix CVE-2017-16876, thanks Dawid Czarnecki

Version 0.8

Released on Oct. 26, 2017

Remove non breaking spaces preprocessing
Remove rev and rel attribute for footnotes
Fix bypassing XSS vulnerability by junorouse

This version is strongly recommended, since it fixed
a security issue.
Version 0.7.4
</code></pre>
<p>Released on Mar. 14, 2017</p>
<ul>
<li>Fix escape_link method by Marcos Ojeda</li>
<li>Handle block HTML with no content by David Baumgold</li>
<li>Use expandtabs for tab</li>
<li>Fix escape option for text renderer</li>
<li>Fix HTML attribute regex pattern</li>
</ul>
<p>Version 0.7.3</p>
<pre><code>
Released on Jun. 28, 2016

Fix strikethrough regex
Fix HTML attribute regex
Fix close tag regex

Version 0.7.2
</code></pre>
<p>Released on Feb. 26, 2016</p>
<ul>
<li>Fix <code>hard_wrap</code> options on renderer.</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/lepture/mistune/commit/cef69acaa506567595e95ab6ecea25a806de622e"><code>cef69ac</code></a> Add change log for v0.8.1</li>
<li><a href="https://github.com/lepture/mistune/commit/5f06d724bc05580e7f203db2d4a4905fc1127f98"><code>5f06d72</code></a> Fix CVE-2017-16876</li>
<li><a href="https://github.com/lepture/mistune/commit/7f7f106a717e6cf58012304e56b41d6fb2b98e5f"><code>7f7f106</code></a> Version bump 0.8</li>
<li><a href="https://github.com/lepture/mistune/commit/f8ac83ff6d49c0e850436b8d9e57b71c3b2c4d57"><code>f8ac83f</code></a> Cleanup appveyor CI</li>
<li><a href="https://github.com/lepture/mistune/commit/dda2ace2c74b534c82ba3a9571ee8e0bddba9e0e"><code>dda2ace</code></a> Fix CI testing</li>
<li><a href="https://github.com/lepture/mistune/commit/ab8f7de8bc78c2a88f9e01522b8a3a0aa8cd9416"><code>ab8f7de</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/lepture/mistune/issues/140">#140</a> from junorouse/master</li>
<li><a href="https://github.com/lepture/mistune/commit/d6f0b6402299bf5a380e7b4e77bd80e8736630fe"><code>d6f0b64</code></a> Fix bypassing XSS vulnerability.</li>
<li><a href="https://github.com/lepture/mistune/commit/5b8c3f7db4321bada0b955a9fb833a3faba4a67f"><code>5b8c3f7</code></a> Change donate link</li>
<li><a href="https://github.com/lepture/mistune/commit/4c117151ab536004599b0d5a8079ccda84cc5472"><code>4c11715</code></a> Add missing regex import to Lexers example (<a href="https://github-redirect.dependabot.com/lepture/mistune/issues/129">#129</a>)</li>
<li><a href="https://github.com/lepture/mistune/commit/e9e2066fee8ea4970cec17f1e480031db96906b9"><code>e9e2066</code></a> Update benchmark for misaka</li>
<li>Additional commits viewable in <a href="https://github.com/lepture/mistune/compare/v0.7...v0.8.1">compare view</a></li>
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		                                    dependencies


	                                 
										opened  by dependabot[bot]  0


	                        
	                           
	                              
	                                 
	                                 
	                                 
	                              
	                              
	                                 
	                                    
	                                    Bump numpy from 1.9.2 to 1.22.0
	                                    
	                                 
	                                  
	                                 
	                                   
		                                   Bumps numpy from 1.9.2 to 1.22.0.

Release notes
Sourced from numpy's releases.

v1.22.0
NumPy 1.22.0 Release Notes
NumPy 1.22.0 is a big release featuring the work of 153 contributors
spread over 609 pull requests. There have been many improvements,
highlights are:

Annotations of the main namespace are essentially complete. Upstream
is a moving target, so there will likely be further improvements,
but the major work is done. This is probably the most user visible
enhancement in this release.
A preliminary version of the proposed Array-API is provided. This is
a step in creating a standard collection of functions that can be
used across application such as CuPy and JAX.
NumPy now has a DLPack backend. DLPack provides a common interchange
format for array (tensor) data.
New methods for quantile, percentile, and related functions. The
new methods provide a complete set of the methods commonly found in
the literature.
A new configurable allocator for use by downstream projects.

