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Re: Finding Clusters
*To*: mathgroup at smc.vnet.net
*Subject*: [mg104644] Re: Finding Clusters
*From*: Szabolcs Horvát <szhorvat at gmail.com>
*Date*: Thu, 5 Nov 2009 03:53:23 -0500 (EST)
*References*: <200911030751.CAA01018@smc.vnet.net> <hcr78s$8c4$1@smc.vnet.net>
On 2009.11.04. 7:34, Fred Simons wrote:
> Here is a very short, very fast but not very simple solution:
>
> components[lst_List] := Module[{f},
> Do[Set @@ f /@ pair, {pair, lst}]; GatherBy[Union @@ lst, f]]
>
I enjoyed Fred Simons's solution tremendously.
I tried to speed it up a bit.
I compared the speed of components[] with the speed of WeakComponents
(from the GraphUtilities package) for random graphs (e.g.
RandomInteger[50000, {30000, 2}]). It seems that components[] is faster
than WeakComponents for as long as the graph doesn't have very large
connected components. However, as soon as large connected components
appear, components[] slows down a lot.
I looked into the source of WeakComponents to find out how it works, but
it turns out it uses undocumented functions, such as
SparseArray`StronglyConnectedComponents
The reason for the slowdown of components[] when large connected
components are present is that the f[] function needs to be evaluated in
several steps. E.g. for the graph {{1,2},{2,3},{3,4}}, the definition
of f will include f[1]=f[2], f[2]=f[3], f[3]=f[4], so the evaluation of
f[1] will take 3 steps.
I tried to remedy this by changing f so that it re-defines itself each
time the left-hand-side of a particular definition can be evaluated
further. With the above example, evaluating f[1] would cause the
definition of f[1] to change from f[1]=f[2] to f[1]=f[4] (as f[2]
evaluates to f[4]). Here's the solution:
setSpecial[lhs_, rhs_] /; rhs =!= lhs :=
(lhs := With[{val = #1}, lhs := #0[val]; val] &[rhs])
components2[lst_List] :=
Module[{f},
Do[setSpecial @@ f /@ pair, {pair, lst}];
GatherBy[Union @@ lst, f]
]
This modified components2[] seems to be faster than WeakComponents[]
even for single-component random graphs, however, it is limited by
$RecursionLimit (which can't be increased indefinitely without risking a
crash)
Szabolcs
P.S. Here's the code I used to compare the speed of components[] and
WeakComponents[]. For 'a' greater than about 0.5 components[] gets slow.
a = 0.7;
tw = Table[
g = RandomInteger[n, {Ceiling[a n], 2}];
{n, First@Timing[WeakComponents[Rule @@@ g]]},
{n, 2^Range[11, 16]}
]
tc = Table[
g = RandomInteger[n, {Ceiling[a n], 2}];
{n, First@Timing[components[g]]},
{n, 2^Range[11, 16]}
]
tc2 = Table[
g = RandomInteger[n, {Ceiling[a n], 2}];
{n, First@Timing[components2[g]]},
{n, 2^Range[11, 16]}
]
ListLogLogPlot[{tw, tc, tc2}, Joined -> True,
PlotMarkers -> Automatic]
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