epydemic
- addition-deletion process
A
process
that adds and removes nodes from a network. The usual modelAdditionDeletionNetworks
adds nodes at a constant rate and with constant degree, removes nodes randomly at a constant rate, and connects new nodes to existing nodes according to some probabilistic attachment kernel.- clustering
The tendency to find small sets of nodes with multiple paths between them. The most common kind of clustering looks for triangles of edges connecting triples of nodes. This can be made precise by defining a clustering coefficient that counts the number of triangles present out of all the possible triangles that could be formed in the network. An example of a network
microstructure
.- community
Another word for
modularity
.- compartments
The possible dynamical states in a
compartmented model of disease
.- compartmented model of disease
A disease model that represents the progression of a disease as a set of discrete compartments with transitions possible between them. Transitions typically occur with some base probability, which might be fixed or might vary across the course of the simulation. See Hethcote
Hethcote-CompartmentedModels
for a survey,- component
A set of nodes connected by edges. A node with a single component is called fully connected.
- contact tree
The way in which individuals were infected during thhe infection. Each node is an infected individual, with edges representing the individuals that individual infected.
While it's common talk of a contact tree, this will only be the case if there is an identifiable "patient zero" from whom all infections arise. In the more general case of multiple people initially infected, the contact tree will actually be a contact forest of multiple independent trees, each one rooted at an initially-infected individual.
- continuous time
A simulation mode in which events occur at unique times represented by real numbers. No two events ever happen simultaneously, but they can be separated by an arbitrarily small interval. Continuous-time simulations can be made statistically exact and run faster for situations in which there are long periods where no events occur.
- degree distribution
The way in which the numbers of neighbours each node has varies. The most basic measure of network topology. More precisely, the degree distribution is the probability pk that a node chosen at random from the network will have degree k, for all values of k. Networks can have the same degree distribution but different kinds of
microstructure
andmesostructure
, so degree distribution isn't always enough on its own to characterise a network completely.- discrete time
A simulation mode in which time progresses in single integer timesteps. During each timestep a collection of events can occur. Discrete-time simulations can be easier to code and understand.
- dynamical state
The state of a node or edge at some point in the simulation. These typically reflect the
compartments
of the simulation, but may be more complex and comprise a vector of information.- epidemic threshold
The critical point of transmissibility at which an outbreak becomes an epidemic and infects a substantial fraction of the network. The existence and value of an epidemic threshold depend on the topology of the network as well as the disease parameters.
- event
A simulation event that changes the state of the underlying network or simulation. Events can occur in
continuous time
ordiscrete time
.- event function
A function called when an
event
fires to perform the action required. Event functions take three arguments: the current simulation time and the element at which the event occurs (which will be selected by the chosenprocess dynamics
). Elements are typically either nodes or edges, depending in thelocus
at which the event occurs.- generating functions
A mathematical tool for working with entire probability distributions, often used in network science research because of its flexibility. They're often used when describing the
degree distribution
of a network. See Newman et aliaArbitraryDegreeDistributions
for a network science introduction and Wilfgeneratingfunctionology
for a more detailed treatment.- giant connected component
In
percolation
(and other) processes, the giant connected component (sometimes called the GCC, or simply "the giant component") is acomponent
that occupies a substantial fraction of the network: basically the GCC forms when the size of thelargest connected component
is "very large". The formal definition of when "large" becomes "giant" is quite complicated and not very practical; a common working definition is that the LCC is "giant" when it includes more that a hundredth of the network's nodesPercolationSmearedPhaseTransition
.- Gillespie simulation
A simulation technique developed initially for ab initio chemistry simulations
Gillespie76,Gillespie77
.- largest connected component
The largest
component
in the network. Often called the LCC, and sometimes called thegiant connected component
when it becomes very large. In some cases we may also be interested in the sizes of other components: for example the second-largest connected component (SLCC) can give useful information.- locus
A "place" at which dynamics can occur, that is to say, where nodes can change compartments and any other tasks can happen. Each
event
is associated with a particular locus: the locus contains the set of nodes or edges to which the event may be applied, while the event defines what happens. All loci are derived from theLocus
class.- mesostructure
A recognisable pattern in the nodes and edges that occupies a substantial fraction of the network. Usually independent of larger-scale properties like
degree distribution
. A common mesostructure ismodularity
.- microstructure
A recognisable pattern or
motif
of nodes and edges that only affects a small number of nodes. The most common kind of microstructure isclustering
.- modularity
Also known as "
community
structure", modular networks consist of sub-networks that are substantially more connected within themselves than they are to each other.- motif
A pattern of a small number of nodes and edges occurring frequently in a network. A triangle is a common motif, as are cycles and cliques. The building blocks of
microstructure
.- network generator
A process that samples a class or ensemble of random networks to create an instance. A typical example is the class of networks with Poisson degree distribution (the ER networks), defined by the order and mean degree of the network. May generate ensembles with specific
microstructure
ormesostructure
.- percolation
A process that randomly "occupies" nodes or edges in a network with a given probability.
- percolation threshold
The occupation probability in a percolation process above which a
giant connected component
forms. The size of the GCC rises rapidly once the threshold is passed, making the threshold generally "crisp".- posted event
An
event
posted for a definite future time. Theprocess dynamics
will execute the posted events at the appropriate time- process
A system that associates a state vector with each node (and possibly edge) in a network, and describes how they evolve over time.
- process dynamics
The simulation approach used, which selects how and when each
event
fires. Process dynamics execute events in time order from two possible sources: a random distribution that chooses an event based on their relative probability or rate; and anyposted event
that has been scheduled.- SEIR
A
compartmented model of disease
where nodes are Exposed to the disease and become infectious for a period before moving to being Infected. This can be used to model pre-symptomatic infectivity.- SIS
A
compartmented model of disease
where nodes go from being Susceptible to the disease, to Infected and able to infect others, and then recover back to Susceptible.- SIR
A
compartmented model of disease
where nodes go from being Susceptible to the disease, to Infected and able to infect others, and are then Removed and take no further part in the dynamics.- stochastic event
An
event
whose occurrence is determined by a probability distribution. In acompartmented model of disease
, for example, the passage of an infection over an edge is a stochastic event, the rate and location of which are determined according to the distribution of infections.- stochastic process
A
process
whose exact progression is determined by random variables drawn from particular probability distributions.- stochastic dynamics
Also known as Gillespie dynamics, this
process dynamics
operates incontinuous time
with one event occurring at each time point.- synchronisation
A
process
that places an oscillator on each node in a network and allow them to interact. In many cases the intention is to have the oscillators converge to a common phase; this can be difficult to achieve, and gives rise to a huge set of interesting possible dynamics.- synchronous dynamics
A
process dynamics
usingdiscrete time
, where a simulation passes through a sequence of discrete timesteps which may include several (or no) events happening.