├── .gitignore ├── CHANGELOG.md ├── LICENSE.md ├── README.md ├── docs ├── bopp.core.html ├── bopp.error-handling.html ├── bopp.helper-functions.html ├── bopp.program-transformations.html ├── css │ ├── default.css │ └── highlight.css ├── examples.chaos.html ├── examples.hmm.html ├── examples.opt.html ├── examples.simple-bimodal.html ├── index.html └── js │ ├── highlight.min.js │ ├── jquery.min.js │ └── page_effects.js ├── gpl-3.0.txt ├── project.clj ├── resources ├── data │ ├── chaos │ │ ├── x1.csv │ │ └── y1.csv │ ├── hmm │ │ ├── gt_x1.csv │ │ ├── gt_x10.csv │ │ ├── gt_x11.csv │ │ ├── gt_x12.csv │ │ ├── gt_x13.csv │ │ ├── gt_x14.csv │ │ ├── gt_x15.csv │ │ ├── gt_x16.csv │ │ ├── gt_x17.csv │ │ ├── gt_x18.csv │ │ ├── gt_x19.csv │ │ ├── gt_x2.csv │ │ ├── gt_x20.csv │ │ ├── gt_x3.csv │ │ ├── gt_x4.csv │ │ ├── gt_x5.csv │ │ ├── gt_x6.csv │ │ ├── gt_x7.csv │ │ ├── gt_x8.csv │ │ ├── gt_x9.csv │ │ ├── y1.csv │ │ ├── y10.csv │ │ ├── y11.csv │ │ ├── y12.csv │ │ ├── y13.csv │ │ ├── y14.csv │ │ ├── y15.csv │ │ ├── y16.csv │ │ ├── y17.csv │ │ ├── y18.csv │ │ ├── y19.csv │ │ ├── y2.csv │ │ ├── y20.csv │ │ ├── y3.csv │ │ ├── y4.csv │ │ ├── y5.csv │ │ ├── y6.csv │ │ ├── y7.csv │ │ ├── y8.csv │ │ └── y9.csv │ └── iris.csv └── matlab │ └── wishart │ ├── logmvgamma.m │ └── wishpdfln.m ├── src ├── bopp │ ├── core.clj │ ├── error_handling.clj │ ├── helper_functions.clj │ └── program_transformations.clj └── examples │ ├── chaos.clj │ ├── hmm.clj │ ├── opt.clj │ └── simple_bimodal.clj ├── test └── bopp │ ├── core_test.clj │ ├── error_handling_test.clj │ └── program_transformations_test.clj └── worksheets ├── chaos.clj ├── hmm.clj ├── opt.clj └── simple_bimodal.clj /.gitignore: -------------------------------------------------------------------------------- 1 | .gorilla-port 2 | *.DS_Store 3 | .nrepl-port (1) 4 | /target 5 | /classes 6 | /checkouts 7 | pom.xml 8 | pom.xml.asc 9 | *.jar 10 | *.class 11 | /.lein-* 12 | /.nrepl-port 13 | .hgignore 14 | .hg/ 15 | -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- 1 | # Change Log 2 | All notable changes to this project will be documented in this file. This change log follows the conventions of [keepachangelog.com](http://keepachangelog.com/). 3 | 4 | ## [Unreleased][unreleased] 5 | ### Changed 6 | - Add a new arity to `make-widget-async` to provide a different widget shape. 7 | 8 | ## [0.1.1] - 2016-10-20 9 | ### Changed 10 | - Documentation on how to make the widgets. 11 | 12 | ### Removed 13 | - `make-widget-sync` - we're all async, all the time. 14 | 15 | ### Fixed 16 | - Fixed widget maker to keep working when daylight savings switches over. 17 | 18 | ## 0.1.0 - 2016-10-20 19 | ### Added 20 | - Files from the new template. 21 | - Widget maker public API - `make-widget-sync`. 22 | 23 | [unreleased]: https://github.com/your-name/bopp/compare/0.1.1...HEAD 24 | [0.1.1]: https://github.com/your-name/bopp/compare/0.1.0...0.1.1 25 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | Copyright © Tom Rainforth, Tuan Anh Le, Jan-Willem van de Meent Michael Osborne, and Frank Wood 2 | 3 | BOPP is free software: you can redistribute it and/or modify 4 | it under the terms of the GNU General Public License as published by 5 | the Free Software Foundation, either version 3 of the License, or 6 | (at your option) any later version. 7 | 8 | BOPP is distributed in the hope that it will be useful, 9 | but WITHOUT ANY WARRANTY; without even the implied warranty of 10 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 | GNU General Public License for more details. 12 | 13 | You should have received a copy of the [GNU General Public License](gpl-3.0.txt) along with BOPP. If not, see [http://www.gnu.org/licenses/](http://www.gnu.org/licenses/). 14 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # BOPP: Bayesian Optimization for Probabilistic Programs 2 | 3 | See our [NIPS Spotlight video](https://www.youtube.com/watch?v=gVzV-NxKa9U) for TLDR. 4 | 5 | Latest release: bopp "0.1.5" 6 | 7 | BOPP is a package for automated marginal maximum a posteriori inference (MMAP) based around the 8 | probabilistic programming system [Anglican](http://www.robots.ox.ac.uk/~fwood/anglican). The 9 | user only needs to write their model in the same manner as existing Anglican programs and by using 10 | the `defopt` construct instead of `defquery`, select the variables to be optimized, with the 11 | rest marginalized out. It can also be used as a means of exploiting the target source code 12 | to improve Bayesian optimization, delivering things such as automatic domain scaling, 13 | unbounded optimization, and implicit constraint satisfaction including equality constraints. 14 | The key idea is to use a series of code transformations to extract from the original program 15 | all the things that are needed to carry out the MMAP problem, such as the target function itself 16 | and a program for optimizing the acquisition function subject to the implicit constraints. These 17 | are then passed to our other package [Deodorant](http://github.com/probprog/deodorant), which uses 18 | these to solve the problem probabilistic programs creates for BO. 19 | The following paper should be referred to for full algorithmic details and we ask that you cite this paper if you 20 | use BOPP in your work. 21 | 22 | Rainforth, T., Le, T. A., van de Meent, J.-W., Osborne, M. A., & Wood, F. (2016). Bayesian Optimization for Probabilistic Programs. In Advances in Neural Information Processing Systems. 23 | 24 | ``` 25 | @incollection{rainforth2016bayesian, 26 | title = {Bayesian Optimization for Probabilistic Programs}, 27 | author = {Rainforth, Tom and Le, Tuan Anh and van de Meent, Jan-Willem and Osborne, Michael A and Wood, Frank}, 28 | booktitle = {Advances in Neural Information Processing Systems 29}, 29 | pages = {280--288}, 30 | year = {2016}, 31 | url = {http://papers.nips.cc/paper/6421-bayesian-optimization-for-probabilistic-programs.pdf} 32 | } 33 | ``` 34 | 35 | ## Installation ## 36 | 37 | To use BOPP in your own [Leiningen](http://leiningen.org/) projects, just include the dependency in your `project.clj`: 38 | ``` 39 | (defproject foo 40 | ... 41 | :dependencies [... 42 | [bopp "0.1.5"] 43 | ...]) 44 | ``` 45 | 46 | In your Clojure files, remember to require functions from `core.clj`, e.g.: 47 | ``` 48 | (ns bar 49 | (require [bopp.core :refer :all])) 50 | ``` 51 | The full documentation can be found [here](https://probprog.github.io/bopp/). Checkout [core/defopt](https://probprog.github.io/bopp/bopp.core.html#var-defopt) and [core/doopt](https://probprog.github.io/bopp/bopp.core.html#var-doopt) in particular. 52 | 53 | Though BOPP currently runs of a snapshot of Anglican that means you don't need to install Anglican explicitly, is does have the same requirements in terms of java, Leiningen etc and so we refer the reader to http://www.robots.ox.ac.uk/~fwood/anglican/usage/index.html and recommend that users follow section 2 in the user start up guide. We also recommend that you familiarize yourself on the syntax of Anglican through the 54 | provided link, as this is the same syntax as Anglican, with the addition of the forms `defopt` and `doopt`. 55 | 56 | ## Usage ## 57 | 58 | ### Defining target programs ### 59 | 60 | BOPP targets are specified using the macro `defopt`. This is identical to `defquery` in [Anglican](http://www.robots.ox.ac.uk/~fwood/anglican) except that it takes as an extra input of the target variables to be optimized. BOPP will optimize the evidence of the program with respect to the variables, whilst marginalizing out over the others. 61 | For example: 62 | 63 | ```lisp 64 | (defopt simple-bimodal [y] [theta] 65 | (let [x (sample (normal 0 1)) 66 | theta (sample (normal x 0.5))] 67 | (observe (normal (sqrt (* theta theta)) 0.5) y))) 68 | ``` 69 | 70 | specifies a model where we wish to optimize `theta`, marginalizing out `x`. 71 | 72 | There are a couple of small restrictions 73 | on the programs that can be specified to ensure that they constitute valid target programs, namely: 74 | 75 | 1. Each target variable must be bound to a value directly by a sample statement with fixed measure-type distribution argument (i.e. not a weird `defdist` distribution object). 76 | 2. The program must be written such that any possible execution trace binds each optimization variable exactly once. 77 | 3. Although any target variable may be lexically multiply bound, it must have the same base measure in all possible execution traces. 78 | 79 | Don't worry, if this doesn't make too much sense, BOPP catches violations of these automatically and gives you 80 | and error telling you what you violated. Please see the [paper](http://papers.nips.cc/paper/6421-bayesian-optimization-for-probabilistic-programs) and [supplementary material](http://www.robots.ox.ac.uk/~twgr/assets/pdf/rainforth2016BOPP.pdf) for more information. 81 | 82 | ### Running BOPP ### 83 | 84 | Calling BOPP is super simple, just call 85 | 86 | `(doopt algorithm opt-query opt-query-args num-samples args)` 87 | 88 | where 89 | - `algorithm` = Inference algorithm used for estimating the marginal [`:smc`, `:pcascade`, `:importance`] 90 | - `opt-query` = Query to be optimized, defined by defopt. 91 | - `opt-query-args` = Fixed inputs of opt-query-args (y in earlier example) 92 | - `num-samples` = Number of samples for constructing the estimator of the marginal. 93 | - `args` = Optional arguments as key-value pairs. See docstring for `doopt`. Note that, by default, 94 | the arguments are setup for speed rather per iteration performance. If you wish to run bopp as 95 | per the setup in the paper, or have a problem where the inference is particularly expensive, you 96 | should include in the option list `:speed-option :careful`. 97 | 98 | This returns a lazy infinite sequence of samples. Call `take` on this will convert it 99 | to a fixed number of outputs. Note that as BOPP is a GP based BO scheme, scaling in N is quite poor 100 | and practically limited to around 400-500. 101 | 102 | ### Examples ### 103 | 104 | A number of worksheets are provided to give example usage in different cases. These can be accessed in a Gorilla REPL by running 105 | `lein gorilla` from the base folder and going through worksheets in the `worksheets/` folder. You can also see (but not run) an example worksheet without installing BOPP [here](http://www.robots.ox.ac.uk/~fwood/anglican/examples/viewer/?source=github&user=probprog&repo=bopp&path=worksheets/chaos.clj). 106 | 107 | ## License ## 108 | 109 | Copyright © Tom Rainforth, Tuan Anh Le, Jan-Willem van de Meent, Michael Osborne and Frank Wood 110 | 111 | BOPP is free software: you can redistribute it and/or modify 112 | it under the terms of the GNU General Public License as published by 113 | the Free Software Foundation, either version 3 of the License, or 114 | (at your option) any later version. 115 | 116 | BOPP is distributed in the hope that it will be useful, 117 | but WITHOUT ANY WARRANTY; without even the implied warranty of 118 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 119 | GNU General Public License for more details. 120 | 121 | You should have received a copy of the [GNU General Public License](gpl-3.0.txt) along with BOPP. If not, see [http://www.gnu.org/licenses/](http://www.gnu.org/licenses/). 122 | -------------------------------------------------------------------------------- /docs/bopp.error-handling.html: -------------------------------------------------------------------------------- 1 | 3 | bopp.error-handling documentation