These are in addition to the ongoing work to provide SIMD support for
commonly used functions, improvements to F2PY, and better documentation.
The Python versions supported in this release are 3.8-3.10, Python 3.7
has been dropped. Note that 32 bit wheels are only provided for Python
3.8 and 3.9 on Windows, all other wheels are 64 bits on account of
Ubuntu, Fedora, and other Linux distributions dropping 32 bit support.
All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix
the occasional problems encountered by folks using truly huge arrays.
Expired deprecations
Deprecated numeric style dtype strings have been removed
Using the strings "Bytes0", "Datetime64", "Str0", "Uint32",
and "Uint64" as a dtype will now raise a TypeError.
(gh-19539)
Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio
numpy.loads was deprecated in v1.15, with the recommendation that
users use pickle.loads instead. ndfromtxt and mafromtxt were both
deprecated in v1.17 - users should use numpy.genfromtxt instead with
the appropriate value for the usemask parameter.
(gh-19615)


... (truncated)


Commits

4adc87d Merge pull request #20685 from charris/prepare-for-1.22.0-release
fd66547 REL: Prepare for the NumPy 1.22.0 release.
125304b wip
c283859 Merge pull request #20682 from charris/backport-20416
5399c03 Merge pull request #20681 from charris/backport-20954
f9c45f8 Merge pull request #20680 from charris/backport-20663
794b36f Update armccompiler.py
d93b14e Update test_public_api.py
7662c07 Update init.py
311ab52 Update armccompiler.py
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										opened  by dependabot[bot]  0
									
	                              
	                           
	                        
	                        
	                           
	                              
	                                 
	                                 
	                                 
	                              
	                              
	                                 
	                                    
	                                    Bump ipython from 3.2.1 to 7.16.3
	                                    
	                                 
	                                  
	                                 
	                                   
		                                   Bumps ipython from 3.2.1 to 7.16.3.

Commits

d43c7c7 release 7.16.3
5fa1e40 Merge pull request from GHSA-pq7m-3gw7-gq5x
8df8971 back to dev
9f477b7 release 7.16.2
138f266 bring back release helper from master branch
5aa3634 Merge pull request #13341 from meeseeksmachine/auto-backport-of-pr-13335-on-7...
bcae8e0 Backport PR #13335: What's new 7.16.2
8fcdcd3 Pin Jedi to <0.17.2.
2486838 release 7.16.1
20bdc6f fix conda build
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										opened  by dependabot[bot]  0
									
	                              
	                           
	                        
	                        
	                           
	                              
	                                 
	                                 
	                                 
	                              
	                              
	                                 
	                                    
	                                    Bump babel from 2.0 to 2.9.1
	                                    
	                                 
	                                  
	                                 
	                                   
		                                   Bumps babel from 2.0 to 2.9.1.

Release notes
Sourced from babel's releases.

Version 2.9.1
Bugfixes

The internal locale-data loading functions now validate the name of the locale file to be loaded and only allow files within Babel's data directory.  Thank you to Chris Lyne of Tenable, Inc. for discovering the issue!

Version 2.9.0
Upcoming version support changes

This version, Babel 2.9, is the last version of Babel to support Python 2.7, Python 3.4, and Python 3.5.

