Merge branch 'network-domains'
This commit is contained in:
Sergiu Ivanov
commit
34fe8a8316
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@ -0,0 +1,47 @@
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@ -436,7 +436,12 @@ tab
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|||
Here's the unsigned syntactic interaction graph of this network:
|
||||
#+NAME: simple-bn-syig
|
||||
#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
|
||||
(dotit (build-syntactic-interaction-graph (unorgv simple-bn)))
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||||
((compose
|
||||
dotit
|
||||
build-syntactic-interaction-graph
|
||||
make-boolean-network-form
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||||
unorgv)
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||||
simple-bn)
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||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/examplejTo8XT.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
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@ -461,7 +466,12 @@ tab
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|||
time constructed according to the canonical definition:
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||||
#+NAME: simple-bn-ig
|
||||
#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
|
||||
(dotit (build-interaction-graph/form (unorgv simple-bn) (make-boolean-domains '(a b c))))
|
||||
((compose
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||||
dotit
|
||||
build-interaction-graph/form
|
||||
make-boolean-network-form
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||||
unorgv)
|
||||
simple-bn)
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||||
#+END_SRC
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||||
|
||||
#+BEGIN_SRC dot :file dots/example1FH1rZ.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
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@ -486,7 +496,12 @@ tab
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|||
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||||
#+NAME: simple-bn-sig
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||||
#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
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||||
(dotit (build-signed-interaction-graph/form (unorgv simple-bn) (make-boolean-domains '(a b c))))
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||||
((compose
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||||
dotit
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||||
build-signed-interaction-graph/form
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||||
make-boolean-network-form
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||||
unorgv)
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||||
simple-bn)
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||||
#+END_SRC
|
||||
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||||
#+BEGIN_SRC dot :file dots/exampledpQygl.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
|
@ -502,28 +517,37 @@ tab
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|||
dynamics:
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||||
#+NAME: simple-bn-sg
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||||
#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
|
||||
(let* ([bn (network-form->network (unorgv simple-bn))]
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||||
[bn-asyn (make-asyn-dynamics bn)])
|
||||
(dotit (pretty-print-state-graph (build-full-boolean-state-graph bn-asyn))))
|
||||
((compose
|
||||
dotit
|
||||
pretty-print-state-graph
|
||||
build-full-state-graph
|
||||
make-asyn-dynamics
|
||||
forms->boolean-network
|
||||
unorgv)
|
||||
simple-bn)
|
||||
#+END_SRC
|
||||
|
||||
|
||||
#+BEGIN_SRC dot :file dots/examplem7LpTs.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
<<simple-bn-sg()>>
|
||||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
[[file:dots/examplem7LpTs.svg]]
|
||||
:END:
|
||||
:end:
|
||||
|
||||
Alternatively, you may prefer a slighty more compact representation
|
||||
of Boolean values as 0 and 1:
|
||||
#+NAME: simple-bn-sg-bool
|
||||
#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
|
||||
(let* ([bn (network-form->network (unorgv simple-bn))]
|
||||
[bn-asyn (make-asyn-dynamics bn)])
|
||||
(dotit (pretty-print-boolean-state-graph (build-full-boolean-state-graph bn-asyn))))
|
||||
((compose
|
||||
dotit
|
||||
pretty-print-boolean-state-graph
|
||||
build-full-state-graph
|
||||
make-asyn-dynamics
|
||||
forms->boolean-network
|
||||
unorgv)
|
||||
simple-bn)
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/examplex1Irnk.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
|
@ -531,9 +555,9 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
[[file:dots/examplex1Irnk.svg]]
|
||||
:END:
|
||||
:end:
|
||||
|
||||
Consider the following state (appearing in the upper left corner of
|
||||
the state graph):
|
||||
|
|
@ -549,7 +573,7 @@ tab
|
|||
#+HEADER: :var simple-bn=munch-sexp(simple-bn)
|
||||
#+HEADER: :var some-state=munch-sexp(some-state)
|
||||
#+BEGIN_SRC racket :results silent
|
||||
(let* ([bn (network-form->network (unorgv simple-bn))]
|
||||
(let* ([bn (forms->boolean-network (unorgv simple-bn))]
|
||||
[bn-asyn (make-asyn-dynamics bn)]
|
||||
[s0 (booleanize-state (unorgv some-state))])
|
||||
(dotit (pretty-print-boolean-state-graph (dds-build-n-step-state-graph bn-asyn (set s0) 2))))
|
||||
|
|
@ -560,17 +584,22 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
[[file:dots/examplecHA6gL.svg]]
|
||||
:END:
|
||||
:end:
|
||||
|
||||
Here is the complete state graph with edges annotated with the
|
||||
modality leading to the update.
|
||||
#+NAME: simple-bn-sg-bool-ann
|
||||
#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
|
||||
(let* ([bn (network-form->network (unorgv simple-bn))]
|
||||
[bn-asyn (make-asyn-dynamics bn)])
|
||||
(dotit (pretty-print-boolean-state-graph (build-full-boolean-state-graph-annotated bn-asyn))))
|
||||
((compose
|
||||
dotit
|
||||
pretty-print-boolean-state-graph
|
||||
build-full-state-graph-annotated
|
||||
make-asyn-dynamics
|
||||
forms->boolean-network
|
||||
unorgv)
|
||||
simple-bn)
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/examplei4we6j.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
|
@ -590,9 +619,14 @@ tab
|
|||
|
||||
#+NAME: bn2-sgr
|
||||
#+BEGIN_SRC racket :results silent :var input-bn=munch-sexp(bn2)
|
||||
(let* ([bn (network-form->network (unorgv input-bn))]
|
||||
[bn-asyn (make-asyn-dynamics bn)])
|
||||
(dotit (pretty-print-boolean-state-graph (build-full-boolean-state-graph-annotated bn-asyn))))
|
||||
((compose
|
||||
dotit
|
||||
pretty-print-boolean-state-graph
|
||||
build-full-state-graph-annotated
|
||||
make-asyn-dynamics
|
||||
forms->boolean-network
|
||||
unorgv)
|
||||
input-bn)
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/examplehsuRqc.svg :results raw drawer :cmd dot :noweb yes
|
||||
|
|
@ -615,14 +649,14 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
| 1 | 0 | 1 |
|
||||
| 1 | 2 | 3 |
|
||||
| 1 | 4 | 5 |
|
||||
| 2 | 0 | 2 |
|
||||
| 2 | 2 | 4 |
|
||||
| 2 | 4 | 6 |
|
||||
:END:
|
||||
:end:
|
||||
|
||||
Here's how you tabulate a Boolean function:
|
||||
#+BEGIN_SRC racket :results table drawer
|
||||
|
|
@ -630,12 +664,12 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
| #f | #f | #f |
|
||||
| #f | #t | #f |
|
||||
| #t | #f | #f |
|
||||
| #t | #t | #t |
|
||||
:END:
|
||||
:end:
|
||||
|
||||
You can tabulate multiple functions taking the same arguments over
|
||||
the same domains together.
