example: Update the section on Boolean networks.
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Sergiu Ivanov
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@ -436,7 +436,12 @@ tab
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Here's the unsigned syntactic interaction graph of this network:
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#+NAME: simple-bn-syig
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#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
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(dotit (build-syntactic-interaction-graph (unorgv simple-bn)))
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((compose
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dotit
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build-syntactic-interaction-graph
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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/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
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#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
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(dotit (build-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-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/example1FH1rZ.svg :results raw drawer :cmd sfdp :noweb yes
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@ -486,7 +496,12 @@ tab
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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
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@ -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)
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(let* ([bn (network-form->network (unorgv simple-bn))]
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[bn-asyn (make-asyn-dynamics bn)])
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(dotit (pretty-print-state-graph (build-full-boolean-state-graph bn-asyn))))
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((compose
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dotit
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pretty-print-state-graph
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build-full-state-graph
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make-asyn-dynamics
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forms->boolean-network
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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/examplem7LpTs.svg :results raw drawer :cmd sfdp :noweb yes
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<<simple-bn-sg()>>
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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:results:
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[[file:dots/examplem7LpTs.svg]]
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:END:
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:end:
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Alternatively, you may prefer a slighty more compact representation
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of Boolean values as 0 and 1:
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#+NAME: simple-bn-sg-bool
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#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
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(let* ([bn (network-form->network (unorgv simple-bn))]
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[bn-asyn (make-asyn-dynamics bn)])
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(dotit (pretty-print-boolean-state-graph (build-full-boolean-state-graph bn-asyn))))
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((compose
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dotit
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pretty-print-boolean-state-graph
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build-full-state-graph
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make-asyn-dynamics
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forms->boolean-network
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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/examplex1Irnk.svg :results raw drawer :cmd sfdp :noweb yes
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@ -531,9 +555,9 @@ tab
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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:results:
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[[file:dots/examplex1Irnk.svg]]
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:END:
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:end:
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Consider the following state (appearing in the upper left corner of
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the state graph):
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@ -549,7 +573,7 @@ tab
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#+HEADER: :var simple-bn=munch-sexp(simple-bn)
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#+HEADER: :var some-state=munch-sexp(some-state)
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#+BEGIN_SRC racket :results silent
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(let* ([bn (network-form->network (unorgv simple-bn))]
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(let* ([bn (forms->boolean-network (unorgv simple-bn))]
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[bn-asyn (make-asyn-dynamics bn)]
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[s0 (booleanize-state (unorgv some-state))])
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(dotit (pretty-print-boolean-state-graph (dds-build-n-step-state-graph bn-asyn (set s0) 2))))
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@ -560,17 +584,22 @@ tab
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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:results:
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[[file:dots/examplecHA6gL.svg]]
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:END:
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:end:
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Here is the complete state graph with edges annotated with the
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modality leading to the update.
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#+NAME: simple-bn-sg-bool-ann
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#+BEGIN_SRC racket :results silent :var simple-bn=munch-sexp(simple-bn)
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(let* ([bn (network-form->network (unorgv simple-bn))]
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[bn-asyn (make-asyn-dynamics bn)])
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(dotit (pretty-print-boolean-state-graph (build-full-boolean-state-graph-annotated bn-asyn))))
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((compose
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dotit
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pretty-print-boolean-state-graph
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build-full-state-graph-annotated
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make-asyn-dynamics
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forms->boolean-network
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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/examplei4we6j.svg :results raw drawer :cmd sfdp :noweb yes
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@ -590,9 +619,14 @@ tab
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#+NAME: bn2-sgr
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#+BEGIN_SRC racket :results silent :var input-bn=munch-sexp(bn2)
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(let* ([bn (network-form->network (unorgv input-bn))]
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[bn-asyn (make-asyn-dynamics bn)])
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(dotit (pretty-print-boolean-state-graph (build-full-boolean-state-graph-annotated bn-asyn))))
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((compose
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dotit
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pretty-print-boolean-state-graph
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build-full-state-graph-annotated
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make-asyn-dynamics
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forms->boolean-network
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unorgv)
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input-bn)
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#+END_SRC
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#+BEGIN_SRC dot :file dots/examplehsuRqc.svg :results raw drawer :cmd dot :noweb yes
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