The cl-bayesnet Reference Manual

Table of Contents

The cl-bayesnet Reference Manual

This is the cl-bayesnet Reference Manual, version 0.1.0, generated automatically by Declt version 3.0 "Montgomery Scott" on Fri Jun 26 10:03:01 2020 GMT+0.

1 Introduction

cl-bayesnet - a Common Lisp Bayesian Network Inference Engine

Overview

cl-bayesnet is a tool for the compilation and probability calculation of discrete, probabilistic Bayesian Networks.

It provides two types of compilation. The first is join-tree compilation. A join-tree is an auxiliary structure which uses message passing to calculate local probabilities given evidence in a network. Compiling a Bayesian Network to a join tree is quick, but message passing is relatively slow. The join tree's space cost should also be taken into account.

The second type of compilation compiles the Bayesian Network into an Arithmetic Circuit, which is written as a series of arithmetic instructions. These instructions can be interpreted on the fly, or written out as source code for a compiler such as gcc. The compilation process is quite slow, but the instructions are evaluated much faster than message passing (using my implementation, anyway). My tests showed approximately 70x speed up of interpreted instructions over message passing, and then the C compiled instructions executed 20x faster than interpreted instructions!

An additional advantage of the arithmetic circuit is that it compiles to a single, standalone function. That means it is perfect for embedded systems, and can be used anywhere, without dependence on any library at all! An absolutely minimal footprint.

## Scope and Goals ##

The scope of cl-bayesnet is just Bayesian Network compilation and probability calculation. There is no API for building or modifying a Bayesian Network. There are no modelling tools. There is no GUI. These tools already exist, and have done for years.

However, there are not many free, open-source Bayesian Network probability calculators. http://sourceforge.net/projects/bnj/ is the only other open-source one I know of. I know of no other project which can compile direct to machine code (through gcc) like cl-bayesnet can.

The goals of this project is to be useful to developers who want to use the results of their Bayesian Network modelling freely in any domain. If there is demand, compilation to pure Java and compilation to pure Lisp can be quickly developed.

## Highlights ##

• Load from dne, ace, xmlbif formats.
• Simple query API.
• Use message passing or arithmetic circuit methods.
• Embeddable C code generation. Other languages such as Java and Lisp are possible.

Using cl-bayesnet

Dependencies

cl-bayesnet uses S-XML to parse xmlbif. It uses trivial-shell to call the C compiler and CFFI to load the resultant shared object file. You can disable the dependencies on CFFI and trivial-shell by adding :cl-bayesnet-no-cffi to your Lisp's features list.

All dependencies are available through quicklisp.

Installation

I suggest using quicklisp. Install that, and then grab the source (via tarball or git) and put it in ~/quicklisp/local-projects/. Symlinks work okay too.

Documentation

See the API-Documentation on github. It may not necessarily be up to date.

Or, use make-api-doc.sbcl in this directory to make the API documentation (cl-bayesnet.html). This assumes you have quicklisp and sbcl installed.

Usage

See tests/test-alarm.lisp for example usage.

Ownership and License

cl-bayesnet's contributors are listed in the AUTHORS file. The authors of cl-bayesnet grant you use of this software under the terms of the Lisp Lesser General Public License (LLGPL). For details see the files COPYING, COPYING.LESSER and COPYING.LISP in this directory.

Contributing

If you find problems with this library please take the time to report the issue. This helps you by increasing the chance the issue will be fixed. It helps motivate me by letting me know the library is being used. It helps everyone when the fixed issue creates a stronger codebase.

To report an issue, use the cl-bayesnet issue tracker at github.com.

For issue fixes and improvements, I prefer pull requests. Simple one or two liner fixes are okay over email for n

2 Systems

The main system appears first, followed by any subsystem dependency.

2.1 cl-bayesnet

Maintainer

Lucas Hope <lucas.r.hope@gmail.com>

Author

Lucas Hope <lucas.r.hope@gmail.com>

License

LLGPL

Description

A Common Lisp Bayesian Network Inference Engine

Version

0.1.0

Dependencies

• s-xml
• trivial-shell
• cffi

Source

cl-bayesnet.asd (file)

Component

src (module)

3 Modules

Modules are listed depth-first from the system components tree.

3.1 cl-bayesnet/src

Parent

cl-bayesnet (system)

Location

src/

Components

• packages.lisp (file)
• utils.lisp (file)
• tries.lisp (file)
• bn-utils.lisp (file)
• bn.lisp (file)
• parse-network.lisp (file)
• clique-tree.lisp (file)
• message.lisp (file)
• evidence.lisp (file)
• compiler.lisp (file)
• emit-c.lisp (file)
• test.lisp (file)

4 Files

Files are sorted by type and then listed depth-first from the systems components trees.

4.1 Lisp

4.1.1 cl-bayesnet.asd

Location

cl-bayesnet.asd

Systems

cl-bayesnet (system)

4.1.2 cl-bayesnet/src/packages.lisp

Parent

src (module)

Location

src/packages.lisp

Packages

cl-bayesnet

4.1.3 cl-bayesnet/src/utils.lisp

Dependency

packages.lisp (file)

Parent

src (module)

Location

src/utils.lisp

Internal Definitions

• *calculation-context* (special variable)
• aif (macro)
• awhen (macro)
• best (function)
• best-in-array (function)
• best-in-hash (function)
• best-in-list (function)
• compose (function)
• copy-array (function)
• cpt-incf (function)
• cpt-index (function)
• make-vector (function)
• map-int (function)
• maparray (function)
• multf (macro)
• normalize (function)
• order-vector (function)
• returnit (macro)
• shuffle (generic function)
• shuffle (method)
• shuffle (method)
• shuffle (method)
• while (macro)
• with-calculation (macro)
• with-calculation-context (macro)
• with-gensyms (macro)

4.1.4 cl-bayesnet/src/tries.lisp

Dependency

utils.lisp (file)

Parent

src (module)