bopp.error-handling

Error handling for BOPP
4 | 

changing-types?

(changing-types? & args)
-------------------------------------------------------------------------------- /docs/bopp.program-transformations.html: -------------------------------------------------------------------------------- 1 | 3 | bopp.program-transformations documentation

bopp.program-transformations

Program transformations for BOPP
 4 | 

->factor-distribution

(->factor-distribution)
Positional factory function for class bopp.program_transformations.factor-distribution.
 5 | 

acq-f-name

acq-query

macro

(acq-query & args)
Returns CPS'd query with the acquisition transformation applied.
 6 | 

factor

(factor)
Factor the value to the log-likelihood terms.
 7 | e.g. (observe (factor) 1) factors the term 1 in the log likelihood as if
 8 | there was an observed value with the likelihood e.

map->factor-distribution

(map->factor-distribution m__6522__auto__)
Factory function for class bopp.program_transformations.factor-distribution, taking a map of keywords to field values.
 9 | 

ml2-query

macro

(ml2-query & args)
Returns CPS'd query with the maximum likelihood (type 2) transformation applied.
10 | 

mmap-query

macro

(mmap-query & args)
Returns CPS'd query with the MMAP transformation applied.
11 | 

optim-args-key

prior-query

macro

(prior-query & args)
Returns CPS'd query with the prior transformation applied.
12 | 

throw-exception

(throw-exception msg)
-------------------------------------------------------------------------------- /docs/css/highlight.css: -------------------------------------------------------------------------------- 1 | /* 2 | github.com style (c) Vasily Polovnyov 3 | */ 4 | 5 | .hljs { 6 | display: block; 7 | overflow-x: auto; 8 | padding: 0.5em; 9 | color: #333; 10 | background: #f8f8f8; 11 | } 12 | 13 | .hljs-comment, 14 | .hljs-quote { 15 | color: #998; 16 | font-style: italic; 17 | } 18 | 19 | .hljs-keyword, 20 | .hljs-selector-tag, 21 | .hljs-subst { 22 | color: #333; 23 | font-weight: bold; 24 | } 25 | 26 | .hljs-number, 27 | .hljs-literal, 28 | .hljs-variable, 29 | .hljs-template-variable, 30 | .hljs-tag .hljs-attr { 31 | color: #008080; 32 | } 33 | 34 | .hljs-string, 35 | .hljs-doctag { 36 | color: #d14; 37 | } 38 | 39 | .hljs-title, 40 | .hljs-section, 41 | .hljs-selector-id { 42 | color: #900; 43 | font-weight: bold; 44 | } 45 | 46 | .hljs-subst { 47 | font-weight: normal; 48 | } 49 | 50 | .hljs-type, 51 | .hljs-class .hljs-title { 52 | color: #458; 53 | font-weight: bold; 54 | } 55 | 56 | .hljs-tag, 57 | .hljs-name, 58 | .hljs-attribute { 59 | color: #000080; 60 | font-weight: normal; 61 | } 62 | 63 | .hljs-regexp, 64 | .hljs-link { 65 | color: #009926; 66 | } 67 | 68 | .hljs-symbol, 69 | .hljs-bullet { 70 | color: #990073; 71 | } 72 | 73 | .hljs-built_in, 74 | .hljs-builtin-name { 75 | color: #0086b3; 76 | } 77 | 78 | .hljs-meta { 79 | color: #999; 80 | font-weight: bold; 81 | } 82 | 83 | .hljs-deletion { 84 | background: #fdd; 85 | } 86 | 87 | .hljs-addition { 88 | background: #dfd; 89 | } 90 | 91 | .hljs-emphasis { 92 | font-style: italic; 93 | } 94 | 95 | .hljs-strong { 96 | font-weight: bold; 97 | } 98 | -------------------------------------------------------------------------------- /docs/examples.simple-bimodal.html: -------------------------------------------------------------------------------- 1 | 3 | examples.simple-bimodal documentation

examples.simple-bimodal

-main

(-main folder-name & opts)

