Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cleanup kmeans() seeding #267

Merged
merged 2 commits into from
Dec 19, 2023
Merged

Cleanup kmeans() seeding #267

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
633d78e
replace updatemin!() with min.()
Dec 19, 2023
0167254
initseeds(KmCentralityAlg): vectorize
Dec 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 4 additions & 15 deletions src/seeding.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -180,9 +180,8 @@ function initseeds!(iseeds::AbstractVector{<:Integer}, alg::KmppAlg,
iseeds[j] = p

# update mincosts
c = view(X, :, p)
colwise!(metric, tmpcosts, X, view(X, :, p))
updatemin!(mincosts, tmpcosts)
mincosts .= min.(mincosts, tmpcosts)
mincosts[p] = 0
end
end
Expand Down Expand Up @@ -211,7 +210,7 @@ function initseeds_by_costs!(iseeds::AbstractVector{<:Integer}, alg::KmppAlg,
iseeds[j] = p

# update mincosts
updatemin!(mincosts, view(costs, :, p))
mincosts .= min.(mincosts, view(costs, :, p))
mincosts[p] = 0
end
end
Expand Down Expand Up @@ -240,21 +239,11 @@ function initseeds_by_costs!(iseeds::AbstractVector{<:Integer}, alg::KmCentralit
k = length(iseeds)
check_seeding_args(n, k)

# compute score for each item
coefs = vec(sum(costs, dims=2))
for i = 1:n
@inbounds coefs[i] = inv(coefs[i])
end

# scores[j] = \sum_j costs[i,j] / (\sum_{j'} costs[i,j'])
# = costs[i,j] * coefs[i]
scores = costs'coefs
scores = costs'vec(mapslices(inv∘sum, costs, dims=2))

# lower score indicates better seeds
sp = sortperm(scores)
for i = 1:k
@inbounds iseeds[i] = sp[i]
end
copyto!(iseeds, 1, sortperm(scores), 1, k)
return iseeds
end

Expand Down
14 changes: 0 additions & 14 deletions src/utils.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,20 +64,6 @@ display_level(s::Symbol) = get(DisplayLevels, s) do
throw(ArgumentError("Invalid option display=:$s ($(join(valid_vals, ", ", ", or ")) expected)"))
end

##### update minimum value

function updatemin!(r::AbstractArray, x::AbstractArray)
n = length(r)
length(x) == n || throw(DimensionMismatch("Inconsistent array lengths."))
@inbounds for i = 1:n
xi = x[i]
if xi < r[i]
r[i] = xi
end
end
return r
end

function check_assignments(assignments::AbstractVector{<:Integer}, nclusters::Union{Integer, Nothing})
nclu = nclusters === nothing ? maximum(assignments) : nclusters
for (j, c) in enumerate(assignments)
Expand Down
Loading