Improvements

CLDR: Use CLDR 37 – Aarni Koskela (#734)
Dates: Handle ZoneInfo objects in get_timezone_location, get_timezone_name - Alessio Bogon (#741)
Numbers: Add group_separator feature in number formatting - Abdullah Javed Nesar (#726)

Bugfixes

Dates: Correct default Format().timedelta format to 'long' to mute deprecation warnings – Aarni Koskela
Import: Simplify iteration code in "import_cldr.py" – Felix Schwarz
Import: Stop using deprecated ElementTree methods "getchildren()" and "getiterator()" – Felix Schwarz
Messages: Fix unicode printing error on Python 2 without TTY. – Niklas Hambüchen
Messages: Introduce invariant that _invalid_pofile() takes unicode line. – Niklas Hambüchen
Tests: fix tests when using Python 3.9 – Felix Schwarz
Tests: Remove deprecated 'sudo: false' from Travis configuration – Jon Dufresne
Tests: Support Py.test 6.x – Aarni Koskela
Utilities: LazyProxy: Handle AttributeError in specified func – Nikiforov Konstantin (#724)
Utilities: Replace usage of parser.suite with ast.parse – Miro Hrončok

Documentation

Update parse_number comments – Brad Martin (#708)
Add iter to Catalog documentation – @CyanNani123

Version 2.8.1
This patch version only differs from 2.8.0 in that it backports in #752.
Version 2.8.0
Improvements

CLDR: Upgrade to CLDR 36.0 - Aarni Koskela (#679)
Messages: Don't even open files with the "ignore" extraction method - @sebleblanc (#678)

Bugfixes

Numbers: Fix formatting very small decimals when quantization is disabled - Lev Lybin, @miluChen (#662)
Messages: Attempt to sort all messages – Mario Frasca (#651, #606)

Docs


... (truncated)


Changelog
Sourced from babel's changelog.

Version 2.9.1
Bugfixes

* The internal locale-data loading functions now validate the name of the locale file to be loaded and only
  allow files within Babel's data directory.  Thank you to Chris Lyne of Tenable, Inc. for discovering the issue!
Version 2.9.0
Upcoming version support changes


This version, Babel 2.9, is the last version of Babel to support Python 2.7, Python 3.4, and Python 3.5.

Improvements

* CLDR: Use CLDR 37 – Aarni Koskela ([#734](https://github.com/python-babel/babel/issues/734))
* Dates: Handle ZoneInfo objects in get_timezone_location, get_timezone_name - Alessio Bogon ([#741](https://github.com/python-babel/babel/issues/741))
* Numbers: Add group_separator feature in number formatting - Abdullah Javed Nesar ([#726](https://github.com/python-babel/babel/issues/726))
Bugfixes