simple-bimodal

BOPP program 'simple-bimodal'
4 | 

simple-bimodal-noisy

BOPP program 'simple-bimodal-noisy'
5 | 
-------------------------------------------------------------------------------- /docs/js/page_effects.js: -------------------------------------------------------------------------------- 1 | function visibleInParent(element) { 2 | var position = $(element).position().top 3 | return position > -50 && position < ($(element).offsetParent().height() - 50) 4 | } 5 | 6 | function hasFragment(link, fragment) { 7 | return $(link).attr("href").indexOf("#" + fragment) != -1 8 | } 9 | 10 | function findLinkByFragment(elements, fragment) { 11 | return $(elements).filter(function(i, e) { return hasFragment(e, fragment)}).first() 12 | } 13 | 14 | function scrollToCurrentVarLink(elements) { 15 | var elements = $(elements); 16 | var parent = elements.offsetParent(); 17 | 18 | if (elements.length == 0) return; 19 | 20 | var top = elements.first().position().top; 21 | var bottom = elements.last().position().top + elements.last().height(); 22 | 23 | if (top >= 0 && bottom <= parent.height()) return; 24 | 25 | if (top < 0) { 26 | parent.scrollTop(parent.scrollTop() + top); 27 | } 28 | else if (bottom > parent.height()) { 29 | parent.scrollTop(parent.scrollTop() + bottom - parent.height()); 30 | } 31 | } 32 | 33 | function setCurrentVarLink() { 34 | $('.secondary a').parent().removeClass('current') 35 | $('.anchor'). 36 | filter(function(index) { return visibleInParent(this) }). 37 | each(function(index, element) { 38 | findLinkByFragment(".secondary a", element.id). 39 | parent(). 40 | addClass('current') 41 | }); 42 | scrollToCurrentVarLink('.secondary .current'); 43 | } 44 | 45 | var hasStorage = (function() { try { return localStorage.getItem } catch(e) {} }()) 46 | 47 | function scrollPositionId(element) { 48 | var directory = window.location.href.replace(/[^\/]+\.html$/, '') 49 | return 'scroll::' + $(element).attr('id') + '::' + directory 50 | } 51 | 52 | function storeScrollPosition(element) { 53 | if (!hasStorage) return; 54 | localStorage.setItem(scrollPositionId(element) + "::x", $(element).scrollLeft()) 55 | localStorage.setItem(scrollPositionId(element) + "::y", $(element).scrollTop()) 56 | } 57 | 58 | function recallScrollPosition(element) { 59 | if (!hasStorage) return; 60 | $(element).scrollLeft(localStorage.getItem(scrollPositionId(element) + "::x")) 61 | $(element).scrollTop(localStorage.getItem(scrollPositionId(element) + "::y")) 62 | } 63 | 64 | function persistScrollPosition(element) { 65 | recallScrollPosition(element) 66 | $(element).scroll(function() { storeScrollPosition(element) }) 67 | } 68 | 69 | function sidebarContentWidth(element) { 70 | var widths = $(element).find('.inner').map(function() { return $(this).innerWidth() }) 71 | return Math.max.apply(Math, widths) 72 | } 73 | 74 | function calculateSize(width, snap, margin, minimum) { 75 | if (width == 0) { 76 | return 0 77 | } 78 | else { 79 | return Math.max(minimum, (Math.ceil(width / snap) * snap) + (margin * 2)) 80 | } 81 | } 82 | 83 | function resizeSidebars() { 84 | var primaryWidth = sidebarContentWidth('.primary') 85 | var secondaryWidth = 0 86 | 87 | if ($('.secondary').length != 0) { 88 | secondaryWidth = sidebarContentWidth('.secondary') 89 | } 90 | 91 | // snap to grid 92 | primaryWidth = calculateSize(primaryWidth, 32, 13, 160) 93 | secondaryWidth = calculateSize(secondaryWidth, 32, 13, 160) 94 | 95 | $('.primary').css('width', primaryWidth) 96 | $('.secondary').css('width', secondaryWidth).css('left', primaryWidth + 1) 97 | 98 | if (secondaryWidth > 0) { 99 | $('#content').css('left', primaryWidth + secondaryWidth + 2) 100 | } 101 | else { 102 | $('#content').css('left', primaryWidth + 1) 103 | } 104 | } 105 | 106 | $(window).ready(resizeSidebars) 107 | $(window).ready(setCurrentVarLink) 108 | $(window).ready(function() { persistScrollPosition('.primary')}) 109 | $(window).ready(function() { 110 | $('#content').scroll(setCurrentVarLink) 111 | $(window).resize(setCurrentVarLink) 112 | }) 113 | -------------------------------------------------------------------------------- /project.clj: -------------------------------------------------------------------------------- 1 | (defproject bopp "0.1.5" 2 | :description "Bayesian Optimization for Probabilistic Programs." 3 | :url "http://github.com/probprog/bopp" 4 | :license {:name "GNU General Public License Version 3" 5 | :url "http://www.gnu.org/licenses/gpl.html"} 6 | :plugins [[lein-codox "0.10.2"] 7 | [lein-gorilla "0.4.0"]] 8 | :dependencies [[org.clojure/clojure "1.8.0"] 9 | [org.clojars.tuananhle/anglican "1.1.1-BOPP"] 10 | [deodorant "0.1.3"] 11 | [clatrix "0.5.0"] 12 | [org.apache.commons/commons-math3 "3.6.1"] 13 | [com.taoensso/tufte "1.0.0-RC2"] 14 | [org.clojure/data.csv "0.1.3"] 15 | [clojure-csv/clojure-csv "2.0.1"]]) 16 | -------------------------------------------------------------------------------- /resources/data/hmm/gt_x1.csv: -------------------------------------------------------------------------------- 1 | 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| 3 433 | 3 434 | 2 435 | 3 436 | 3 437 | 3 438 | 3 439 | 2 440 | 2 441 | 2 442 | 3 443 | 3 444 | 3 445 | 3 446 | 3 447 | 2 448 | 2 449 | 1 450 | 1 451 | 1 452 | 1 453 | 2 454 | 2 455 | 1 456 | 1 457 | 2 458 | 1 459 | 2 460 | 2 461 | 2 462 | 1 463 | 2 464 | 2 465 | 2 466 | 2 467 | 2 468 | 2 469 | 2 470 | 2 471 | 2 472 | 2 473 | 2 474 | 1 475 | 1 476 | 1 477 | 2 478 | 2 479 | 3 480 | 3 481 | 2 482 | 3 483 | 3 484 | 3 485 | 2 486 | 1 487 | 1 488 | 1 489 | 1 490 | 2 491 | 2 492 | 2 493 | 2 494 | 3 495 | 3 496 | 3 497 | 3 498 | 2 499 | 2 500 | 2 501 | 2 502 | 2 503 | 1 504 | 1 505 | 1 506 | 1 507 | 2 508 | 2 509 | 2 510 | 2 511 | 2 512 | 1 513 | 1 514 | 1 515 | 2 516 | 2 517 | 2 518 | 3 519 | 2 520 | 2 521 | 2 522 | 2 523 | 2 524 | 3 525 | 3 526 | 3 527 | 2 528 | 1 529 | 1 530 | 1 531 | 2 532 | 2 533 | 2 534 | 1 535 | 1 536 | 1 537 | 1 538 | 1 539 | 1 540 | 1 541 | 1 542 | 1 543 | 1 544 | 1 545 | 2 546 | 2 547 | 1 548 | 2 549 | 2 550 | 2 551 | 2 552 | 2 553 | 3 554 | 3 555 | 2 556 | 2 557 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| 2 808 | 2 809 | 2 810 | 2 811 | 2 812 | 1 813 | 1 814 | 2 815 | 2 816 | 3 817 | 3 818 | 3 819 | 2 820 | 1 821 | 1 822 | 1 823 | 1 824 | 2 825 | 2 826 | 1 827 | 2 828 | 2 829 | 3 830 | 2 831 | 2 832 | 1 833 | 1 834 | 1 835 | 1 836 | 1 837 | 2 838 | 2 839 | 2 840 | 2 841 | 2 842 | 1 843 | 1 844 | 1 845 | 1 846 | 1 847 | 1 848 | 1 849 | 2 850 | 1 851 | 1 852 | 1 853 | 1 854 | 2 855 | 2 856 | 2 857 | 2 858 | 2 859 | 2 860 | 2 861 | 3 862 | 3 863 | 3 864 | 3 865 | 2 866 | 3 867 | 2 868 | 2 869 | 1 870 | 1 871 | 1 872 | 2 873 | 2 874 | 2 875 | 2 876 | 1 877 | 1 878 | 1 879 | 1 880 | 2 881 | 3 882 | 1 883 | 1 884 | 1 885 | 1 886 | 2 887 | 2 888 | 2 889 | 2 890 | 2 891 | 2 892 | 3 893 | 3 894 | 3 895 | 3 896 | 3 897 | 3 898 | 3 899 | 3 900 | 3 901 | 3 902 | 3 903 | 3 904 | 3 905 | 3 906 | 3 907 | 1 908 | 1 909 | 1 910 | 1 911 | 1 912 | 1 913 | 2 914 | 2 915 | 2 916 | 2 917 | 2 918 | 1 919 | 1 920 | 2 921 | 3 922 | 3 923 | 3 924 | 1 925 | 1 926 | 2 927 | 2 928 | 2 929 | 2 930 | 1 931 | 2 932 | 2 933 | 2 934 | 3 935 | 2 936 | 2 937 | 2 938 | 2 939 | 2 940 | 2 941 | 2 942 | 1 943 | 1 944 | 1 945 | 2 946 | 1 947 | 1 948 | 1 949 | 2 950 | 2 951 | 2 952 | 2 953 | 2 954 | 2 955 | 2 956 | 3 957 | 3 958 | 3 959 | 3 960 | 3 961 | 3 962 | 3 963 | 3 964 | 3 965 | 1 966 | 1 967 | 1 968 | 1 969 | 1 970 | 1 971 | 2 972 | 2 973 | 2 974 | 2 975 | 3 976 | 1 977 | 2 978 | 2 979 | 2 980 | 2 981 | 2 982 | 2 983 | 3 984 | 2 985 | 1 986 | 1 987 | 1 988 | 1 989 | 1 990 | 2 991 | 2 992 | 1 993 | 1 