From 1f1d18060a9ac99879f53895375741fc4619f01e Mon Sep 17 00:00:00 2001
From: Christian Guinard <28689358+christiangnrd@users.noreply.github.com>
Date: Wed, 9 Apr 2025 10:47:05 -0300
Subject: [PATCH 1/4] Implement Adjusted Mutual Information

---
 Project.toml               | 11 ++++++-
 ext/SpecialFunctionsExt.jl | 64 ++++++++++++++++++++++++++++++++++++++
 src/Clustering.jl          |  4 +++
 src/mutualinfo.jl          | 63 +++++++++++++++++++++++++++++++------
 test/mutualinfo.jl         | 26 +++++++++++++---
 test/runtests.jl           |  1 +
 6 files changed, 155 insertions(+), 14 deletions(-)
 create mode 100644 ext/SpecialFunctionsExt.jl

diff --git a/Project.toml b/Project.toml
index b68444e7..f6460845 100644
--- a/Project.toml
+++ b/Project.toml
@@ -9,12 +9,20 @@ NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
+[weakdeps]
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+
+[extensions]
+SpecialFunctionsExt = "SpecialFunctions"
+
 [compat]
 Distances = "0.10.9"
 NearestNeighbors = "0.4"
+SpecialFunctions = ">= 0.8"
 Statistics = "1"
 StatsBase = "0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.31, 0.32, 0.33, 0.34"
 julia = "1"
@@ -26,9 +34,10 @@ Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["CodecZlib", "Statistics", "LinearAlgebra", "SparseArrays", "Distances", "Random", "DelimitedFiles", "StableRNGs", "Test"]
+test = ["CodecZlib", "Statistics", "LinearAlgebra", "SparseArrays", "Distances", "Random", "DelimitedFiles", "SpecialFunctions", "StableRNGs", "Test"]
diff --git a/ext/SpecialFunctionsExt.jl b/ext/SpecialFunctionsExt.jl
new file mode 100644
index 00000000..d4289cd1
--- /dev/null
+++ b/ext/SpecialFunctionsExt.jl
@@ -0,0 +1,64 @@
+module SpecialFunctionsExt # Should be same name as the file (just like a normal package)
+
+using SpecialFunctions: loggamma
+using StatsBase: counts
+using Statistics: middle
+
+import Clustering: _mutualinfo
+
+function _mutualinfo(::Val{:adjusted}, a, b; aggregate::Symbol = :mean)
+    norm_f = if aggregate === :mean
+        middle
+    elseif aggregate === :geomean
+        (a,b) -> sqrt(a*b)
+    elseif aggregate === :max
+        max
+    elseif aggregate === :min
+        min
+    else
+        throw(ArgumentError("Valid options for `aggregate` are: `mean`, `geomean`, `max`, `min`"))
+    end
+
+    return _mutualinfo(counts(a, b)) do hck, hc, hk, rows, cols, N
+        mi = hc - hck
+        emi = _expectedmutualinfo(rows, cols, N)
+        normalizer = norm_f(hc, hk)
+        denominator = normalizer - emi
+        (mi - emi) / denominator
+    end
+end
+
+# Adjusted Mutual Information
+
+function _expectedmutualinfo(a, b, n_samples)
+    nijs = 1:max(maximum(a), maximum(b))
+
+    term1 = nijs ./ n_samples
+
+    log_ab = [log(a[i]) + log(b[j]) for i in eachindex(a), j in eachindex(b)]
+    log_Nnij = log(n_samples) .+ log.(nijs)
+
+    gln_a = loggamma.(a .+ 1)
+    gln_b = loggamma.(b .+ 1)
+    gln_Na = loggamma.(n_samples .- a .+ 1)
+    gln_Nb = loggamma.(n_samples .- b .+ 1)
+    gln_Nnij = loggamma.(nijs .+ 1) .+ loggamma.(n_samples + 1)
+
+    emi = zero(Float64)
+    for i in eachindex(a), j in eachindex(b)
+        nij_idxs = max(1, a[i] - n_samples + b[j]):min(a[i], b[j])
+        for nij in nij_idxs
+            term2 = log_Nnij[nij] - log_ab[i,j]
+            gln = (
+                gln_a[i] + gln_b[j] + gln_Na[i] + gln_Nb[j] - gln_Nnij[nij] -
+                loggamma(a[i] - nij + 1) - loggamma(b[j] - nij + 1) -
+                loggamma(n_samples - a[i] - b[j] + nij + 1)
+            )
+            term3 = exp(gln)
+            emi += (term1[nij] * term2 * term3)
+        end
+    end
+    return emi
+end
+
+end # module
diff --git a/src/Clustering.jl b/src/Clustering.jl
index fae9ee82..0c5ee6d3 100644
--- a/src/Clustering.jl
+++ b/src/Clustering.jl
@@ -100,4 +100,8 @@ module Clustering
     include("hclust.jl")
 
     include("deprecate.jl")
+
+    if !isdefined(Base, :get_extension)
+        include("../ext/SpecialFunctionsExt.jl")
+    end
 end
diff --git a/src/mutualinfo.jl b/src/mutualinfo.jl
index 65b0a527..817ba413 100644
--- a/src/mutualinfo.jl
+++ b/src/mutualinfo.jl
@@ -1,6 +1,6 @@
 # Mutual Information
 