|
||||
|
|
@ -644,21 +678,21 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
| #f | #f | #f | #f |
|
||||
| #f | #t | #f | #t |
|
||||
| #t | #f | #f | #t |
|
||||
| #t | #t | #t | #t |
|
||||
:END:
|
||||
:end:
|
||||
|
||||
Here's how to tabulate the network =simple-bn=, defined at the top
|
||||
of this section:
|
||||
#+BEGIN_SRC racket :results table drawer :var in-bn=munch-sexp(simple-bn)
|
||||
(tabulate-boolean-network (network-form->network (unorgv in-bn)))
|
||||
(tabulate-network (forms->boolean-network (unorgv in-bn)))
|
||||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
| a | b | c | f-a | f-b | f-c |
|
||||
| #f | #f | #f | #f | #f | #t |
|
||||
| #f | #f | #t | #f | #t | #f |
|
||||
|
|
@ -668,7 +702,7 @@ tab
|
|||
| #t | #f | #t | #f | #f | #f |
|
||||
| #t | #t | #f | #t | #f | #t |
|
||||
| #t | #t | #t | #t | #f | #f |
|
||||
:END:
|
||||
:end:
|
||||
|
||||
** Random functions and networks
|
||||
To avoid having different results every time a code block in this
|
||||
|
|
@ -691,7 +725,7 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
| a | b | c | f |
|
||||
| #f | 1 | cold | 4 |
|
||||
| #f | 1 | hot | 5 |
|
||||
|
|
@ -701,17 +735,17 @@ tab
|
|||
| #t | 1 | hot | 6 |
|
||||
| #t | 2 | cold | 4 |
|
||||
| #t | 2 | hot | 5 |
|
||||
:END:
|
||||
:end:
|
||||
|
||||
We can build an entire random network over these domains:
|
||||
#+BEGIN_SRC racket :results table drawer :var simple-domains=munch-sexp(simple-domains)
|
||||
(random-seed 0)
|
||||
(define n (random-network (unorgv simple-domains)))
|
||||
(tabulate-network n (unorgv simple-domains))
|
||||
(tabulate-network n)
|
||||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
| a | b | c | f-a | f-b | f-c |
|
||||
| #f | 1 | cold | #f | 2 | hot |
|
||||
| #f | 1 | hot | #f | 2 | cold |
|
||||
|
|
@ -721,7 +755,7 @@ tab
|
|||
| #t | 1 | hot | #t | 1 | cold |
|
||||
| #t | 2 | cold | #f | 2 | hot |
|
||||
| #t | 2 | hot | #t | 1 | cold |
|
||||
:END:
|
||||
:end:
|
||||
|
||||
Let's snapshot this random network and give it a name.
|
||||
#+NAME: rnd-network
|
||||
|
|
@ -735,16 +769,16 @@ tab
|
|||
| #t | 2 | cold | #f | 2 | hot |
|
||||
| #t | 2 | hot | #t | 1 | cold |
|
||||
|
||||
Here's how we can read back this table as a Boolean network:
|
||||
Here's how we can read back this table as a network:
|
||||
#+HEADER: :var rnd-network=munch-sexp(rnd-network)
|
||||
#+BEGIN_SRC racket :results output drawer
|
||||
(string->any rnd-network)
|
||||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
'(("a" "b" "c" "f-a" "f-b" "f-c") ("#f" 1 "cold" "#f" 2 "hot") ("#f" 1 "hot" "#f" 2 "cold") ("#f" 2 "cold" "#t" 1 "cold") ("#f" 2 "hot" "#t" 2 "hot") ("#t" 1 "cold" "#f" 2 "cold") ("#t" 1 "hot" "#t" 1 "cold") ("#t" 2 "cold" "#f" 2 "hot") ("#t" 2 "hot" "#t" 1 "cold"))
|
||||
:END:
|
||||
:end:
|
||||
|
||||
You can use =table->network= to convert a table such as [[rnd-network][rnd-network]]
|
||||
to a network.
|
||||
|
|
@ -754,19 +788,23 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
'#hash((a . #<procedure:...dds/networks.rkt:518:4>) (b . #<procedure:...dds/networks.rkt:518:4>) (c . #<procedure:...dds/networks.rkt:518:4>))
|
||||
:END:
|
||||
:results:
|
||||
(network '#hash((a . #<procedure:...ds/functions.rkt:145:4>) (b . #<procedure:...ds/functions.rkt:145:4>) (c . #<procedure:...ds/functions.rkt:145:4>)) '#hash((a . (#f #t)) (b . (1 2)) (c . (cold hot))))
|
||||
:end:
|
||||
|
||||
Here's the state graph of [[rnd-network][rnd-network]].
|
||||
#+NAME: rnd-network-sg
|
||||
#+HEADER: :var rnd-network=munch-sexp(rnd-network)
|
||||
#+HEADER: :var simple-domains=munch-sexp(simple-domains)
|
||||
#+BEGIN_SRC racket :results silent drawer
|
||||
(define n (table->network (unorg rnd-network)))
|
||||
(define rnd-asyn (make-asyn-dynamics n))
|
||||
(define states (list->set (build-all-states (unorgv simple-domains))))
|
||||
(dotit (pretty-print-state-graph (dds-build-state-graph-annotated rnd-asyn states)))
|
||||
((compose
|
||||
dotit
|
||||
pretty-print-state-graph
|
||||
build-full-state-graph-annotated
|
||||
make-asyn-dynamics
|
||||
table->network
|
||||
unorg)
|
||||
rnd-network)
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/exampleHc023j.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
|
@ -774,17 +812,21 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
[[file:dots/exampleHc023j.svg]]
|
||||
:END:
|
||||
:end:
|
||||
|
||||
Here's the signed interaction graph of [[rnd-network][rnd-network]].
|
||||
#+NAME: rnd-network-ig
|
||||
#+HEADER: :var rnd-network=munch-sexp(rnd-network)
|
||||
#+HEADER: :var simple-domains=munch-sexp(simple-domains)
|
||||
#+BEGIN_SRC racket :results silent drawer
|
||||
(define n (table->network (unorg rnd-network)))
|
||||
(dotit (build-signed-interaction-graph n (unorgv simple-domains)))
|
||||
((compose
|
||||
dotit
|
||||
build-signed-interaction-graph
|
||||
table->network
|
||||
unorg)
|
||||
rnd-network)
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/examplePIN5ac.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
|
@ -792,13 +834,9 @@ tab
|
|||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
:RESULTS:
|
||||
:results:
|
||||
[[file:dots/examplePIN5ac.svg]]
|
||||
:END:
|
||||
|
||||
Note that =build-signed-interaction-graph= only includes the + and
|
||||
the - arcs in the graph, as it does not have access to the symbolic
|
||||
description of the function.
|
||||
:end:
|
||||
|
||||
** Standalone threshold Boolean functions (TBF)
|
||||
/Note:/ Before using the objects described in this section,
|
||||
|
|
@ -1071,7 +1109,11 @@ tab
|
|||
|
||||
#+NAME: tbfs-nots-sg
|
||||
#+BEGIN_SRC racket :results silent drawer :var tbfs-nots=munch-sexp(tbfs-nots)
|
||||
(dotit (build-tbn-state-graph (read-org-tbn tbfs-nots)))
|
||||
((compose
|
||||
dotit
|
||||
build-tbn-state-graph
|
||||
read-org-tbn)
|
||||
tbfs-nots)
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/examplew206DH.svg :results raw drawer :cmd sfdp :noweb yes
|
||||
|
|
@ -1174,7 +1216,12 @@ tab
|
|||
|
||||
#+NAME: tbfs-nots-ig-pp
|
||||
#+BEGIN_SRC racket :results silent drawer :var tbfs-nots=munch-sexp(tbfs-nots)
|
||||
(dotit (pretty-print-tbn-interaction-graph (tbn-interaction-graph (read-org-tbn tbfs-nots))))
|
||||
((compose
|
||||
dotit
|
||||
pretty-print-tbn-interaction-graph
|
||||
tbn-interaction-graph
|
||||
read-org-tbn)
|
||||
tbfs-nots)
|
||||
#+END_SRC
|
||||
|
||||
#+BEGIN_SRC dot :file dots/exampleQLHMVK.svg :results raw drawer :cmd dot :noweb yes
|
||||
|
|
|
|||
435
networks.rkt
435
networks.rkt
|
|
@ -18,25 +18,30 @@
|
|||
(contract-out [struct tbf/state ([weights (hash/c variable? number?)]
