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Examples for Probabilistic System Anglican

Clojure 100.00%

anglican-examples's Introduction

Anglican Examples

A repository of programs written in the probabilistic programming language Anglican with browser-based interaction via Gorilla REPL.

Install

Download and install Leiningen
Use git to fork and clone this repository

Usage

In your local repository type "lein gorilla"
Open the indicated local website in a browser.
Use the menu in the upper right hand corner to load and run any of the included examples.

Contributing

Give back: issue pull requests to include new examples you've written in this shared repository.
Add comments and make suggestions in the issue tracker.

anglican-examples's People

Contributors

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gbaydin talesa lsaldyt jonasseglare orolle perov

anglican-examples's Issues

The branching model has non-deterministic error

The branching model in the branching_aistats.clj file has some non-deterministic error.

(defn fib [n]
  "returns the n-th number in the Fibonacci sequence"
  (loop [a 0 b 1 m 0]
    (if (= m n)
      a
      (recur b (+ a b) (inc m)))))

(with-primitive-procedures [fib]
  (defquery branching
      "A simple example illustrating flow control with
      dependence on random choices"
      []
      (let [count-prior (poisson 4)
            r (sample count-prior)
            l (if (< 4 r)
                6
                (+ (fib (* 3 r))
                   (sample count-prior)))]
        (observe (poisson l) 6)
        (predict :r r)
        (predict :l l))))

If I run it with a lot of particles with SMC sampler, it sometimes give Error during inference: org.apache.commons.math3.exception.NotStrictlyPositiveException: mean (0) (but sometimes not). If the # of particles is large (say 500,000), it will be broken nearly every time.

`lein gorilla` fails

When I run lein gorilla as instructed in the Readme, I get the following error. I am using a fresh install of clojure verion 1.10.

