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Alpha renaming of bound variables #148

Merged
merged 19 commits into from
Jun 25, 2019
Merged

Alpha renaming of bound variables #148

merged 19 commits into from
Jun 25, 2019

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@eb8680 eb8680 commented May 30, 2019 •
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Resolves #96. Blocking #130.

This PR makes the following changes to substitution and interpretation:

  1. Adds eager alpha-renaming whenever a variable is newly bound
  2. Adds .fresh and .bound attributes to each term (empty by default) which are frozensets of names of fresh variables introduced by a term and variables newly bound by a term respectively. These must be manually populated in the __init__ method of each new term if they are not empty for that term.
  3. Changes the semantics of the Subs term slightly: there is now a substitute function that calls itself recursively, as opposed to Subs calling eager_subs methods which in turn recursively call Subs. A Subs term now represents a lazy call to substitute. I did this instead of manually changing every call to Subs inside an eager_subs method into recursive eager_subs calls.
  4. Makes substitution more generic, removing the need for .eager_subs implementations in terms that don't introduce fresh variables and simplifying the implementation of new terms. Hopefully most eager_subs methods of terms that don't introduce fresh variables can be removed in a followup PR.

Tasks:

  • Add .fresh and .bound to any remaining terms missing them and add some tests checking
  • Fix various minor regressions (Affine, Joint, Stack, Lambda, Independent, etc)
  • Add new tests exercising alpha-renaming (which would currently trigger NotImplementedErrors)

Triaged:

  • Make funsor.adjoint compatible with alpha-renaming

@eb8680 eb8680 added the WIP label May 30, 2019
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Thanks for implementing this!

@fritzo fritzo merged commit 7e456e6 into master Jun 25, 2019
This was referenced Jun 26, 2019
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eb8680 added a commit that referenced this pull request Jun 28, 2019
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Squashed commit of the following:
216f3da 
commit 3a80b29
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Thu Jun 27 14:17:26 2019 -0700

    Make substitution an interpretation (#155)

    * make substitute into an interpretation

    * simplify interpretation and add numpy+tco test to Makefile

    * tweak Independent

    * remove substitute_funsor

    * uncomment long examples

    * conditionally xfail some numpy tests

    * update semantics of Independent to be compatible with substitution changes

    * add Module to ground types

commit ce5cdeb
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Wed Jun 26 10:18:32 2019 -0700

    Remove eager_subs method from Joint (#154)

commit ba0dfcb
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Tue Jun 25 15:04:38 2019 -0700

    Separate generic and fresh variables in substitute (#153)

commit 14766ef
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Tue Jun 25 14:52:19 2019 -0700

    Remove most eager_subs methods from terms with no fresh variables (#152)

commit 7e456e6
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Tue Jun 25 13:34:58 2019 -0700

    Alpha renaming of bound variables (#148)

commit 3edfb0f
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Wed Jun 5 09:58:30 2019 -0700

    Use classifiers to specify the license (#150)

commit d1cd1d2
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Fri May 24 11:10:14 2019 -0700

    Add an explicit stack-based interpreter (#147)

commit ac02dcc
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Mon May 6 11:02:20 2019 -0700

    Update badge to point to travis-ci.com (#143)

commit 416cff6
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Thu May 2 14:45:10 2019 -0700

    Promote Einsum to a funsor for pattern matching (#142)

commit 30e4255
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Thu May 2 10:46:24 2019 -0700

    Update CI to use PyTorch 1.1.0 (#141)

    * Update CI to use PyTorch 1.1.0

    * Fix travis version

    * Accommodate change to torch.max return type

commit 00c467d
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Wed May 1 22:57:54 2019 -0700

    Add model and guide auxiliary variable elimination to minipyro.elbo (#126)

    * add auxiliary variable elimination to minipyro.elbo to mimic TraceEnum_ELBO

    * optional partial_sum_product

    * Common subexpression elimination

    * add a test for traceenum_elbo

    * add two more tests, one of which is xfailing...