994 | 1 995 | 1 996 | 1 997 | 1 998 | 1 999 | 1 1000 | 1 1001 | -------------------------------------------------------------------------------- /resources/data/iris.csv: -------------------------------------------------------------------------------- 1 | 5.1,3.5,1.4,0.2,Iris-setosa 2 | 4.9,3.0,1.4,0.2,Iris-setosa 3 | 4.7,3.2,1.3,0.2,Iris-setosa 4 | 4.6,3.1,1.5,0.2,Iris-setosa 5 | 5.0,3.6,1.4,0.2,Iris-setosa 6 | 5.4,3.9,1.7,0.4,Iris-setosa 7 | 4.6,3.4,1.4,0.3,Iris-setosa 8 | 5.0,3.4,1.5,0.2,Iris-setosa 9 | 4.4,2.9,1.4,0.2,Iris-setosa 10 | 4.9,3.1,1.5,0.1,Iris-setosa 11 | 5.4,3.7,1.5,0.2,Iris-setosa 12 | 4.8,3.4,1.6,0.2,Iris-setosa 13 | 4.8,3.0,1.4,0.1,Iris-setosa 14 | 4.3,3.0,1.1,0.1,Iris-setosa 15 | 5.8,4.0,1.2,0.2,Iris-setosa 16 | 5.7,4.4,1.5,0.4,Iris-setosa 17 | 5.4,3.9,1.3,0.4,Iris-setosa 18 | 5.1,3.5,1.4,0.3,Iris-setosa 19 | 5.7,3.8,1.7,0.3,Iris-setosa 20 | 5.1,3.8,1.5,0.3,Iris-setosa 21 | 5.4,3.4,1.7,0.2,Iris-setosa 22 | 5.1,3.7,1.5,0.4,Iris-setosa 23 | 4.6,3.6,1.0,0.2,Iris-setosa 24 | 5.1,3.3,1.7,0.5,Iris-setosa 25 | 4.8,3.4,1.9,0.2,Iris-setosa 26 | 5.0,3.0,1.6,0.2,Iris-setosa 27 | 5.0,3.4,1.6,0.4,Iris-setosa 28 | 5.2,3.5,1.5,0.2,Iris-setosa 29 | 5.2,3.4,1.4,0.2,Iris-setosa 30 | 4.7,3.2,1.6,0.2,Iris-setosa 31 | 4.8,3.1,1.6,0.2,Iris-setosa 32 | 5.4,3.4,1.5,0.4,Iris-setosa 33 | 5.2,4.1,1.5,0.1,Iris-setosa 34 | 5.5,4.2,1.4,0.2,Iris-setosa 35 | 4.9,3.1,1.5,0.1,Iris-setosa 36 | 5.0,3.2,1.2,0.2,Iris-setosa 37 | 5.5,3.5,1.3,0.2,Iris-setosa 38 | 4.9,3.1,1.5,0.1,Iris-setosa 39 | 4.4,3.0,1.3,0.2,Iris-setosa 40 | 5.1,3.4,1.5,0.2,Iris-setosa 41 | 5.0,3.5,1.3,0.3,Iris-setosa 42 | 4.5,2.3,1.3,0.3,Iris-setosa 43 | 4.4,3.2,1.3,0.2,Iris-setosa 44 | 5.0,3.5,1.6,0.6,Iris-setosa 45 | 5.1,3.8,1.9,0.4,Iris-setosa 46 | 4.8,3.0,1.4,0.3,Iris-setosa 47 | 5.1,3.8,1.6,0.2,Iris-setosa 48 | 4.6,3.2,1.4,0.2,Iris-setosa 49 | 5.3,3.7,1.5,0.2,Iris-setosa 50 | 5.0,3.3,1.4,0.2,Iris-setosa 51 | 7.0,3.2,4.7,1.4,Iris-versicolor 52 | 6.4,3.2,4.5,1.5,Iris-versicolor 53 | 6.9,3.1,4.9,1.5,Iris-versicolor 54 | 5.5,2.3,4.0,1.3,Iris-versicolor 55 | 6.5,2.8,4.6,1.5,Iris-versicolor 56 | 5.7,2.8,4.5,1.3,Iris-versicolor 57 | 6.3,3.3,4.7,1.6,Iris-versicolor 58 | 4.9,2.4,3.3,1.0,Iris-versicolor 59 | 6.6,2.9,4.6,1.3,Iris-versicolor 60 | 5.2,2.7,3.9,1.4,Iris-versicolor 61 | 5.0,2.0,3.5,1.0,Iris-versicolor 62 | 5.9,3.0,4.2,1.5,Iris-versicolor 63 | 6.0,2.2,4.0,1.0,Iris-versicolor 64 | 6.1,2.9,4.7,1.4,Iris-versicolor 65 | 5.6,2.9,3.6,1.3,Iris-versicolor 66 | 6.7,3.1,4.4,1.4,Iris-versicolor 67 | 5.6,3.0,4.5,1.5,Iris-versicolor 68 | 5.8,2.7,4.1,1.0,Iris-versicolor 69 | 6.2,2.2,4.5,1.5,Iris-versicolor 70 | 5.6,2.5,3.9,1.1,Iris-versicolor 71 | 5.9,3.2,4.8,1.8,Iris-versicolor 72 | 6.1,2.8,4.0,1.3,Iris-versicolor 73 | 6.3,2.5,4.9,1.5,Iris-versicolor 74 | 6.1,2.8,4.7,1.2,Iris-versicolor 75 | 6.4,2.9,4.3,1.3,Iris-versicolor 76 | 6.6,3.0,4.4,1.4,Iris-versicolor 77 | 6.8,2.8,4.8,1.4,Iris-versicolor 78 | 6.7,3.0,5.0,1.7,Iris-versicolor 79 | 6.0,2.9,4.5,1.5,Iris-versicolor 80 | 5.7,2.6,3.5,1.0,Iris-versicolor 81 | 5.5,2.4,3.8,1.1,Iris-versicolor 82 | 5.5,2.4,3.7,1.0,Iris-versicolor 83 | 5.8,2.7,3.9,1.2,Iris-versicolor 84 | 6.0,2.7,5.1,1.6,Iris-versicolor 85 | 5.4,3.0,4.5,1.5,Iris-versicolor 86 | 6.0,3.4,4.5,1.6,Iris-versicolor 87 | 6.7,3.1,4.7,1.5,Iris-versicolor 88 | 6.3,2.3,4.4,1.3,Iris-versicolor 89 | 5.6,3.0,4.1,1.3,Iris-versicolor 90 | 5.5,2.5,4.0,1.3,Iris-versicolor 91 | 5.5,2.6,4.4,1.2,Iris-versicolor 92 | 6.1,3.0,4.6,1.4,Iris-versicolor 93 | 5.8,2.6,4.0,1.2,Iris-versicolor 94 | 5.0,2.3,3.3,1.0,Iris-versicolor 95 | 5.6,2.7,4.2,1.3,Iris-versicolor 96 | 5.7,3.0,4.2,1.2,Iris-versicolor 97 | 5.7,2.9,4.2,1.3,Iris-versicolor 98 | 6.2,2.9,4.3,1.3,Iris-versicolor 99 | 5.1,2.5,3.0,1.1,Iris-versicolor 100 | 5.7,2.8,4.1,1.3,Iris-versicolor 101 | 6.3,3.3,6.0,2.5,Iris-virginica 102 | 5.8,2.7,5.1,1.9,Iris-virginica 103 | 7.1,3.0,5.9,2.1,Iris-virginica 104 | 6.3,2.9,5.6,1.8,Iris-virginica 105 | 6.5,3.0,5.8,2.2,Iris-virginica 106 | 7.6,3.0,6.6,2.1,Iris-virginica 107 | 4.9,2.5,4.5,1.7,Iris-virginica 108 | 7.3,2.9,6.3,1.8,Iris-virginica 109 | 6.7,2.5,5.8,1.8,Iris-virginica 110 | 7.2,3.6,6.1,2.5,Iris-virginica 111 | 6.5,3.2,5.1,2.0,Iris-virginica 112 | 6.4,2.7,5.3,1.9,Iris-virginica 113 | 6.8,3.0,5.5,2.1,Iris-virginica 114 | 5.7,2.5,5.0,2.0,Iris-virginica 115 | 5.8,2.8,5.1,2.4,Iris-virginica 116 | 6.4,3.2,5.3,2.3,Iris-virginica 117 | 6.5,3.0,5.5,1.8,Iris-virginica 118 | 7.7,3.8,6.7,2.2,Iris-virginica 119 | 7.7,2.6,6.9,2.3,Iris-virginica 120 | 6.0,2.2,5.0,1.5,Iris-virginica 121 | 6.9,3.2,5.7,2.3,Iris-virginica 122 | 5.6,2.8,4.9,2.0,Iris-virginica 123 | 7.7,2.8,6.7,2.0,Iris-virginica 124 | 6.3,2.7,4.9,1.8,Iris-virginica 125 | 6.7,3.3,5.7,2.1,Iris-virginica 126 | 7.2,3.2,6.0,1.8,Iris-virginica 127 | 6.2,2.8,4.8,1.8,Iris-virginica 128 | 6.1,3.0,4.9,1.8,Iris-virginica 129 | 6.4,2.8,5.6,2.1,Iris-virginica 130 | 7.2,3.0,5.8,1.6,Iris-virginica 131 | 7.4,2.8,6.1,1.9,Iris-virginica 132 | 7.9,3.8,6.4,2.0,Iris-virginica 133 | 6.4,2.8,5.6,2.2,Iris-virginica 134 | 6.3,2.8,5.1,1.5,Iris-virginica 135 | 6.1,2.6,5.6,1.4,Iris-virginica 136 | 7.7,3.0,6.1,2.3,Iris-virginica 137 | 6.3,3.4,5.6,2.4,Iris-virginica 138 | 6.4,3.1,5.5,1.8,Iris-virginica 139 | 6.0,3.0,4.8,1.8,Iris-virginica 140 | 6.9,3.1,5.4,2.1,Iris-virginica 141 | 6.7,3.1,5.6,2.4,Iris-virginica 142 | 6.9,3.1,5.1,2.3,Iris-virginica 143 | 5.8,2.7,5.1,1.9,Iris-virginica 144 | 6.8,3.2,5.9,2.3,Iris-virginica 145 | 6.7,3.3,5.7,2.5,Iris-virginica 146 | 6.7,3.0,5.2,2.3,Iris-virginica 147 | 6.3,2.5,5.0,1.9,Iris-virginica 148 | 6.5,3.0,5.2,2.0,Iris-virginica 149 | 6.2,3.4,5.4,2.3,Iris-virginica 150 | 5.9,3.0,5.1,1.8,Iris-virginica 151 | -------------------------------------------------------------------------------- /resources/matlab/wishart/logmvgamma.m: -------------------------------------------------------------------------------- 1 | 2 | % From here: https://github.com/areslp/matlab/blob/master/vbgm/logmvgamma.m 3 | 4 | function y = logmvgamma(x,d) 5 | % Compute logarithm multivariate Gamma function. 6 | % Gamma_p(x) = pi^(p(p-1)/4) prod_(j=1)^p Gamma(x+(1-j)/2) 7 | % log Gamma_p(x) = p(p-1)/4 log pi + sum_(j=1)^p log Gamma(x+(1-j)/2) 8 | % Written by Michael Chen (sth4nth@gmail.com). 9 | s = size(x); 10 | x = reshape(x,1,prod(s)); 11 | x = bsxfun(@plus,repmat(x,d,1),(1-(1:d)')/2); 12 | y = d*(d-1)/4*log(pi)+sum(gammaln(x),1); 13 | y = reshape(y,s); 14 | -------------------------------------------------------------------------------- /resources/matlab/wishart/wishpdfln.m: -------------------------------------------------------------------------------- 1 | 2 | % From Wikipedia: http://en.wikipedia.org/wiki/Wishart_distribution 3 | 4 | function lnpdf = wishpdfln(X, n, V) 5 | p = size(X,1); 6 | lnpdf = 0; 7 | lnpdf = lnpdf + ((n - p - 1) / 2.0) * log(det(X)); 8 | lnpdf = lnpdf - (trace(inv(V) * X) / 2.0); 9 | lnpdf = lnpdf - ((n * p) / 2.0) * log(2.0); 10 | lnpdf = lnpdf - (n / 2.0) * log(det(V)); 11 | lnpdf = lnpdf - logmvgamma(n / 2.0, p); 12 | -------------------------------------------------------------------------------- /src/bopp/error_handling.clj: -------------------------------------------------------------------------------- 1 | (ns bopp.error-handling 2 | "Error handling for BOPP") 3 | 4 | (defn- dist-type [dist-symbol] 5 | "Given a distribution object symbol, returns either 'continuous or 6 | 'discrete." 7 | (cond (some #(= dist-symbol %) 8 | ['bernoulli 'binomial 'categorical 'discrete 'flip 'poisson 9 | 'uniform-discrete]) 10 | 'discrete 11 | 12 | (some #(= dist-symbol %) 13 | ['beta 'gamma 'dirichlet 'exponential 'chi-squared 'normal 14 | 'uniform-continuous 'mvn 'multivariate-t 'wishart]) 15 | 'continuous 16 | 17 | :else 18 | (throw (Exception. (str "Distribution " dist-symbol " not supported."))))) 19 | 20 | (defn- detect-types [ast optim-args types] 21 | "Given an abstract syntax tree of an optimization query, collect types of 22 | distribution objects being assigned to optimization variables in optim-args. 23 | 24 | Returns a map with optim-arg as key and {list of types of distributions being 25 | assigned to this optim-arg} as value. E.g. 26 | 27 | {'theta ['continuous 'continuous 'discrete] 28 | 'psi ['continuous]}. 29 | 30 | Used as a helper function for changing-types?." 31 | (if (list? ast) 32 | (let [root (first ast)] 33 | (if (= root 'let) 34 | (loop [bindings (second ast) 35 | ;; Initialize new-types to contain types from statemets after 36 | ;; the binding vector 37 | new-types (reduce (partial merge-with concat) {} 38 | (map #(detect-types % optim-args {}) (drop 2 ast)))] 39 | (if (empty? bindings) 40 | (merge-with concat types new-types) 41 | (let [[name value] (take 2 bindings)] 42 | (recur (drop 2 bindings) 43 | (if (some #(= name %) optim-args) 44 | (update new-types name #(conj % (dist-type (first (second value))))) 45 | (merge-with concat new-types (detect-types value optim-args {}))))))) 46 | (reduce (partial merge-with concat) 47 | types 48 | (map #(detect-types % optim-args {}) (rest ast))))) 49 | types)) 50 | 51 | (defn changing-types? 52 | [& args] 53 | "Given an optimization query, detect whether there are assignments to the 54 | same optimization variables that change type from continuous to discrete or 55 | vice-versa. 56 | Returns true or false." 57 | (let [value (first args) 58 | optim-args (second args) 59 | source (drop 2 args) 60 | types (detect-types (apply list (conj source 'do)) optim-args {})] 61 | (not (every? (partial apply =) 62 | (vals types))))) 63 | -------------------------------------------------------------------------------- /src/bopp/helper_functions.clj: -------------------------------------------------------------------------------- 1 | (ns bopp.helper-functions 2 | "Helper functions" 3 | (:require [clojure.core.matrix :as m] 4 | [clojure.core.matrix.linear :as ml])) 5 | 6 | ;; matrix library uses vectorz for protocol implementations 7 | (m/set-current-implementation :vectorz) 8 | 9 | (defn argmax 10 | "Index of maximum of a collection" 11 | [coll] 12 | (first 13 | (apply max-key 14 | second 15 | (map vector 16 | (range (count coll)) 17 | coll)))) 18 | 19 | (defn indexed-max 20 | "Returns an indexed maximum. Accepts a function f and a collection 21 | coll. Returns a pair [y-max i-max] in which y-max is the largest 22 | value (f x-max) and i-max is the index such that (nth coll i-max) 23 | returns x-max." 24 | [f coll] 25 | (loop [best [(/ 1 (- 0.0)) 0] 26 | i 0 27 | xs coll] 28 | (if-let [x (first xs)] 29 | (let [[y-max i-max] best 30 | y (f x)] 31 | (recur (if (> y y-max) 32 | [y i] 33 | best) 34 | (inc i) 35 | (rest xs))) 36 | best))) 37 | 38 | (defn cartesian [colls] 39 | (if (empty? colls) 40 | '(()) 41 | (for [x (first colls) 42 | more (cartesian (rest colls))] 43 | (cons x more)))) 44 | 45 | ;; Functions ported from Anglican 46 | 47 | ;; erf 48 | (defn erf 49 | "error function" 50 | [x] 51 | (org.apache.commons.math3.special.Erf/erf x)) 52 | 53 | ;; mean 54 | (defn sum 55 | "sums array slices along specified dimension" 56 | ([a dimension] 57 | (reduce 58 | m/add 59 | (m/slices a dimension))) 60 | ([a] 61 | (sum a 0))) 62 | 63 | (defn mean 64 | "mean of array slices along specified dimension" 65 | ([a dimension] 66 | (m/div (sum a dimension) 67 | (get (m/shape a) dimension))) 68 | ([a] 69 | (mean a 0))) 70 | 71 | ;; distributions 72 | (defprotocol distribution 73 | "random distribution" 74 | (sample* [this] 75 | "draws a sample from the distribution") 76 | (observe* [this value] 77 | "return the probability [density] of the value")) 78 | 79 | (def RNG 80 | "random number generator; 81 | used by Apache Commons Math distribution objects" 82 | (org.apache.commons.math3.random.SynchronizedRandomGenerator. 83 | (org.apache.commons.math3.random.Well19937c.))) 84 | 85 | (defn ^:private qualify 86 | "accepts a symbol, returns the qualified symbol; 87 | intended to be called from a macro" 88 | [s] 89 | (symbol (format "%s/%s" *ns* s))) 90 | 91 | (defmacro defdist 92 | "defines distribution" 93 | [name & args] 94 | (let [[docstring parameters & args] 95 | (if (string? (first args)) 96 | args 97 | `(~(format "%s distribution" name) ~@args)) 98 | [bindings & methods] 99 | (if (vector? (first args)) 100 | args 101 | `[[] ~@args]) 102 | record-name (symbol (format "%s-distribution" name)) 103 | variables (take-nth 2 bindings)] 104 | `(do 105 | (declare ~name) 106 | (defrecord ~record-name [~@parameters ~@variables] 107 | Object 108 | (toString [~'this] 109 | (str (list '~(qualify name) ~@parameters))) 110 | distribution 111 | ~@methods) 112 | (defn ~name ~docstring ~parameters 113 | (let ~bindings 114 | (~(symbol (format "->%s" record-name)) 115 | ~@parameters ~@variables))) 116 | (defmethod print-method ~record-name 117 | [~'o ~'m] 118 | (print-simple (str ~'o) ~'m))))) 119 | 120 | (defmacro ^:private from-apache 121 | "wraps Apache Commons Math distribution" 122 | [name args type [apache-name & apache-args]] 123 | (let [dist (gensym "dist")] 124 | `(defdist ~(symbol name) 125 | ~(format "%s distribution (imported from apache)" name) 126 | ~args 127 | [~dist (~(symbol (format "org.apache.commons.math3.distribution.%sDistribution." apache-name)) 128 | RNG ~@apache-args)] 129 | (~'sample* [~'this] (.sample ~dist)) 130 | (~'observe* [~'this ~'value] 131 | ~(case type 132 | :discrete `(~'.logProbability ~dist ~'value) 133 | :continuous `(~'.logDensity ~dist ~'value)))))) 134 | 135 | (defprotocol multivariate-distribution 136 | "additional methods for multivariate distributions" 137 | (transform-sample [this samples] 138 | "accepts a vector of random values and generates 139 | a sample from the multivariate distribution")) 140 | 141 | (from-apache normal [mean sd] :continuous 142 | (Normal (double mean) (double sd))) 143 | 144 | (defdist mvn 145 | "multivariate normal" 146 | [mean cov] [k (m/ecount mean) ; number of dimensions 147 | Lcov (:L (ml/cholesky (m/matrix cov))) 148 | unit-normal (normal 0 1) 149 | Z (delay (let [|Lcov| (reduce * (m/diagonal Lcov))] 150 | (+ (* 0.5 k (Math/log (* 2 Math/PI))) 151 | (Math/log |Lcov|)))) 152 | iLcov (delay (m/inverse Lcov)) 153 | transform-sample (fn [samples] 154 | (m/add mean (m/mmul Lcov samples)))] 155 | (sample* [this] (transform-sample 156 | (repeatedly k #(sample* unit-normal)))) 157 | (observe* [this value] 158 | (let [dx (m/mmul @iLcov (m/sub value mean))] 159 | (- (* -0.5 (m/dot dx dx)) @Z))) 160 | multivariate-distribution 161 | (transform-sample [this samples] (transform-sample samples))) 162 | -------------------------------------------------------------------------------- /src/examples/simple_bimodal.clj: -------------------------------------------------------------------------------- 1 | (ns examples.simple-bimodal 2 | (require [bopp.core :refer :all] 3 | [clojure.data.json :as json] 4 | [anglican.runtime :refer :all] 5 | [taoensso.tufte :as tufte :refer (defnp p profiled profile)])) 6 | 7 | 8 | (defopt simple-bimodal [y] [theta] 9 | (let [theta (sample (normal 0 0.5))] 10 | (observe 11 | (normal (sqrt (* theta theta)) 0.5) y))) 12 | 13 | (defopt simple-bimodal-noisy [y] [theta] 14 | (let [theta (sample (normal 0 5)) 15 | sig-n (sample (normal 0 0.35)) 16 | t (+ theta sig-n)] 17 | (observe 18 | (normal (sqrt (* t t)) 0.5) y))) 19 | 20 | (defn -main [folder-name & opts] 21 | (let [[num-steps num-samples num-init plot-aq model] (map read-string (take 5 opts)) 22 | num-steps (or num-steps 1) 23 | num-samples (or num-samples 1000) 24 | num-init (or num-init 2) 25 | plot-aq (or plot-aq false) 26 | model (or (eval model) simple-bimodal) 27 | _ (println :model-type (type model))] 28 | (->> (doopt 29 | :importance model [5] 30 | num-samples 31 | :bo-options {:num-initial-thetas num-init 32 | :debug-folder folder-name 33 | :plot-aq plot-aq 34 | :verbose 1}) 35 | (take num-steps) 36 | (json/write-str) 37 | (spit (str folder-name ".json"))))) 38 | 39 | (tufte/add-basic-println-handler! {}) 40 | 41 | (tufte/profile 42 | {} 43 | (-main "simple-bimodal-dump" "10" "2" "5" "false" "simple-bimodal")) 44 | -------------------------------------------------------------------------------- /test/bopp/core_test.clj: -------------------------------------------------------------------------------- 1 | (ns bopp.core-test 2 | (:require [clojure.test :refer :all] 3 | [bopp.core :refer :all] 4 | [anglican.runtime :refer :all] 5 | [anglican.smc] 6 | [anglican.importance] 7 | [anglican.inference :refer [infer]])) 8 | 9 | (defopt q [y] [theta] 10 | (let [a (sample (normal 0 1)) 11 | theta (sample (gamma 1 1)) 12 | b (sample (normal a theta))] 13 | (observe (normal (+ a b) theta) y) 14 | [a b])) 15 | 16 | (deftest doopt-test 17 | (let [mmap-states (doopt :smc q [2] 100 :bo-options {:verbose 1} :opt-type :mmap) 18 | ml2-states (doopt :smc q [2] 100 :bo-options {:verbose 1} :opt-type :ml2)] 19 | (is (first mmap-states) 20 | "testing whether mmap runs.") 21 | (is (first ml2-states) 22 | "testing whether ml2 runs."))) 23 | 24 | ;; ;; This should throw an Exception 25 | ;; (defopt q2 [y] [theta] 26 | ;; (let [a (sample (normal 0 1)) 27 | ;; theta (sample (gamma 1 1)) 28 | ;; b (sample (normal a theta)) 29 | ;; theta (sample (discrete 1 1))] 30 | ;; (observe (normal (+ a b) theta) y) 31 | ;; [a b])) 32 | 33 | ;; ;; This shouldn't throw an Exception 34 | ;; (defopt q3 [y] [theta] 35 | ;; (let [a (sample (normal 0 1)) 36 | ;; theta (sample (gamma 1 1)) 37 | ;; b (sample (normal a theta)) 38 | ;; theta (sample (normal 1 1))] 39 | ;; (observe (normal (+ a b) theta) y) 40 | ;; [a b])) 41 | 42 | ;; ;; This should detect multiple instances of declarations of theta during runtime 43 | ;; (defopt q4 [y] [theta] 44 | ;; (let [a (sample (normal 0 1)) 45 | ;; theta (sample (gamma 1 1)) 46 | ;; b (sample (normal a theta)) 47 | ;; theta (sample (normal 1 1))] 48 | ;; (observe (normal (+ a b) theta) y) 49 | ;; [a b])) 50 | ;; (def mmap-states (doopt :smc q4 [2] 100 :bo-options {:verbose 1} :opt-type :mmap)) 51 | 52 | ;; ;; This should be slow because there is an expensive operation before sampling all optim-vars 53 | ;; (defopt q5 [y] [theta psi] 54 | ;; (let [a (sample (normal 0 1)) 55 | ;; psi (sample (normal 1 2)) 56 | ;; x (doall (repeatedly 1e5 #(sample (mvn [1 0] [[1 0] [0 1]])))) 57 | ;; theta (sample (gamma 1 1)) 58 | ;; b (sample (normal a theta))] 59 | ;; (observe (normal (+ a b) theta) y) 60 | ;; [a b])) 61 | 62 | ;; (time (first (infer :importance (:prior-query q5) [2]))) 63 | 64 | ;; ;; This should be fast 65 | ;; (defopt q6 [y] [theta psi] 66 | ;; (let [a (sample (normal 0 1)) 67 | ;; psi (sample (normal 1 2)) 68 | ;; theta (sample (gamma 1 1)) 69 | ;; x (doall (repeatedly 1e5 #(sample (mvn [1 0] [[1 0] [0 1]])))) 70 | ;; b (sample (normal a theta))] 71 | ;; (observe (normal (+ a b) theta) y) 72 | ;; [a b])) 73 | 74 | ;; (time (first (infer :importance (:prior-query q6) [2]))) 75 | 76 | ;; (run-tests 'bopp.core-test) 77 | -------------------------------------------------------------------------------- /test/bopp/error_handling_test.clj: -------------------------------------------------------------------------------- 1 | (ns bopp.error-handling-test 2 | (:require [clojure.test :refer :all]) 3 | (:require [bopp.error-handling :refer :all])) 4 | 5 | (deftest changing-types?-test 6 | (is (= true 7 | (apply changing-types? '([y] [theta] 8 | (let [a (sample (normal 0 10)) 9 | theta (sample (normal a 20)) 10 | b (sample (normal a (* theta theta))) 11 | theta (sample (discrete [a 20]))] 12 | (observe (normal (* a theta) (* b b)) y) 13 | [a b])))) 14 | (str "normal and discrete are different types.")) 15 | (is (= false 16 | (apply changing-types? '([y] [theta] 17 | (let [a (sample (normal 0 10)) 18 | theta (sample (normal a 20)) 19 | b (sample (normal a (* theta theta))) 20 | theta (sample (wishart nil nil))] 21 | (observe (normal (* a theta) (* b b)) y) 22 | [a b])))) 23 | (str "normal and wishart are same type.")) 24 | (is (= false 25 | (apply changing-types? '([y] [theta] 26 | (let [a (sample (discrete [0 10])) 27 | theta (sample (discrete a 20)) 28 | b (sample (normal a (* theta theta))) 29 | theta (sample (categorical nil nil))] 30 | (observe (normal (* a theta) (* b b)) y) 31 | [a b])))) 32 | (str "discrete and categorical is different types.")) 33 | (is (= true 34 | (apply changing-types? '([y] [theta] 35 | (let [a (sample (discrete [0 10])) 36 | b (sample (normal a (* theta theta)))] 37 | (if condition 38 | (let [theta (sample (discrete a 20))] 39 | (+ 1 theta)) 40 | (let [theta (sample (normal nil nil))] 41 | (+ 2 theta))) 42 | (observe (normal (* a theta) (* b b)) y) 43 | [a b])))) 44 | (str "discrete and normal in different branches are different types."))) 45 | 46 | ;; (run-tests 'bopp.error-handling-test) 47 | -------------------------------------------------------------------------------- /test/bopp/program_transformations_test.clj: -------------------------------------------------------------------------------- 1 | (ns bopp.program-transformations-test 2 | (:require [bopp.program-transformations :refer :all] 3 | [anglican.runtime :refer [normal flip]])) 4 | 5 | ;;; Prior transformation 6 | 7 | ;; (def a (prior-query [y] [theta] 8 | ;; (let [a (sample (normal 0 10)) 9 | ;; theta (sample (normal a 20)) 10 | ;; b (sample (normal a (* theta theta)))] 11 | ;; (observe (normal (* a theta) (* b b)) y) 12 | ;; [a b]))) 13 | 14 | ;; (:source (meta a)) ;; Returns: 15 | ;; ;; (query [y] 16 | ;; ;; (do 17 | ;; ;; (let [a (sample (normal 0 10)) 18 | ;; ;; theta (let [value (sample (normal a 20))] 19 | ;; ;; (if (retrieve (symbol "OPTIM_ARGS") 20 | ;; ;; (symbol "theta")) 21 | ;; ;; (throw-exception "WARNING: Multiple instances of declaration of optimization variable theta detected!")) 22 | 23 | ;; ;; (store (symbol "OPTIM_ARGS") 24 | ;; ;; (symbol "theta") 25 | ;; ;; value) 26 | 27 | ;; ;; (if (= (set (keys (retrieve (symbol "OPTIM_ARGS")))) 28 | ;; ;; (set [(symbol "theta")])) 29 | ;; ;; (do 30 | ;; ;; (println "exiting the program early") 31 | ;; ;; (return (map (fn [x] (retrieve (symbol "OPTIM_ARGS") x)) 32 | ;; ;; [(symbol "theta")])))) 33 | 34 | ;; ;; value) 35 | ;; ;; b (sample (normal a (* theta theta)))] 36 | ;; ;; nil 37 | ;; ;; [a b]) 38 | ;; ;; (map (fn [x] (retrieve (symbol "OPTIM_ARGS") x)) [(symbol "theta")]))) 39 | 40 | ;;; Acq transformation 41 | 42 | ;; (def c (acq-query [y] [theta] 43 | ;; (let [a (sample (normal 0 10)) 44 | ;; theta (sample (normal a 20)) 45 | ;; b (sample (normal a (* theta theta)))] 46 | ;; (observe (normal (* a theta) (* b b)) y) 47 | ;; [a b]))) 48 | 49 | ;; (:source (meta c)) ; Returns: 50 | ;; ;; (query [y ACQ_F] 51 | ;; ;; (do (let [a (sample (normal 0 10)) 52 | ;; ;; theta (let [value (sample (normal a 20))] 53 | ;; ;; (if (retrieve (symbol "OPTIM_ARGS") 54 | ;; ;; (symbol "theta")) 55 | ;; ;; (throw-exception "WARNING: Multiple instances of declaration of optimization variable theta detected!")) 56 | 57 | ;; ;; (store (symbol "OPTIM_ARGS") 58 | ;; ;; (symbol "theta") 59 | ;; ;; value) 60 | 61 | ;; ;; (if (= (set (keys (retrieve (symbol "OPTIM_ARGS")))) 62 | ;; ;; (set [(symbol "theta")])) 63 | ;; ;; (do (println "exiting the program early") 64 | ;; ;; (return 65 | ;; ;; (do 66 | ;; ;; (observe (factor) (ACQ_F (map (fn [x] (retrieve (symbol "OPTIM_ARGS") x)) [(symbol "theta")]))) 67 | ;; ;; (map (fn [x] (retrieve (symbol "OPTIM_ARGS") x)) 68 | ;; ;; [(symbol "theta")]))))) 69 | 70 | ;; ;; value) 71 | ;; ;; b (sample (normal a (* theta theta)))] 72 | ;; ;; nil 73 | ;; ;; [a b]) 74 | ;; ;; (observe (factor) (ACQ_F (map (fn [x] (retrieve (symbol "OPTIM_ARGS") x)) [(symbol "theta")]))) 75 | ;; ;; (map (fn [x] (retrieve (symbol "OPTIM_ARGS") x)) [(symbol "theta")]))) 76 | 77 | ;;; MMAP transformation 78 | 79 | ;; (def d (mmap-query [y] [theta] 80 | ;; (let [a (sample (normal 0 10)) 81 | ;; c (sample (normal a 20)) 82 | ;; b (sample (normal a (* c c))) 83 | ;; d (let [theta (sample (normal a (* b c)))] 84 | ;; theta)] 85 | ;; (observe (normal (* a d) (* b b)) y) 86 | ;; [a b]))) 87 | 88 | ;; (:source (meta d)) 89 | 90 | ;;; ML2 transformation 91 | 92 | ;; (def e (ml2-query [y] [theta] 93 | ;; (if (sample (flip 0.3)) 94 | ;; (let [a (sample (normal 0 1)) 95 | ;; theta (sample (normal a 1))] 96 | ;; (observe (normal a (* theta theta)) 1) 97 | ;; a) 98 | ;; (let [a (sample (normal 0 12)) 99 | ;; theta (sample (normal a 21))] 100 | ;; (observe (normal a (* theta theta)) 31) 101 | ;; theta)))) 102 | 103 | ;; (meta e) 104 | 105 | 106 | -------------------------------------------------------------------------------- /worksheets/hmm.clj: -------------------------------------------------------------------------------- 1 | ;; gorilla-repl.fileformat = 1 2 | 3 | ;; ** 4 | ;;; # Hidden Markov Model with Unknown Number of States 5 | ;; ** 6 | 7 | ;; @@ 8 | (ns worksheets.hmm 9 | (:require [gorilla-plot.core :as plot] 10 | [anglican.core :refer [doquery]] 11 | [bopp.core :refer :all] 12 | [bopp.helper-functions :refer [argmax]] 13 | [clojure-csv.core :refer :all] 14 | [clojure.data.csv :as csv] 15 | [clojure.java.io :as io] 16 | [clojure.core.matrix :as m] 17 | [clojure.data.json :as json]) 18 | (:use 19 | clojure.repl 20 | [anglican 21 | runtime 22 | emit 23 | smc 24 | pcascade 25 | stat 26 | [state :only [get-result get-log-weight]] 27 | [inference :only [log-marginal rand-roulette]]])) 28 | ;; @@ 29 | 30 | ;; ** 31 | ;;; ## The Problem 32 | ;;; 33 | ;;; We consider a hidden Markov model (HMM) with an unknown number of states. This example demonstrates how BOPP can be applied to models which conceptually have an unknown number of variables, by generating all possible variables that might be needed, but then leaving some variables unused for some execution traces. This avoids problems of varying base measures so that the MMAP problem is well defined and provides a function with a fixed number of inputs as required by the BO scheme. From the BO perspective, the target function is simply constant for variations in an unused variable. 34 | ;;; 35 | ;;; HMMs are Markovian state space models with discrete latent variables. Each latent state @@x\_t \in\{1,\dots,K\}, t=1,\dots,T@@ is defined conditionally on @@x\_{t-1}@@ through a set of discrete transition probabilities, whilst each output @@y\_t\in\mathbb{R}@@ is considered to be generated i.i.d. given @@x\_t@@. We consider the following HMM, in which the number of states @@K@@, is also a random variable: 36 | ;;; 37 | ;;; @@\begin{align} 38 | ;;; K & \sim \text{Discrete}\{1,2,3,4,5\} \\\\ 39 | ;;; T\_k &\sim \text{Dirichlet}\\{{1}\_{1:K}\\}, \quad \forall k=1,\dots,K \\\\ 40 | ;;; \phi\_k &\sim \text{Uniform}[0,1], \quad \forall k=1,\dots,K \\\\ 41 | ;;; \mu\_0 &\leftarrow \min \\{y\_{1:T}\\} \\\\ 42 | ;;; \mu\_k &\leftarrow \mu\_{k-1}+\phi\_k \cdot (\max \\{y\_{1:T}\\} -\mu\_{k-1}), \quad \forall k=1,\dots,K \\\\ 43 | ;;; x\_1 &\leftarrow 1 \\\\ 44 | ;;; x\_t | x\_{t-1} &\sim \text{Discrete}\\{T\_{x\_{t-1}}\\} \\\\ 45 | ;;; y\_t | x\_t &\sim\mathcal{N}(\mu(x\_{t-1}),0.2). 46 | ;;; \end{align}@@ 47 | ;;; 48 | ;;; Our experiment is based on applying BOPP to the above model to do MMAP estimation with a single synthetic dataset, generated using @@K=3, \;\mu\_1 = -1, \;\mu\_2 = 0, \;\mu\_3 = 4, \;T\_1 = [0.9,0.1,0], \;T\_2=[0.2,0.75,0.05]@@ and @@T\_3=[0.1,0.2,0.7]@@. Lets first first load the data and set the known parameters. 49 | ;;; 50 | ;; ** 51 | 52 | ;; @@ 53 | (defn hmm-data [n] 54 | (let [ground-truth-x (mapv read-string 55 | (into [] 56 | (flatten 57 | (csv/read-csv 58 | (slurp 59 | (io/reader 60 | (io/resource (str "data/hmm/gt_x" n ".csv")))))))) 61 | y (mapv read-string 62 | (into [] 63 | (flatten 64 | (csv/read-csv 65 | (slurp 66 | (io/reader 67 | (io/resource (str "data/hmm/y" n ".csv"))))))))] 68 | [ground-truth-x y])) 69 | 70 | (def T 500) 71 | 72 | (def observations (take T (second (hmm-data 1)))) 73 | 74 | (defn index->ind 75 | "converts a collection of indices to a matrix of indicator vectors" 76 | [values] 77 | (let [max-v (reduce max values) 78 | zero-vec (into [] (repeat (inc max-v) 0))] 79 | (m/matrix (map #(assoc zero-vec % 1) values)))) 80 | 81 | (defn square 82 | [x] 83 | (m/mul x x)) 84 | 85 | (def sig 0.2) 86 | ;; @@ 87 | 88 | ;; ** 89 | ;;; ## Solution using BOPP 90 | ;;; 91 | ;;; We now use BOPP to optimize both the number of states @@K@@ and the stick-breaking parameters @@\phi_k@@, with full inference performed on the other parameters. BOPP therefore aims to maximize 92 | ;;; 93 | ;;; @@\begin{align} 94 | ;;; p(K,\phi\_{k=1:5}|y\_{t=1:T}) = \iint p(K,\phi\_{k=1:5},x\_{t=1:T},T\_{k=1:K}|y\_{t=1:T}) \mathrm{d}x\_{t=1:T} \mathrm{d}T\_{k=1:K}. 95 | ;;; \end{align}@@ 96 | ;;; 97 | ;;; First we define our model using defopt 98 | ;; ** 99 | 100 | ;; @@ 101 | (defopt hmm-simple-opt 102 | [] 103 | [n-states phi1 phi2 phi3 phi4 phi5] 104 | (let [opt-min (apply min observations) 105 | opt-max (apply max observations) 106 | n-states (sample (uniform-discrete 1 6)) 107 | init-dist (discrete (apply conj [1] (repeat (dec n-states) 0))) 108 | trans-dist-mem (mem (fn [n] (discrete (sample (dirichlet (into [] (repeat n-states 1))))))) 109 | 110 | phi1 (sample (uniform-continuous 0 1)) 111 | phi2 (sample (uniform-continuous 0 1)) 112 | phi3 (sample (uniform-continuous 0 1)) 113 | phi4 (sample (uniform-continuous 0 1)) 114 | phi5 (sample (uniform-continuous 0 1)) 115 | 116 | mus (let [left (- 1 phi1) 117 | mu1 phi1] 118 | (if (< n-states 2) 119 | [mu1] 120 | (let [diff2 (* phi2 left) 121 | left (- left diff2) 122 | mu2 (- 1 left)] 123 | (if (< n-states 3) 124 | [mu1 mu2] 125 | (let [diff3 (* phi3 left) 126 | left (- left diff3) 127 | mu3 (- 1 left)] 128 | (if (< n-states 4) 129 | [mu1 mu2 mu3] 130 | (let [diff4 (* phi4 left) 131 | left (- left diff4) 132 | mu4 (- 1 left)] 133 | (if (< n-states 5) 134 | [mu1 mu2 mu3 mu4] 135 | (let [diff5 (* phi5 left) 136 | left (- left diff5) 137 | mu5 (- 1 left)] 138 | [mu1 mu2 mu3 mu4 mu5]))))))))) 139 | mus (map #(+ opt-min (* % (- opt-max opt-min))) mus)] 140 | ;; Return states, n-states, mus and transition distribution 141 | {:states 142 | (reduce 143 | (fn [states obs] 144 | (let [state (sample (trans-dist-mem (peek states)))] 145 | (observe (normal (nth mus state) sig) obs) 146 | (conj states state))) 147 | [(sample init-dist)] 148 | observations) 149 | :n-states n-states 150 | :mus mus 151 | :transition-dist {0 (trans-dist-mem 0) 152 | 1 (trans-dist-mem 1) 153 | 2 (trans-dist-mem 2) 154 | 3 (trans-dist-mem 3) 155 | 4 (trans-dist-mem 4)}})) 156 | ;; @@ 157 | 158 | ;; ** 159 | ;;; Now we carry out the MMAP estimation by calling BOPP 160 | ;; ** 161 | 162 | ;; @@ 163 | (def samples (->> (doopt :pcascade 164 | hmm-simple-opt 165 | [] 166 | 200 ;; Number of particles 167 | :bo-options {:verbose 1} 168 | :inf-options {:number-of-threads 400 :number-of-particles 200}) 169 | (take 50) ;; Number of optimization iterations to do 170 | doall 171 | (mapv #(take 2 %)))) 172 | ;; @@ 173 | 174 | ;; @@ 175 | samples 176 | ;; @@ 177 | 178 | ;; @@ 179 | 180 | ;; @@ 181 | -------------------------------------------------------------------------------- /worksheets/opt.clj: -------------------------------------------------------------------------------- 1 | ;; gorilla-repl.fileformat = 1 2 | 3 | ;; ** 4 | ;;; # Optimization Benchmarks 5 | ;; ** 6 | 7 | ;; @@ 8 | (ns worksheets.opt 9 | (:require [gorilla-plot.core :as plot] 10 | [clojure.core.matrix :as mat] 11 | [bopp.core :refer :all]) 12 | (:use [anglican runtime emit])) 13 | ;; @@ 14 | ;; => 15 | ;;; {"type":"html","content":"nil","value":"nil"} 16 | ;; <= 17 | 18 | ;; ** 19 | ;;; In this worksheet we consider simply using BOPP as an optimizer on some classic Bayesian optimization benchmark problems. Results for some popular packages on the same problems are presented in the paper. 