Error here

clojure.lang.Compiler$CompilerException: Syntax error compiling at (org/httpkit/server.clj:1:1).
#:clojure.error{:phase :compile-syntax-check, :line 1, :column 1, :source "org/httpkit/server.clj"}
 at clojure.lang.Compiler.load (Compiler.java:7647)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:463)
    clojure.lang.RT.load (RT.java:428)
    clojure.core$load$fn__6824.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:703)
    gorilla_repl.core$eval668$loading__6706__auto____669.invoke (core.clj:5)
    gorilla_repl.core$eval668.invokeStatic (core.clj:5)
    gorilla_repl.core$eval668.invoke (core.clj:5)
    clojure.lang.Compiler.eval (Compiler.java:7176)
    clojure.lang.Compiler.eval (Compiler.java:7165)
    clojure.lang.Compiler.load (Compiler.java:7635)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:463)
    clojure.lang.RT.load (RT.java:428)
    clojure.core$load$fn__6824.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:436)
    leiningen.gorilla$eval662$loading__6706__auto____663.invoke (gorilla.clj:7)
    leiningen.gorilla$eval662.invokeStatic (gorilla.clj:7)
    leiningen.gorilla$eval662.invoke (gorilla.clj:7)
    clojure.lang.Compiler.eval (Compiler.java:7176)
    clojure.lang.Compiler.eval (Compiler.java:7165)
    clojure.lang.Compiler.load (Compiler.java:7635)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:463)
    clojure.lang.RT.load (RT.java:428)
    clojure.core$load$fn__6824.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    leiningen.core.utils$require_resolve.invokeStatic (utils.clj:102)
    leiningen.core.utils$require_resolve.invoke (utils.clj:95)
    leiningen.core.utils$require_resolve.invokeStatic (utils.clj:105)
    leiningen.core.utils$require_resolve.invoke (utils.clj:95)
    leiningen.core.main$lookup_task_var.invokeStatic (main.clj:69)
    leiningen.core.main$lookup_task_var.invoke (main.clj:65)
    leiningen.core.main$pass_through_help_QMARK_.invokeStatic (main.clj:79)
    leiningen.core.main$pass_through_help_QMARK_.invoke (main.clj:73)
    leiningen.core.main$task_args.invokeStatic (main.clj:82)
    leiningen.core.main$task_args.invoke (main.clj:81)
    leiningen.core.main$resolve_and_apply.invokeStatic (main.clj:339)
    leiningen.core.main$resolve_and_apply.invoke (main.clj:336)
    leiningen.core.main$_main$fn__6681.invoke (main.clj:452)
    leiningen.core.main$_main.invokeStatic (main.clj:442)
    leiningen.core.main$_main.doInvoke (main.clj:439)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.core$apply.invokeStatic (core.clj:665)
    clojure.main$main_opt.invokeStatic (main.clj:491)
    clojure.main$main_opt.invoke (main.clj:487)
    clojure.main$main.invokeStatic (main.clj:598)
    clojure.main$main.doInvoke (main.clj:561)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.main.main (main.java:37)
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.DatatypeConverter
 at java.net.URLClassLoader.findClass (URLClassLoader.java:471)
    clojure.lang.DynamicClassLoader.findClass (DynamicClassLoader.java:69)
    java.lang.ClassLoader.loadClass (ClassLoader.java:588)
    clojure.lang.DynamicClassLoader.loadClass (DynamicClassLoader.java:77)
    java.lang.ClassLoader.loadClass (ClassLoader.java:521)
    java.lang.Class.forName0 (Class.java:-2)
    java.lang.Class.forName (Class.java:398)
    clojure.lang.RT.classForName (RT.java:2207)
    clojure.lang.RT.classForNameNonLoading (RT.java:2220)
    org.httpkit.server$eval2688$loading__6706__auto____2689.invoke (server.clj:1)
    org.httpkit.server$eval2688.invokeStatic (server.clj:1)
    org.httpkit.server$eval2688.invoke (server.clj:1)
    clojure.lang.Compiler.eval (Compiler.java:7176)
    clojure.lang.Compiler.eval (Compiler.java:7165)
    clojure.lang.Compiler.load (Compiler.java:7635)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:463)
    clojure.lang.RT.load (RT.java:428)
    clojure.core$load$fn__6824.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:703)
    gorilla_repl.core$eval668$loading__6706__auto____669.invoke (core.clj:5)
    gorilla_repl.core$eval668.invokeStatic (core.clj:5)
    gorilla_repl.core$eval668.invoke (core.clj:5)
    clojure.lang.Compiler.eval (Compiler.java:7176)
    clojure.lang.Compiler.eval (Compiler.java:7165)
    clojure.lang.Compiler.load (Compiler.java:7635)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:463)
    clojure.lang.RT.load (RT.java:428)
    clojure.core$load$fn__6824.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:436)
    leiningen.gorilla$eval662$loading__6706__auto____663.invoke (gorilla.clj:7)
    leiningen.gorilla$eval662.invokeStatic (gorilla.clj:7)
    leiningen.gorilla$eval662.invoke (gorilla.clj:7)
    clojure.lang.Compiler.eval (Compiler.java:7176)
    clojure.lang.Compiler.eval (Compiler.java:7165)
    clojure.lang.Compiler.load (Compiler.java:7635)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:463)
    clojure.lang.RT.load (RT.java:428)
    clojure.core$load$fn__6824.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    leiningen.core.utils$require_resolve.invokeStatic (utils.clj:102)
    leiningen.core.utils$require_resolve.invoke (utils.clj:95)
    leiningen.core.utils$require_resolve.invokeStatic (utils.clj:105)
    leiningen.core.utils$require_resolve.invoke (utils.clj:95)
    leiningen.core.main$lookup_task_var.invokeStatic (main.clj:69)
    leiningen.core.main$lookup_task_var.invoke (main.clj:65)
    leiningen.core.main$pass_through_help_QMARK_.invokeStatic (main.clj:79)
    leiningen.core.main$pass_through_help_QMARK_.invoke (main.clj:73)
    leiningen.core.main$task_args.invokeStatic (main.clj:82)
    leiningen.core.main$task_args.invoke (main.clj:81)
    leiningen.core.main$resolve_and_apply.invokeStatic (main.clj:339)
    leiningen.core.main$resolve_and_apply.invoke (main.clj:336)
    leiningen.core.main$_main$fn__6681.invoke (main.clj:452)
    leiningen.core.main$_main.invokeStatic (main.clj:442)
    leiningen.core.main$_main.doInvoke (main.clj:439)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.core$apply.invokeStatic (core.clj:665)
    clojure.main$main_opt.invokeStatic (main.clj:491)
    clojure.main$main_opt.invoke (main.clj:487)
    clojure.main$main.invokeStatic (main.clj:598)
    clojure.main$main.doInvoke (main.clj:561)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.main.main (main.java:37)

typo in :require ?

Thank you for this beautiful repo!

At linear_regression clj, I see :require [plotting :as plot].
https://github.com/probprog/anglican-examples/blob/master/worksheets/linear_regression.clj#L9

Is it supposed to be :require [gorilla-plot.core :as plot] ?

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