    * Simplify test and minipyro (#140)

    * Add smoke test for gaussian-probit model

    * Remove bogus assertion

    * Fix TraceEnum_ELBO to use EnumerateMessenger

    * remove EnumerateMessenger

    * add optional optimization to traceenum_elbo and mark monte carlo test xfail

commit c77dc99
Author: JP <jonathanp.chen@gmail.com>
Date:   Wed May 1 21:26:07 2019 -0700

    rtd fix to not install torch 1.0 (#139)

commit 2e5fd40
Author: JP <jonathanp.chen@gmail.com>
Date:   Wed May 1 14:10:27 2019 -0700

    deploy documentation (#138)

commit cb09325
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Wed May 1 12:19:14 2019 -0700

    Add generic Bernoulli wrapper around probs,logits version (#137)

commit 45e0434
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Wed May 1 12:11:03 2019 -0700

    Refactor elbos (#136)

    * Refactor elbos

    * Fix jit classes

commit 1f5f602
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Tue Apr 30 23:57:13 2019 -0700

    Add BernoulliLogits distribution (#135)

commit df25607
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Tue Apr 30 15:51:38 2019 -0700

    Avoid legacy constructors (#134)

commit 92e85c3
Author: Fritz Obermeyer <fritzo@uber.com>
Date:   Mon Apr 29 11:14:31 2019 -0700

    Add JitTrace_ELBO class to minipyro (#133)

    * Add JitTrace_ELBO class to minipyro

    * Enable minipyro --jit test

    * Simplify JitTrace_ELBO

    * Make Gaussian math jit compatible

    * Add unit tests for BlockVector and BlockMatrix

    * Fix docs

    * Tweak docs

commit 5053f55
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Apr 12 14:09:23 2019 -0400

    Remove dependency on pyro ParamStoreDict (#129)

commit 79a8621
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Thu Apr 11 21:15:00 2019 -0700

    Support constraints in funsor.minipyro (#128)

    * Support constraints in funsor.minipyro

    * Make minipyro tests a little stronger

    * Save metadata to value.unconstrained()

commit a7f3b8a
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Tue Apr 9 21:29:29 2019 -0700

    Reinstate examples/minipyro.py, forked from pyro/examples (#125)

    * Reinstate examples/minipyro.py, forked from pyro/examples

    * Add a rule for eager evaluation of (p.exp() * f).reduce(ops.add) and a failing test showing numerical instability

    * compute most of expectation in log-space in minipyro

    * handle plates?

    * add

commit 48fa3f7
Author: Neeraj Pradhan <prad.neeraj@gmail.com>
Date:   Mon Apr 8 11:17:29 2019 -0700

    Add Beta, Dirichlet, and Binomial distributions (#120)

commit f74df0a
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Sat Apr 6 19:28:39 2019 -0700

    Add rule for creating Gaussians from Affine inputs (#119)

commit 8fa1c32
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Sat Apr 6 15:21:33 2019 -0700

    Add an Affine term to represent multilinear functions of real Variables (#116)

commit 627711e
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sat Apr 6 10:09:42 2019 -0700

    Support wrapping PyTorch builtin functions (#118)

commit 216626c
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sat Apr 6 09:06:51 2019 -0700

    Add a torch_tensordot operation (#117)

    * Add a torch_tensordot op

    * Fix docstrings to avoid sphinx warning

commit fcb4670
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Apr 5 10:30:03 2019 -0700

    Add moment_matching interpretation + SLDS example (#115)

    * Sketch imm example (no inference yet)

    * Sketch Gaussian.moment_matching_reduce

    * Use moment-matching interpretation in IMM example

    * Rename example to slds.py

    * Make SLDS params more interesting

    * Relax assumptions regarding reduced_vars

commit fd0dfe4
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Tue Apr 2 15:04:43 2019 -0700