|
||||
[threshold number?])]
|
||||
[struct dynamics ([network network?]
|
||||
[mode mode?])])
|
||||
[mode mode?])]
|
||||
[struct network ([functions (hash/c variable? procedure?)]
|
||||
[domains domain-mapping/c])]
|
||||
[struct network-form ([forms variable-mapping?]
|
||||
[domains domain-mapping/c])])
|
||||
;; Functions
|
||||
(contract-out [update (-> network? state? (set/c variable? #:kind 'dont-care) state?)]
|
||||
(contract-out [make-boolean-network (-> (hash/c variable? procedure?) network?)]
|
||||
[make-01-network (-> (hash/c variable? procedure?) network?)]
|
||||
[update (-> network? state? (set/c variable? #:kind 'dont-care) state?)]
|
||||
[make-state (-> (listof (cons/c symbol? any/c)) state?)]
|
||||
[make-state-booleanize (-> (listof (cons/c symbol? (or/c 0 1))) state?)]
|
||||
[booleanize-state (-> state? state?)]
|
||||
[make-network-from-functions (-> (listof (cons/c symbol? update-function/c)) network?)]
|
||||
[update-function-form->update-function (-> update-function-form? update-function/c)]
|
||||
[network-form->network (-> network-form? network?)]
|
||||
[make-network-from-forms (-> (listof (cons/c symbol? update-function-form?))
|
||||
network?)]
|
||||
[make-boolean-network-form (-> variable-mapping? network-form?)]
|
||||
[forms->boolean-network (-> variable-mapping? network?)]
|
||||
[list-syntactic-interactions (-> network-form? variable? (listof variable?))]
|
||||
[build-syntactic-interaction-graph (-> network-form? graph?)]
|
||||
[interaction? (-> network? domain-mapping/c variable? variable? boolean?)]
|
||||
[get-interaction-sign (-> network? domain-mapping/c variable? variable? (or/c #f -1 0 1))]
|
||||
[build-interaction-graph (-> network? domain-mapping/c graph?)]
|
||||
[build-interaction-graph/form (-> network-form? domain-mapping/c graph?)]
|
||||
[build-signed-interaction-graph (-> network? domain-mapping/c graph?)]
|
||||
[build-signed-interaction-graph/form (-> network-form? domain-mapping/c graph?)]
|
||||
[interaction? (-> network? variable? variable? boolean?)]
|
||||
[get-interaction-sign (-> network? variable? variable? (or/c #f -1 0 1))]
|
||||
[build-interaction-graph (-> network? graph?)]
|
||||
[build-interaction-graph/form (-> network-form? graph?)]
|
||||
[build-signed-interaction-graph (-> network? graph?)]
|
||||
[build-signed-interaction-graph/form (-> network-form? graph?)]
|
||||
[build-all-states (-> domain-mapping/c (listof state?))]
|
||||
[make-same-domains (-> (listof variable?) generic-set? domain-mapping/c)]
|
||||
[make-boolean-domains (-> (listof variable?) (hash/c variable? (list/c #f #t)))]
|
||||
|
|
@ -48,8 +53,6 @@
|
|||
[make-dynamics-from-func (-> network? (-> (listof variable?) mode?) dynamics?)]
|
||||
[make-asyn-dynamics (-> network? dynamics?)]
|
||||
[make-syn-dynamics (-> network? dynamics?)]
|
||||
[read-org-network-make-asyn (-> string? dynamics?)]
|
||||
[read-org-network-make-syn (-> string? dynamics?)]
|
||||
[dds-step-one (-> dynamics? state? (set/c state?))]
|
||||
[dds-step-one-annotated (-> dynamics? state? (set/c (cons/c modality? state?)))]
|
||||
[dds-step (-> dynamics? (set/c state? #:kind 'dont-care) (set/c state?))]
|
||||
|
|
@ -64,10 +67,8 @@
|
|||
[ppsg (-> graph? graph?)]
|
||||
[pretty-print-boolean-state-graph (-> graph? graph?)]
|
||||
[ppsgb (-> graph? graph?)]
|
||||
[build-full-boolean-state-graph (-> dynamics? graph?)]
|
||||
[build-full-boolean-state-graph-annotated (-> dynamics? graph?)]
|
||||
[build-full-01-state-graph (-> dynamics? graph?)]
|
||||
[build-full-01-state-graph-annotated (-> dynamics? graph?)]
|
||||
[build-full-state-graph (-> dynamics? graph?)]
|
||||
[build-full-state-graph-annotated (-> dynamics? graph?)]
|
||||
[tabulate-state (->* (procedure? domain-mapping/c) (#:headers boolean?)
|
||||
(listof (listof any/c)))]
|
||||
[tabulate-state* (->* ((non-empty-listof procedure?) domain-mapping/c) (#:headers boolean?)
|
||||
|
|
@ -76,10 +77,8 @@
|
|||
(listof (listof any/c)))]
|
||||
[tabulate-state*/boolean (->* ((non-empty-listof procedure?) (listof variable?)) (#:headers boolean?)
|
||||
(listof (listof any/c)))]
|
||||
[tabulate-network (->* (network? domain-mapping/c) (#:headers boolean?)
|
||||
[tabulate-network (->* (network?) (#:headers boolean?)
|
||||
(listof (listof any/c)))]
|
||||
[tabulate-boolean-network (->* (network?) (#:headers boolean?)
|
||||
(listof (listof any/c)))]
|
||||
[table->network (->* ((listof (*list/c any/c any/c))) (#:headers boolean?) network?)]
|
||||
[random-function/state (domain-mapping/c generic-set? . -> . procedure?)]
|
||||
[random-boolean-function/state ((listof variable?) . -> . procedure?)]
|
||||
|
|
@ -138,7 +137,6 @@
|
|||
(contract-out [variable? (-> any/c boolean?)]
|
||||
[state? (-> any/c boolean?)]
|
||||
[update-function-form? (-> any/c boolean?)]
|
||||
[network-form? (-> any/c boolean?)]
|
||||
[modality? (-> any/c boolean?)]
|
||||
[mode? (-> any/c boolean?)]
|
||||
[sbf/state? (-> any/c boolean?)])
|
||||
|
|
@ -173,20 +171,46 @@
|
|||
;;; state.
|
||||
(define update-function/c (-> state? any/c))
|
||||
|
||||
;;; A network is a mapping from its variables to its update functions.
|
||||
;;; A domain mapping is a hash set mapping variables to the lists of
|
||||
;;; values in their domains.
|
||||
(define domain-mapping/c (hash/c variable? list?))
|
||||
|
||||
;;; A network consists of a mapping from its variables to its update
|
||||
;;; variables, as a well as of a mapping from its variables to
|
||||
;;; their domains.
|
||||
;;;
|
||||
;;; Note that the domains of the variables of the network are not part
|
||||
;;; of the network definition. This is because the variables of some
|
||||
;;; networks may have infinite domains, which can be restricted in
|
||||
;;; multiple different ways.
|
||||
(define network? (hash/c variable? procedure?))
|
||||
;;; The domain mapping does not have to assign domains to all
|
||||
;;; variables (e.g., it may be empty), but in this case the functions
|
||||
;;; which need to know the domains will not work.
|
||||
(struct network (functions domains) #:transparent)
|
||||
|
||||
;;; Builds a network from a given hash table assigning functions to
|
||||
;;; variables by attributing Boolean domains to every variable.