* Dates: Correct default Format().timedelta format to 'long' to mute deprecation warnings – Aarni Koskela
* Import: Simplify iteration code in &quot;import_cldr.py&quot; – Felix Schwarz
* Import: Stop using deprecated ElementTree methods &quot;getchildren()&quot; and &quot;getiterator()&quot; – Felix Schwarz
* Messages: Fix unicode printing error on Python 2 without TTY. – Niklas Hambüchen
* Messages: Introduce invariant that _invalid_pofile() takes unicode line. – Niklas Hambüchen
* Tests: fix tests when using Python 3.9 – Felix Schwarz
* Tests: Remove deprecated 'sudo: false' from Travis configuration – Jon Dufresne
* Tests: Support Py.test 6.x – Aarni Koskela
* Utilities: LazyProxy: Handle AttributeError in specified func – Nikiforov Konstantin ([#724](https://github.com/python-babel/babel/issues/724))
* Utilities: Replace usage of parser.suite with ast.parse – Miro Hrončok
Documentation
</code></pre>
<ul>
<li>Update parse_number comments – Brad Martin (<a href="https://github-redirect.dependabot.com/python-babel/babel/issues/708">#708</a>)</li>
<li>Add <strong>iter</strong> to Catalog documentation – <a href="https://github.com/CyanNani123"><code>@CyanNani123</code></a></li>
</ul>
<h2>Version 2.8.1</h2>
<p>This is solely a patch release to make running tests on Py.test 6+ possible.</p>
<p>Bugfixes</p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/python-babel/babel/commit/a99fa2474c808b51ebdabea18db871e389751559"><code>a99fa24</code></a> Use 2.9.0's setup.py for 2.9.1</li>
<li><a href="https://github.com/python-babel/babel/commit/60b33e083801109277cb068105251e76d0b7c14e"><code>60b33e0</code></a> Become 2.9.1</li>
<li><a href="https://github.com/python-babel/babel/commit/412015ef642bfcc0d8ba8f4d05cdbb6aac98d9b3"><code>412015e</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/python-babel/babel/issues/782">#782</a> from python-babel/locale-basename</li>
<li><a href="https://github.com/python-babel/babel/commit/5caf717ceca4bd235552362b4fbff88983c75d8c"><code>5caf717</code></a> Disallow special filenames on Windows</li>
<li><a href="https://github.com/python-babel/babel/commit/3a700b5b8b53606fd98ef8294a56f9510f7290f8"><code>3a700b5</code></a> Run locale identifiers through <code>os.path.basename()</code></li>
<li><a href="https://github.com/python-babel/babel/commit/5afe2b2f11dcdd6090c00231d342c2e9cd1bdaab"><code>5afe2b2</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/python-babel/babel/issues/754">#754</a> from python-babel/github-ci</li>
<li><a href="https://github.com/python-babel/babel/commit/58de8342f865df88697a4a166191e880e3c84d82"><code>58de834</code></a> Replace Travis + Appveyor with GitHub Actions (WIP)</li>
<li><a href="https://github.com/python-babel/babel/commit/d1bbc08e845d03d8e1f0dfa0e04983d755f39cb5"><code>d1bbc08</code></a> import_cldr: use logging; add -q option</li>
<li><a href="https://github.com/python-babel/babel/commit/156b7fb9f377ccf58c71cf01dc69fb10c7b69314"><code>156b7fb</code></a> Quiesce CLDR download progress bar if requested (or not a TTY)</li>
<li><a href="https://github.com/python-babel/babel/commit/613dc1700f91c3d40b081948c0dd6023d8ece057"><code>613dc17</code></a> Make the import warnings about unsupported number systems less verbose</li>
<li>Additional commits viewable in <a href="https://github.com/python-babel/babel/compare/2.0...v2.9.1">compare view</a></li>
</ul>
</details>
<br />


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										opened  by dependabot[bot]  0
									
	                              

	                           

	                        

	                        
	                           
	                              
	                                 
	                                 
	                                 
	                              
	                              
	                                 
	                                    
	                                    Bump py from 1.4.30 to 1.10.0
	                                    
	                                 
	                                  
	                                 
	                                   
		                                   Bumps py from 1.4.30 to 1.10.0.

Changelog
Sourced from py's changelog.

1.10.0 (2020-12-12)

Fix a regular expression DoS vulnerability in the py.path.svnwc SVN blame functionality (CVE-2020-29651)
Update vendored apipkg: 1.4 => 1.5
Update vendored iniconfig: 1.0.0 => 1.1.1

1.9.0 (2020-06-24)


Add type annotation stubs for the following modules:

py.error
py.iniconfig
py.path (not including SVN paths)
py.io
py.xml

There are no plans to type other modules at this time.
The type annotations are provided in external .pyi files, not inline in the
code, and may therefore contain small errors or omissions. If you use py
in conjunction with a type checker, and encounter any type errors you believe
should be accepted, please report it in an issue.


1.8.2 (2020-06-15)

On Windows, py.path.locals which differ only in case now have the same
Python hash value. Previously, such paths were considered equal but had
different hashes, which is not allowed and breaks the assumptions made by
dicts, sets and other users of hashes.

1.8.1 (2019-12-27)


Handle FileNotFoundError when trying to import pathlib in path.common
on Python 3.4 (#207).


py.path.local.samefile now works correctly in Python 3 on Windows when dealing with symlinks.


1.8.0 (2019-02-21)


add "importlib" pyimport mode for python3.5+, allowing unimportable test suites
to contain identically named modules.


fix LocalPath.as_cwd() not calling os.chdir() with None, when
being invoked from a non-existing directory.




