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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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Issue #64: added n_init to kmeans
lbollar Sep 30, 2016
f85cce7
cleaned up for PR
lbollar Sep 30, 2016
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removed tabs
lbollar Sep 30, 2016
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removed line breaks to conform with style
lbollar Oct 5, 2016
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fixed another whitespace conflict
lbollar Oct 5, 2016
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used vim command to hopefully fix trailing whitespace issues
lbollar Oct 5, 2016
b8b381b
extraneous newline
lbollar Oct 5, 2016
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Merge branch 'master' into n_init
kmsquire Aug 26, 2017
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54 changes: 35 additions & 19 deletions src/kmeans.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,19 @@ type KmeansResult{T<:AbstractFloat} <: ClusteringResult
counts::Vector{Int} # number of samples assigned to each cluster (k)
cweights::Vector{Float64} # cluster weights (k)
totalcost::Float64 # total cost (i.e. objective) (k)
iterations::Int # number of elapsed iterations
iterations::Int # number of elapsed iterations
converged::Bool # whether the procedure converged
end

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,
maxiter::Integer=_kmeans_default_maxiter,
maxiter::Integer=_kmeans_default_maxiter,
tol::Real=_kmeans_default_tol,
display::Symbol=_kmeans_default_display)

Expand All @@ -34,27 +35,42 @@ function kmeans!{T<:AbstractFloat}(X::Matrix{T}, centers::Matrix{T};
counts = Array(Int, k)
cweights = Array(Float64, k)

_kmeans!(X, conv_weights(T, n, weights), centers,
assignments, costs, counts, cweights,
_kmeans!(X, conv_weights(T, n, weights), centers,
assignments, costs, counts, cweights,
round(Int, maxiter), tol, display_level(display))
end

function kmeans(X::Matrix, k::Int;
function kmeans(X::Matrix, k::Int;
weights=nothing,
init=_kmeans_default_init,
maxiter::Integer=_kmeans_default_maxiter,
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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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 @@ -68,8 +84,8 @@ function _kmeans!{T<:AbstractFloat}(
costs::Vector{T}, # out: costs of the resultant assignments (n)
counts::Vector{Int}, # out: the number of samples assigned to each cluster (k)
cweights::Vector{Float64}, # out: the weights of each cluster
maxiter::Int, # in: maximum number of iterations
tol::Real, # in: tolerance of change at convergence
maxiter::Int, # in: maximum number of iterations
tol::Real, # in: tolerance of change at convergence
displevel::Int) # in: the level of display

# initialize
Expand Down Expand Up @@ -153,7 +169,7 @@ function _kmeans!{T<:AbstractFloat}(
end
end

return KmeansResult(centers, assignments, costs, counts, cweights,
return KmeansResult(centers, assignments, costs, counts, cweights,
@compat(Float64(objv)), t, converged)
end

Expand Down Expand Up @@ -245,7 +261,7 @@ function update_centers!{T<:AbstractFloat}(
n::Int = size(x, 2)
k::Int = size(centers, 2)

# initialize center weights
# initialize center weights
for i = 1 : k
if to_update[i]
cweights[i] = 0.
Expand Down Expand Up @@ -299,7 +315,7 @@ function update_centers!{T<:AbstractFloat}(
n::Int = size(x, 2)
k::Int = size(centers, 2)

# initialize center weights
# initialize center weights
for i = 1 : k
if to_update[i]
cweights[i] = 0.
Expand All @@ -314,7 +330,7 @@ function update_centers!{T<:AbstractFloat}(
if wj > 0
@inbounds cj = assignments[j]
1 <= cj <= k || error("assignment out of boundary.")

if to_update[cj]
rj = view(centers, :, cj)
xj = view(x, :, j)
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