20 | ;; ** 21 | 22 | ;; @@ 23 | (defdist factor 24 | [] 25 | (sample* [this] 0) 26 | (observe* [this value] value)) 27 | ;; @@ 28 | ;; => 29 | ;;; {"type":"html","content":"#multifn[print-method 0x1d79a227]","value":"#multifn[print-method 0x1d79a227]"} 30 | ;; <= 31 | 32 | ;; ** 33 | ;;; ## Branin 34 | ;; ** 35 | 36 | ;; ** 37 | ;;; @@f(x) = -\left(x\_2-\frac{5.1}{4\pi^2}x\_1^2+\frac{5}{\pi}x\_1-6\right)^2-10(1-\frac{1}{8\pi}\cos(x\_1))-10@@ 38 | ;;; 39 | ;;; Bounds @@-5 \le x\_1 \le 10@@ and @@0 \le x\_2 \le 15@@. 40 | ;;; 41 | ;;; There are three global maximum, @@f(x^\*) = -0.397887@@ at @@x^\* = (-\pi,12,1275), (\pi,2.275) ~\rm{and}~ (9.42478,2.475)@@. 42 | ;; ** 43 | 44 | ;; ** 45 | ;;; First lets define the problem. 46 | ;; ** 47 | 48 | ;; @@ 49 | (with-primitive-procedures [factor] 50 | (defopt branin-opt [] [x1 x2] 51 | (let [x1 (sample (uniform-continuous -5 10)) 52 | x2 (sample (uniform-continuous 0 15)) 53 | t1 (- (+ (- x2 (* (pow x1 2) (/ 5.1 (* 4 (pow Math/PI 2))))) 54 | (* x1 (/ 5 Math/PI))) 55 | 6) 56 | t2 (* 10 57 | (- 1 (/ 1 (* 8 Math/PI))) 58 | (cos x1))] 59 | (observe (factor) (+ (pow t1 2) t2 10))))) 60 | ;; @@ 61 | ;; => 62 | ;;; {"type":"html","content":"#'worksheets.opt/branin-opt","value":"#'worksheets.opt/branin-opt"} 63 | ;; <= 64 | 65 | ;; ** 66 | ;;; Now we can run BOPP in a single simple call and collect the results. Note performance is likely to be worse than the paper as we are using the default lightweight options setup rather than the more careful one from the paper. 67 | ;; ** 68 | 69 | ;; @@ 70 | (def branin-samples (->> (doopt :importance 71 | branin-opt 72 | [] 73 | 1 74 | :bo-options {:verbose 1 75 | :b-deterministic true} 76 | :opt-type :risk-minimization) 77 | (take 100) ;; Number of optimization iterations to do 78 | doall 79 | (mapv #(take 2 %)))) 80 | ;; @@ 81 | 82 | ;; @@ 83 | branin-samples 84 | ;; @@ 85 | 86 | ;; ** 87 | ;;; ## Hartmann 6D 88 | ;; ** 89 | 90 | ;; ** 91 | ;;; @@\begin{align} 92 | ;;; f(x) &= -\sum\_{i=1}^{4} \alpha\_i \exp \left(-\sum\_{j=1}^{6} A\_{i,j}(x\_j-P\_{i,j})^2\right), \quad \rm{where} \\\\ 93 | ;;; \alpha &= (1,1.2,3,3.2)^T \\\\ 94 | ;;; A &= \left(\begin{matrix} 95 | ;;; 10 & 3 & 17 & 3.5 & 1.6 & 8 \\\\ 96 | ;;; 0.05 & 10 & 17 & 0.1 & 8 & 14 \\\\ 97 | ;;; 3 & 3.5 & 1.7 & 10 & 17 & 8 \\\\ 98 | ;;; 17 & 8 & 0.05 & 10 & 0.1 & 14 99 | ;;; \end{matrix}\right) \\\\ 100 | ;;; P &= 10^{-4} \left( 101 | ;;; \begin{matrix} 102 | ;;; 1312 & 1696 & 5569 & 124 & 8283 & 5886\\\\ 103 | ;;; 2329 & 4135 & 8307 & 3736 & 1004 & 9991 \\\\ 104 | ;;; 2358 & 1451 & 3522 & 2883 & 3047 & 6650 \\\\ 105 | ;;; 4047 & 8828 & 8732 & 5743 & 1091 & 381 106 | ;;; \end{matrix} 107 | ;;; \right) 108 | ;;; \end{align}@@ 109 | ;;; 110 | ;;; Bounds @@0 \le x\_i \le 1, \; \forall i \in \\{1,\dots,6\\}@@ 111 | ;;; 112 | ;;; The function has 6 local minima and one global minima at 113 | ;;; @@\begin{align} 114 | ;;; x^\* &= (0.20169,0.150011,0.476874,0.275332,0.311652,0.6573), 115 | ;;; \end{align}@@ 116 | ;;; with @@f(x^\*) = -3.32237@@. 117 | ;; ** 118 | 119 | ;; @@ 120 | (def A 121 | [[10 3 17 3.5 1.7 8] 122 | [0.05 10 17 0.1 8 14] 123 | [3 3.5 1.7 10 17 8] 124 | [17 8 0.05 10 0.1 14]]) 125 | 126 | (def P 127 | [[0.1312 0.1696 0.5569 0.0124 0.8283 0.5886] 128 | [0.2329 0.4135 0.8307 0.3736 0.1004 0.9991] 129 | [0.2348 0.1451 0.3522 0.2883 0.3047 0.6650] 130 | [0.4047 0.8828 0.8732 0.5743 0.1091 0.0381]]) 131 | 132 | (def alpha 133 | [1 1.2 3 3.2]) 134 | 135 | (defn hartmann-6d [x1 x2 x3 x4 x5 x6] 136 | (let [x [x1 x2 x3 x4 x5 x6] 137 | dxP (mat/pow 138 | (mat/sub P x) 139 | 2) 140 | terms (mat/transpose 141 | (mat/mul A dxP)) 142 | terms-reduced (reduce mat/add terms) 143 | exp-terms (mat/exp 144 | (mat/sub 0 terms-reduced)) 145 | f (- 0 146 | (reduce + (mat/mul alpha exp-terms)))] 147 | f)) 148 | 149 | (with-primitive-procedures [factor hartmann-6d] 150 | (defopt hartmann-opt [] [x1 x2 x3 x4 x5 x6] 151 | (let [x1 (sample (uniform-continuous 0 1)) 152 | x2 (sample (uniform-continuous 0 1)) 153 | x3 (sample (uniform-continuous 0 1)) 154 | x4 (sample (uniform-continuous 0 1)) 155 | x5 (sample (uniform-continuous 0 1)) 156 | x6 (sample (uniform-continuous 0 1)) 157 | f (hartmann-6d x1 x2 x3 x4 x5 x6)] 158 | (observe (factor) f)))) 159 | ;; @@ 160 | ;; => 161 | ;;; {"type":"html","content":"#'worksheets.opt/hartmann-opt","value":"#'worksheets.opt/hartmann-opt"} 162 | ;; <= 163 | 164 | ;; ** 165 | ;;; Again its a simple call to use BOPP. 166 | ;; ** 167 | 168 | ;; @@ 169 | (def hartmann6d-samples (->> (doopt :importance 170 | hartmann-opt 171 | [] 172 | 1 173 | :bo-options {:verbose 1 174 | :b-deterministic true} 175 | :opt-type :risk-minimization) 176 | (take 100) ;; Number of optimization iterations to do 177 | doall 178 | (mapv #(take 2 %)))) 179 | ;; @@ 180 | 181 | ;; @@ 182 | hartmann6d-samples 183 | ;; @@ 184 | -------------------------------------------------------------------------------- /worksheets/simple_bimodal.clj: -------------------------------------------------------------------------------- 1 | ;; gorilla-repl.fileformat = 1 2 | 3 | ;; ** 4 | ;;; # Simple Bimodal Modal 5 | ;; ** 6 | 7 | ;; @@ 8 | (ns examples.simple-bimodal 9 | (require [bopp.core :refer :all] 10 | [anglican.runtime :refer :all])) 11 | ;; @@ 12 | ;; => 13 | ;;; {"type":"html","content":"nil","value":"nil"} 14 | ;; <= 15 | 16 | ;; ** 17 | ;;; In this simple example, we demonstrate the ability of BOPP to carry out unbounded optimization on a 1D problem with a significant prior-posterior mismatch, namely @@p \left(\theta\right)={\rm Normal}(0, 0.5)@@ and @@p \left(Y|\theta\right)={\rm Normal}(5-\left|\theta\right|,0.5)@@ where we want to optimize @@p(\theta | Y)@@ with respec to @@\theta@@. This requires BOPP to adapt to the target and effectively establish maxima in the presence of multiple modes. It should be noted that this is a deterministic optimization problem. 18 | ;; ** 19 | 20 | ;; @@ 21 | (defopt simple-bimodal [y] [theta] 22 | (let [theta (sample (normal 0 0.5))] 23 | (observe 24 | (normal (sqrt (* theta theta)) 0.5) y))) 25 | ;; @@ 26 | ;; => 27 | ;;; {"type":"html","content":"#'examples.simple-bimodal/simple-bimodal","value":"#'examples.simple-bimodal/simple-bimodal"} 28 | ;; <= 29 | 30 | ;; @@ 31 | (def samples (->> (doopt :importance 32 | simple-bimodal 33 | [5] 34 | 1 ;; Number of particles 35 | :bo-options {:verbose 1}) 36 | (take 50) ;; Number of optimization iterations to do 37 | doall 38 | (mapv #(take 2 %)))) 39 | ;; @@ 40 | 41 | ;; @@ 42 | samples 43 | ;; @@ 44 | --------------------------------------------------------------------------------