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Add more TUDatasets
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* MUTAG and Mutagenicity
* NCI1 and NCI109
* PTCDatasets
* PROTEINS datasets
* Add fingerprint dataset
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@simonschoelly
simonschoelly authored Feb 10, 2021
1 parent 4ce6763 commit e126df5
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16 changes: 1 addition & 15 deletions README.md
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Expand Up @@ -19,21 +19,7 @@ julia> list_datasets()
TUDatasets.AIDSDataset
TUDatasets.AspirinDataset
TUDatasets.BZRDataset
TUDatasets.BZR_MDDataset
TUDatasets.BenzeneDataset
TUDatasets.COIL_DELDataset
TUDatasets.COIL_RAGDataset
TUDatasets.COLLABDataset
TUDatasets.COLORS_3Dataset
TUDatasets.DBLP_v1Dataset
TUDatasets.DDDataset
TUDatasets.ENZYMESDataset
TUDatasets.QM9Dataset
TUDatasets.REDDIT_BINARYDataset
TUDatasets.SYNTHETICDataset
TUDatasets.SYNTHETICnewDataset
TUDatasets.SynthieDataset
TUDatasets.TRIANGLESDataset
[...]

# Load QM9 from TUDatasets. This dataset contains 129433 molecules represented as graphs.
# The resulting ValGraphCollection is an immutable collection of graphs.
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248 changes: 248 additions & 0 deletions src/TUDatasets.jl
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Expand Up @@ -235,10 +235,21 @@ function __init__()
BenzeneDataset(),
BZRDataset(),
BZR_MDDataset(),
MutagenicityDataset(),
MUTAGDataset(),
NCI1Dataset(),
NCI109Dataset(),
PTC_FMDataset(),
PTC_FRDataset(),
PTC_MMDataset(),
PTC_MRDataset(),
DDDataset(),
ENZYMESDataset(),
PROTEINSDataset(),
PROTEINS_fullDataset(),
COIL_DELDataset(),
COIL_RAGDataset(),
FingerprintDataset(),
COLLABDataset(),
DBLP_v1Dataset(),
REDDIT_BINARYDataset(),
Expand Down Expand Up @@ -362,6 +373,177 @@ node_labels_map(::BenzeneDataset, i) = ("C", "O", "H")[i + 1]

graph_attributes_type(::BenzeneDataset) = NamedTuple{(:total_energy,), Tuple{Float64}}

## --------------------------------------
## Mutagenicity
## --------------------------------------

struct MutagenicityDataset <: TUDataset end

dataset_name(::MutagenicityDataset) = "Mutagenicity"

dataset_hash(::MutagenicityDataset) = "6230f94ba246b76834fb51ffa138370477b7bf8a784ade92c5e0586780d2ae0e"

dataset_references(::MutagenicityDataset) = [16, 20]

readme_name(::MutagenicityDataset) = "Mutagenicity_label_readme.txt"

node_labels_type(::MutagenicityDataset) = NamedTuple{(:chem,), Tuple{String}}
node_labels_map(::MutagenicityDataset, i) = ("C", "O", "Cl", "H", "N", "F", "Br", "S", "P", "I", "Na", "K", "Li", "Ca")[i + 1]

edge_labels_type(::MutagenicityDataset) = NamedTuple{(:valence,), Tuple{Int8}}
edge_labels_map(::MutagenicityDataset, i) = (1, 2, 3)[i + 1]

graph_labels_type(::MutagenicityDataset) = NamedTuple{(:class,), Tuple{String}}
graph_labels_map(::MutagenicityDataset, i) = ("mutagen", "nonmutagen")[i + 1]

## --------------------------------------
## MUTAG
## --------------------------------------

struct MUTAGDataset <: TUDataset end

dataset_name(::MUTAGDataset) = "MUTAG"

dataset_hash(::MUTAGDataset) = "c419bdc853c367d2d83da4973c45100954ae15e10f5ae2cddde6ca431f8207f6"

dataset_references(::MUTAGDataset) = [1, 23]

readme_name(::MUTAGDataset) = "README.txt"

node_labels_type(::MUTAGDataset) = NamedTuple{(:chem,), Tuple{String}}
node_labels_map(::MUTAGDataset, i) = ("C", "N", "O", "F", "I", "Cl", "Br")[i + 1]

edge_labels_type(::MUTAGDataset) = NamedTuple{(:bond_type,), Tuple{String}}
edge_labels_map(::MUTAGDataset, i) = ("aromatic", "single", "double", "triple")[i + 1]

graph_labels_type(::MUTAGDataset) = Tuple{Int8}

## --------------------------------------
## NCI1
## --------------------------------------

struct NCI1Dataset <: TUDataset end

dataset_name(::NCI1Dataset) = "NCI1"

dataset_hash(::NCI1Dataset) = "10e1458f3bd9224f14e6d7627e74dcfd13e48d376d73935e7bd2900590ef1d82"

dataset_references(::NCI1Dataset) = [8, 9, 22]

readme_name(::NCI1Dataset) = "README.txt"

node_labels_type(::NCI1Dataset) = Tuple{Int8}

graph_labels_type(::NCI1Dataset) = Tuple{Bool}

## --------------------------------------
## NCI109
## --------------------------------------

struct NCI109Dataset <: TUDataset end

dataset_name(::NCI109Dataset) = "NCI109"

dataset_hash(::NCI109Dataset) = "96e521a294e3e9c088540e9e9caccf55e4ca6e97cf468d68445814467956abaf"

dataset_references(::NCI109Dataset) = [8, 9, 22]

readme_name(::NCI109Dataset) = "README.txt"

node_labels_type(::NCI109Dataset) = Tuple{Int8}

graph_labels_type(::NCI109Dataset) = Tuple{Bool}

## --------------------------------------
## PTC_FM
## --------------------------------------

struct PTC_FMDataset <: TUDataset end

dataset_name(::PTC_FMDataset) = "PTC_FM"

dataset_hash(::PTC_FMDataset) = "a06c80761db8ffd739a171f0d90cfa1f4dc965e1ea716ee5a25cc6cf5f4ae682"

dataset_references(::PTC_FMDataset) = [2, 23]

readme_name(::PTC_FMDataset) = "README.txt"

node_labels_type(::PTC_FMDataset) = Tuple{String}
# Note that each PTC dataset has slightly different atoms in slightly different order.
node_labels_map(::PTC_FMDataset, i) = ("In", "P", "C", "O", "N", "Cl", "S", "Br", "Na", "F", "As", "K", "Cu", "I", "Ba", "Sn", "Pb", "Ca")[i + 1]

edge_labels_type(::PTC_FMDataset) = Tuple{String}
# This is weird, as single and double have different order here than for other PTC datasets
edge_labels_map(::PTC_FMDataset, i) = ("triple", "single", "double", "aromatic")[i + 1]

graph_labels_type(::PTC_FMDataset) = Tuple{Int8}

## --------------------------------------
## PTC_FR
## --------------------------------------

struct PTC_FRDataset <: TUDataset end

dataset_name(::PTC_FRDataset) = "PTC_FR"

dataset_hash(::PTC_FRDataset) = "c4b0083af725aaff27b41228591294922968bd5509179d24c6ea4d3996ed6072"

dataset_references(::PTC_FRDataset) = [2, 23]

readme_name(::PTC_FRDataset) = "README.txt"

node_labels_type(::PTC_FRDataset) = Tuple{String}
node_labels_map(::PTC_FRDataset, i) = ("In", "P", "O", "N", "Na", "C", "Cl", "S", "Br", "F", "As", "K", "Cu", "Zn", "I", "Sn", "Pb", "Te", "Ca")[i + 1]

edge_labels_type(::PTC_FRDataset) = Tuple{String}
edge_labels_map(::PTC_FRDataset, i) = ("triple", "double", "single", "aromatic")[i + 1]

graph_labels_type(::PTC_FRDataset) = Tuple{Int8}

## --------------------------------------
## PTC_MM
## --------------------------------------

struct PTC_MMDataset <: TUDataset end

dataset_name(::PTC_MMDataset) = "PTC_MM"

dataset_hash(::PTC_MMDataset) = "3846d6697330a446d46a1274b8708fcc153acdbcf59f649871bc0844bb012e4f"

dataset_references(::PTC_MMDataset) = [2, 23]

readme_name(::PTC_MMDataset) = "README.txt"

node_labels_type(::PTC_MMDataset) = Tuple{String}
node_labels_map(::PTC_MMDataset, i) = ("In", "P", "O", "N", "Na", "C", "Cl", "S", "Br", "F", "As", "K", "B", "Cu", "Zn", "I", "Ba", "Sn", "Pb", "Ca")[i + 1]

edge_labels_type(::PTC_MMDataset) = Tuple{String}
edge_labels_map(::PTC_MMDataset, i) = ("triple", "double", "single", "aromatic")[i + 1]

graph_labels_type(::PTC_MMDataset) = Tuple{Int8}

## --------------------------------------
## PTC_MR
## --------------------------------------

struct PTC_MRDataset <: TUDataset end

dataset_name(::PTC_MRDataset) = "PTC_MR"

dataset_hash(::PTC_MRDataset) = "5699a6d9f1bc5b3d71495f09ef50de53fa3e6bb24ead1150da678500229f5237"

dataset_references(::PTC_MRDataset) = [2, 23]

readme_name(::PTC_MRDataset) = "README.txt"

node_labels_type(::PTC_MRDataset) = Tuple{String}
node_labels_map(::PTC_MRDataset, i) = ("In", "P", "O", "N", "Na", "C", "Cl", "S", "Br", "F", "K", "Cu", "Zn", "I", "Ba", "Sn", "Pb", "Ca")[i + 1]

edge_labels_type(::PTC_MRDataset) = Tuple{String}
edge_labels_map(::PTC_MRDataset, i) = ("triple", "double", "single", "aromatic")[i + 1]

graph_labels_type(::PTC_MRDataset) = Tuple{Int8}


## --------------------------------------
## QM9
Expand Down Expand Up @@ -429,6 +611,48 @@ graph_labels_type(::ENZYMESDataset) = Tuple{Int8}
node_labels_type(::ENZYMESDataset) = Tuple{Int8}
node_attributes_type(::ENZYMESDataset) = NTuple{18, Float64}

## --------------------------------------
## PROTEINS
## --------------------------------------

struct PROTEINSDataset <: TUDataset end

dataset_name(::PROTEINSDataset) = "PROTEINS"

dataset_hash(::PROTEINSDataset) = "2da8de15284b88edabca2888ce5444d62f364ed41159260977088c4e53d4d848"

readme_name(::PROTEINSDataset) = "README.txt"

dataset_references(::PROTEINSDataset) = [4, 6]

graph_eltype(::PROTEINSDataset) = Int16

graph_labels_type(::PROTEINSDataset) = Tuple{Int8}

node_labels_type(::PROTEINSDataset) = Tuple{Int8}
node_attributes_type(::PROTEINSDataset) = Tuple{Float64}

## --------------------------------------
## PROTEINS_full
## --------------------------------------

struct PROTEINS_fullDataset <: TUDataset end

dataset_name(::PROTEINS_fullDataset) = "PROTEINS_full"

dataset_hash(::PROTEINS_fullDataset) = "3b7782403ce98754df3330a67e9b2aff32e69520aa1245bf515c48cc0119c562"

readme_name(::PROTEINS_fullDataset) = "README.txt"

dataset_references(::PROTEINS_fullDataset) = [4, 6]

graph_eltype(::PROTEINS_fullDataset) = Int16

graph_labels_type(::PROTEINS_fullDataset) = Tuple{Int8}

node_labels_type(::PROTEINS_fullDataset) = Tuple{Int8}
node_attributes_type(::PROTEINS_fullDataset) = NTuple{29, Float64}

## --------------------------------------
## COIL-DEL
## --------------------------------------
Expand Down Expand Up @@ -473,6 +697,30 @@ edge_attributes_type(::COIL_RAGDataset) = NamedTuple{(:boundary,), Tuple{Float32

graph_labels_type(::COIL_RAGDataset) = Tuple{Int8} # TODO not sure what the labels mean

## --------------------------------------
## Fingerprint
## --------------------------------------

struct FingerprintDataset <: TUDataset end

dataset_name(::FingerprintDataset) = "Fingerprint"

dataset_hash(::FingerprintDataset) = "6c53fc4e71a26b192681375b7a860afd49a24367cb1a15bda6b57067c467154d"

dataset_references(::FingerprintDataset) = [16, 19]

readme_name(::FingerprintDataset) = "Fingerprint_label_readme.txt"

node_attributes_type(::FingerprintDataset) = @NamedTuple{x::Float64, y::Float64}

edge_attributes_type(::FingerprintDataset) = @NamedTuple{orient::Float64, angle::Float64}

graph_labels_type(::FingerprintDataset) = @NamedTuple{class::String}
graph_labels_map(::FingerprintDataset, i) =
("L", "TR", "A", "TA", "W", "R", "T", "WR", "TL", "LT", "AT", "RT", "WL", "RW", "AR")[i + 1]



## --------------------------------------
## COLLAB
## --------------------------------------
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Registration pull request created: JuliaRegistries/General/29788

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.1.0 -m "<description of version>" e126df56fb495bc68dc31468e33e194ade98fe8d
git push origin v0.1.0

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