-function _mutualinfo(A::AbstractMatrix{<:Integer}, normed::Bool)
+@inline function _mutualinfo(f, A::AbstractMatrix{<:Integer})
     N = sum(A)
     (N == 0.0) && return 0.0
 
@@ -14,16 +14,21 @@ function _mutualinfo(A::AbstractMatrix{<:Integer}, normed::Bool)
     hc = entArows/N + log(N)
     hk = entAcols/N + log(N)
 
-    mi = hc - hck
-    return if normed
-        2*mi/(hc+hk)
+    f(hck,hc,hk,rows,cols,N)
+end
+
+function _mutualinfo(::Val{T}, a, b; kwargs...) where T
+    if T === :adjusted && isempty(kwargs)
+        error("Error: mutualinfo(): `method=:adjusted` requires SpecialFunctions package to be loaded")
+    elseif T !== :classic && T !== :normalized
+        throw(ArgumentError("mutualinfo(): `method=:$(T)` is not supported"))
     else
-        mi
+        throw(ArgumentError("mutualinfo(): unsupported kwargs used. See the `mutualinfo` docstring for more information"))
     end
 end
 
 """
-    mutualinfo(a, b; normed=true) -> Float64
+    mutualinfo(a, b; method=:normalized, kwargs...) -> Float64
 
 Compute the *mutual information* between the two clusterings of the same
 data points.
@@ -31,11 +36,51 @@ data points.
 `a` and `b` can be either [`ClusteringResult`](@ref) instances or
 assignments vectors (`AbstractVector{<:Integer}`).
 
-If `normed` parameter is `true` the return value is the normalized mutual information (symmetric uncertainty),
-see "Data Mining Practical Machine Tools and Techniques", Witten & Frank 2005.
+`method` can be one of `:classic`, `:normalized` (default), or `:adjusted`, to calculate the
+original mutual information score, the normalized mutual information, or the adjusted mutual
+information respectively.
+
+When `method=:adjusted`, the `aggregate` kwarg determines how the normalizer
+in the denominator is computed. It can be one of:
+- `:mean`: The arithmetic mean of two values
+- `:geomean`:  The geometric mean of two values
+- `:max`: The highest of two values
+- `:min`: The lowest of two values
 
 # References
 > Vinh, Epps, and Bailey, (2009). *Information theoretic measures for clusterings comparison*.
 > Proceedings of the 26th Annual International Conference on Machine Learning - ICML ‘09.
+
+> "Data Mining Practical Machine Tools and Techniques", Witten & Frank 2005.
 """
-mutualinfo(a, b; normed::Bool=true) = _mutualinfo(counts(a, b), normed)
+function mutualinfo(a, b; method::Union{Nothing, Symbol} = nothing, normed::Union{Nothing, Bool} = nothing, kwargs...)
+    # Disallow `method` and `normed` to be used together
+    if isnothing(method)
+        isnothing(normed) || Base.depwarn("`normed` kwarg is deprecated, please use `method=:normalized` instead of `normed=true`, and `method=:classic` instead of `normed=false'", :mutualinfo)
+        method = if isnothing(normed) || normed
+            :normalized
+        else
+            :classic
+        end
+    else
+        isnothing(normed) || throw(ArgumentError("`normed` kwarg is not compatible with `method` kwarg"))
+    end
+    # Little hack to ensure the correct error is thrown
+    if method === :adjusted && length(kwargs) >= 1 && :aggregate ∉ keys(kwargs)
+        method = :classic
+    end
+
+    _mutualinfo(Val(method), a, b; kwargs...)
+end
+
+function _mutualinfo(::Val{:normalized}, a, b)
+    return _mutualinfo(counts(a, b)) do hck, hc, hk, _, _, _
+        mi = hc - hck
+        2*mi/(hc+hk)
+    end
+end
+function _mutualinfo(::Val{:classic}, a, b)
+    return _mutualinfo(counts(a, b)) do hck, hc, _, _, _, _
+        hc - hck
+    end
+end
diff --git a/test/mutualinfo.jl b/test/mutualinfo.jl
index f2caeed3..a29e203b 100644
--- a/test/mutualinfo.jl
+++ b/test/mutualinfo.jl
@@ -6,13 +6,31 @@ using Clustering
     # https://nlp.stanford.edu/IR-book/html/htmledition/evaluation-of-clustering-1.html
     a1 = [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3]
     a2 = [1, 1, 1, 1, 1, 2, 3, 3, 1, 2, 2, 2, 2, 2, 3, 3, 3]
-    @test mutualinfo(a1, a2, normed=false) ≈ 0.39 atol=1.0e-2
-    @test mutualinfo(a1, a2) ≈ 0.36 atol=1.0e-2
+    @test mutualinfo(a1, a2; method=:classic) ≈ 0.39 atol=1.0e-2
+    @test mutualinfo(a1, a2;) ≈ 0.36 atol=1.0e-2
+    @test mutualinfo(a1, a2; method=:adjusted) ≈ 0.2602 atol=1.0e-4
+    @test mutualinfo(a1, a2; method=:adjusted, aggregate=:geomean) ≈ 0.2602 atol=1.0e-4
+    @test mutualinfo(a1, a2; method=:adjusted, aggregate=:max) ≈ 0.2547 atol=1.0e-4
+    @test mutualinfo(a1, a2; method=:adjusted, aggregate=:min) ≈ 0.2659 atol=1.0e-4
+
+    # test deprecated kwarg
+    @test mutualinfo(a1, a2; normed=false) ≈ 0.39 atol=1.0e-2
+    @test mutualinfo(a1, a2; normed=true) ≈ 0.36 atol=1.0e-2
 
