dds/scribblings/networks.scrbl

#lang scribble/manual
@(require (for-label racket graph "../networks.rkt" "../utils.rkt" "../functions.rkt" racket/random racket/hash))

@title[#:tag "networks"]{dds/networks: Formal Dynamical Networks}

@defmodule[dds/networks]

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

@section[#:tag "networks-basics"]{Basic definitions}

@section{Syntactic description of networks}

@section{Inferring interaction graphs}

This section provides inference of both unsigned and signed interaction graphs.
Since the inference of signed interaction 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 @emph{syntactic} interaction graphs and
interaction graphs generated from the dynamics of the network.
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.

@section{Dynamics of networks}

This section contains definitions for building and analysing the dynamics
of networks.

@section{Tabulating functions and networks}

@section{Constructing functions and networks}

@section{Random functions and networks}

@section{TBF/TBN and SBF/SBN}

This section defines threshold Boolean functions (TBF) and networks (TBN), as
well as sign Boolean functions (SBF) and networks (SBN).