... (truncated)


Commits

e5ff378 Update CHANGELOG for 1.10.0
94cf44f Update vendored libs
5e8ded5 testing: comment out an assert which fails on Python 3.9 for now
afdffcc Rename HOWTORELEASE.rst to RELEASING.rst
2de53a6 Merge pull request #266 from nicoddemus/gh-actions
fa1b32e Merge pull request #264 from hugovk/patch-2
887d6b8 Skip test_samefile_symlink on pypy3 on Windows
e94e670 Fix test_comments() in test_source
fef9a32 Adapt test
4a694b0 Add GitHub Actions badge to README
Additional commits viewable in compare view





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										opened  by dependabot[bot]  0

MCMC samplers for Bayesian estimation in Python, including Metropolis-Hastings, NUTS, and Slice

Related tags

Overview

Sampyl

Dependencies

Installation

Documentation

Tests

License

Comments

Version 2.0.2

Version 2.0.1

Version 2.0.0

Version 2.0.0 RC1

Version 2.0.0 Alpha 1

Version 0.8.4

Changelog

v1.21.0

NumPy 1.21.0 Release Notes

New functions

Add PCG64DXSM BitGenerator

Expired deprecations

Changelog

v1.22.0

NumPy 1.22.0 Release Notes

Expired deprecations

Deprecated numeric style dtype strings have been removed

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

Version 2.9.1

Bugfixes

Version 2.9.0

Upcoming version support changes

Improvements

Bugfixes

Documentation

Version 2.8.1

Version 2.8.0

Improvements

Bugfixes

Docs

Version 2.9.1

Version 2.9.0

1.10.0 (2020-12-12)

1.9.0 (2020-06-24)

1.8.2 (2020-06-15)

1.8.1 (2019-12-27)

1.8.0 (2019-02-21)

Owner

Mat Leonard

We have implemented shaDow-GNN as a general and powerful pipeline for graph representation learning. For more details, please find our paper titled Deep Graph Neural Networks with Shallow Subgraph Samplers, available on arXiv (https//arxiv.org/abs/2012.01380).

TorchGeo is a PyTorch domain library, similar to torchvision, that provides datasets, transforms, samplers, and pre-trained models specific to geospatial data.

A solution to the 2D Ising model of ferromagnetism, implemented using the Metropolis algorithm

The Python ensemble sampling toolkit for affine-invariant MCMC

PyTorch implementation of Algorithm 1 of "On the Anatomy of MCMC-Based Maximum Likelihood Learning of Energy-Based Models"

zeus is a Python implementation of the Ensemble Slice Sampling method.

SANet: A Slice-Aware Network for Pulmonary Nodule Detection

The undersampled DWI image using Slice-Interleaved Diffusion Encoding (SIDE) method can be reconstructed by the UNet network.

Re-implementation of the Noise Contrastive Estimation algorithm for pyTorch, following "Noise-contrastive estimation: A new estimation principle for unnormalized statistical models." (Gutmann and Hyvarinen, AISTATS 2010)

pyhsmm - library for approximate unsupervised inference in Bayesian Hidden Markov Models (HMMs) and explicit-duration Hidden semi-Markov Models (HSMMs), focusing on the Bayesian Nonparametric extensions, the HDP-HMM and HDP-HSMM, mostly with weak-limit approximations.

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

Bayesian-Torch is a library of neural network layers and utilities extending the core of PyTorch to enable the user to perform stochastic variational inference in Bayesian deep neural networks

Hierarchical-Bayesian-Defense - Towards Adversarial Robustness of Bayesian Neural Network through Hierarchical Variational Inference (Openreview)

TorchDistiller - a collection of the open source pytorch code for knowledge distillation, especially for the perception tasks, including semantic segmentation, depth estimation, object detection and instance segmentation.

pytorch implementation of openpose including Hand and Body Pose Estimation.

Web service for facial landmark detection, head pose estimation, facial action unit recognition, and eye-gaze estimation based on OpenFace 2.0

OpenFace – a state-of-the art tool intended for facial landmark detection, head pose estimation, facial action unit recognition, and eye-gaze estimation.

Monocular Depth Estimation - Weighted-average prediction from multiple pre-trained depth estimation models

Light-weight network, depth estimation, knowledge distillation, real-time depth estimation, auxiliary data.

Expired deprecations for `loads`, `ndfromtxt`, and `mafromtxt` in npyio