    Add initial sphinx docs (#114)

commit 51b5489
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sun Mar 31 23:14:38 2019 -0700

    Add a VAE example using the monte_carlo interpretation (#95)

    * Sketch Monte Carlo interpretation of logaddexp reduction

    * Use AssociativeOp in patterns

    * Fix op pattern matcher

    * Try eager before monte_carlo

    * Drop ops.sample, ops.marginal

    * Sketch VAE example using monte carlo interpretation

    * Refactor, focusing on .sample() and .monte_carlo_logsumexp() methods

    * Fix vae example

    * Sketch Tensor.sample() (untested)

    * Fix cyclic import

    * Sketch Gaussian.sample() (untested)

    * Implement Delta.sample()

    * Sketch Expectation class

    * Sketch sampler implementations

    * Delete Expectation in favor of Integrate in a separate PR

    * Revert .sample() sketch

    * Update VAE example to use multi-output Functions

    * Fix reductions in VAE

    * Sketch support for multiple args in __getitem__

    * Fix bugs in getitem_tensor_tensor

    * Add stronger tests for tensor getitem

    * Add support for string indexing

    * Simplify vae example using multi-getitem

    * Add stub for Integrate

    * Fix typo

    * Sketch monte_carlo registration of Gaussian-Gaussian things

    * Add stubs for Joint integration

    * Fix typos

    * Sketch support for multiple samples

    * Fix test usage of registry

    * Fix bugs in gaussian integral

    * Handle scale factors in Funsor.sample()

    * Use Integrate in test_samplers.py

    * Fix bug in Integrate; be less clever

    * Add implementations of gaussian-linear integrals

    * Add interpretation logging controlled by FUNSOR_DEBUG

    * Simplify debug printing

    * Fix lazy reduction for Joint.reduce()

    * Fix recursion bug

    * Get univariate Gaussian sampling to mostly work

    * Fix bug in Tensor.eager_reduce with nontrivial output

    * Fix output shape broadcasting in Tensor

    * Fix assert_close in test_samplers.py

    * Fix cholesky bugs

    * Fix bug in _trace_mm()

    * Fixes for examples/vae.py

    * Remove examples/vae.py

    * Revert "Remove examples/vae.py"

    This reverts commit bee75b9.

    * Use funsor.Lambda in VAE example

    * Add a Lambda funsor, inverse to getitem

    * Use lazy substitution rather than Lambda

    * Add --pdb argument to examples/vae.py

    * Add function logging and filename logging when FUNSOR_DEBUG=1

    * Enable more functions to be logged

    * Little fixes

    * Fixes to support vae example

    * Fix comment

    * Revert product sample rules

    * WIP sketch plates

    * Simplify vae example (still not working)

    * Sketch Uncurry funsor

    * Sketch Uncurry-Delta-Lambda pattern

    * Sketch Joint-Uncurry-Delta rule

    * Sketch uncurry-distribution test

    * Change to_funsor second arg from dtype to Domain

    * Add Funsor.__contains__

    * Use Uncurry in VAE example

    * Fix test_normal_uncurry

    * Rename Uncurry to Independent

    * Revert irrelevant changes

    * Support sampling from mixtures

    * Update VAE example to use Independent

    * Get VAE example to start working

    * Flake8

    * Revert nan validation

    * Add torchvision to setup.py

commit 306aca6
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sun Mar 31 22:51:42 2019 -0700

    Add Lambda and Independent funsors (#97)

    * Add a Lambda funsor, inverse to getitem

    * Sketch Uncurry funsor

    * Sketch Uncurry-Delta-Lambda pattern

    * Sketch Joint-Uncurry-Delta rule

    * Sketch uncurry-distribution test

    * Change to_funsor second arg from dtype to Domain

    * Add Funsor.__contains__

    * Fix test_normal_uncurry

    * Rename Uncurry to Independent

commit 89313ef
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sun Mar 31 13:40:43 2019 -0700