|
||||
(define (make-boolean-network funcs)
|
||||
(network funcs (make-boolean-domains (hash-keys funcs))))
|
||||
|
||||
;;; Build a network from a given hash table assigning functions to
|
||||
;;; variables by attributing the domain {0,1} to every variable.
|
||||
(define (make-01-network funcs)
|
||||
(network funcs (make-01-domains (hash-keys funcs))))
|
||||
|
||||
(module+ test
|
||||
(test-case "make-boolean-network"
|
||||
(define f1 (λ (s) (let ([x1 (hash-ref s 'x1)]
|
||||
[x2 (hash-ref s 'x2)])
|
||||
(and x1 (not x2)))))
|
||||
(define f2 (λ (s) (let ([x2 (hash-ref s 'x2)])
|
||||
(not x2))))
|
||||
(define bn (make-boolean-network (hash 'x1 f1 'x2 f2)))
|
||||
(check-equal? (network-domains bn) (hash 'x1 '(#f #t) 'x2 '(#f #t)))))
|
||||
|
||||
;;; Given a state s updates all the variables from xs.
|
||||
(define (update network s xs)
|
||||
(define funcs (network-functions network))
|
||||
(for/fold ([new-s s])
|
||||
([x xs])
|
||||
(let ([f (hash-ref network x)])
|
||||
(hash-set new-s x (f s)))))
|
||||
(define fx (hash-ref funcs x))
|
||||
(hash-set new-s x (fx s))))
|
||||
|
||||
(module+ test
|
||||
(test-case "basic definitions"
|
||||
|
|
@ -195,7 +219,7 @@
|
|||
(and x1 (not x2)))))
|
||||
(define f2 (λ (s) (let ([x2 (hash-ref s 'x2)])
|
||||
(not x2))))
|
||||
(define bn (make-network-from-functions `((x1 . ,f1) (x2 . ,f2))))
|
||||
(define bn (make-boolean-network (hash 'x1 f1 'x2 f2)))
|
||||
(define s1 (make-state '((x1 . #t) (x2 . #f))))
|
||||
(define new-s1 (update bn s1 '(x2 x1)))
|
||||
(define s2 (make-state '((x1 . #f) (x2 . #f))))
|
||||
|
|
@ -218,6 +242,10 @@
|
|||
[(cons var 0) (cons var #f)]
|
||||
[(cons var 1) (cons var #t)]))))
|
||||
|
||||
;;; Booleanizes a given state: replaces 0 with #f and 1 with #t.
|
||||
(define (booleanize-state s)
|
||||
(for/hash ([(x val) s]) (match val [0 (values x #f)] [1 (values x #t)])))
|
||||
|
||||
(module+ test
|
||||
(test-case "make-state, make-state-booleanize, booleanize-state"
|
||||
(check-equal? (make-state-booleanize '((a . 0) (b . 1)))
|
||||
|
|
@ -225,13 +253,6 @@
|
|||
(check-equal? (booleanize-state (make-state '((a . 0) (b . 1))))
|
||||
(make-state '((a . #f) (b . #t))))))
|
||||
|
||||
;;; Booleanizes a given state: replaces 0 with #f and 1 with #t.
|
||||
(define (booleanize-state s)
|
||||
(for/hash ([(x val) s]) (match val [0 (values x #f)] [1 (values x #t)])))
|
||||
|
||||
;;; A version of make-immutable-hash restricted to creating networks.
|
||||
(define (make-network-from-functions funcs) (make-immutable-hash funcs))
|
||||
|
||||
|
||||
;;; =================================
|
||||
;;; Syntactic description of networks
|
||||
|
|
@ -242,9 +263,14 @@
|
|||
;;; '(and x y (not z)) or '(+ 1 a (- b 10)).
|
||||
(define update-function-form? any/c)
|
||||
|
||||
;;; A Boolean network form is a mapping from its variables to the
|
||||
;;; forms of their update functions.
|
||||
(define network-form? variable-mapping?)
|
||||
;;; A network form consists of a mapping from variables to the forms
|
||||
;;; of their update functions, together with a mapping from its
|
||||
;;; variables to its update functions.
|
||||
;;;
|
||||
;;; The domain mapping does not have to assign domains to all
|
||||
;;; variables (e.g., it may be empty), but in this case the functions
|
||||
;;; which need to know the domains will not work.
|
||||
(struct network-form (forms domains) #:transparent)
|
||||
|
||||
;;; Build an update function from an update function form.
|
||||
(define (update-function-form->update-function form)
|
||||
|
|
@ -257,27 +283,46 @@
|
|||
(check-equal? (f s) #f)))
|
||||
|
||||
;;; Build a network from a network form.
|
||||
(define (network-form->network bnf)
|
||||
(for/hash ([(x form) bnf])
|
||||
(values x (update-function-form->update-function form))))
|
||||
(define (network-form->network nf)
|
||||
(network
|
||||
(for/hash ([(x form) (in-hash (network-form-forms nf))])
|
||||
(values x (update-function-form->update-function form)))
|
||||
(network-form-domains nf)))
|
||||
|
||||
(module+ test
|
||||
(test-case "network-form->network"
|
||||
(define bn (network-form->network
|
||||
(make-hash '((a . (and a b)) (b . (not b))))))
|
||||
(network-form (hash 'a '(and a b)
|
||||
'b '(not b))
|
||||
(hash 'a '(#f #t)
|
||||
'b '(#f #t)))))
|
||||
(define s (make-state '((a . #t) (b . #t))))
|
||||
(check-equal? ((hash-ref bn 'a) s) #t)))
|
||||
(check-equal? ((hash-ref (network-functions bn) 'a) s) #t)))
|
||||
|
||||
;;; Build a network from a list of pairs of forms of update functions.
|
||||
(define (make-network-from-forms forms)
|
||||
(network-form->network (make-immutable-hash forms)))
|
||||
;;; Build a Boolean network form from a given mapping assigning forms
|
||||
;;; to variables.
|
||||
(define (make-boolean-network-form forms)
|
||||
(network-form forms (make-boolean-domains (hash-keys forms))))
|
||||
|
||||
(module+ test
|
||||
(test-case "make-network-from-forms"
|
||||
(define bn (make-network-from-forms '((a . (and a b))
|
||||
(b . (not b)))))
|
||||
(define s (make-state '((a . #t) (b . #t))))
|
||||
(check-equal? ((hash-ref bn 'a) s) #t)))
|
||||
(test-case "make-boolean-network-form"
|
||||
(check-equal? (make-boolean-network-form (hash 'a '(and a b)
|
||||
'b '(not b)))
|
||||
(network-form
|
||||
'#hash((a . (and a b)) (b . (not b)))
|
||||
'#hash((a . (#f #t)) (b . (#f #t)))))))
|
||||
|
||||
;;; Build a Boolean network from a given mapping assigning forms
|
||||
;;; to variables.
|
||||
(define forms->boolean-network
|
||||
(compose network-form->network make-boolean-network-form))
|
||||
|
||||
(module+ test
|
||||
(test-case "forms->boolean-network"
|
||||
(define n (forms->boolean-network (hash 'a '(and a b)
|
||||
'b '(not b))))
|
||||
(check-equal? (network-domains n) (hash 'a '(#f #t)
|
||||
'b '(#f #t)))))
|
||||
|
||||
|
||||
;;; ============================
|
||||
|
|
@ -289,18 +334,27 @@
|
|||
;;; graphs is based on analysing the dynamics of the networks, it may
|
||||
;;; be quite resource-consuming, especially since I allow any
|
||||
;;; syntactic forms in the definitions of the functions.
