Rewrite bn without types, rename it to networks.
I tried generalising my code from Boolean networks to any kinds of networks, but got tired of having to fight the type system (for now at least). The last drop was the fact that the graph library does not seem to have a typed version. So I decided to go with contracts instead.
This commit is contained in:
Sergiu Ivanov
parent
009c6109a9
commit
cf19859be8
3 changed files with 131 additions and 126 deletions
115
bn.rkt
115
bn.rkt
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#lang racket
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;;; dds/bn
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;;; This module provides some quick definitions for running Boolean
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;;; networks. A Boolean network is a set of Boolean variables which
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;;; are updated according to their corresponding update functions.
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;;; The variables to be updated at each step are given by the mode.
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(require "utils.rkt")
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(provide
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;; Functions
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update make-state make-bn-funcs update-func-form->update-func
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bn-form->bn make-bn-forms
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;; Syntax
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st bn)
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;;; =================
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;;; Basic definitions
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;;; =================
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(define-type Variable Symbol)
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;;; A state of a Boolean network is a mapping from the variables of the
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;;; network to their Boolean values.
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(define-type State (HashTable Variable Boolean))
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;;; An update function is a Boolean function computing a Boolean value
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;;; from the given state.
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(define-type UpdateFunc (-> State Boolean))
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;;; A Boolean network is a mapping from its variables to its update
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;;; functions.
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(define-type Network (HashTable Variable UpdateFunc))
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;;; Given a state s updates all the variables from xs. This
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;;; corresponds to a parallel mode.
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(: update (-> Network State (Listof Variable) State))
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(define (update bn ; the Boolean network
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s ; the state to operate on
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xs) ; the variables to update
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(let ([new-s : State (hash-copy s)])
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(for ([x xs])
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(let ([f (hash-ref bn x)])
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(hash-set! new-s x (f s))))
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new-s))
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;;; A version of make-hash restricted to creating Boolean states.
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(: make-state (-> (Listof (Pairof Variable Boolean)) State))
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(define (make-state mappings)
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(make-hash mappings))
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;;; A shortcut for make-state.
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(define-syntax-rule (st mappings) (make-state mappings))
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;;; A version of make-hash restricted to creating Boolean networks.
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(: make-bn-funcs (-> (Listof (Pairof Variable UpdateFunc)) Network))
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(define (make-bn-funcs funcs)
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(make-hash funcs))
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;;; =========================================
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;;; Syntactic description of Boolean networks
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;;; =========================================
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;;; An UpdateFuncForm is any form which can appear as a body of a
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;;; Boolean function and which can be evaluated with eval. For
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;;; example, '(and x y (not z)).
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(define-type UpdateFuncForm Any)
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;;; A Boolean network form is a mapping from its variables to the
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;;; forms of their update functions.
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(define-type NetworkForm (HashTable Variable UpdateFuncForm))
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;;; Build an update function from an update function form.
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#;(: update-func-form->update-func (-> UpdateFuncForm UpdateFunc))
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(define (update-func-form->update-func form)
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(lambda ([s : State])
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(cast (eval-with1 (cast s (HashTable Variable Any)) form) Boolean)))
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;;; Build a Network from a Network form.
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(: bn-form->bn (-> NetworkForm Network))
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(define (bn-form->bn bnf)
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(make-hash
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(hash-map bnf (lambda ([x : Variable] [form : UpdateFuncForm])
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(cons x (update-func-form->update-func form))))))
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;;; Build a network from a list of pairs of forms of update functions.
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(: make-bn-forms (-> (Listof (Pairof Variable UpdateFuncForm)) Network))
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(define (make-bn-forms forms)
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(bn-form->bn (make-hash forms)))
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;;; A shortcut for make-bn-forms.
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(define-syntax-rule (bn forms) (make-bn-forms forms))
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;;; ============================
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;;; Inferring interaction graphs
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;;; ============================
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;;; I allow any syntactic forms in definitions of Boolean functions.
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;;; I can still find out which Boolean variables appear in those
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;;; syntactic form, but I have no reliable syntactic means of finding
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;;; out what kind of action do they have (inhibition or activation)
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;;; since I cannot do Boolean minimisation (e.g., I cannot rely on not
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;;; appearing before a variable, since (not (not a)) is equivalent
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;;; to a). On the other hand, going through all Boolean states is
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;;; quite resource-consuming and thus not always useful.
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;;;
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;;; In this section I provide inference of both unsigned and signed
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;;; interaction graphs, but since the inference of signed interaction
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;;; graphs is based on analysing the dynamics of the networks, it may
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;;; be quite resource-consuming.
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@ -1,21 +1,21 @@
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#lang typed/racket
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#lang racket
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;;; Tests for dds/bn.
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;;; Tests for dds/networks.
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(require typed/rackunit "bn.rkt")
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(require rackunit "networks.rkt")
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;;; This test case sets up the following Boolean network:
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;;; x1 = x1 AND NOT x2
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;;; x2 = NOT x2
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(test-case "Basic definitions"
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(let* ([f1 (λ ([s : State])
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(let* ([f1 (λ (s)
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(let ([x1 (hash-ref s 'x1)]
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[x2 (hash-ref s 'x2)])
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(and x1 (not x2))))]
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[f2 (λ ([s : State])
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[f2 (λ (s)
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(let ([x2 (hash-ref s 'x2)])
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(not x2)))]
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[bn (make-bn-funcs `((x1 . ,f1) (x2 . ,f2)))])
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[bn (make-network-from-functions `((x1 . ,f1) (x2 . ,f2)))])
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(test-case "One-step syncronous update"
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(let* ([s (make-state '((x1 . #t) (x2 . #f)))]
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@ -33,12 +33,12 @@
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(test-case "Syntactic description of Boolean networks"
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(let ([s (make-state '((x . #t) (y . #f)))]
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[f (update-func-form->update-func '(and x y))])
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[f (update-function-form->update-function '(and x y))])
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(check-equal? (f s) #f))
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(let ([bn1 (bn-form->bn (make-hash '((a . (and a b)) (b . (not b)))))]
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[bn2 (make-bn-forms '((a . (and a b))
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(b . (not b))))]
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[bn3 (bn '((a . (and a b))
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(let ([bn1 (network-form->network (make-hash '((a . (and a b)) (b . (not b)))))]
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[bn2 (make-network-from-forms '((a . (and a b))
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(b . (not b))))]
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[bn3 (nn '((a . (and a b))
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(b . (not b))))]
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[s (st '((a . #t) (b . #t)))])
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(check-equal? ((hash-ref bn1 'a) s) #t)
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120
networks.rkt
Normal file
120
networks.rkt
Normal file
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@ -0,0 +1,120 @@
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#lang racket
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;;; dds/networks
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;;; This module provides some quick definitions for and analysing
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;;; network models. A network is a set of variables which are updated
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;;; according to their corresponding update functions. The variables
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;;; to be updated at each step are given by the mode.
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;;;
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;;; This model can generalise Boolean networks, TBANs, multivalued
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;;; networks, etc.
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(require "utils.rkt")
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(provide
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;; Functions with contracts
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(contract-out [update (-> network? state? (listof variable?) state?)]
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[make-state (-> (listof (cons/c symbol? any/c)) state?)]
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[make-network-from-functions (-> (listof (cons/c symbol? update-function?)) network?)]
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[update-function-form->update-function (-> update-function-form? update-function?)]
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[network-form->network (-> network-form? network?)]
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[make-network-from-forms (-> (listof (cons/c symbol? update-function-form?))
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network?)])
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;; Functions
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variable? state? update-function? update-function-form? network-form?
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;; Contracts
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state/c network/c
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;; Syntax
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st nn)
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;;; =================
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;;; Basic definitions
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;;; =================
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(define variable? symbol?)
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;;; A state of a network is a mapping from the variables of the
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;;; network to their values.
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(define state? variable-mapping?)
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(define state/c (flat-named-contract 'state state?))
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;;; An update function is a function computing a value from the given
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;;; state.
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(define update-function? (-> state? any/c))
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;;; A network is a mapping from its variables to its update functions.
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(define network? variable-mapping?)
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(define network/c (flat-named-contract 'network network?))
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;;; Given a state s updates all the variables from xs. This
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;;; corresponds to a parallel mode.
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(define (update bn ; the Boolean network
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s ; the state to operate on
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xs) ; the variables to update
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(let ([new-s (hash-copy s)])
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(for ([x xs])
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(let ([f (hash-ref bn x)])
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(hash-set! new-s x (f s))))
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new-s))
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;;; A version of make-hash restricted to creating network states (see
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;;; contract).
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(define (make-state mappings) (make-hash mappings))
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;;; A shortcut for make-state.
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(define-syntax-rule (st mappings) (make-state mappings))
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;;; A version of make-hash restricted to creating networks.
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(define (make-network-from-functions funcs) (make-hash funcs))
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;;; =================================
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;;; Syntactic description of networks
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;;; =================================
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;;; An update function form is any form which can appear as a body of
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;;; a function and which can be evaluated with eval. For example,
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;;; '(and x y (not z)) or '(+ 1 a (- b 10)).
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(define update-function-form? any/c)
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;;; A Boolean network form is a mapping from its variables to the
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;;; forms of their update functions.
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(define network-form? variable-mapping?)
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;;; Build an update function from an update function form.
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(define (update-function-form->update-function form)
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(lambda (s) (eval-with s form)))
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;;; Build a network from a network form.
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(define (network-form->network bnf)
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(make-hash
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(hash-map bnf (lambda (x form)
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(cons x (update-function-form->update-function form))))))
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;;; Build a network from a list of pairs of forms of update functions.
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(define (make-network-from-forms forms)
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(network-form->network (make-hash forms)))
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;;; A shortcut for make-network-from-forms.
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(define-syntax-rule (nn forms) (make-network-from-forms forms))
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;;; ============================
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;;; Inferring interaction graphs
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;;; ============================
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;;; I allow any syntactic forms in definitions of Boolean functions.
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;;; I can still find out which Boolean variables appear in those
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;;; syntactic form, but I have no reliable syntactic means of finding
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;;; out what kind of action do they have (inhibition or activation)
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;;; since I cannot do Boolean minimisation (e.g., I cannot rely on not
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;;; appearing before a variable, since (not (not a)) is equivalent
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;;; to a). On the other hand, going through all Boolean states is
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;;; quite resource-consuming and thus not always useful.
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;;;
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;;; In this section I provide inference of both unsigned and signed
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;;; interaction graphs, but since the inference of signed interaction
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;;; graphs is based on analysing the dynamics of the networks, it may
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;;; be quite resource-consuming.
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