Location

src/tries.lisp

Internal Definitions

• %trie-map-key-value (function)
• %trie-map-trie (function)
• +trie-hash-threshold+ (constant)
• copy-trie (function)
• do-trie-branches (macro)
• do-trie-values (macro)
• hash-to-trie (function)
• make-trie (function)
• make-trie-hash (function)
• trie (structure)
• trie-bottom-p (function)
• trie-branch (function)
• (setf trie-branch) (function)
• trie-branch-count (function)
• trie-branch-values (function)
• trie-clear (function)
• trie-count (function)
• (setf trie-count) (function)
• trie-insert (function)
• trie-list-bottom (function)
• trie-list-depth (function)
• trie-list-values (function)
• trie-map-b (function)
• trie-map-branches (function)
• trie-map-key-value (function)
• trie-map-trie (function)
• trie-map-values (function)
• trie-p (function)
• trie-prune (function)
• trie-search (function)
• trie-test (function)
• (setf trie-test) (function)
• trie-value (function)
• (setf trie-value) (function)

4.1.5 cl-bayesnet/src/bn-utils.lisp

Dependency

tries.lisp (file)

Parent

src (module)

Location

src/bn-utils.lisp

Internal Definitions

• *temporary-directory* (special variable)
• degen-prob (function)
• do-upper (macro)
• edge< (function)
• edge= (function)
• find-temporary-file (function)
• float-to-fixnums (function)
• map-pairs (function)
• multiply-floats (macro)
• node-combinations (function)
• random-choose (function)
• reset-potential (macro)
• split (function)
• split-probs (function)
• sum-floats (macro)
• symmetric (function)
• (setf symmetric) (function)
• vecfn (function)
• vlength (macro)

4.1.6 cl-bayesnet/src/bn.lisp

Dependency

bn-utils.lisp (file)

Parent

src (module)

Location

src/bn.lisp

Exported Definitions

• add-evidence (generic function)
• add-evidence (method)
• add-evidence (method)
• clear-evidence (generic function)
• clear-evidence (method)
• clear-evidence (method)
• evidence (generic function)
• evidence (method)
• evidence (method)
• (setf evidence) (generic function)
• evidence-index (generic function)
• evidence-index (method)
• evidence-index (method)
• name (generic function)
• name (method)
• name (method)
• net (generic function)
• net (method)
• net (class)
• node (generic function)
• node (method)
• node (method)
• node (class)
• node-order (generic function)
• node-order (method)
• num-nodes (generic function)
• num-nodes (method)
• num-states (generic function)
• num-states (method)
• parents (generic function)
• parents (method)
• query (function)
• states (generic function)
• states (method)
• with-evidence (macro)

Internal Definitions

• %evidence (method)
• (setf %evidence) (method)
• %evidence-1 (function)
• %query (generic function)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• compiled (method)
• (setf compiled) (method)
• evidence-1 (generic function)
• evidence-1 (method)
• gen-parameter (function)
• index (method)
• (setf index) (method)
• node-vec (method)
• (setf node-vec) (method)
• nodes (method)
• num-arcs (function)
• num-nodes-1 (function)
• num-states-1 (function)
• parent-indices (method)
• (setf parent-indices) (method)
• parent-vec (method)
• (setf parent-vec) (method)
• preprocess-network (function)
• preprocess-node (function)
• properties (method)
• properties (method)
• save-evidence (macro)
• set-name (method)
• set-name (method)
• set-net (method)
• set-node-order (method)
• set-parents (method)
• set-states (method)
• statep (function)
• table (method)
• (setf table) (method)
• table-lookup (function)

4.1.7 cl-bayesnet/src/parse-network.lisp

Dependency

bn.lisp (file)

Parent

src (module)

Location

src/parse-network.lisp

Exported Definitions

• load-ace (function)
• load-dne (function)
• load-xmlbif (function)

Internal Definitions

• dimension-list (function)
• dimension-list-but-one (function)
• keyify (function)
• parse-ace-node (function)
• parse-ace-potential (function)
• parse-ace-stream (function)
• parse-netica-net (function)
• parse-netica-node (function)
• parse-netica-stream (function)
• xmlbif-add-definition (function)
• xmlbif-add-variable (function)

4.1.8 cl-bayesnet/src/clique-tree.lisp

Dependency

parse-network.lisp (file)

Parent

src (module)

Location

src/clique-tree.lisp

Internal Definitions

• assign-nodes (function)
• best-root (function)
• clique-tree (function)
• cluster-node (function)
• connect (function)
• cycle (function)
• delete-node (function)
• floyd-warshall (function)
• gen-cliques (function)
• moral (function)
• neighbour (function)
• neighbours (function)
• net-masks (function)
• path (function)
• roots (function)
• sep-cost (function)
• sep-mass (function)
• sep-sets (function)
• traverse (function)
• tree-depth (function)
• weight-cluster (function)

4.1.9 cl-bayesnet/src/message.lisp

Dependency

clique-tree.lisp (file)

Parent

src (module)

Location

src/message.lisp

Exported Definitions

• join-tree (class)
• name (method)
• net (method)
• states (method)

Internal Definitions

• all-sep-sets (method)
• assignment (method)
• assignment (method)
• clean-potential (method)
• cluster (class)
• clusters (method)
• collect-evidence (function)
• consistent (method)
• (setf consistent) (method)
• distribute-evidence (function)
• evi (method)
• (setf evi) (method)
• evi (method)
• index (method)
• join-tree-of (method)
• (setf join-tree-of) (method)
• jt-node (class)
• jt-obs (function)
• jt-prob (function)
• jt-propagate (function)
• jt-retract (function)
• links (method)
• make-join-tree (function)
• make-potential (function)
• marginalise (function)
• mark (method)
• (setf mark) (method)
• mask (method)
• message-pass (generic function)
• message-pass (method)
• nodes (method)
• obs (method)
• (setf obs) (method)
• obs (method)
• (setf obs) (method)
• potential (method)
• (setf potential) (method)
• potential-container (class)
• sep-set (class)

4.1.10 cl-bayesnet/src/evidence.lisp

Dependency

message.lisp (file)

Parent

src (module)

Location

src/evidence.lisp

Exported Definitions

• add-evidence (method)
• clear-evidence (method)
• evidence (method)
• evidence (method)
• evidence-index (method)
• evidence-index (method)
• node (method)
• node (method)
• use-join-tree (function)

Internal Definitions

• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• evidence-1 (method)

4.1.11 cl-bayesnet/src/compiler.lisp

Dependency

evidence.lisp (file)

Parent

src (module)

Location

src/compiler.lisp

Exported Definitions

• instructions (class)
• use-interpreted (function)

Internal Definitions

• *-lookup (method)
• +-lookup (method)
• add-form (function)
• assignment (method)
• (setf assignment) (method)
• best-traversal (function)
• cliques (method)
• (setf cliques) (method)
• form-count (method)
• (setf form-count) (method)
• forms (method)
• (setf forms) (method)
• gen-clique (function)
• gen-evidence (function)
• gen-instructions (function)
• gen-separator (function)
• get-* (function)
• get-+ (function)
• get-match (function)
• interpret (function)
• match (function)
• match-lookup (method)
• post-process-plus (function)
• post-process-times (function)
• push-form (function)
• set-* (function)
• set-+ (function)
• set-match (function)
• tree (method)
• (setf tree) (method)

4.1.12 cl-bayesnet/src/emit-c.lisp

Dependency

compiler.lisp (file)

Parent

src (module)

Location

src/emit-c.lisp

Exported Definitions

use-compiled-c (function)

Internal Definitions

• *gcc-format-string* (special variable)
• emit-c-double (function)
• emit-c-forms (function)
• emit-c-net (function)
• emit-c-preamble (function)

4.1.13 cl-bayesnet/src/test.lisp

Dependency

emit-c.lisp (file)

Parent

src (module)

Location

src/test.lisp

Internal Definitions

• junction-p (function)
• net-graph (function)
• random-evidence (function)
• random-graph (function)
• random-network (function)
• random-prob (function)
• random-table (function)
• test-net-random (function)

5 Packages

Packages are listed by definition order.

5.1 cl-bayesnet

A Common Lisp Bayesian Network Inference Engine

Source

packages.lisp (file)

Nickname

bn

Use List

common-lisp

Exported Definitions

• add-evidence (generic function)
• add-evidence (method)
• add-evidence (method)
• add-evidence (method)
• clear-evidence (generic function)
• clear-evidence (method)
• clear-evidence (method)
• clear-evidence (method)
• evidence (generic function)
• evidence (method)
• evidence (method)
• evidence (method)
• evidence (method)
• (setf evidence) (generic function)
• evidence-index (generic function)
• evidence-index (method)
• evidence-index (method)
• evidence-index (method)
• evidence-index (method)
• instructions (class)
• join-tree (class)
• load-ace (function)
• load-dne (function)
• load-xmlbif (function)
• name (generic function)
• name (method)
• name (method)
• name (method)
• net (generic function)
• net (method)
• net (method)
• net (class)
• node (generic function)
• node (method)
• node (method)
• node (method)
• node (method)
• node (class)
• node-order (generic function)
• node-order (method)
• num-nodes (generic function)
• num-nodes (method)
• num-states (generic function)
• num-states (method)
• parents (generic function)
• parents (method)
• query (function)
• states (generic function)
• states (method)
• states (method)
• use-compiled-c (function)
• use-interpreted (function)
• use-join-tree (function)
• with-evidence (macro)

Internal Definitions

• %evidence (generic function)
• %evidence (method)
• (setf %evidence) (method)
• (setf %evidence) (generic function)
• %evidence-1 (function)
• %query (generic function)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %trie-map-key-value (function)
• %trie-map-trie (function)
• *-lookup (generic function)
• *-lookup (method)
• *calculation-context* (special variable)
• *gcc-format-string* (special variable)
• *temporary-directory* (special variable)
• +-lookup (generic function)
• +-lookup (method)
• +trie-hash-threshold+ (constant)
• add-form (function)
• aif (macro)
• all-sep-sets (generic function)
• all-sep-sets (method)
• assign-nodes (function)
• assignment (generic function)
• assignment (method)
• (setf assignment) (method)
• assignment (method)
• assignment (method)
• (setf assignment) (generic function)
• awhen (macro)
• best (function)
• best-in-array (function)
• best-in-hash (function)
• best-in-list (function)
• best-root (function)
• best-traversal (function)
• clean-potential (generic function)
• clean-potential (method)
• clique-tree (function)
• cliques (generic function)
• cliques (method)
• (setf cliques) (method)
• (setf cliques) (generic function)
• cluster (class)
• cluster-node (function)
• clusters (generic function)
• clusters (method)
• collect-evidence (function)
• compiled (generic function)
• compiled (method)
• (setf compiled) (method)
• (setf compiled) (generic function)
• compose (function)
• connect (function)
• consistent (generic function)
• consistent (method)
• (setf consistent) (method)
• (setf consistent) (generic function)
• copy-array (function)
• copy-trie (function)
• cpt-incf (function)
• cpt-index (function)
• cycle (function)
• degen-prob (function)
• delete-node (function)
• dimension-list (function)
• dimension-list-but-one (function)
• distribute-evidence (function)
• do-trie-branches (macro)
• do-trie-values (macro)
• do-upper (macro)
• edge< (function)
• edge= (function)
• emit-c-double (function)
• emit-c-forms (function)
• emit-c-net (function)
• emit-c-preamble (function)
• evi (generic function)
• evi (method)
• (setf evi) (method)
• evi (method)
• (setf evi) (generic function)
• evidence-1 (generic function)
• evidence-1 (method)
• evidence-1 (method)
• find-temporary-file (function)
• float-to-fixnums (function)
• floyd-warshall (function)
• form-count (generic function)
• form-count (method)
• (setf form-count) (method)
• (setf form-count) (generic function)
• forms (generic function)
• forms (method)
• (setf forms) (method)
• (setf forms) (generic function)
• gen-clique (function)
• gen-cliques (function)
• gen-evidence (function)
• gen-instructions (function)
• gen-parameter (function)
• gen-separator (function)
• get-* (function)
• get-+ (function)
• get-match (function)
• hash-to-trie (function)
• index (generic function)
• index (method)
• index (method)
• (setf index) (method)
• (setf index) (generic function)
• interpret (function)
• join-tree-of (generic function)
• join-tree-of (method)
• (setf join-tree-of) (method)
• (setf join-tree-of) (generic function)
• jt-node (class)
• jt-obs (function)
• jt-prob (function)
• jt-propagate (function)
• jt-retract (function)
• junction-p (function)
• keyify (function)
• links (generic function)
• links (method)
• make-join-tree (function)
• make-potential (function)
• make-trie (function)
• make-trie-hash (function)
• make-vector (function)
• map-int (function)
• map-pairs (function)
• maparray (function)
• marginalise (function)
• mark (generic function)
• mark (method)
• (setf mark) (method)
• (setf mark) (generic function)
• mask (generic function)
• mask (method)
• match (function)
• match-lookup (generic function)
• match-lookup (method)
• message-pass (generic function)
• message-pass (method)
• moral (function)
• multf (macro)
• multiply-floats (macro)
• neighbour (function)
• neighbours (function)
• net-graph (function)
• net-masks (function)
• node-combinations (function)
• node-vec (generic function)
• node-vec (method)
• (setf node-vec) (method)
• (setf node-vec) (generic function)
• nodes (generic function)
• nodes (method)
• nodes (method)
• normalize (function)
• num-arcs (function)
• num-nodes-1 (function)
• num-states-1 (function)
• obs (generic function)
• obs (method)
• (setf obs) (method)
• obs (method)
• (setf obs) (method)
• (setf obs) (generic function)
• order-vector (function)
• parent-indices (generic function)
• parent-indices (method)
• (setf parent-indices) (method)
• (setf parent-indices) (generic function)
• parent-vec (generic function)
• parent-vec (method)
• (setf parent-vec) (method)
• (setf parent-vec) (generic function)
• parse-ace-node (function)
• parse-ace-potential (function)
• parse-ace-stream (function)
• parse-netica-net (function)
• parse-netica-node (function)
• parse-netica-stream (function)
• path (function)
• post-process-plus (function)
• post-process-times (function)
• potential (generic function)
• potential (method)
• (setf potential) (method)
• (setf potential) (generic function)
• potential-container (class)
• preprocess-network (function)
• preprocess-node (function)
• properties (generic function)
• properties (method)
• properties (method)
• push-form (function)
• random-choose (function)
• random-evidence (function)
• random-graph (function)
• random-network (function)
• random-prob (function)
• random-table (function)
• reset-potential (macro)
• returnit (macro)
• roots (function)
• save-evidence (macro)
• sep-cost (function)
• sep-mass (function)
• sep-set (class)
• sep-sets (function)
• set-* (function)
• set-+ (function)
• set-match (function)
• set-name (generic function)
• set-name (method)
• set-name (method)
• set-net (generic function)
• set-net (method)
• set-node-order (generic function)
• set-node-order (method)
• set-parents (generic function)
• set-parents (method)
• set-states (generic function)
• set-states (method)
• shuffle (generic function)
• shuffle (method)
• shuffle (method)
• shuffle (method)
• split (function)
• split-probs (function)
• statep (function)
• sum-floats (macro)
• symmetric (function)
• (setf symmetric) (function)
• table (generic function)
• table (method)
• (setf table) (method)
• (setf table) (generic function)
• table-lookup (function)
• test-net-random (function)
• traverse (function)
• tree (generic function)
• tree (method)
• (setf tree) (method)
• (setf tree) (generic function)
• tree-depth (function)
• trie (structure)
• trie-bottom-p (function)
• trie-branch (function)
• (setf trie-branch) (function)
• trie-branch-count (function)
• trie-branch-values (function)
• trie-clear (function)
• trie-count (function)
• (setf trie-count) (function)
• trie-insert (function)
• trie-list-bottom (function)
• trie-list-depth (function)
• trie-list-values (function)
• trie-map-b (function)
• trie-map-branches (function)
• trie-map-key-value (function)
• trie-map-trie (function)
• trie-map-values (function)
• trie-p (function)
• trie-prune (function)
• trie-search (function)
• trie-test (function)
• (setf trie-test) (function)
• trie-value (function)
• (setf trie-value) (function)
• vecfn (function)
• vlength (macro)
• weight-cluster (function)
• while (macro)
• with-calculation (macro)
• with-calculation-context (macro)
• with-gensyms (macro)
• xmlbif-add-definition (function)
• xmlbif-add-variable (function)

6 Definitions

Definitions are sorted by export status, category, package, and then by lexicographic order.

6.1 Exported definitions

6.1.1 Macros

Macro: with-evidence (NET &rest EVIDENCE) &body BODY

Saves the existing evidence in the net and sets the evidence to evidence. Restores the net to its previous state after leaving the with-evidence block.

Package

cl-bayesnet

Source

bn.lisp (file)

6.1.2 Functions

Function: load-ace FILE

Load a file in ace file format. Returns a net.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: load-dne FILE

Load a file in Netica’s dne file format. Returns a net.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: load-xmlbif FILE

Load a file in xmlbif file format. Returns a net.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: query OBJECT &optional QUERY

Queries a net or node object.

node only - A probability vector for the states of node.

node and integer - The probability the node is in that numbered state (according to (states node)).

node and symbol - The probability the node is in that state.

node and list - A probability vector for the states of node given list, which is a plist of node-state pairs.

net only - The joint probability for the whole net.

net and vector - The joint probability for the whole net, given the vector. Vector has the num-nodes length, and contains either a state number for each node, or -1 if the node state is unknown.

net and symbol - A probability vector for the states of the node designated by symbol.

net and list - The joint probability for the whole net, given list, which is a plist of node-state pairs.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: use-compiled-c NET &optional SOURCE-LOCATION

Writes out arithmetic circuit instructions to a c file, compiles it with gcc, loads the shared object, and prepares the net to use the loaded function. If source-location is specified, writes the c file there. Otherwise uses a temporary file.

Returns the closure used, the raw cffi function pointer, and the number of instructions.

Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: use-interpreted NET

Use interpreted arithmetic circuit instructions for the net. Returns the instructions object.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: use-join-tree NET

Use a join-tree to evaluate this net. Returns the join-tree object.

Package

cl-bayesnet

Source

evidence.lisp (file)

6.1.3 Generic functions

Generic Function: add-evidence OBJECT EVIDENCE

Sets the evidence in a node via state index or symbol. For a net or join-tree, adds the evidence as a plist of node-state pairs.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: add-evidence (JT join-tree) (EVIDENCE list)

Source

evidence.lisp (file)

Method: add-evidence OBJECT EVIDENCE

Method: add-evidence (NET net) (EVIDENCE list)

Generic Function: clear-evidence OBJECT

Clear all evidence from object.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: clear-evidence (JT join-tree)

Source

evidence.lisp (file)

Method: clear-evidence (NET net)

Method: clear-evidence (NODE node)

Generic Function: evidence OBJECT

Returns the evidence in a node as its state symbol (nil if no evidence), and for nets and join-trees a plist of node-state pairs. Settable.

Package

cl-bayesnet

Source

bn.lisp (file)

Writer

(setf evidence) (generic function)

Methods

Method: evidence (NODE jt-node)

Source

evidence.lisp (file)

Method: evidence (JT join-tree)

Source

evidence.lisp (file)

Method: evidence (NET net)

Method: evidence (NODE node)

Generic Function: (setf evidence) EVIDENCE OBJECT

Sets the evidence in a node via state index or symbol. For a net or join-tree, sets the evidence as either a plist of node-state pairs, or a vector of state indices (or -1 for unobserved) corresponding to the net’s node-order.

Package

cl-bayesnet

Source

bn.lisp (file)

Reader

evidence (generic function)

Generic Function: evidence-index OBJECT

Returns the evidence in a node as a state index and nets as a vector of state indices. -1 indicates no evidence.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: evidence-index (NODE jt-node)

Source

evidence.lisp (file)

Method: evidence-index (JT join-tree)

Source

evidence.lisp (file)

Method: evidence-index (NET net)

Method: evidence-index (NODE node)

Generic Function: name NET/NODE

For a net, a string identifier and for a node, a keyword identifier.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: name (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: name (NODE node)

automatically generated reader method

Method: name (NET net)

automatically generated reader method

Generic Function: net NODE/JOIN-TREE

Returns the containing net for a node or join-tree.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: net (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Method: net (NODE node)

automatically generated reader method

Generic Function: node NAME/INDEX NET/JOIN-TREE

Retrieve the node represented by a keyword name or index from the given net or join-tree.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: node (INDEX fixnum) (JT join-tree)

Source

evidence.lisp (file)

Method: node (NAME symbol) (JT join-tree)

Source

evidence.lisp (file)

Method: node (INDEX fixnum) (NET net)

Method: node (NAME symbol) (NET net)

Generic Function: node-order NET

Returns a list of node-names as keywords. The ordering matches their index order. This is set as part of the network compilation process.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: node-order (NET net)

automatically generated reader method

Generic Function: num-nodes NET

The amount of nodes in the network.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: num-nodes (NET net)

automatically generated reader method

Generic Function: num-states NODE

The amount of states for the given node.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: num-states (NODE node)

automatically generated reader method

Generic Function: parents NODE

A vector of parent names as keywords for the given node.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: parents (NODE node)

automatically generated reader method

Generic Function: states NODE

A vector of state names as keywords for the given node.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods

Method: states (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: states (NODE node)

automatically generated reader method

6.1.4 Classes

Class: instructions ()

Package

cl-bayesnet

Source

compiler.lisp (file)

Direct superclasses

standard-object (class)

Direct methods

• initialize-instance (method)
• tree (method)
• tree (method)
• cliques (method)
• cliques (method)
• assignment (method)
• assignment (method)
• form-count (method)
• form-count (method)
• *-lookup (method)
• +-lookup (method)
• match-lookup (method)
• forms (method)
• forms (method)

Direct slots

Slot: forms

Type

list

Readers

forms (generic function)

Writers

(setf forms) (generic function)

Slot: match-lookup

Readers

match-lookup (generic function)

Slot: +-lookup

Readers

+-lookup (generic function)

Slot: *-lookup

Readers

*-lookup (generic function)

Slot: form-count

Type

fixnum

Initform

0

Readers

form-count (generic function)

Writers

(setf form-count) (generic function)

Slot: assignment

Type

(simple-array fixnum *)

Readers

assignment (generic function)

Writers

(setf assignment) (generic function)

Slot: cliques

Type

simple-vector

Readers

cliques (generic function)

Writers

(setf cliques) (generic function)

Slot: tree

Type

simple-vector

Readers

tree (generic function)

Writers

(setf tree) (generic function)

Class: join-tree ()

Package

cl-bayesnet

Source

message.lisp (file)

Direct superclasses

standard-object (class)

Direct methods

• %query (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• evidence (method)
• evidence (method)
• add-evidence (method)
• evidence (method)
• evidence-1 (method)
• evidence-index (method)
• clear-evidence (method)
• node (method)
• node (method)
• message-pass (method)
• evi (method)
• obs (method)
• obs (method)
• assignment (method)
• consistent (method)
• consistent (method)
• all-sep-sets (method)
• links (method)
• clusters (method)
• nodes (method)
• net (method)

Direct slots

Slot: net

Initargs

:net

Readers

net (generic function)

Slot: nodes

Initargs

:nodes

Readers

nodes (generic function)

Slot: clusters

Initargs

:clusters

Readers

clusters (generic function)

Slot: links

Initargs

:links

Readers

links (generic function)

Slot: all-sep-sets

Initargs

:sep-sets

Readers

all-sep-sets (generic function)

Slot: consistent

Readers

consistent (generic function)

Writers

(setf consistent) (generic function)

Slot: assignment

Initargs

:assignment

Readers

assignment (generic function)

Slot: obs

Initargs

:obs

Readers

obs (generic function)

Writers

(setf obs) (generic function)

Slot: evidence

Initargs

:evidence

Readers

evi (generic function)

Class: net ()

Package

cl-bayesnet

Source

bn.lisp (file)

Direct superclasses

standard-object (class)

Direct methods

• initialize-instance (method)
• %query (method)
• %query (method)
• %query (method)
• %query (method)
• evidence-1 (method)
• evidence (method)
• evidence (method)
• add-evidence (method)
• evidence (method)
• evidence-index (method)
• clear-evidence (method)
• node (method)
• node (method)
• properties (method)
• nodes (method)
• node-vec (method)
• node-vec (method)
• num-nodes (method)
• set-node-order (method)
• node-order (method)
• compiled (method)
• compiled (method)
• set-name (method)
• name (method)

Direct slots

Slot: name

Readers

name (generic function)

Writers

set-name (generic function)

Slot: compiled

Readers

compiled (generic function)

Writers

(setf compiled) (generic function)

Slot: node-order

Readers

node-order (generic function)

Writers

set-node-order (generic function)

Slot: num-nodes

Readers

num-nodes (generic function)

Slot: node-vec

Readers

node-vec (generic function)

Writers

(setf node-vec) (generic function)

Slot: nodes

Initform

(make-hash-table)

Readers

nodes (generic function)

Slot: properties

Initform

(make-hash-table)

Readers

properties (generic function)

Class: node ()

Package

cl-bayesnet

Source

bn.lisp (file)

Direct superclasses

standard-object (class)

Direct methods

• %query (method)
• %query (method)
• %query (method)
• %query (method)
• evidence (method)
• evidence (method)
• evidence (method)
• evidence (method)
• evidence-index (method)
• clear-evidence (method)
• properties (method)
• %evidence (method)
• %evidence (method)
• index (method)
• index (method)
• num-states (method)
• parent-indices (method)
• parent-indices (method)
• parent-vec (method)
• parent-vec (method)
• set-parents (method)
• parents (method)
• set-states (method)
• states (method)
• table (method)
• table (method)
• set-net (method)
• net (method)
• set-name (method)
• name (method)

Direct slots

Slot: name

Readers

name (generic function)

Writers

set-name (generic function)

Slot: net

Initargs

:net

Readers

net (generic function)

Writers

set-net (generic function)

Slot: table

Readers

table (generic function)

Writers

(setf table) (generic function)

Slot: states

Readers

states (generic function)

Writers

set-states (generic function)

Slot: parents

Readers

parents (generic function)

Writers

set-parents (generic function)

Slot: parent-vec

Readers

parent-vec (generic function)

Writers

(setf parent-vec) (generic function)

Slot: parent-indices

Type

(simple-array fixnum *)

Readers

parent-indices (generic function)

Writers

(setf parent-indices) (generic function)

Slot: num-states

Readers

num-states (generic function)

Slot: index

Readers

index (generic function)

Writers

(setf index) (generic function)

Slot: evidence

Initform

-1

Readers

%evidence (generic function)

Writers

(setf %evidence) (generic function)

Slot: properties

Initform

(make-hash-table)

Readers

properties (generic function)

6.2 Internal definitions

6.2.1 Constants

Constant: +trie-hash-threshold+

Package

cl-bayesnet

Source

tries.lisp (file)

6.2.2 Special variables

Special Variable: *calculation-context*

Used by with-calculation(-context) to define a limited caching environment.

Package

cl-bayesnet

Source

utils.lisp (file)

Special Variable: *gcc-format-string*

String to pass to format. First arg is source, second is target.

Package

cl-bayesnet

Source

emit-c.lisp (file)

Special Variable: *temporary-directory*

Temporary work directory for C-based network compilation

Package

cl-bayesnet

Source

bn-utils.lisp (file)

6.2.3 Macros

Macro: aif TEST-FORM THEN-FORM &optional ELSE-FORM

Anaphoric if. (lexically sets ’it’ to the test-form, which can then be referenced in then-form and else-form.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: awhen TEST-FORM &body BODY

Anaphoric when. See aif.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: do-trie-branches (NEXT-TRIE TRIE &optional RESULT) &body BODY

Loop over the trie’s branches.

Package

cl-bayesnet

Source

tries.lisp (file)

Macro: do-trie-values (VALUE TRIE &optional RETVAL) &body BODY

Package

cl-bayesnet

Source

tries.lisp (file)

Macro: do-upper (I J LEN &optional RESULT) &body BODY

do for upper triangular i and j. i from 0 to len, j from i+1 to len.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: multf REF MULTIPLIER

(setf ref (* ref multiplier)). Like incf.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: multiply-floats FLOATS

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: reset-potential PLACE

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: returnit VAL &body BODY

An anaphorous macro. binds the first val to ‘it’, allows possible modifications in the body, then returns the values. A more general prog1.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: save-evidence OBJECT &body BODY

Package

cl-bayesnet

Source

bn.lisp (file)

Macro: sum-floats FLOATS

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: vlength VEC

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: while EXPR &body BODY

Continue performing body until expr is false.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: with-calculation LABEL &body BODY

Unless label is nil, caches the calculation performed by body using label. If there is no calculation-context, does not evaluate label, so don’t rely on side effects.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: with-calculation-context (&optional TEST) &body BODY

Defines a calculation context within which calculations performed within with-calculation are cached according to their label.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: with-gensyms (&rest SYMBOLS) &body BODY

Package

cl-bayesnet

Source

utils.lisp (file)

6.2.4 Functions

Function: %evidence-1 NET ARRAY

Package

cl-bayesnet

Source

bn.lisp (file)

Function: %trie-map-key-value FN KEY TRIE NEW-TRIE

Create a new trie with the same structure as trie, applying fn to the key and the old trie node.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: %trie-map-trie FN NEW-TRIE TRIE &rest TRIES

Create a new trie with the same structure as trie, applying fn to each trie-node in turn.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: add-form FORM INS &optional DEPTH

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: assign-nodes NET CLIQUES

Returns an assignment of a clique node for each net node. Since lookup within a clique is sequential, just uses an array of lists. An array of assignments from the node perspective is returned as a second value.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: best SEQ/HASH COMPARE &key KEY

Returns the best value in seq/hash, along with its position (or key for the hash), according to compare. The comparison value is returned as a third value. key extracts the value to be used for comparison.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-in-array ARRAY COMPARE &key KEY

return the best value in array, along with its position and its comparison value. See best.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-in-hash HASH COMPARE &key KEY

return the best value in hash along with its hash-key and its comparison value. See best.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-in-list LIST COMPARE &key KEY

return the best value in list, along with its position and its comparison value. See best.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-root TREE

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: best-traversal NET INS

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: clique-tree NET

Builds a clique-tree for dag. The tree is represented by an upper triangular matrix which has lists of clique-nodes in its diagonal.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: cluster-node GRAPH NODE

Generates a list of added links (node1 . node2) which are necessary to form a cluster around node. Uses an (edge-tree).

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: collect-evidence JT CLUSTER

Package

cl-bayesnet

Source

message.lisp (file)

Function: compose &rest FNS

Create a function which is the composition of the given functions.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: connect GRAPH A B

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: copy-array ARRAY

Package

cl-bayesnet

Source

utils.lisp (file)

Function: copy-trie INSTANCE

Package

cl-bayesnet

Source

tries.lisp (file)

Function: cpt-incf ATT-STATE ATT-MASK

Increments att-state according to att-mask; att-state and att-mask are vectors. att-mask is nil for non-included attributes and the number of values for included attributes. It takes (reduce
#’* (remove nil att-mask)) to iterate through att-state. att-state must be a positive integer below the mask’s value, wherever mask is non-nil.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: cpt-index MASK ATT-STATE

Given the mask and att-state, return an index. Used to map attribute values to a single lookup value in a table.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: cycle GRAPH A

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: degen-prob I LENGTH

Creates a 0-vector of the given length, with the i’th argument set to 1.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: delete-node GRAPH NODE

Remove references to the node from graph. Replaces the node with t

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: dimension-list LIST

Calculates the dimensionality of the list. EG: (make-array (dimension-list list) :initial-contents list)))

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: dimension-list-but-one LIST

Calculates the dimensionality of the list, minus one. EG: (make-array (dimension-list list) :initial-contents list)))

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: distribute-evidence JT CLUSTER

Package

cl-bayesnet

Source

message.lisp (file)

Function: edge< EDGE1 EDGE2

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: edge= EDGE1 EDGE2

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: emit-c-double DOUBLE

Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: emit-c-forms FUNC-NAME NET-SPEC FORMS STREAM

Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: emit-c-net NET STREAM

Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: emit-c-preamble FUNC-NAME NET-SPEC STREAM

Write out the matching function for state and val. Returns 1.0 if state is negative (missing) or state = val. Returns 0.0 otherwise.

Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: find-temporary-file PREFIX SUFFIX &optional DIRECTORY

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: float-to-fixnums FLOAT

This converts a float to a list of fixnums, useful for hashing floats using fixnum-based schemes.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: floyd-warshall GRAPH

This finds all shortest paths in graph. I could make it more efficient by using the fact that the paths are symmetric.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: gen-clique NET INS NET-STATE TRAVERSAL DEPTH

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: gen-cliques NET GRAPH

Graph is an array of (itree), where each tree contains that node’s neighbours. Returns a list of cliques obtained from triangulating the graph. The triangulation can be recovered by starting with a moral graph and ensuring each clique is completely connected. Each clique is an itree of nodes. Destroys graph.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: gen-evidence NET NET-STATE NODE-NUM

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: gen-instructions NET

Generate an arithmetic circuit for the bn represented by a
net (bn.lisp). Note that this version assumes the clique-tree is a single tree (which is correct at 15/12/2007).

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: gen-parameter NET NET-STATE NODE-NUM

Generate a parameter for the net with the given net-state and node-num.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: gen-separator NET INS NET-STATE TRAVERSAL DEPTH

bn - a net object.
clique-tree - a clique-tree built from the bn’s dag. Symmetric array with node-num lists on the diagonal and t where connected. node-assignment - (aref node-assignment node-num) == node’s clique index. net-state - array of the current node states. Nil means the node hasn’t been processed.
traversal - the current traversal to operate on: (clique trav1 ... travn) depth - the current depth of the traversal.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: get-* INS VALS DEPTH

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: get-+ INS VALS DEPTH

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: get-match INS NODE-NUM VALUE

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: hash-to-trie HASH &key TRIE TRIE-KEY TRIE-VALUE BAGP

Add the elements of hash to the given trie (if no trie is given, make one with the same test as the hash table. trie-key (default #’identity) is a function to apply to the hash-key. It should convert the hash-key to a list of atoms which are compatible with the trie’s test. trie-value (default #’identity) is a function to extract the value of interest from the actual value (or the key if bagp is non-nil) held in the hash.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: interpret INS NET-SPEC

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: jt-obs JT NODE-NUM OBS

Enter the observation that node-num is obs.

Package

cl-bayesnet

Source

message.lisp (file)

Function: jt-prob JT NODE-NUM

Calculates the probability of node-num given junction tree jt.

Package

cl-bayesnet

Source

message.lisp (file)

Function: jt-propagate JT

Package

cl-bayesnet

Source

message.lisp (file)

Function: jt-retract JT

Package

cl-bayesnet

Source

message.lisp (file)

Function: junction-p CLIQUES TREE

Test whether the tree is in fact a junction tree, meaning for each pair of cliques, all cliques in between contain their intersection.

Package

cl-bayesnet

Source

test.lisp (file)

Function: keyify STRING

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: make-join-tree NET

Package

cl-bayesnet

Source

message.lisp (file)

Function: make-potential NET CLUSTER ASSIGNMENT

Package

cl-bayesnet

Source

message.lisp (file)

Function: make-trie &key (VALUE VALUE) (COUNT COUNT) (TEST TEST) (BRANCH BRANCH)

Package

cl-bayesnet

Source

tries.lisp (file)

Function: make-trie-hash ALIST &key TEST

Converts a trie alist to a trie-specific hash.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: make-vector LEN &optional INITARG

Package

cl-bayesnet

Source

utils.lisp (file)

Function: map-int FN N

Map fn across integers from 0 below n, returning the results in an (ordered) list.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: map-pairs FN LIST

applies fn to each pair of items and returns a list of the resulting values. > (map-pairs #’cons ’(1 2 3 4))
=> ((1 . 2) (1 . 3) (1 . 4) (2 . 3) (2 . 4) (3 . 4))

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: maparray FN ARRAY

maparray applies fn to all elements in array, returning the result in an array the same dimension as the first array

Package

cl-bayesnet

Source

utils.lisp (file)

Function: marginalise SEP-SET CLUSTER

Return a new potential for sep-set to match cluster.

Package

cl-bayesnet

Source

message.lisp (file)

Function: match VAL1 VAL2

Matches evidence.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: moral NET

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: neighbour GRAPH A B

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: neighbours GRAPH NODE-NUM

Generates a list of neighbours of the node.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: net-graph NET

Output the net’s structure in a viewable form.

Package

cl-bayesnet

Source

test.lisp (file)

Function: net-masks NET CLIQUES TRAVERSAL

Shadowing traversal, returns (tree-node node-mask combinations) for each tree-node in traversal.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: node-combinations INITIAL NODE-MASK

Returns a vector of all node index combinations built from initial. node-mask is a vector which is nil for non-incremented nodes and numstates for included nodes. DEPRECATED for being horribly slow.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: normalize VEC &optional SMOOTHING-FACTOR

Normalize a vector. Optionally adds smoothing-factor (which should be a number) to each element first. If tot is less than or equal to 0.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: num-arcs NET

Package

cl-bayesnet

Source

bn.lisp (file)

Function: num-nodes-1 NET

Package

cl-bayesnet

Source

bn.lisp (file)

Function: num-states-1 NODE

Package

cl-bayesnet

Source

bn.lisp (file)

Function: order-vector END &optional START

Create a vector of length (end - start), filled with numbers from start...(end - 1). Start defaults to 0.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: parse-ace-node NAME LIST

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-ace-potential NET PARENTS DATA-LIST

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-ace-stream STREAM &key NET

Idea taken from trivial-configuration-parser by Brian Mastenbrook.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-netica-net LIST &key NET

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-netica-node NAME LIST

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-netica-stream STREAM &key NET

Idea taken from trivial-configuration-parser by Brian Mastenbrook.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: path GRAPH A B

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: post-process-plus DEPTH ARGS INS

Puts the form in canonical form for insertion.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: post-process-times DEPTH ARGS INS

Puts the form in canonical form for insertion.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: preprocess-network NET

Readies the network for efficient lookup.
Sets a node ordering for the network. Also sets node parent-vec and parent-indices.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: preprocess-node NODE

Store information for efficient lookup.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: push-form FORM INS &optional DEPTH

Pushes a form onto instructions, and returns an index into forms. Won’t actually add a form if a matching one exists (acts like pushnew).

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: random-choose SEQ

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: random-evidence NET &optional NET-SPEC ARR

Package

cl-bayesnet

Source

test.lisp (file)

Function: random-graph NUM-NODES NUM-ARCS &key ENSURE-CONNECTED

Package

cl-bayesnet

Source

test.lisp (file)

Function: random-network MAX-STATES &rest RANDOM-GRAPH-ARGS

Package

cl-bayesnet

Source

test.lisp (file)

Function: random-prob NUM-STATES

Package

cl-bayesnet

Source

test.lisp (file)

Function: random-table NODE

Package

cl-bayesnet

Source

test.lisp (file)

Function: roots GRAPH

Returns the roots of the graph as a list.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: sep-cost A B STATES

Find prod states of x in X + prod states of y in Y. clique1 and clique2 are lists, states is a vector.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: sep-mass A B

Find |intersection| of lists clique1 and clique2

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: sep-sets CLIQUES STATES

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: set-* INS VALS FORM-NUM DEPTH

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: set-+ INS VALS FORM-NUM DEPTH

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: set-match INS NODE-NUM VALUE FORM-NUM

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: split P X

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: split-probs PROBS PROB-LENGTH

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: statep NODE STATE

Package

cl-bayesnet

Source

bn.lisp (file)

Function: symmetric ARRAY X Y

Treat 2D array as a symmetric array. Settable.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Writer

(setf symmetric) (function)

Function: (setf symmetric) VAL ARRAY X Y

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Reader

symmetric (function)

Function: table-lookup TABLE INDICES

Package

cl-bayesnet

Source

bn.lisp (file)

Function: test-net-random NET &optional ITERATIONS

Package

cl-bayesnet

Source

test.lisp (file)

Function: traverse TREE &optional ROOT

Builds a traversal for the undirected tree structure tree. Structure is ;(tree-node subtraversal1 ... subtraversaln)

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: tree-depth TREE ROOT

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: trie-bottom-p TRIE

Returns t if the given trie has no branches.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-branch INSTANCE

Function: (setf trie-branch) VALUE INSTANCE

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-branch-count TRIE

Count the number of branches of trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-branch-values TRIE

Return (key . trie-value) for each branch of trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-clear TRIE

Empties the trie, but leaves the test as is.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-count INSTANCE

Function: (setf trie-count) VALUE INSTANCE

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-insert VALUE TRIE KEY

Insert the value in the trie with the given key. Returns the accessed trie node.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-list-bottom TRIE

List all values at the bottom of the trie (i.e. values of all tries with no branches).

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-list-depth TRIE DEPTH

List all values at the given depth (0 is the top level).

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-list-values TRIE

Recursively list all values in the trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-b FN TRIE

Apply fn to each branch of trie. Returns the trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-branches FN TRIE

Apply fn to each branch of trie. Returns a list of the returned values.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-key-value FN TRIE

Create a new trie with the same structure as trie, applying fn to the key and the old trie node.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-trie FN TRIE &rest TRIES

Apply fn to the given trie and its children, returning the results as the values of a matching trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-values FN TRIE

Apply fn to the given trie’s non-nil values, returning the results as the values of a matching trie.

Package

cl-bayesnet

Source

tries.lisp (file)