|
||||
;;;
|
||||
;;; Note the fine difference between syntactic interaction graphs and
|
||||
;;; interaction graphs generated from the dynamics of the network.
|
||||
;;; The syntactic interaction graphs are based on the whether
|
||||
;;; a variable appears or not in the form of the function for another
|
||||
;;; variable. On the other hand, the normal, conventional interaction
|
||||
;;; graph records the fact that one variable has an impact on the
|
||||
;;; dynamics of the other variable. Depending on the model, these may
|
||||
;;; or may not be the same.
|
||||
|
||||
;;; Lists the variables of the network form appearing in the update
|
||||
;;; function form for x.
|
||||
(define (list-syntactic-interactions nf x)
|
||||
(set-intersect
|
||||
(extract-symbols (hash-ref nf x))
|
||||
(hash-keys nf)))
|
||||
(extract-symbols (hash-ref (network-form-forms nf) x))
|
||||
(hash-keys (network-form-forms nf))))
|
||||
|
||||
(module+ test
|
||||
(test-case "list-syntactic-interactions"
|
||||
(define n #hash((a . (+ a b c))
|
||||
(b . (- b c))))
|
||||
(define n (make-boolean-network-form #hash((a . (+ a b c))
|
||||
(b . (- b c)))))
|
||||
(check-true (set=? (list-syntactic-interactions n 'a) '(a b)))
|
||||
(check-true (set=? (list-syntactic-interactions n 'b) '(b)))))
|
||||
|
||||
|
|
@ -320,12 +374,13 @@
|
|||
(define (build-syntactic-interaction-graph n)
|
||||
(transpose
|
||||
(unweighted-graph/adj
|
||||
(for/list ([(var _) n]) (cons var (list-syntactic-interactions n var))))))
|
||||
(for/list ([(var _) (in-hash (network-form-forms n))])
|
||||
(cons var (list-syntactic-interactions n var))))))
|
||||
|
||||
(module+ test
|
||||
(test-case "build-syntactic-interaction-graph"
|
||||
(define n #hash((a . (+ a b c))
|
||||
(b . (- b c))))
|
||||
(define n (make-boolean-network-form #hash((a . (+ a b c))
|
||||
(b . (- b c)))))
|
||||
(define ig (build-syntactic-interaction-graph n))
|
||||
(check-true (has-vertex? ig 'a))
|
||||
(check-true (has-vertex? ig 'b))
|
||||
|
|
@ -336,10 +391,6 @@
|
|||
(check-false (has-edge? ig 'c 'b))
|
||||
(check-false (has-edge? ig 'c 'a))))
|
||||
|
||||
;;; A domain mapping is a hash set mapping variables to the lists of
|
||||
;;; values in their domains.
|
||||
(define domain-mapping/c (hash/c variable? list?))
|
||||
|
||||
;;; Given a hash-set mapping variables to generic sets of their
|
||||
;;; possible values, constructs the list of all possible states.
|
||||
(define (build-all-states vars-domains)
|
||||
|
|
@ -412,10 +463,11 @@
|
|||
;;; interact, i.e. that there exists such a state s with the property
|
||||
;;; that s' which is s with a different value for x yields such a new
|
||||
;;; state f(s') in which the value for y is different from f(s).
|
||||
(define (interaction? network doms x y)
|
||||
(define (interaction? network x y)
|
||||
(define doms (network-domains network))
|
||||
(define states-not-x (build-all-states (hash-remove doms x)))
|
||||
(define dom-x (hash-ref doms x))
|
||||
(define y-func (hash-ref network y))
|
||||
(define y-func (hash-ref (network-functions network) y))
|
||||
(define (different-ys-exist? st)
|
||||
(define x-states (for/list ([x-val (in-list dom-x)])
|
||||
(hash-set st x x-val)))
|
||||
|
|
@ -430,20 +482,19 @@
|
|||
|
||||
(module+ test
|
||||
(test-case "interaction?"
|
||||
(define n-bool (network-form->network
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z))))
|
||||
(define bool-doms (make-boolean-domains '(x y z)))
|
||||
(check-true (interaction? n-bool bool-doms 'x 'y))
|
||||
(check-true (interaction? n-bool bool-doms 'y 'x))
|
||||
(check-false (interaction? n-bool bool-doms 'x 'z))
|
||||
(define n-multi (network-form->network
|
||||
(hash 'x '(max (+ y 1) 2)
|
||||
'y '(min (- y 1) 0))))
|
||||
(define n1 (forms->boolean-network
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z))))
|
||||
(check-true (interaction? n1 'x 'y))
|
||||
(check-true (interaction? n1 'y 'x))
|
||||
(check-false (interaction? n1 'x 'z))
|
||||
(define n-multi (hash 'x '(max (+ y 1) 2)
|
||||
'y '(min (- y 1) 0)))
|
||||
(define 123-doms (make-same-domains '(x y) '(0 1 2)))
|
||||
(check-false (interaction? n-multi 123-doms 'x 'y))
|
||||
(check-true (interaction? n-multi 123-doms 'y 'x))))
|
||||
(define n2 (network-form->network (network-form n-multi 123-doms)))
|
||||
(check-false (interaction? n2 'x 'y))
|
||||
(check-true (interaction? n2 'y 'x))))
|
||||
|
||||
;;; Given two variables x and y of a network f, checks whether they
|
||||
;;; interact, and if they interact, returns 1 if increasing x leads to
|
||||
|
|
@ -452,10 +503,11 @@
|
|||
;;;
|
||||
;;; Use interaction? if you only need to know whether two variables
|
||||
;;; interact, because interaction? will be often faster.
|
||||
(define (get-interaction-sign network doms x y)
|
||||
(define (get-interaction-sign network x y)
|
||||
(define doms (network-domains network))
|
||||
(define dom-x (hash-ref doms x))
|
||||
(define dom-y (hash-ref doms y))
|
||||
(define y-func (hash-ref network y))
|
||||
(define y-func (hash-ref (network-functions network) y))
|
||||
(define (collect-impacts-on-y st)
|
||||
;; The way in which the values are ordered in the domains gives
|
||||
;; a total order on these values. This means that considering
|
||||
|
|
@ -489,45 +541,44 @@
|
|||
|
||||
(module+ test
|
||||
(test-case "get-interaction-sign"
|
||||
(define n-bool (network-form->network
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z)
|
||||
't '(or (and (not x) y)
|
||||
(and x (not y))))))
|
||||
(define bool-doms (make-boolean-domains '(x y z t)))
|
||||
(check-equal? (get-interaction-sign n-bool bool-doms 'x 'y) 1)
|
||||
(check-equal? (get-interaction-sign n-bool bool-doms 'y 'x) -1)
|
||||
(check-false (get-interaction-sign n-bool bool-doms 'x 'z))
|
||||
(check-equal? (get-interaction-sign n-bool bool-doms 'y 'z) 1)
|
||||
(check-equal? (get-interaction-sign n-bool bool-doms 'x 't) 0)
|
||||
(define n-multi (network-form->network
|
||||
(hash 'x '(min (+ y 1) 2)
|
||||
'y '(max (- y 1) 0)
|
||||
'z '(- 2 y)
|
||||
't '(abs (- y 1)))))
|
||||
(define n1 (forms->boolean-network
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z)
|
||||
't '(or (and (not x) y)
|
||||
(and x (not y))))))
|
||||
(check-equal? (get-interaction-sign n1 'x 'y) 1)
|
||||
(check-equal? (get-interaction-sign n1 'y 'x) -1)
|
||||
(check-false (get-interaction-sign n1 'x 'z))
|
||||
(check-equal? (get-interaction-sign n1 'y 'z) 1)
|
||||
(check-equal? (get-interaction-sign n1 'x 't) 0)
|
||||
(define n-multi (hash 'x '(min (+ y 1) 2)
|
||||
'y '(max (- y 1) 0)
|
||||
'z '(- 2 y)
|
||||
't '(abs (- y 1))))
|
||||
(define 123-doms (make-same-domains '(x y z t) '(0 1 2)))
|
||||
(check-false (get-interaction-sign n-multi 123-doms 'x 'y))
|
||||
(check-equal? (get-interaction-sign n-multi 123-doms 'y 'x) 1)
|
||||
(check-equal? (get-interaction-sign n-multi 123-doms 'y 'z) -1)
|
||||
(check-equal? (get-interaction-sign n-multi 123-doms 'y 't) 0)
|
||||
(check-equal? (get-interaction-sign n-multi 123-doms 'y 'y) 1)))
|
||||
(define n2 (network-form->network (network-form n-multi 123-doms)))
|
||||
(check-false (get-interaction-sign n2 'x 'y))
|
||||
(check-equal? (get-interaction-sign n2 'y 'x) 1)
|
||||
(check-equal? (get-interaction-sign n2 'y 'z) -1)
|
||||
(check-equal? (get-interaction-sign n2 'y 't) 0)
|
||||
(check-equal? (get-interaction-sign n2 'y 'y) 1)))
|
||||
|
||||
;;; Given a network, builds its interaction graph. The graph has
|
||||
;;; variables as nodes and has a directed edge from x to y if
|
||||
;;; interaction? returns #t for these variables, in this order.