     # https://doi.org/10.1186/1471-2105-7-380
     a1 = [1, 1, 1, 1, 1, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 2]
     a2 = [1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4]
-    @test mutualinfo(a1, a2, normed=false) ≈ 0.6 atol=0.1
-    @test mutualinfo(a1, a2) ≈ 0.5 atol=0.1
+    @test mutualinfo(a1, a2; method=:classic) ≈ 0.6 atol=0.1
+    @test mutualinfo(a1, a2; method=:normalized) ≈ 0.5 atol=0.1
+    @test mutualinfo(a1, a2; method=:adjusted, aggregate=:mean) ≈ 0.3839 atol=1.0e-4
+    @test mutualinfo(a1, a2; method=:adjusted, aggregate=:geomean) ≈ 0.3861 atol=1.0e-4
+    @test mutualinfo(a1, a2; method=:adjusted, aggregate=:max) ≈ 0.3437 atol=1.0e-4
+    @test mutualinfo(a1, a2; method=:adjusted, aggregate=:min) ≈ 0.4348 atol=1.0e-4
+
+    # test errors
+    @test_throws "ArgumentError: `normed` kwarg is not compatible with `method` kwarg" mutualinfo(a1, a2; method=:adjusfted, normed=false)
+    @test_throws "ArgumentError: mutualinfo(): `method=:adjusfted` is not supported" mutualinfo(a1, a2; method=:adjusfted, aggregate=:min)
+    @test_throws "ArgumentError: mutualinfo(): unsupported kwargs used." mutualinfo(a1, a2; method=:adjusted, notaggregate=:min)
+    @test_throws "ArgumentError: mutualinfo(): unsupported kwargs used." mutualinfo(a1, a2; method=:classic, notaggregate=:min)
 
 end
diff --git a/test/runtests.jl b/test/runtests.jl
index 2e6a7894..2dfe14da 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -3,6 +3,7 @@ using Test
 using Random
 using LinearAlgebra
 using SparseArrays
+using SpecialFunctions
 using StableRNGs
 using Statistics
 

From 5a539ac4efd1f8f0d36e694b4d1a0f09cb7527dd Mon Sep 17 00:00:00 2001
From: Christian Guinard <28689358+christiangnrd@users.noreply.github.com>
Date: Sun, 18 May 2025 10:56:13 -0300
Subject: [PATCH 2/4] tests: Fix tests for older Julia

Also a couple of clarity fixes
---
 src/mutualinfo.jl  | 10 +++++-----
 test/mutualinfo.jl | 17 ++++++++++++-----
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/mutualinfo.jl b/src/mutualinfo.jl
index 817ba413..65b0afca 100644
--- a/src/mutualinfo.jl
+++ b/src/mutualinfo.jl
@@ -55,17 +55,17 @@ in the denominator is computed. It can be one of:
 """
 function mutualinfo(a, b; method::Union{Nothing, Symbol} = nothing, normed::Union{Nothing, Bool} = nothing, kwargs...)
     # Disallow `method` and `normed` to be used together
-    if isnothing(method)
-        isnothing(normed) || Base.depwarn("`normed` kwarg is deprecated, please use `method=:normalized` instead of `normed=true`, and `method=:classic` instead of `normed=false'", :mutualinfo)
-        method = if isnothing(normed) || normed
+    if method === nothing
+        (normed === nothing) || Base.depwarn("`normed` kwarg is deprecated, please use `method=:normalized` instead of `normed=true`, and `method=:classic` instead of `normed=false'", :mutualinfo)
+        method = if (normed === nothing) || normed
             :normalized
         else
             :classic
         end
     else
-        isnothing(normed) || throw(ArgumentError("`normed` kwarg is not compatible with `method` kwarg"))
+        (normed === nothing) || throw(ArgumentError("`normed` kwarg is not compatible with `method` kwarg"))
     end
-    # Little hack to ensure the correct error is thrown
+    # Little hack to ensure the invalid kwargs error is thrown
     if method === :adjusted && length(kwargs) >= 1 && :aggregate ∉ keys(kwargs)
         method = :classic
     end
diff --git a/test/mutualinfo.jl b/test/mutualinfo.jl
index a29e203b..9fe89ecb 100644
--- a/test/mutualinfo.jl
+++ b/test/mutualinfo.jl
@@ -27,10 +27,17 @@ using Clustering
     @test mutualinfo(a1, a2; method=:adjusted, aggregate=:max) ≈ 0.3437 atol=1.0e-4
     @test mutualinfo(a1, a2; method=:adjusted, aggregate=:min) ≈ 0.4348 atol=1.0e-4
 
-    # test errors
-    @test_throws "ArgumentError: `normed` kwarg is not compatible with `method` kwarg" mutualinfo(a1, a2; method=:adjusfted, normed=false)
-    @test_throws "ArgumentError: mutualinfo(): `method=:adjusfted` is not supported" mutualinfo(a1, a2; method=:adjusfted, aggregate=:min)
-    @test_throws "ArgumentError: mutualinfo(): unsupported kwargs used." mutualinfo(a1, a2; method=:adjusted, notaggregate=:min)
-    @test_throws "ArgumentError: mutualinfo(): unsupported kwargs used." mutualinfo(a1, a2; method=:classic, notaggregate=:min)
+    # test errors. More precise tests on Julia 1.8+ when supported
 
+    if VERSION >= v"1.8"
+        @test_throws "ArgumentError: `normed` kwarg is not compatible with `method` kwarg" mutualinfo(a1, a2; method=:adjusted, normed=false)
+        @test_throws "ArgumentError: mutualinfo(): `method=:adjusfted` is not supported" mutualinfo(a1, a2; method=:adjusfted, aggregate=:min)
+        @test_throws "ArgumentError: mutualinfo(): unsupported kwargs used." mutualinfo(a1, a2; method=:adjusted, notaggregate=:min)
+        @test_throws "ArgumentError: mutualinfo(): unsupported kwargs used." mutualinfo(a1, a2; method=:classic, notaggregate=:min)
+    else
+        @test_throws ArgumentError mutualinfo(a1, a2; method=:adjusted, normed=false)
+        @test_throws ArgumentError mutualinfo(a1, a2; method=:adjusfted, aggregate=:min)
+        @test_throws ArgumentError mutualinfo(a1, a2; method=:adjusted, notaggregate=:min)
+        @test_throws ArgumentError mutualinfo(a1, a2; method=:classic, notaggregate=:min)
+    end
 end

From b4dd79472474ab824f3eac7cfd9d0706d74740a1 Mon Sep 17 00:00:00 2001
From: Christian Guinard <28689358+christiangnrd@users.noreply.github.com>
Date: Thu, 10 Apr 2025 12:11:43 -0300
Subject: [PATCH 3/4] Project.toml: Clean up

---
 Project.toml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/Project.toml b/Project.toml
index f6460845..b793659d 100644
--- a/Project.toml
+++ b/Project.toml
@@ -30,14 +30,11 @@ julia = "1"
 [extras]
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["CodecZlib", "Statistics", "LinearAlgebra", "SparseArrays", "Distances", "Random", "DelimitedFiles", "SpecialFunctions", "StableRNGs", "Test"]
+test = ["CodecZlib", "LinearAlgebra", "SparseArrays", "DelimitedFiles", "SpecialFunctions", "StableRNGs", "Test"]

From 275b9dc90d00dd36b5cd7cf28986798d91f0b192 Mon Sep 17 00:00:00 2001
From: Christian Guinard <28689358+christiangnrd@users.noreply.github.com>
Date: Sun, 18 May 2025 11:26:36 -0300
Subject: [PATCH 4/4] CI: Fix codecov and macOS arch

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 788566ec..85694bf1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
             arch: x64
           - os: macos-latest
             version: '1'
-            arch: x64
+            arch: aarch64
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
@@ -48,7 +48,7 @@ jobs:
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          files: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest