dds/example/example.org

Examples of usage of dds

• Introduction
• Org-mode, Racket, and dds <<intro>>
  • Importing a module from file
  • Output formats for results of evaluation of code blocks
    • A note about printing update function forms
  • Reading Org-mode tables<<tabread>>
  • Inline graph visualisation with Graphviz
• dds/networks
  • Boolean networks
  • Network functions
• Reaction systems

Introduction

This document shows some examples of usage of the modules in dds with Org-mode. It relies on emacs-ob-racket.

The following section describes how Org-mode can interact with Racket, and how this interaction can be used for a fluid workflow with dds. In particular, the code block munch-sexp is defined in this section.

The subsequent sections show off some the functionalities of the submodules of dds.

Org-mode, Racket, and dds <<intro>>

Importing a module from file

To require the modules from the files of dds, you can use the following code (I only reset the prelude here because I set at the top of this file):

#lang racket
(require (file "~/Candies/prj/racket/dds/networks.rkt"))
(require (file "~/Candies/prj/racket/dds/utils.rkt"))

Note that this code will not work with :results value. I think it is because in this case the code is not really evaluated at top level.

These initialisation lines can be put into the prologue of every code block in a subtree by setting :prologue via :header-args:racket: in the properties drawer. Check out the properties drawer of this section for an example.

Alternatively, this property can be set via a #+PROPERTY line at the top the file. For example, this file has such a line. Whenever this property line changes, refresh the setup of the file by hitting C-c C-c on the property line. This will update the prologue for all racket code blocks.

Finally, you can also set :prologue (and other properties with long values) in the following way:

(st '((a . 1)))

'#hash((a . 1))

Output formats for results of evaluation of code blocks

This section of the Org manual describes various different formats for presenting the results of code blocks. I find the following three particularly useful as of [2020-02-22 Sat]: output, list, and table.

The output result format is the simplest and the most natural ones. It works as if the code block were inserted into a module which would then be evaluated.

(println "This is the first line of output.")
(println (+ 1 2))
(println "This the third line of output.")

"This is the first line of output." 3 "This the third line of output."

The list result format typesets the result of the last line in the code block as a list:

'(1 "hello" (and x y))

• 1
• "hello"
• (and x y)

Note how nested lists are not recursively shown as nested Org-mode lists.

For some reason, the list output format does not work with the result drawer:

'(1 "hello" (and x y))

• (1 "\"hello\"" (and x y))

Finally, the table result format typesets the output as a table:

'((a . #t) (b . #f))

a	#t
b	#f

This is clearly very useful for printing states (and hash tables, more generally):

(st '((a . 1) (b . #f) (c . "hello")))

a	1
b	#f
c	"hello"

A note about printing update function forms

Automatic table typesetting may go in the way of readability for hash tables whose values are lists, as the following example shows:

#hash((a . (and a b)) (b . (not b)))

a	and	a	b
b	not	b

To tackle this issue, dds/utils provides stringify-variable-mapping (with the shortcut sgfy) which converts all the values of a given variable mapping to strings:

(sgfy #hash((a . (and a b)) (b . (not b))))

a	"(and a b)"
b	"(not b)"

Reading Org-mode tables<<tabread>>

Org-mode allows supplying tables as arguments for code blocks.

a	"(and a b)"
b	(or b (not a))

tab

((a (and a b)) (b (or b (not a))))

Unfortunately, the same trick does not work with Racket directly, because Racket interprets the first elements in the parentheses as function applications:

tab

application: not a procedure; expected a procedure that can be applied to arguments given: "a" arguments…: "(and a b)" context…: "/tmp/babel-qkvrRR/org-babel-c4wuju.rkt": [running body] temp37_0 for-loop run-module-instance!125 perform-require!78

Fortunately, we can easily remedy this problem by creating a named parameterised Elisp source block which will explicitly convert the table to a string:

(prin1 sexp)

(("a" "(and a b)") ("b" "(or b (not a))"))

We can now correctly receive this table in a Racket source code block by threading it through munch-sexp:

(println tab)

"((\"a\" \"(and a b)\") (\"b\" \"(or b (not a))\"))"

dds/utils has several functions for parsing such strings, and notably read-org-variable-mapping, with the shortcut unorg:

(unorg tab)

'#hash((a . (and a b)) (b . (or b (not a))))

Of course, we can use munch-sexp to prepare any other table than test-table for use with Racket:

a	(not a)
b	(and a c)
c	(and a (not b))

(unorg tab)

'#hash((a . (not a)) (b . (and a c)) (c . (and a (not b))))

Inline graph visualisation with Graphviz

Some functions in dds build graphs:

(build-interaction-graph (unorg bf))

#<unweighted-graph>

The graph library allows building a Graphviz description of the constructed graph. (Note that you have to install the graph library by running raco pkg install graph and require it. The long property line at the top of this file defining the prologue for racket source code blocks takes care of requiring graph.)

(display (graphviz (build-interaction-graph (unorg bf))))

digraph G { node0 [label="c"]; node1 [label="b"]; node2 [label="a"]; subgraph U { edge [dir=none]; node0 -> node1; node2 -> node2; } subgraph D { node2 -> node0; node2 -> node1; } }

You can have an inline drawing of this graph by calling the previous code block (igraph) via a noweb reference in Graphviz/DOT source block:

<<igraph()>>

Note that the graph library draws self-loops as undirected edges. It also draws double-sided edges as undirected edges (e.g., in the preceding graph, b depends on c and c depends on b).

dds/networks

The dds/networks is a module for working with different network models. A network is a set of variables which are updated according to their corresponding update functions. The variables to be updated at each step are given by the mode. This model can generalise Boolean networks, TBANs, multivalued networks, etc.