    Refactor .unscaled_sample() interface (#113)

commit 366e9e3
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sun Mar 31 13:39:35 2019 -0700

    Change to_funsor second arg from dtype to Domain (#112)

commit bddcc2c
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sat Mar 30 18:15:54 2019 -0700

    Support event_dim kwarg in pyro.param (#111)

    * Support event_dim kwarg in pyro.param

    * Use local-param branch of Pyro

    * Use pyro dev for CI

commit 36e57ae
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 29 13:00:36 2019 -0700

    Add a working minipyro with tests (#100)

    * Add pristine copy of pyro/contrib/minipyro.py

    * First pass at fixing minipyro

    * First pass at transformed distributions

    * Add test for sampling transformed Gaussian

    * Add test for renaming a Gaussian variable

    * Add dist.LogNormal distribution and density test

    * Add xfailing test for LogNormal sampler

    * Attempt to fix minipyro.elbo

    * Implement negation and subtraction ops for R-N derivatives

    * Fix bug in log_joint.process of sample

    * Implement reduction along a plate dimension

    * Implement correct but non-monte-carlo elbo

    * Fix bugs in Gaussian

    * Implement plate reductions for Gaussian, Joint

    * Use Expectation(...) in elbo computation

    * Fix typos in elbo

    * Add tests for plate reduction

    * Use Expectation interface by default

    * Add initial test_minipyro.py

    * Add more minipyro tests

    * Add shape assertions to gaussian math

    * Refactor minipyro

    * Add an observation to plate test

    * Add more plates tests

    * Support sampling in funsor.minipyro

commit b9cdbac
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 29 11:02:00 2019 -0700

    Implement plate reductions for Gaussian, Joint (#108)

commit 37ce962
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Thu Mar 28 14:43:45 2019 -0700

    Make distributions lazy when used Pyro-style (#107)

commit 16a2fbb
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Wed Mar 27 18:04:50 2019 -0700

    Add Contract to optimizer (#105)

commit c339f1a
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Wed Mar 27 17:57:22 2019 -0700

    Implement negation and subtraction ops for R-N derivatives (#104)

commit 830e430
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Wed Mar 27 14:58:14 2019 -0700

    Implement basic transformed distributions (#103)

    * First pass at transformed distributions

    * Add test for sampling transformed Gaussian

    * Add test for renaming a Gaussian variable

    * Add dist.LogNormal distribution and density test

    * Add xfailing test for LogNormal sampler

commit a54defa
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Wed Mar 27 14:02:34 2019 -0700

    Support for pattern matching with the unification library (#78)

commit 364745e
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Tue Mar 26 19:08:23 2019 -0700

    Remove modified version of minipyro (#102)

commit ea7feb2
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Tue Mar 26 13:29:12 2019 -0700

    Log function and filename when FUNSOR_DEBUG=1 (#101)

    * Add function logging and filename logging when FUNSOR_DEBUG=1

    * Enable more functions to be logged

commit 951630c
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Tue Mar 26 00:14:21 2019 -0700

    Resurrect lazy Subs funsor (again) (#99)

    * Sketch Monte Carlo interpretation of logaddexp reduction

    * Use AssociativeOp in patterns

    * Fix op pattern matcher

    * Try eager before monte_carlo

    * Drop ops.sample, ops.marginal

    * Sketch VAE example using monte carlo interpretation

    * Refactor, focusing on .sample() and .monte_carlo_logsumexp() methods

    * Fix vae example

    * Sketch Tensor.sample() (untested)

    * Fix cyclic import

    * Sketch Gaussian.sample() (untested)

    * Implement Delta.sample()

    * Sketch Expectation class

    * Sketch sampler implementations

    * Delete Expectation in favor of Integrate in a separate PR

    * Revert .sample() sketch

    * Update VAE example to use multi-output Functions

    * Fix reductions in VAE

    * Sketch support for multiple args in __getitem__

    * Fix bugs in getitem_tensor_tensor

    * Add stronger tests for tensor getitem

    * Add support for string indexing

    * Simplify vae example using multi-getitem

    * Add stub for Integrate

    * Fix typo

    * Sketch monte_carlo registration of Gaussian-Gaussian things

    * Add stubs for Joint integration

    * Fix typos

    * Sketch support for multiple samples

    * Fix test usage of registry

    * Fix bugs in gaussian integral

    * Handle scale factors in Funsor.sample()

    * Use Integrate in test_samplers.py

    * Fix bug in Integrate; be less clever

    * Add implementations of gaussian-linear integrals

    * Add interpretation logging controlled by FUNSOR_DEBUG

    * Simplify debug printing

    * Fix lazy reduction for Joint.reduce()

    * Fix recursion bug

    * Get univariate Gaussian sampling to mostly work

    * Fix bug in Tensor.eager_reduce with nontrivial output

    * Fix output shape broadcasting in Tensor

    * Fix assert_close in test_samplers.py

    * Fix cholesky bugs

    * Fix bug in _trace_mm()

    * Fixes for examples/vae.py

    * Remove examples/vae.py

    * Add docstrings

    * Resurrect lazy Subs funsor (again)

    * Fix typo

    * Allow completely lazy eager_subs method

commit 15b0c73
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Mon Mar 25 17:04:45 2019 -0700

    Implement Monte Carlo interpretation of Integrate (#54)

    * Sketch Monte Carlo interpretation of logaddexp reduction

    * Use AssociativeOp in patterns

    * Fix op pattern matcher

    * Try eager before monte_carlo

    * Drop ops.sample, ops.marginal

    * Sketch VAE example using monte carlo interpretation

    * Refactor, focusing on .sample() and .monte_carlo_logsumexp() methods

    * Fix vae example

    * Sketch Tensor.sample() (untested)

    * Fix cyclic import

    * Sketch Gaussian.sample() (untested)

    * Implement Delta.sample()

    * Sketch Expectation class

    * Sketch sampler implementations

    * Delete Expectation in favor of Integrate in a separate PR

    * Revert .sample() sketch

    * Update VAE example to use multi-output Functions

    * Fix reductions in VAE

    * Sketch support for multiple args in __getitem__

    * Fix bugs in getitem_tensor_tensor

    * Add stronger tests for tensor getitem

    * Add support for string indexing

    * Simplify vae example using multi-getitem

    * Add stub for Integrate

    * Fix typo

    * Sketch monte_carlo registration of Gaussian-Gaussian things

    * Add stubs for Joint integration

    * Fix typos

    * Sketch support for multiple samples

    * Fix test usage of registry

    * Fix bugs in gaussian integral

    * Handle scale factors in Funsor.sample()

    * Use Integrate in test_samplers.py

    * Fix bug in Integrate; be less clever

    * Add implementations of gaussian-linear integrals

    * Add interpretation logging controlled by FUNSOR_DEBUG

    * Simplify debug printing

    * Fix lazy reduction for Joint.reduce()

    * Fix recursion bug

    * Get univariate Gaussian sampling to mostly work

    * Fix bug in Tensor.eager_reduce with nontrivial output

    * Fix output shape broadcasting in Tensor

    * Fix assert_close in test_samplers.py

    * Fix cholesky bugs

    * Fix bug in _trace_mm()

    * Fixes for examples/vae.py

    * Remove examples/vae.py

    * Add docstrings

    * Updates per review

    * Revert accidental change

commit d2d4c4a
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sat Mar 23 13:44:16 2019 -0700

    Fix lazy reduction for Joint.reduce() (#94)

    * Fix lazy reduction for Joint.reduce()

    * Fix recursion bug

commit 270d168
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 22 16:44:01 2019 -0700

    Add interpretation logging controlled by FUNSOR_DEBUG=1 (#93)

    * Add interpretation logging controlled by FUNSOR_DEBUG

    * Simplify debug printing

    * Improve pretty printing of Stack and Joint

commit 5d0a291
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 22 12:55:34 2019 -0700

    Implement advanced indexing in Funsor.__getitem__() (#88)

    * Sketch support for multiple args in __getitem__

    * Fix bugs in getitem_tensor_tensor

    * Add stronger tests for tensor getitem

    * Add support for string indexing

commit 028f640
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Thu Mar 21 15:45:29 2019 -0700

    Add isort command to Makefile (#92)

commit 7bbfb3a
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Thu Mar 21 13:39:40 2019 -0700

    Sketched a simple PCFG example (#87)

commit 3fe2581
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Thu Mar 21 13:39:14 2019 -0700

    Refactor contract dependencies (#91)

    * Refactor contract dependencies

    * Fix optimize(Contract, Tensor, Tensor)

    * Fix dtype computation

    * Address review comment

    * Fix typo

commit 7cca0f8
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Wed Mar 20 12:22:44 2019 -0700

    Implement Contract term (#77)

commit 876070f
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Wed Mar 20 00:19:26 2019 -0700

    Add a to_data() helper (#84)

    * Add a to_nonfunsor() helper

    * Fix typo; add more tests

    * Rename to_nonfunsor to to_data

commit 05649ae
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Tue Mar 19 20:50:04 2019 -0700

    Support torch functions that return nested tuples of tensors (#82)

commit 2b8c0e5
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Tue Mar 19 14:39:51 2019 -0700

    Rename funsor.contract module to funsor.sum_product (#81)

commit 0139a70
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 15 15:58:11 2019 -0700

    Implement monte carlo .sample() methods (#75)

commit b5ea615
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 15 15:40:08 2019 -0700

    Implement sequential interpretation (#76)

commit 5fa7fa6
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Wed Mar 13 11:29:21 2019 -0700

    Implement a Joint normal form funsor (#69)

    * Add a simple delta distribution

    * Add tests for nontrivial event dim

    * Simplify unit test

    * Sketch a general Delta funsor class

    * Simplify to binding a single name in Delta

    * Add some tests for Delta

    * Add test for ground substitution

    * Add tests for reduction

    * Add test for conversion from dist.Delta to Delta

    * Sketch JointNormalForm funsor

    * Settle on Joint interface

    * Add more + handling

    * Remove .log_density field from Delta funsor

    * Drop handling of .log_density from Joint

    * Add logic promoting various Binary(-,-) to Joint

    * Revert "Remove .log_density field from Delta funsor"

    This reverts commit 897f523.

    * Revert "Drop handling of .log_density from Joint"

    This reverts commit a7d0082.

    * Simplify Gaussian funsor

    * WIP Refactor Joint patterns

    * Get Gaussian working with Joint

    * Add a smoke test for Joint

    * Add test for reduction

    * Make xfail more targeted

    * Update docstring on Joint

    * Remove unnecessary handling of Binary(ops.add,...)

commit 9dbb231
Author: Neeraj Pradhan <prad.neeraj@gmail.com>
Date:   Tue Mar 12 18:46:00 2019 -0700

     Separate out ops implementations based on backend (#74)

    * Separate out ops implementations based on backend

    * rebase with master

    * fix failing tests

    * fix error in safediv; get tests working

    * use object for binary ops

    * address comment

    * address comments

commit b130f17
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Mon Mar 11 16:21:14 2019 -0700

    Implement a general Delta funsor (#65)

    * Add a simple delta distribution

    * Add tests for nontrivial event dim

    * Simplify unit test

    * Sketch a general Delta funsor class

    * Simplify to binding a single name in Delta

    * Add some tests for Delta

    * Add test for ground substitution

    * Add tests for reduction

    * Add test for conversion from dist.Delta to Delta

    * Remove .log_density field from Delta funsor

    * Revert "Remove .log_density field from Delta funsor"

    This reverts commit 897f523.

    * Fix failing test

    * Add tests for log_density

    * Update __init__.py

commit 34a1d9c
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Mon Mar 11 15:53:09 2019 -0700

    Implement MultivariateNormal distribution (#73)

    * Add multivariate distribution

    * Reduce test tolerance to fix CI build

commit 8108b78
Author: Neeraj Pradhan <prad.neeraj@gmail.com>
Date:   Mon Mar 11 12:48:37 2019 -0700

    Add numpy backend for funsor (#58)

commit 89540d6
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Mon Mar 11 12:43:22 2019 -0700

    Add prototype funsor.adjoint module (#64)

commit 27b4a76
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sun Mar 10 19:38:57 2019 -0700

    Make reduction methods operate over events (#66)

    * Make reduction ops operate over events

    * Update existing tests

    * Update examples

    * Update README.md

    * Add tests for event reduction ops

    * Fix shape bug

    * Update README.md

commit db497c4
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Sat Mar 9 19:43:27 2019 -0800

    Add lazy option to HMM examples (#67)

commit e46c2df
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Sat Mar 9 01:56:27 2019 -0800

    Refactor contract (#60)

    * Sketch funsor.contract module

    * Add unit test for _partition

    * Add tests for partial_sum_product()

    * Fix test in python 3

commit 97153c7
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 8 16:37:47 2019 -0800

    Match Op type rather than object (#63)

commit d960182
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 8 15:56:34 2019 -0800

    Add type check in Funsor.__call__() (#62)

commit 72fedac
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 8 15:14:15 2019 -0800

    Update minipyro storyboard to correctly handle plates (#56)

    * Update minipyro storyboard to correctly handle plates

    * Revert changes to einsum.py

commit 52f4366
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Fri Mar 8 14:57:21 2019 -0800

    Implement Op wrapper class to enable pattern matching (#55)

commit e64a730
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Wed Mar 6 17:41:20 2019 -0800

    Add a simple Delta distribution (#49)

    * Add a simple delta distribution

    * Add tests for nontrivial event dim

    * Simplify unit test

commit c47a17f
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Wed Mar 6 09:12:29 2019 -0800

    Fix path evaluation order in optimizer (#47)

commit 4537e90
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Tue Mar 5 18:27:36 2019 -0800

    Add plated einsum implementation (#46)

commit 448c1fa
Author: Fritz Obermeyer <fritz.obermeyer@gmail.com>
Date:   Mon Mar 4 17:12:54 2019 -0800

    Implement general Gaussian funsor (#37)

    * WIP sketch Gaussian funsor

    * Partially implement binary_gaussian_gaussian

    * Implement marginalization along a dimension; add smoke test

    * Add more comments

    * Implement binary_gaussian_gaussian

    * Sketch to_affine() and Affine funsor

    * Add xfailing test for to_affine()

    * Sketch more of eager_subs

    * Remove affine stuff

    * WIP fix align_gaussian() using align_tensor()

    * Refactor and simplify align_tensor()

    * Fix eager_subs

    * Get smoke tests working

    * Switch from scale_tril to precision representation

    * Implement basic Normal -> Gaussian transform

    * Rename normal conversions

    * Fix filling in of defaults for distribution classes

    * Add test for binary_gaussian_number

    * Add test for binary_gaussian_tensor

    * Add xfailing test for gaussian + gaussian

    * Add more tests

    * Add test of Normal vs Gaussian

    * Fix math error in Gaussian .logsumexp()

    * Fix bugs in Gaussian+Gaussian, align_gaussian()

    * Fix kalman_filter.py, add to make test

    * Add more distribution tests

commit d333418
Author: eb8680 <eb8680@users.noreply.github.com>
Date:   Sun Mar 3 10:35:23 2019 -0800

    Reinstate opt_einsum-based optimizer (#40)
@eb8680 eb8680 mentioned this pull request Jul 17, 2019
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Implement alpha conversion logic
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