More unified interface

Author: gdalle

docs/Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.0-beta2"
+julia_version = "1.9.3"
 manifest_format = "2.0"
 project_hash = "8f377c7585a608434bf87f0689076fc3a3224468"
 
@@ -212,7 +212,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.5+1"
+version = "1.0.5+0"
 
 [[deps.ConstructionBase]]
 deps = ["LinearAlgebra"]
@@ -230,6 +230,11 @@ git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781"
 uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
 version = "0.6.2"
 
+[[deps.Crayons]]
+git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
+uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
+version = "4.1.1"
+
 [[deps.DataAPI]]
 git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
@@ -713,12 +718,12 @@ version = "0.3.1"
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
-version = "0.6.4"
+version = "0.6.3"
 
 [[deps.LibCURL_jll]]
 deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
 uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
-version = "8.0.1+1"
+version = "7.84.0+0"
 
 [[deps.LibGit2]]
 deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
@@ -727,7 +732,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 [[deps.LibSSH2_jll]]
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
 uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
-version = "1.11.0+1"
+version = "1.10.2+0"
 
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
@@ -838,6 +843,12 @@ git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e"
 uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900"
 version = "0.4.2"
 
+[[deps.MarchingCubes]]
+deps = ["PrecompileTools", "StaticArrays"]
+git-tree-sha1 = "c8e29e2bacb98c9b6f10445227a8b0402f2f173a"
+uuid = "299715c1-40a9-479a-aaf9-4a633d36f717"
+version = "0.1.8"
+
 [[deps.Markdown]]
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
@@ -856,7 +867,7 @@ version = "0.5.6"
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
-version = "2.28.2+1"
+version = "2.28.2+0"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
@@ -880,7 +891,7 @@ version = "0.3.4"
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
-version = "2023.1.10"
+version = "2022.10.11"
 
 [[deps.Multisets]]
 git-tree-sha1 = "8d852646862c96e226367ad10c8af56099b4047e"
@@ -929,7 +940,7 @@ version = "1.3.5+1"
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.23+2"
+version = "0.3.21+4"
 
 [[deps.OpenEXR]]
 deps = ["Colors", "FileIO", "OpenEXR_jll"]
@@ -946,7 +957,7 @@ version = "3.1.4+0"
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
-version = "0.8.1+2"
+version = "0.8.1+0"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -980,7 +991,7 @@ version = "1.6.2"
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15"
-version = "10.42.0+1"
+version = "10.42.0+0"
 
 [[deps.PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
@@ -1039,7 +1050,7 @@ version = "0.42.2+0"
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-version = "1.10.0"
+version = "1.9.2"
 
 [[deps.PkgVersion]]
 deps = ["Pkg"]
@@ -1127,7 +1138,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[deps.Random]]
-deps = ["SHA"]
+deps = ["SHA", "Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[deps.RangeArrays]]
@@ -1291,7 +1302,6 @@ version = "1.1.1"
 [[deps.SparseArrays]]
 deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-version = "1.10.0"
 
 [[deps.SpecialFunctions]]
 deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
@@ -1359,7 +1369,7 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"]
     StatsFunsInverseFunctionsExt = "InverseFunctions"
 
 [[deps.StochasticBlockModelVariants]]
-deps = ["DensityInterface", "DocStringExtensions", "Graphs", "LinearAlgebra", "PrecompileTools", "ProgressMeter", "Random", "SimpleWeightedGraphs", "SparseArrays", "SpecialFunctions", "Statistics"]
+deps = ["DensityInterface", "DocStringExtensions", "ForwardDiff", "Graphs", "LinearAlgebra", "Optim", "PrecompileTools", "ProgressMeter", "Random", "SimpleWeightedGraphs", "SparseArrays", "SpecialFunctions", "Statistics", "UnicodePlots"]
 path = ".."
 uuid = "37adabcb-1964-4c56-850d-39a4302c0c39"
 version = "0.1.0"
@@ -1377,7 +1387,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 [[deps.SuiteSparse_jll]]
 deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
-version = "7.2.0+1"
+version = "5.10.1+6"
 
 [[deps.TOML]]
 deps = ["Dates"]
@@ -1451,6 +1461,27 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf"
 uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1"
 version = "0.4.1"
 
+[[deps.UnicodePlots]]
+deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "LinearAlgebra", "MarchingCubes", "NaNMath", "PrecompileTools", "Printf", "Requires", "SparseArrays", "StaticArrays", "StatsBase"]
+git-tree-sha1 = "b96de03092fe4b18ac7e4786bee55578d4b75ae8"
+uuid = "b8865327-cd53-5732-bb35-84acbb429228"
+version = "3.6.0"
+
+    [deps.UnicodePlots.extensions]
+    FreeTypeExt = ["FileIO", "FreeType"]
+    ImageInTerminalExt = "ImageInTerminal"
+    IntervalSetsExt = "IntervalSets"
+    TermExt = "Term"
+    UnitfulExt = "Unitful"
+
+    [deps.UnicodePlots.weakdeps]
+    FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+    FreeType = "b38be410-82b0-50bf-ab77-7b57e271db43"
+    ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254"
+    IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+    Term = "22787eb5-b846-44ae-b979-8e399b8463ab"
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
 [[deps.WoodburyMatrices]]
 deps = ["LinearAlgebra", "SparseArrays"]
 git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3"
@@ -1520,7 +1551,7 @@ version = "1.5.0+0"
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.13+1"
+version = "1.2.13+0"
 
 [[deps.isoband_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1543,7 +1574,7 @@ version = "0.15.1+0"
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.8.0+1"
+version = "5.8.0+0"
 
 [[deps.libfdk_aac_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1572,12 +1603,12 @@ version = "1.3.7+1"
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
-version = "1.52.0+1"
+version = "1.48.0+0"
 
 [[deps.p7zip_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
-version = "17.4.0+2"
+version = "17.4.0+0"
 
 [[deps.x264_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]

docs/plots_csbm.jl

@@ -1,7 +1,7 @@
 using Base.Threads
 using CairoMakie
 using LinearAlgebra
-using Random: default_rng
+using Random: default_rng, rand!
 using Statistics
 using StochasticBlockModelVariants
 using ProgressMeter
@@ -17,11 +17,13 @@ function compute_fig1_csbm(; α, d, μ, ρ, N_values, λ_values, trials)
     prog = Progress(I * J * K; desc="CSBM - Fig 1")
     for i in 1:I
         for j in 1:J
-            @threads for k in 1:K
-                N, λ = N_values[i], λ_values[j]
-                P = ceil(Int, N / α)
-                csbm = CSBM(; N, P, d, μ, λ, ρ)
-                (qu, qv, converged) = evaluate_amp(rng, csbm)
+            N, λ = N_values[i], λ_values[j]
+            P = ceil(Int, N / α)
+            csbm = CSBM(; N, P, d, μ, λ, ρ)
+            B = rand(rng, csbm).observations.B
+            for k in 1:K  # don't parallelize
+                (; latents, observations) = rand!(rng, B, csbm)
+                (qu, qv, converged) = evaluate_amp(rng, csbm, latents, observations)
                 qu_values[i, j, k] = qu
                 qv_values[i, j, k] = qv
                 converged_values[i, j, k] = converged

docs/plots_glmsbm.jl

@@ -1,7 +1,7 @@
 using Base.Threads
 using CairoMakie
 using LinearAlgebra
-using Random: default_rng
+using Random: default_rng, rand!
 using Statistics
 using StochasticBlockModelVariants
 using ProgressMeter
@@ -17,11 +17,13 @@ function compute_fig1_glmsbm(; N, c, ρ, Pʷ, α_values, λ_values, trials)
     prog = Progress(I * J * K; desc="CSBM - Fig 1")
     for i in 1:I
         for j in 1:J
-            @threads for k in 1:K
-                α, λ = α_values[i], λ_values[j]
-                M = ceil(Int, N / α)
-                glmsbm = GLMSBM(; N, M, c, λ, ρ, Pʷ)
-                (qs, qw, converged) = evaluate_amp(rng, glmsbm)
+            α, λ = α_values[i], λ_values[j]
+            M = ceil(Int, N / α)
+            glmsbm = GLMSBM(; N, M, c, λ, ρ, Pʷ)
+            F = rand(rng, glmsbm).observations.F
+            for k in 1:K  # don't parallelize
+                (; latents, observations) = rand!(rng, F, glmsbm)
+                (qs, qw, converged) = evaluate_amp(rng, glmsbm, latents, observations)
                 qs_values[i, j, k] = qs
                 qw_values[i, j, k] = qw
                 converged_values[i, j, k] = converged
@@ -43,8 +45,8 @@ function plot_fig1_glmsbm(res; α_values, λ_values)
         lines!(ax1, λ_values, qs_means; label="α=$α")
         errorbars!(ax1, λ_values, qs_means, qs_stds; label=nothing)
 
-        qw_means = dropdims(mean(qs_values[i, :, :]; dims=2); dims=2)
-        qw_stds = dropdims(std(qs_values[i, :, :]; dims=2); dims=2)
+        qw_means = dropdims(mean(qw_values[i, :, :]; dims=2); dims=2)
+        qw_stds = dropdims(std(qw_values[i, :, :]; dims=2); dims=2)
         lines!(ax2, λ_values, qw_means; label="α=$α")
         errorbars!(ax2, λ_values, qw_means, qw_stds; label=nothing)
     end
@@ -58,6 +60,6 @@ Pʷ = GaussianWeightPrior()
 α_values = reverse([0.3, 1, 3, 10, 30])
 α_values = reverse([0.3, 1])
 λ_values = 0:0.1:2
-trials = 10
+trials = 1
 res1 = compute_fig1_glmsbm(; N, c, ρ, Pʷ, α_values, λ_values, trials)  # kills Julia
 plot_fig1_glmsbm(res1; α_values, λ_values)

src/StochasticBlockModelVariants.jl

@@ -15,7 +15,7 @@ using Graphs: AbstractGraph, neighbors
 using LinearAlgebra: LinearAlgebra, dot, mul!, norm
 using PrecompileTools: @compile_workload
 using ProgressMeter: Progress, next!
-using Random: AbstractRNG, default_rng
+using Random: Random, AbstractRNG, default_rng, rand!, randn!
 using SimpleWeightedGraphs: SimpleWeightedGraph
 using SpecialFunctions: erf
 using Statistics: mean, std
@@ -26,7 +26,7 @@ export nb_features, average_degree, communities_snr, affinities, features_snr, e
 export CSBM, LatentsCSBM, ObservationsCSBM
 export GLMSBM, LatentsGLMSBM, ObservationsGLMSBM
 export GaussianWeightPrior, RademacherWeightPrior
-export init_amp, update_amp!, run_amp, evaluate_amp
+export init_amp, update_amp!, run_amp, evaluate_amp, semisupervised_loss_amp
 export discrete_overlap, continuous_overlap
 
 include("utils.jl")