|
||||
(define (build-interaction-graph network doms)
|
||||
(define vars (hash-keys network))
|
||||
(define (build-interaction-graph network)
|
||||
(define vars (hash-keys (network-functions network)))
|
||||
(unweighted-graph/directed
|
||||
(for*/list ([x (in-list vars)]
|
||||
[y (in-list vars)]
|
||||
#:when (interaction? network doms x y))
|
||||
#:when (interaction? network x y))
|
||||
(list x y))))
|
||||
|
||||
;;; Like build-interaction-graph, but accepts a network form and
|
||||
;;; converts it a to a network.
|
||||
(define (build-interaction-graph/form form doms)
|
||||
(build-interaction-graph (network-form->network form) doms))
|
||||
(define build-interaction-graph/form
|
||||
(compose build-interaction-graph network-form->network))
|
||||
|
||||
(module+ test
|
||||
(test-case "build-interaction-graph"
|
||||
|
|
@ -535,41 +586,40 @@
|
|||
[skip-expensive-tests?
|
||||
(displayln "Skipping test case build-interaction-graph.")]
|
||||
[else
|
||||
(define n-bool
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z)
|
||||
't '(or (and (not x) y)
|
||||
(and x (not y)))))
|
||||
(define bool-doms (make-boolean-domains '(x y z t)))
|
||||
(check-equal? (graphviz (build-interaction-graph/form n-bool bool-doms))
|
||||
(define n1 (make-boolean-network-form
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z)
|
||||
't '(or (and (not x) y)
|
||||
(and x (not y))))))
|
||||
(check-equal? (graphviz (build-interaction-graph/form n1))
|
||||
"digraph G {\n\tnode0 [label=\"y\"];\n\tnode1 [label=\"z\"];\n\tnode2 [label=\"x\"];\n\tnode3 [label=\"t\"];\n\tsubgraph U {\n\t\tedge [dir=none];\n\t\tnode0 -> node2;\n\t\tnode1 -> node1;\n\t}\n\tsubgraph D {\n\t\tnode0 -> node3;\n\t\tnode0 -> node1;\n\t\tnode2 -> node3;\n\t}\n}\n")
|
||||
(define n-multi
|
||||
(hash 'x '(min (+ y 1) 2)
|
||||
'y '(max (- y 1) 0)
|
||||
'z '(- 2 y)
|
||||
't '(abs (- y 1))))
|
||||
(define n-multi (hash 'x '(min (+ y 1) 2)
|
||||
'y '(max (- y 1) 0)
|
||||
'z '(- 2 y)
|
||||
't '(abs (- y 1))))
|
||||
(define 123-doms (make-same-domains '(x y z t) '(0 1 2)))
|
||||
(check-equal? (graphviz (build-interaction-graph/form n-multi 123-doms))
|
||||
(define n2 (network-form n-multi 123-doms))
|
||||
(check-equal? (graphviz (build-interaction-graph/form n2))
|
||||
"digraph G {\n\tnode0 [label=\"y\"];\n\tnode1 [label=\"z\"];\n\tnode2 [label=\"x\"];\n\tnode3 [label=\"t\"];\n\tsubgraph U {\n\t\tedge [dir=none];\n\t\tnode0 -> node0;\n\t}\n\tsubgraph D {\n\t\tnode0 -> node2;\n\t\tnode0 -> node3;\n\t\tnode0 -> node1;\n\t}\n}\n")])))
|
||||
|
||||
;;; Given a network, builds its signed interaction graph. The graph
|
||||
;;; has variables as nodes and has a directed edge from x to
|
||||
;;; y labelled by the value get-interaction-sign for these variables,
|
||||
;;; in that order, unless this value is #f.
|
||||
(define (build-signed-interaction-graph network doms)
|
||||
(define vars (hash-keys network))
|
||||
(define (build-signed-interaction-graph network)
|
||||
(define vars (hash-keys (network-functions network)))
|
||||
(weighted-graph/directed
|
||||
(for*/list ([x (in-list vars)]
|
||||
[y (in-list vars)]
|
||||
[sign (in-value (get-interaction-sign network doms x y))]
|
||||
[sign (in-value (get-interaction-sign network x y))]
|
||||
#:unless (eq? sign #f))
|
||||
(list sign x y))))
|
||||
|
||||
;;; Like build-signed-interaction-graph, but takes a network form and
|
||||
;;; converts it a to a network.
|
||||
(define (build-signed-interaction-graph/form form doms)
|
||||
(build-signed-interaction-graph (network-form->network form) doms))
|
||||
(define build-signed-interaction-graph/form
|
||||
(compose build-signed-interaction-graph network-form->network))
|
||||
|
||||
(module+ test
|
||||
(test-case "build-signed-interaction-graph"
|
||||
|
|
@ -577,22 +627,21 @@
|
|||
[skip-expensive-tests?
|
||||
(displayln "Skipping test case build-signed-interaction-graph.")]
