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Issue #64: added n_init to kmeans #78

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Issue #64: added n_init to kmeans #78

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775eefc
Issue #64: added n_init to kmeans
lbollar Sep 30, 2016
f85cce7
cleaned up for PR
lbollar Sep 30, 2016
3ea7c39
removed tabs
lbollar Sep 30, 2016
fd296d4
removed line breaks to conform with style
lbollar Oct 5, 2016
50f0654
fixed another whitespace conflict
lbollar Oct 5, 2016
a9cb7ab
used vim command to hopefully fix trailing whitespace issues
lbollar Oct 5, 2016
b8b381b
extraneous newline
lbollar Oct 5, 2016
5ae2901
Merge branch 'master' into n_init
kmsquire Aug 26, 2017
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32 changes: 25 additions & 7 deletions src/kmeans.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ const _kmeans_default_init = :kmpp
const _kmeans_default_maxiter = 100
const _kmeans_default_tol = 1.0e-6
const _kmeans_default_display = :none
const _kmeans_default_n_init = 10

function kmeans!{T<:AbstractFloat}(X::Matrix{T}, centers::Matrix{T};
weights=nothing,
Expand All @@ -43,18 +44,33 @@ function kmeans(X::Matrix, k::Int;
weights=nothing,
init=_kmeans_default_init,
maxiter::Integer=_kmeans_default_maxiter,
n_init::Integer=_kmeans_default_n_init,
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I understand that n_init comes from Python's sklearn (#64), but it doesn't sound like a best choice for me.
Maybe something like n_tries to reflect that the parameter defines how many times the algorithm, rather than some initialization procedure, is run?

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@wildart wildart Sep 28, 2018 •
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or ntries? And wouldn't be an overkill to run 10 times? I recommend default value 1, because usually a quick partitioning is required and not necessarily best one. And, if one needs to find a best clustering, this parameter can be set to larger value explicitly.

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10 is what sklearn does at it sounds reasonable to me.
It isn't unusual to run 1000s of times, (that was done as the baseline for the affinity propagation paper)
If some need a quick partition they can ask for it.

The default shouldn't be so sensitive to random factors.

I think 10 strikes the right balance.
Though I could see argument for 3 or 30

tol::Real=_kmeans_default_tol,
display::Symbol=_kmeans_default_display)

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Another unrelated whitespace change


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One last remaining extraneous newline.

m, n = size(X)
(2 <= k < n) || error("k must have 2 <= k < n.")
iseeds = initseeds(init, X, k)
centers = copyseeds(X, iseeds)
kmeans!(X, centers;
weights=weights,
maxiter=maxiter,
tol=tol,
display=display)
n_init > 0 || throw(ArgumentError("n_init must be greater than 0"))

lowestcost::Float64 = Inf
local bestresult::KmeansResult

for i = 1:n_init
iseeds = initseeds(init, X, k)
centers = copyseeds(X, iseeds)
result = kmeans!(X, centers;
weights=weights,
maxiter=maxiter,
tol=tol,
display=display)

if result.totalcost < lowestcost
lowestcost = result.totalcost
bestresult = result
end
end
return bestresult
end

#### Core implementation
Expand All @@ -72,6 +88,8 @@ function _kmeans!{T<:AbstractFloat}(
tol::Real, # in: tolerance of change at convergence
displevel::Int) # in: the level of display



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Please remove the excess whitespace here and above. The change is unrelated to the PR.

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Trailing whitespace. I don't know what editor you use, but I think Atom trims trailing whitespace by default, and in Vim you can do :%s/\s\+$//g to remove it.

# initialize

k = size(centers, 2)
Expand Down
6 changes: 3 additions & 3 deletions test/kmeans.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ k = 10
x = rand(m, n)

# non-weighted
r = kmeans(x, k; maxiter=50)
r = kmeans(x, k; maxiter=50, n_init=2)
@test isa(r, KmeansResult{Float64})
@test size(r.centers) == (m, k)
@test length(r.assignments) == n
Expand All @@ -24,7 +24,7 @@ r = kmeans(x, k; maxiter=50)
@test_approx_eq sum(r.costs) r.totalcost

# non-weighted (float32)
r = kmeans(@compat(map(Float32, x)), k; maxiter=50)
r = kmeans(@compat(map(Float32, x)), k; maxiter=50, n_init=2)
@test isa(r, KmeansResult{Float32})
@test size(r.centers) == (m, k)
@test length(r.assignments) == n
Expand All @@ -37,7 +37,7 @@ r = kmeans(@compat(map(Float32, x)), k; maxiter=50)

# weighted
w = rand(n)
r = kmeans(x, k; maxiter=50, weights=w)
r = kmeans(x, k; maxiter=50, weights=w, n_init=2)
@test isa(r, KmeansResult{Float64})
@test size(r.centers) == (m, k)
@test length(r.assignments) == n
Expand Down