Added mutagenesis dataset

Author: racinmat

Project.toml

@@ -9,6 +9,7 @@ DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 FixedPointNumbers = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"

README.md

@@ -30,6 +30,7 @@ Find below a list of available datasets and links to their documentation.
 #### Miscellaneous
   - [BostonHousing](https://juliaml.github.io/MLDatasets.jl/dev/datasets/BostonHousing/)
   - [Iris](https://juliaml.github.io/MLDatasets.jl/dev/datasets/Iris/)
+  - [Mutagenesis](https://relational.fit.cvut.cz/dataset/Mutagenesis)
 
 #### Text
   - [PTBLM](https://juliaml.github.io/MLDatasets.jl/dev/datasets/PTBLM/)

docs/make.jl

@@ -33,6 +33,7 @@ makedocs(
             "Miscellaneous" => Any[
                 "Iris" => "datasets/Iris.md",
                 "Boston Housing" => "datasets/BostonHousing.md",
+                "´Mutagenesis" => "datasets/Mutagenesis.md",
             ],
 
             "Text" => Any[

docs/src/datasets/Mutagenesis.md

@@ -0,0 +1,16 @@
+# Mutagenesis
+
+The `Mutagenesis` dataset comprises 188 molecules trialed for mutagenicity on Salmonella typhimurium, available from
+ [relational.fit.cvut.cz](https://relational.fit.cvut.cz/dataset/Mutagenesis) and
+ [CTUAvastLab/datasets](https://github.com/CTUAvastLab/datasets/tree/main/mutagenesis). 
+
+Train, test and validation data can be loaded using:
+```julia
+train_x, train_y = Mutagenesis.traindata()
+test_x, test_y = Mutagenesis.testdata()
+val_x, val_y = Mutagenesis.valdata()
+```
+
+```@docs
+Mutagenesis
+```

src/MLDatasets.jl

@@ -39,6 +39,7 @@ include("download.jl")
 # Misc.
 include("BostonHousing/BostonHousing.jl")
 include("Iris/Iris.jl")
+include("Mutagenesis/Mutagenesis.jl")
 
 # Vision
 include("CIFAR10/CIFAR10.jl")

src/Mutagenesis/Mutagenesis.jl

@@ -0,0 +1,62 @@
+export Mutagenesis
+module Mutagenesis
+
+    using DataDeps, JSON
+    using ..MLDatasets: datafile
+
+    function __init__()
+        DEPNAME = "Mutagenesis"
+        ORIGINAL_LINK = "https://relational.fit.cvut.cz/dataset/Mutagenesis"
+        DATA_LINK = "https://raw.githubusercontent.com/CTUAvastLab/datasets/main/mutagenesis"
+        DATA = "data.json"
+        METADATA = "meta.json"
+
+        register(DataDep(
+            DEPNAME,
+            """
+            Dataset: The $DEPNAME dataset.
+            Website: $ORIGINAL_LINK
+            License: CC0
+            """,
+            "$DATA_LINK/" .* [DATA, METADATA],
+        ))
+    end
+
+    traindata(; dir = nothing) = traindata(dir)
+    testdata(; dir = nothing) = testdata(dir)
+    valdata(; dir = nothing) = valdata(dir)
+
+    function traindata(dir)
+        samples, targets, train_idxs, val_idxs, test_idxs = load_data(dir)
+        samples[train_idxs], targets[train_idxs]
+    end
+
+    function testdata(dir)
+        samples, targets, train_idxs, val_idxs, test_idxs = load_data(dir)
+        samples[test_idxs], targets[test_idxs]
+    end
+
+    function valdata(dir)
+        samples, targets, train_idxs, val_idxs, test_idxs = load_data(dir)
+        samples[val_idxs], targets[val_idxs]
+    end
+
+    function load_data(dir)
+        data_path = datafile(DEPNAME, DATA, dir)
+        metadata_path = datafile(DEPNAME, METADATA, dir)
+        samples = read_data(data_path)
+        metadata = read_metadata(metadata_path)
+        labelkey = metadata["label"]
+        targets = map(i -> i[labelkey], samples)
+        val_num = metadata["val_samples"]
+        test_num = metadata["test_samples"]
+        train_idxs = 1:length(samples)-val_num-test_num
+        val_idxs = length(samples)-val_num-test_num+1:length(samples)-test_num
+        test_idxs = length(samples)-test_num+1:length(samples)
+        samples, targets, train_idxs, val_idxs, test_idxs
+    end
+
+    read_data(path) = Vector{Dict}(open(JSON.parse, path))
+    read_metadata(path) = open(JSON.parse, path)
+
+end # module

test/runtests.jl

@@ -10,6 +10,7 @@ tests = [
     # misc
     "tst_iris.jl",
     "tst_boston_housing.jl",
+    "tst_mutagenesis.jl",
     # vision
     "tst_cifar10.jl",
     "tst_cifar100.jl",

test/tst_mutagenesis.jl

@@ -0,0 +1,13 @@
+data_dir = withenv("DATADEPS_ALWAY_ACCEPT"=>"true") do
+    datadep"Mutagenesis"
+end
+
+@testset "Mutagenesis" begin
+    train_x, train_y = Mutagenesis.traindata()
+    test_x, test_y = Mutagenesis.testdata()
+    val_x, val_y = Mutagenesis.valdata()
+
+    @test length(train_x) == length(train_y) == 100
+    @test length(test_x) == length(test_y) == 44
+    @test length(val_x) == length(val_y) == 44
+end