|
||||
[else
|
||||
(define n-bool
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z)
|
||||
't '(or (and (not x) y)
|
||||
(and x (not y)))))
|
||||
(define bool-doms (make-boolean-domains '(x y z t)))
|
||||
(check-equal? (graphviz (build-signed-interaction-graph/form n-bool bool-doms))
|
||||
(define n1 (make-boolean-network-form
|
||||
(hash 'x '(not y)
|
||||
'y 'x
|
||||
'z '(and y z)
|
||||
't '(or (and (not x) y)
|
||||
(and x (not y))))))
|
||||
(check-equal? (graphviz (build-signed-interaction-graph/form n1))
|
||||
"digraph G {\n\tnode0 [label=\"y\"];\n\tnode1 [label=\"z\"];\n\tnode2 [label=\"x\"];\n\tnode3 [label=\"t\"];\n\tsubgraph U {\n\t\tedge [dir=none];\n\t\tnode1 -> node1 [label=\"1\"];\n\t}\n\tsubgraph D {\n\t\tnode0 -> node2 [label=\"-1\"];\n\t\tnode0 -> node3 [label=\"0\"];\n\t\tnode0 -> node1 [label=\"1\"];\n\t\tnode2 -> node3 [label=\"0\"];\n\t\tnode2 -> node0 [label=\"1\"];\n\t}\n}\n")
|
||||
(define n-multi
|
||||
(hash 'x '(min (+ y 1) 2)
|
||||
'y '(max (- y 1) 0)
|
||||
'z '(- 2 y)
|
||||
't '(abs (- y 1))))
|
||||
(define n-multi (hash 'x '(min (+ y 1) 2)
|
||||
'y '(max (- y 1) 0)
|
||||
'z '(- 2 y)
|
||||
't '(abs (- y 1))))
|
||||
(define 123-doms (make-same-domains '(x y z t) '(0 1 2)))
|
||||
(check-equal? (graphviz (build-signed-interaction-graph/form n-multi 123-doms))
|
||||
(define n2 (network-form n-multi 123-doms))
|
||||
(check-equal? (graphviz (build-signed-interaction-graph/form n2))
|
||||
"digraph G {\n\tnode0 [label=\"y\"];\n\tnode1 [label=\"z\"];\n\tnode2 [label=\"x\"];\n\tnode3 [label=\"t\"];\n\tsubgraph U {\n\t\tedge [dir=none];\n\t\tnode0 -> node0 [label=\"1\"];\n\t}\n\tsubgraph D {\n\t\tnode0 -> node2 [label=\"1\"];\n\t\tnode0 -> node3 [label=\"0\"];\n\t\tnode0 -> node1 [label=\"-1\"];\n\t}\n}\n")])))
|
||||
|
||||
;;; ====================
|
||||
|
|
@ -634,7 +683,7 @@
|
|||
;;; Given a network, applies a function for building a mode to its
|
||||
;;; variables and returns the corresponding network dynamics.
|
||||
(define (make-dynamics-from-func network mode-func)
|
||||
(dynamics network (mode-func (hash-keys network))))
|
||||
(dynamics network (mode-func (hash-keys (network-functions network)))))
|
||||
|
||||
;;; Creates the asynchronous dynamics for a given network.
|
||||
(define (make-asyn-dynamics network)
|
||||
|
|
@ -646,7 +695,7 @@
|
|||
|
||||
(module+ test
|
||||
(test-case "make-asyn-dynamics, make-syn-dynamics"
|
||||
(define n (network-form->network #hash((a . (not a)) (b . b))))
|
||||
(define n (forms->boolean-network #hash((a . (not a)) (b . b))))
|
||||
(define asyn (make-asyn-dynamics n))
|
||||
(define syn (make-syn-dynamics n))
|
||||
(check-equal? (dynamics-network asyn) n)
|
||||
|
|
@ -654,14 +703,6 @@
|
|||
(check-equal? (dynamics-network syn) n)
|
||||
(check-equal? (dynamics-mode syn) (set (set 'a 'b)))))
|
||||
|
||||
;;; Reads an Org-mode-produced sexp, converts it into a network, and
|
||||
;;; builds the asyncronous dynamics out of it.
|
||||
(define read-org-network-make-asyn (compose make-asyn-dynamics network-form->network read-org-variable-mapping))
|
||||
|
||||
;;; Reads an Org-mode-produced sexp, converts it into a network, and
|
||||
;;; builds the synchronous dynamics out of it.
|
||||
(define read-org-network-make-syn (compose make-syn-dynamics network-form->network read-org-variable-mapping))
|
||||
|
||||
;;; Pretty-prints a state of the network.
|
||||
(define (pretty-print-state s)
|
||||
(string-join (hash-map s (λ (key val) (format "~a:~a" key val)) #t)))
|
||||
|
|
@ -701,20 +742,26 @@
|
|||
(define ppsgb pretty-print-boolean-state-graph)
|
||||
|
||||
;;; Builds the full state graph of a Boolean network.
|
||||
(define (build-full-boolean-state-graph dyn)
|
||||
(define (build-full-state-graph dyn)
|
||||
(dds-build-state-graph
|
||||
dyn
|
||||
(list->set (build-all-boolean-states (hash-keys (dynamics-network dyn))))))
|
||||
((compose list->set
|
||||
build-all-states
|
||||
network-domains
|
||||
dynamics-network) dyn)))
|
||||
|
||||
;;; Build the full annotated state graph of a Boolean network.
|
||||
(define (build-full-boolean-state-graph-annotated dyn)
|
||||
(define (build-full-state-graph-annotated dyn)
|
||||
(dds-build-state-graph-annotated
|
||||
dyn
|
||||
(list->set (build-all-boolean-states (hash-keys (dynamics-network dyn))))))
|
||||
((compose list->set
|
||||
build-all-states
|
||||
network-domains
|
||||
dynamics-network) dyn)))
|
||||
|
||||
(module+ test
|
||||
(test-case "Dynamics of networks"
|
||||
(define n (network-form->network #hash((a . (not a)) (b . b))))
|
||||
(define n (forms->boolean-network #hash((a . (not a)) (b . b))))
|
||||
(define asyn (make-asyn-dynamics n))
|
||||
(define syn (make-syn-dynamics n))
|
||||
(define s (make-state '((a . #t) (b . #f))))
|
||||
|
|
@ -724,8 +771,8 @@
|
|||
(define gr-full (dds-build-state-graph asyn (set s)))
|
||||
(define gr-full-pp (pretty-print-state-graph gr-full))
|
||||
(define gr-full-ppb (pretty-print-boolean-state-graph gr-full))
|
||||
(define gr-complete-bool (build-full-boolean-state-graph asyn))
|
||||
(define gr-complete-bool-ann (build-full-boolean-state-graph-annotated asyn))
|
||||
(define gr-complete-bool (build-full-state-graph asyn))
|
||||
(define gr-complete-bool-ann (build-full-state-graph-annotated asyn))
|
||||
(check-equal? (dds-step-one asyn s) (set (make-state '((a . #f) (b . #f)))
|
||||
(make-state '((a . #t) (b . #f)))))
|
||||
(check-equal? (dds-step-one-annotated asyn s)
|
||||
|
|
@ -801,20 +848,6 @@
|
|||
#hash((a . #f) (b . #t)) #hash((a . #t) (b . #t)))
|
||||
(set (set 'a)))))
|
||||
|
||||
;;; Like build-full-boolean-state-graph, but the states are expressed
|
||||
;;; in 0 and 1, instead of #f and #t.
|
||||
(define (build-full-01-state-graph dyn)
|
||||
(dds-build-state-graph
|
||||
dyn
|
||||
(list->set (build-all-01-states (hash-keys (dynamics-network dyn))))))
|
||||
|
||||
;;; Like build-full-boolean-state-graph-annotated, but the states are expressed
|
||||
;;; in 0 and 1, instead of #f and #t.
|
||||
(define (build-full-01-state-graph-annotated dyn)
|
||||
(dds-build-state-graph-annotated
|
||||
dyn
|
||||
(list->set (build-all-01-states (hash-keys (dynamics-network dyn))))))
|
||||
|
||||
|
||||
;;; =================================
|
||||
;;; Tabulating functions and networks
|
||||
|
|
@ -887,13 +920,13 @@
|
|||
;;; network. If headers is #t, prepends a list of variable names and
|
||||
;;; update functions (f-x, where x is the name of the corresponding
|
||||
;;; variable) to the result.
|
||||
(define (tabulate-network network domains #:headers [headers #t])
|
||||
(define (tabulate-network network #:headers [headers #t])
|
||||
;; I use hash-map with try-order? set to #t to ask the hash table to
|
||||
;; sort the keys for me.
