networks: Remove the old functions for building interaction graphs.
These functions mix interaction graphs derived from the expressions defining the network with deriving the interactions from the dynamics, which does not always yield the same result. Also, some functions only worked for Boolean networks, including get-interaction-sign. Additionally, these functions are among the first ones I wrote in dds, so there are a couple of things which can be written in a better way.
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Sergiu Ivanov
parent
70de0ec718
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1 changed files with 0 additions and 185 deletions
185
networks.rkt
185
networks.rkt
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@ -37,11 +37,6 @@
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[make-01-domains (-> (listof variable?) (hash/c variable? (list/c 0 1)))]
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[make-01-domains (-> (listof variable?) (hash/c variable? (list/c 0 1)))]
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[build-all-boolean-states (-> (listof variable?) (listof state?))]
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[build-all-boolean-states (-> (listof variable?) (listof state?))]
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[build-all-01-states (-> (listof variable?) (listof state?))]
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[build-all-01-states (-> (listof variable?) (listof state?))]
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[get-interaction-sign (-> network? domain-mapping/c variable? variable? (or/c '+ '- '0))]
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[build-signed-interaction-graph/form (-> network-form? domain-mapping/c graph?)]
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[build-boolean-signed-interaction-graph/form (-> network-form? graph?)]
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[build-signed-interaction-graph (-> network? domain-mapping/c graph?)]
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[build-boolean-signed-interaction-graph (-> network? graph?)]
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[make-asyn (-> (listof variable?) mode?)]
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[make-asyn (-> (listof variable?) mode?)]
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[make-syn (-> (listof variable?) mode?)]
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[make-syn (-> (listof variable?) mode?)]
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[make-dynamics-from-func (-> network? (-> (listof variable?) mode?) dynamics?)]
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[make-dynamics-from-func (-> network? (-> (listof variable?) mode?) dynamics?)]
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@ -402,186 +397,6 @@
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#hash((a . 1) (b . 0))
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#hash((a . 1) (b . 0))
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#hash((a . 1) (b . 1))))))
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#hash((a . 1) (b . 1))))))
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;;; Given two interacting variables of a network and the domains
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;;; of the variables, returns '+ if the interaction is monotonously
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;;; increasing, '- if it is monotonously decreasing, and '0 otherwise.
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;;;
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;;; This function does not check whether the two variables indeed
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;;; interact. Its behaviour is undefined if the variables do not
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;;; interact.
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;;;
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;;; /!\ This function iterates through almost all of the states of the
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;;; network, so its performance decreases very quickly with network
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;;; size.
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(define (get-interaction-sign network doms x y)
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(let* ([dom-x (hash-ref doms x)]
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[dom-y (hash-ref doms y)]
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;; Replace the domain of x by a dummy singleton.
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[doms-no-x (hash-set doms x '(#f))]
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;; Build all the states, but as if x were not there: since I
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;; replace its domain by a singleton, all states will contain
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;; the same value for x.
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[states-no-x (build-all-states doms-no-x)]
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;; Go through all states, then through all ordered pairs of
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;; values of x, generate pairs of states (s1, s2) such that x
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;; has a smaller value in s1, and check that updating y in s1
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;; yields a smaller value than updating y in s2. I rely on
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;; the fact that the domains are ordered.
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[x-y-interactions (for*/list ([s states-no-x]
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[x1 dom-x] ; ordered pairs of values of x
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[x2 (cdr (member x1 dom-x))])
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(let* ([s1 (hash-set s x x1)] ; s1(x) < s2(x)
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[s2 (hash-set s x x2)]
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[y1 ((hash-ref network y) s1)]
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[y2 ((hash-ref network y) s2)])
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;; y1 <= y2?
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(<= (index-of dom-y y1) (index-of dom-y y2))))])
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(cond
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;; If, in all interactions, y1 <= y2, then we have an
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;; increasing/promoting interaction between x and y.
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[(andmap (λ (x) (eq? x #t)) x-y-interactions) '+]
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;; If, in all interactions, y1 > y2, then we have an
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;; decreasing/inhibiting interaction between x and y.
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[(andmap (λ (x) (eq? x #f)) x-y-interactions) '-]
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;; Otherwise the interaction is neither increasing nor
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;; decreasing.
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[else '0])))
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(module+ test
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(test-case "get-interaction-sign"
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(define n #hash((a . (not b)) (b . a)))
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(define doms (make-boolean-domains '(a b)))
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(check-equal? (get-interaction-sign (network-form->network n) doms 'a 'b) '+)
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(check-equal? (get-interaction-sign (network-form->network n) doms 'b 'a) '-)))
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;;; Constructs a signed interaction graph of a given network form,
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;;; given the ordered domains of its variables. The order on the
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;;; domains determines the signs which will appear on the interaction
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;;; graph.
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;;;
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;;; /!\ This function iterates through almost all states of the
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;;; network for every arrow in the unsigned interaction graph, so its
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;;; performance decreases very quickly with the size of the network.
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(define (build-signed-interaction-graph/form network-form doms)
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(let ([ig (build-syntactic-interaction-graph network-form)]
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[network (network-form->network network-form)])
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;; Label every edge of the interaction graph with the sign.
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(define sig
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(weighted-graph/directed
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(for/list ([e (in-edges ig)])
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(match-let ([(list x y) e])
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(list (get-interaction-sign network doms x y)
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x y)))))
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;; Ensure that every variable of the network appears in the signed
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;; interaction graph as well.
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(for ([v (in-vertices ig)])
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(add-vertex! sig v))
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sig))
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(module+ test
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(test-case "build-signed-interaction-graph/form"
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(define n #hash((a . (not b)) (b . a)))
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(define doms (make-boolean-domains '(a b)))
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(define sig1 (build-signed-interaction-graph/form n doms))
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(check-true (has-vertex? sig1 'a))
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(check-true (has-vertex? sig1 'b))
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(check-false (has-vertex? sig1 'c))
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(check-false (has-edge? sig1 'a 'a))
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(check-true (has-edge? sig1 'b 'a))
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(check-false (has-edge? sig1 'b 'b))
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(check-false (has-edge? sig1 'c 'b))
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(check-false (has-edge? sig1 'c 'a))
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(check-equal? (edge-weight sig1 'a 'b) '+)
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(check-equal? (edge-weight sig1 'b 'a) '-)))
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;;; Calls build-signed-interaction-graph with the Boolean domain for
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;;; all variable.
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;;;
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;;; /!\ The same performance warning applies as for
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;;; build-signed-interaction-graph.
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(define (build-boolean-signed-interaction-graph/form network-form)
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(build-signed-interaction-graph/form
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network-form
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(make-boolean-domains (hash-keys network-form))))
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(module+ test
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(test-case "build-boolean-signed-interaction-graph/form"
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(define n #hash((a . (not b)) (b . a)))
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(define sig2 (build-boolean-signed-interaction-graph/form n))
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(check-true (has-vertex? sig2 'a))
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(check-true (has-vertex? sig2 'b))
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(check-false (has-vertex? sig2 'c))
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(check-false (has-edge? sig2 'a 'a))
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(check-true (has-edge? sig2 'b 'a))
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(check-false (has-edge? sig2 'b 'b))
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(check-false (has-edge? sig2 'c 'b))
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(check-false (has-edge? sig2 'c 'a))
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(check-equal? (edge-weight sig2 'a 'b) '+)
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(check-equal? (edge-weight sig2 'b 'a) '-)))
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;;; Similar to build-signed-interaction-graph/form, but operates on a
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;;; network rather than a form. The resulting graph only includes the
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;;; edges for positive or negative interactions.
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;;;
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;;; This function has operates with much less knowledge than
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;;; build-signed-interaction-graph/form, so prefer using the latter
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;;; when you can get a network form.
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;;;
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;;; /!\ This function iterates through all states of the network for
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;;; every arrow in the unsigned interaction graph, so its performance
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;;; decreases very quickly with the size of the network.
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(define (build-signed-interaction-graph network doms)
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(define sig
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(weighted-graph/directed
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(for*/fold ([edges '()])
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([(x _) (in-hash network)]
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[(y _) (in-hash network)])
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(match (get-interaction-sign network doms x y)
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['0 edges]
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[sign (cons (list sign x y) edges)]))))
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;; Ensure that all variables of the network appear in the signed
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;; interaction graph.
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(for ([(v _) (in-hash network)])
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(add-vertex! sig v))
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sig)
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;;; Calls build-signed-interaction-graph assuming that the domains of
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;;; all variables are Boolean.
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;;;
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;;; This function has operates with much less knowledge than
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;;; build-boolean-signed-interaction-graph/form, so prefer using the
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;;; latter when you can get a network form.
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;;;
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;;; /!\ This function iterates through all states of the network for
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;;; every arrow in the unsigned interaction graph, so its performance
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;;; decreases very quickly with the size of the network.
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(define (build-boolean-signed-interaction-graph network)
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(build-signed-interaction-graph network (make-boolean-domains (hash-keys network))))
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(module+ test
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(test-case "build-signed-interaction-graph, build-boolean-signed-interaction-graph"
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(define n #hash((a . (not b)) (b . a)))
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(define sig3 (build-boolean-signed-interaction-graph (network-form->network n)))
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(check-true (has-vertex? sig3 'a))
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(check-true (has-vertex? sig3 'b))
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(check-equal? (edge-weight sig3 'a 'a) '+)
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(check-equal? (edge-weight sig3 'b 'b) '+)
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(check-equal? (edge-weight sig3 'a 'b) '+)
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(check-equal? (edge-weight sig3 'b 'a) '-)))
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;;; Interaction graphs for networks without interactions must still
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;;; contain all nodes.
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(module+ test
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(test-case "Interaction must graphs always contain all nodes."
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(define n #hash((a . #t) (b . #t)))
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(define ig (build-syntactic-interaction-graph n))
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(define sig-nf (build-boolean-signed-interaction-graph/form n))
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(define sig (build-boolean-signed-interaction-graph (network-form->network n)))
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(check-equal? (get-vertices ig) '(b a))
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(check-true (empty? (get-edges ig)))
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(check-equal? (get-vertices sig-nf) '(b a))
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(check-true (empty? (get-edges sig-nf)))
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(check-equal? (get-vertices sig) '(b a))))
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;;; ====================
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;;; ====================
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