Boolean networks

Consider the following Boolean network:

a	b
b	(and (not a) c)
c	(not c)

Note that if you define the formula of a as 0, it will set a to 1, because 0 is not #f. For example, (if 0 1 2) evaluates to 1, and not to 2.

Here's the unsigned interaction graph of this network:

(dotit (build-interaction-graph (unorg simple-bn)))

<<simple-bn-ig()>>

Here's the signed interaction graph of this network:

(dotit (build-boolean-signed-interaction-graph (unorg simple-bn)))

<<simple-bn-sig()>>

For the interaction a → b, note indeed that when c is #f, b is always #f (positive interaction). On the other hand, when c is #t, b becomes (not a) (negative interaction). Therefore, the influence of a on b is neither activating nor inhibiting.

Here is the full state graph of this network under the asynchronous dynamics:

(let* ([bn (nn (unorg simple-bn))]
    [bn-asyn (make-asyn-dynamics bn)])
(dotit (ppsg (build-full-boolean-state-graph bn-asyn))))

<<simple-bn-sg()>>

Alternatively, you may prefer a slighty more compact representation of Boolean values as 0 and 1:

(let* ([bn (nn (unorg simple-bn))]
    [bn-asyn (make-asyn-dynamics bn)])
(dotit (ppsgb (build-full-boolean-state-graph bn-asyn))))

<<simple-bn-sg-bool()>>

Consider the following state (appearing in the upper left corner of the state graph):

a	0
c	1
b	1

These are the states which can be reached from it in at most 2 steps:

(let* ([bn (nn (unorg simple-bn))]
    [bn-asyn (make-asyn-dynamics bn)]
    [s0 (stb (unorg some-state))])
(dotit (ppsgb (dds-build-n-step-state-graph bn-asyn (set s0) 2))))

<<simple-bn-some-state()>>

Here is the complete state graph with edges annotated with the modality leading to the update.

(let* ([bn (nn (unorg simple-bn))]
    [bn-asyn (make-asyn-dynamics bn)])
(dotit (ppsgb (build-full-boolean-state-graph-annotated bn-asyn))))

<<simple-bn-sg-bool-ann()>>

For some networks, a single transition between two states may be due to different modalities. Consider the following network:

a	(not b)
b	b

(let* ([bn (nn (unorg input-bn))]
    [bn-asyn (make-asyn-dynamics bn)])
(dotit (ppsgb (build-full-boolean-state-graph-annotated bn-asyn))))

<<bn2-sgr()>>

Network functions

dds/networks provides some basic primitives for working with individual functions which may appear in a network model. Clearly, these primitives can be applied in contexts not necessarily directly related to networks.

Here's how you can tabulate a function. The domain of x is {1, 2}, and the domain of y is {0, 2, 4}. The first column in the output corresponds to x, the second to y, and the third corresponds to the value of the function.

(tabulate (λ (x y) (+ x y)) '(1 2) '(0 2 4))

1	0	1
1	2	3
1	4	5
2	0	2
2	2	4
2	4	6

Here's how you tabulate a Boolean function:

(tabulate/boolean (λ (x y) (and x y)))

#f	#f	#f
#f	#t	#f
#t	#f	#f
#t	#t	#t

Reaction systems

Consider the following reaction system:

a	x t	y	z
b	x	q	z

Here is how we read this reaction into Racket code:

(unorg-rs input-rs)

(hash 'a (reaction (set 'x 't) (set 'y) (set 'z)) 'b (reaction (set 'x) (set 'q) (set 'z)))

Here is how we can put it back into an Org-mode table:

(org-rs (unorg-rs input-rs))

a	"t x"	"y"	"z"
b	"x"	"q"	"z"

Here is how we can apply this reaction system to a state:

(let ([rs (unorg-rs input-rs)])
(apply-rs rs (set 'x 't)))

(set 'z)

Let's see which reactions got applied:

(let ([rs (unorg-rs input-rs)])
(list-enabled rs (set 'x 't)))

• a
• b

You can also give a name to a list and read it with munch-sexp:

• x y
• z
• t

(read-ctx input-ctx)

(list (set 'x 'y) (set 'z) (set) (set 't))

Let's see what the evolution of rs1 looks like with the context sequence ctx1.

(dotit (ppsg (build-interactive-process-graph (unorg-rs input-rs) (read-ctx input-ctx))))

digraph G { node0 [label="C:{}{t}\nD:{}"]; node1 [label="C:{z}{}{t}\nD:{z}"]; node2 [label="C:{t}\nD:{}"]; node3 [label="C:{x y}{z}{}{t}\nD:{}"]; node4 [label="C:\nD:{}"]; subgraph U { edge [dir=none]; node4 -> node4 [label="{}"]; } subgraph D { node0 -> node2 [label="{}"]; node1 -> node0 [label="{}"]; node2 -> node4 [label="{}"]; node3 -> node1 [label="{b}"]; } }

<<rs1-sgr()>>

Note that we need to keep the full context sequence in the name of each state to avoid merging states with the same result and contexts, but which occur at different steps of the evolution.

The graphical presentation for interactive processes is arguably less readable than just listing the contexts and the results explicitly. Here is how you can do it.

(build-interactive-process (unorg-rs input-rs) (read-ctx input-ctx))

(y x)	nil
(z)	(z)
nil	nil
(t)	nil
nil	nil

The first column of this table shows the current context. The second column shows the result of application of the reactions to the previous state. The interactive process contains one more step with respect to the context sequence. This is to show the effect of the last context.

Note that empty sets are printed as nil.