|
||||
(define-values (vars funcs) (for/lists (l1 l2)
|
||||
([pair (hash-map network cons #t)])
|
||||
([pair (hash-map (network-functions network) cons #t)])
|
||||
(values (car pair) (cdr pair))))
|
||||
(define tab (tabulate-state* funcs domains #:headers headers))
|
||||
(define tab (tabulate-state* funcs (network-domains network) #:headers headers))
|
||||
(cond
|
||||
[headers
|
||||
;; Replace the names of the functions tabulate-state* gave us by
|
||||
|
|
@ -904,17 +937,12 @@
|
|||
(cons (append (take hdrs (length vars)) fnames) vals)])]
|
||||
[else tab]))
|
||||
|
||||
;;; Like tabulate-network, but assumes all the variables are Boolean.
|
||||
(define (tabulate-boolean-network bn #:headers [headers #t])
|
||||
(tabulate-network bn (make-boolean-domains (hash-map bn (λ (x y) x) #t))
|
||||
#:headers headers))
|
||||
|
||||
(module+ test
|
||||
(test-case "tabulate-boolean-network"
|
||||
(define bn (network-form->network #hash((a . (not a)) (b . b))))
|
||||
(check-equal? (tabulate-boolean-network bn)
|
||||
(test-case "tabulate-network"
|
||||
(define bn (forms->boolean-network #hash((a . (not a)) (b . b))))
|
||||
(check-equal? (tabulate-network bn)
|
||||
'((a b f-a f-b) (#f #f #t #f) (#f #t #t #t) (#t #f #f #f) (#t #t #f #t)))
|
||||
(check-equal? (tabulate-boolean-network bn #:headers #f)
|
||||
(check-equal? (tabulate-network bn #:headers #f)
|
||||
'((#f #f #t #f) (#f #t #t #t) (#t #f #f #f) (#t #t #f #t)))))
|
||||
|
||||
|
||||
|
|
@ -935,6 +963,10 @@
|
|||
;;;
|
||||
;;; This function relies on table->function, so the same caveats
|
||||
;;; apply.
|
||||
;;;
|
||||
;;; The domains of the network is a mapping assigning to each variable
|
||||
;;; the set of values which can appear in its column in the table.
|
||||
;;; This function does not check whether the table is complete.
|
||||
(define (table->network table #:headers [headers #t])
|
||||
(define n (/ (length (car table)) 2))
|
||||
;; Get the variable names from the table or generate them, if
|
||||
|
|
@ -956,8 +988,15 @@
|
|||
(define funcs (for/list ([out func-lines])
|
||||
(table->function (for/list ([in st-ins] [o out])
|
||||
(list in o)))))
|
||||
;; Infer the domains.
|
||||
(define domains (for/hash [(dom (in-list (lists-transpose ins)))
|
||||
(x (in-list var-names))]
|
||||
(values x (remove-duplicates dom))))
|
||||
;; Construct the network.
|
||||
(make-network-from-functions (map cons var-names funcs)))
|
||||
(network (for/hash ([x (in-list var-names)]
|
||||
[f (in-list funcs)])
|
||||
(values x f))
|
||||
domains))
|
||||
|
||||
(module+ test
|
||||
(test-case "table->network"
|
||||
|
|
@ -966,8 +1005,8 @@
|
|||
(#f #t #f #t)
|
||||
(#t #f #t #f)
|
||||
(#t #t #t #t))))
|
||||
(define f1 (hash-ref n 'x1))
|
||||
(define f2 (hash-ref n 'x2))
|
||||
(define f1 (hash-ref (network-functions n) 'x1))
|
||||
(define f2 (hash-ref (network-functions n) 'x2))
|
||||
|
||||
(check-false (f1 (make-state '((x1 . #f) (x2 . #f)))))
|
||||
(check-false (f1 (make-state '((x1 . #f) (x2 . #t)))))
|
||||
|
|
@ -977,7 +1016,10 @@
|
|||
(check-false (f2 (make-state '((x1 . #f) (x2 . #f)))))
|
||||
(check-true (f2 (make-state '((x1 . #f) (x2 . #t)))))
|
||||
(check-false (f2 (make-state '((x1 . #t) (x2 . #f)))))
|
||||
(check-true (f2 (make-state '((x1 . #t) (x2 . #t)))))))
|
||||
(check-true (f2 (make-state '((x1 . #t) (x2 . #t)))))
|
||||
|
||||
(check-equal? (network-domains n)
|
||||
#hash((x1 . (#f #t)) (x2 . (#f #t))))))
|
||||
|
||||
|
||||
;;; =============================
|
||||
|
|
@ -1005,7 +1047,7 @@
|
|||
(check-equal? (tabulate-state/boolean f '(x1 x2) #:headers #f)
|
||||
'((#f #f #f) (#f #t #f) (#t #f #t) (#t #t #t)))
|
||||
(define bn (random-boolean-network/vars 3))
|
||||
(check-equal? (tabulate-boolean-network bn)
|
||||
(check-equal? (tabulate-network bn)
|
||||
'((x0 x1 x2 f-x0 f-x1 f-x2)
|
||||
(#f #f #f #f #t #f)
|
||||
(#f #f #t #t #f #f)
|
||||
|
|
@ -1018,8 +1060,9 @@
|
|||
|
||||
;;; Generates a random network from the given domain mapping.
|
||||
(define (random-network domains)
|
||||
(for/hash ([(x x-dom) (in-hash domains)])
|
||||
(values x (random-function/state domains x-dom))))
|
||||
(network (for/hash ([(x x-dom) (in-hash domains)])
|
||||
(values x (random-function/state domains x-dom)))
|
||||
domains))
|
||||
|
||||
;;; Generates a random Boolean network with the given variables.
|
||||
(define (random-boolean-network vars)
|
||||
|
|
@ -1379,8 +1422,8 @@
|
|||
|
||||
;;; Constructs a network from a network form defining a TBN.
|
||||
(define (tbn->network tbn)
|
||||
(for/hash ([(var tbf) (in-hash tbn)])
|
||||
(values var ((curry apply-tbf/state) tbf))))
|
||||
(make-01-network (for/hash ([(var tbf) (in-hash tbn)])
|
||||
(values var ((curry apply-tbf/state) tbf)))))
|
||||
|
||||
(module+ test
|
||||
(test-case "tbn->network"
|
||||
|
|
@ -1390,13 +1433,15 @@
|
|||
(define s1 (make-state '((a . 0) (b . 0))))
|
||||
(check-equal? (update n s1 '(a b))
|
||||
(make-state '((a . 0) (b . 1))))
|
||||
(check-equal? (network-domains n) #hash((a . (0 1)) (b . (0 1))))
|
||||
|
||||
(define sbn (make-sbn `((a . ,(make-sbf/state '((b . -1))))
|
||||
(b . ,(make-sbf/state '((a . 1)))))))
|
||||
(define sn (tbn->network sbn))
|
||||
(define s2 (make-state '((a . 1) (b . 1))))
|
||||
(check-equal? (update sn s2 '(a b))
|
||||
(make-state '((a . 0) (b . 1))))))
|
||||
(make-state '((a . 0) (b . 1))))
|
||||
(check-equal? (network-domains sn) #hash((a . (0 1)) (b . (0 1))))))
|
||||
|
||||
;;; A helper function for read-org-tbn and read-org-sbn. It reads a
|
||||
;;; TBN from an Org-mode sexp containing a list of lists of numbers.
|
||||
|
|
@ -1529,7 +1574,7 @@
|
|||
;;; A shortcut for building the state graphs of TBN.
|
||||
(define build-tbn-state-graph
|
||||
(compose pretty-print-state-graph
|
||||
build-full-01-state-graph
|
||||
build-full-state-graph
|
||||
make-syn-dynamics
|
||||
tbn->network))
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue