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Add more TUDatasets #2

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Feb 10, 2021
Merged

Add more TUDatasets #2

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b4c4a59
Add MUTAG and Mutagenicity datasets
simonschoelly Feb 4, 2021
14abe3f
Add NCI1 and NCI109 datasets
simonschoelly Feb 6, 2021
06c3280
Add PTCDatasets
simonschoelly Feb 6, 2021
f565c9a
Add PROTEINS datasets
simonschoelly Feb 7, 2021
f3228c4
Add fingerprint dataset
simonschoelly Feb 7, 2021
51469e3
Merge branch 'master' of github.com:simonschoelly/GraphDatasets.jl in…
simonschoelly Feb 10, 2021
9c3edcd
Update README
simonschoelly Feb 10, 2021
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16 changes: 1 addition & 15 deletions README.md
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Original file line number Diff line number Diff line change
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
## --------------------------------------
Expand Down