This project provides the daphne probabilistic programming compiler. It is built closely following the book An Introduction to Probabilistic Programming.

The compiler transforms a first order programming language, i.e. a language without recursion and therefore a fixed number of random variables, in Clojure syntax into an intermediate graph representation that lends itself to different inference methods, JSON exports and automatic translation to an amortizing neural network as is described further down.

To run this compiler you need to have leiningen and a JVM for Java 8 or later installed. To see all the options provided by the compiler run:

lein run graph --help

in the directory where you have checked out this repository.

To generate the arithmetic circuit program from our paper provided as the following file in programs/arithmetic_circuit.daphne,

(let [z0 (sample (laplace 20.0 2.0))
      z1 (sample (laplace 10.0 2.0))

      z2 (sample (normal (+ z0 z1) 0.1))
      z3 (sample (normal (* z0 z1) 0.1))

      z4 (sample (normal 7.0 2.0))
      z5 (sample (normal z3 z4))

      x0 (observe (normal (+ z3) 0.1) 0.2)
      x1 (observe (normal z5 0.1) -3.5)]
  [z0 z1 z2 z3 z4 z5])

you can run

lein run graph -i programs/arithmetic_circuit.daphne -o output.json

with the input program as the first argument and the output path as the second argument. By default the compiler emits JSON, but it can also emit the more expressive edn format of Clojure. This will emit a data structure describing the graphical model structure of the following form:

[{},
 {"V":["sample5","sample0","observe6","observe7","sample4","sample2","sample1","sample3"],
  "A":{"sample0":["sample2","sample3"],
       "sample1":["sample2","sample3"],
       "sample4":["sample5"],
       "sample3":["sample5","observe6"],
       "sample5":["observe7"]},
  "P":{"sample0":["sample*",["laplace",20.0,2.0]],
       "sample1":["sample*",["laplace",10.0,2.0]],
       "sample2":["sample*",["normal",["+","sample0","sample1"],0.1]],
       "sample3":["sample*",["normal",["*","sample0","sample1"],0.1]],
       "sample4":["sample*",["normal",7.0,2.0]],
       "sample5":["sample*",["normal","sample3","sample4"]],
       "observe6":["observe*",["normal",["+","sample3"],0.1],0.2],
       "observe7":["observe*",["normal","sample5",0.1],-3.5]},
  "Y":{"observe6":0.2,"observe7":-3.5}},
 ["sample0","sample1","sample2","sample3","sample4","sample5"]]

The first entry in the triple contains all functions defined in the input file, here none. The second contains a dictionary of the graphical model with "V" denoting all random variable vertices, "A" the forward pointing adjacency information, "P" the symbolic expressions of the link functions in the deterministic target language and "Y" all observe statements. The last entry in the triple is the return value of the program, here corresponding to [z0 z1 z2 z3 z4 z5].

Alternatively you can emit a desugared AST (see the book) by using the desugar command:

lein run desugar -i programs/arithmetic_circuit.daphne -o output.json

[["let",["z0",["sample",["laplace",20.0,2.0]]],
  ["let",["z1",["sample",["laplace",10.0,2.0]]],
   ["let",["z2",["sample",["normal",["+","z0","z1"],0.1]]],
    ["let",["z3",["sample",["normal",["*","z0","z1"],0.1]]],
     ["let",["z4",["sample",["normal",7.0,2.0]]],
      ["let",["z5",["sample",["normal","z3","z4"]]],
       ["let",["x0",["observe",["normal",["+","z3"],0.1],0.2]],
        ["let",["x1",["observe",["normal","z5",0.1],-3.5]],
         ["vector","z0","z1","z2","z3","z4","z5"]]]]]]]]]]

Note that the let binding is now nested with an expression for each individual binding and the vector in the final expression is explicitly denoted through a starting "vector" expression to distinguish it from the normal lists. This format makes it easy to write custom interpreters in any language that can read JSON.

If you are using daphne compiler for the UBC CS532: Probabilistic Programming course then you are good to go as long as you can run the lein commands described above. You do not need to have the "python export" functionality, described below, working.

To create a Python class instead of a JSON graphical model you can use the python-class command,

lein run python-class -i programs/arithmetic_circuit.daphne -o autogen_arithmetic_circuit.py

Note that we have prepended autogen_ here, which is necessary to distinguish this model from the ones we already included in models.py in our Python codebase. If you do not use our amortization setup you can pick the filename freely. You can compile convolution.daphne in the same way.

Make sure that you have hy-lang for Python 3 installed and check for hy2py on your path. The Python dependencies are documented in requirements.txt.

We can now use the provided Python files to train a neural network with

python3 main.py with train_steps=100 gmodel_name=autogen_convolution -F ./runs

Sacred will store the resulting files in the ./runs directory.

We provide plotting code for the loss curves in the paper in the ./plots directory (WIP).

The Python code base for training is derived from FFJORD,

To augment nodes in the graphical model as described in our paper you can provide the following argument

python3 main.py with train_steps=100 gmodel_name=autogen_convolution to_augment=[0,1,2,3,4,5] -F ./runs

Which will add one augmenting node to the nodes one to five.

The compiler consists of multiple passes and provides an extended partial evaluation fix point operator that allows expressions such as

(foreach (count input) ...)

where input is some value provided to the program and the loop counter expression can be partially evaluated to an integer at compile time. This facilitates the provision of a small linear algebra and neural network library in the linalg.clj file (WIP).

The compiler also integrates the structural faithful inversion algorithm for graphical models, which was inspired by the book "Probabilistic Graphical Models" by Daphne Koller and Nir Friedman. This is used by the amortizing Python code.

Clojure recently got fairly seamless bindings including zero copy support to Clojure tensor libraries for Python and Julia. This allows interleaving the expressive metaprogramming facilities of Clojure during the compilation with many numerical algorithms and facilities of these ecosystems. Clojure itself also has flexible high performance numerical libraries through the uncomplicate ecosystem that operate on the same memory layouts as numpy and Julia ndarrays.

Since the codebase is also used to teach the probabilistic programming course CPSC 539W of Frank Wood at UBC, it also contains a few examples and many unit tests corresponding to former exercises.

This is also the codebase accompanying our AISTATS 2020 paper

@inproceedings{DBLP:conf/aistats/WeilbachBWH20,
  author    = {Christian Weilbach and
               Boyan Beronov and
               William Harvey and
               Frank Wood},
  editor    = {Silvia Chiappa and
               Roberto Calandra},
  title     = {Structured Conditional Continuous Normalizing Flows for Efficient
               Amortized Inference in Graphical Models},
  booktitle = {The 23rd International Conference on Artificial Intelligence and Statistics,
               {AISTATS} 2020, 26-28 August 2020, Online [Palermo, Sicily, Italy]},
  series    = {Proceedings of Machine Learning Research},
  volume    = {108},
  pages     = {4441--4451},
  publisher = {{PMLR}},
  year      = {2020},
  url       = {http://proceedings.mlr.press/v108/weilbach20a.html},
  timestamp = {Mon, 29 Jun 2020 18:03:58 +0200},
  biburl    = {https://dblp.org/rec/conf/aistats/WeilbachBWH20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

• add convolution code
• provide sacred local filesystem loader for the plot routines
• provide plotting code for deconvolution figure

Copyright © 2018-2021 Christian Weilbach

This program and the accompanying materials are made available under the terms of the Eclipse Public License 2.0 which is available at http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary Licenses when the conditions for such availability set forth in the Eclipse Public License, v. 2.0 are satisfied: GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html.