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Benchmark GAT model on the ESOL dataset
Benchmark DTNN model on the QM7 dataset
Benchmark MPNN model on the Tox21 dataset (with Masked Loss)
MolGraph
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Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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P
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R
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S
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T
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U
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V
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W
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__call__() (molgraph.chemistry.ConformerGenerator method)
(molgraph.chemistry.Feature method)
(molgraph.chemistry.features.Aromatic method)
(molgraph.chemistry.features.BondType method)
(molgraph.chemistry.features.ChiralCenter method)
(molgraph.chemistry.features.CIPCode method)
(molgraph.chemistry.features.Conjugated method)
(molgraph.chemistry.features.CrippenLogPContribution method)
(molgraph.chemistry.features.CrippenMolarRefractivityContribution method)
(molgraph.chemistry.features.Degree method)
(molgraph.chemistry.features.FormalCharge method)
(molgraph.chemistry.features.GasteigerCharge method)
(molgraph.chemistry.features.Hetero method)
(molgraph.chemistry.features.Hybridization method)
(molgraph.chemistry.features.HydrogenAcceptor method)
(molgraph.chemistry.features.HydrogenDonor method)
(molgraph.chemistry.features.LabuteASAContribution method)
(molgraph.chemistry.features.NumRadicalElectrons method)
(molgraph.chemistry.features.Ring method)
(molgraph.chemistry.features.RingSize method)
(molgraph.chemistry.features.Rotatable method)
(molgraph.chemistry.features.Stereo method)
(molgraph.chemistry.features.Symbol method)
(molgraph.chemistry.features.TotalNumHs method)
(molgraph.chemistry.features.TotalValence method)
(molgraph.chemistry.features.TPSAContribution method)
(molgraph.chemistry.Featurizer method)
(molgraph.chemistry.MolecularGraphEncoder method)
(molgraph.chemistry.MolecularGraphEncoder3D method)
(molgraph.chemistry.Tokenizer method)
(molgraph.models.GradientActivationMapping method)
(molgraph.models.IntegratedSaliencyMapping method)
(molgraph.models.SaliencyMapping method)
(molgraph.models.SmoothGradSaliencyMapping method)
__getattr__() (molgraph.tensors.graph_tensor.GraphTensor method)
__getitem__() (molgraph.tensors.graph_tensor.GraphTensor method)
_build() (molgraph.layers.GNNLayer method)
_call() (molgraph.layers.GNNLayer method)
A
adapt() (molgraph.layers.CenterScaling method)
(molgraph.layers.EmbeddingLookup method)
(molgraph.layers.MinMaxScaling method)
(molgraph.layers.StandardScaling method)
(molgraph.layers.VarianceThreshold method)
Aromatic (class in molgraph.chemistry.features)
AttentiveFPConv (class in molgraph.layers)
AttentiveFPReadout (class in molgraph.layers)
available_embedding_methods (molgraph.chemistry.ConformerGenerator property)
available_force_field_methods (molgraph.chemistry.ConformerGenerator property)
B
BondType (class in molgraph.chemistry.features)
build() (molgraph.models.DMPNN method)
(molgraph.models.GIN method)
(molgraph.models.MPNN method)
build_from_signature() (molgraph.layers.AttentiveFPConv method)
(molgraph.layers.GNNLayer method)
C
call() (molgraph.layers.AttentiveFPConv method)
(molgraph.layers.AttentiveFPReadout method)
(molgraph.layers.CenterScaling method)
(molgraph.layers.DotProductIncident method)
(molgraph.layers.DTNNConv method)
(molgraph.layers.EdgeConv method)
(molgraph.layers.EdgeDropout method)
(molgraph.layers.EmbeddingLookup method)
(molgraph.layers.ExtractField method)
(molgraph.layers.FeatureMasking method)
(molgraph.layers.FeatureProjection method)
(molgraph.layers.GATConv method)
(molgraph.layers.GatedGCNConv method)
(molgraph.layers.GatherIncident method)
(molgraph.layers.GATv2Conv method)
(molgraph.layers.GCFConv method)
(molgraph.layers.GCNConv method)
(molgraph.layers.GCNIIConv method)
(molgraph.layers.GINConv method)
(molgraph.layers.GMMConv method)
(molgraph.layers.GNNLayer method)
(molgraph.layers.GraphSageConv method)
(molgraph.layers.GTConv method)
(molgraph.layers.LaplacianPositionalEncoding method)
(molgraph.layers.MinMaxScaling method)
(molgraph.layers.MPNNConv method)
(molgraph.layers.NodeDropout method)
(molgraph.layers.NodeReadout method)
(molgraph.layers.SegmentPoolingReadout method)
(molgraph.layers.SetGatherReadout method)
(molgraph.layers.StandardScaling method)
(molgraph.layers.TransformerEncoderReadout method)
(molgraph.layers.VarianceThreshold method)
(molgraph.models.DMPNN method)
(molgraph.models.GIN method)
(molgraph.models.MPNN method)
CenterScaling (class in molgraph.layers)
ChiralCenter (class in molgraph.chemistry.features)
CIPCode (class in molgraph.chemistry.features)
compile() (molgraph.models.GraphAutoEncoder method)
(molgraph.models.GraphMasking method)
(molgraph.models.GraphVariationalAutoEncoder method)
compute_edge_weights_from_degrees() (in module molgraph.layers.gnn_ops)
compute_output_shape() (molgraph.layers.AttentiveFPConv method)
(molgraph.layers.AttentiveFPReadout method)
(molgraph.layers.DTNNConv method)
(molgraph.layers.EdgeConv method)
(molgraph.layers.GATConv method)
(molgraph.layers.GatedGCNConv method)
(molgraph.layers.GATv2Conv method)
(molgraph.layers.GCFConv method)
(molgraph.layers.GCNConv method)
(molgraph.layers.GCNIIConv method)
(molgraph.layers.GINConv method)
(molgraph.layers.GMMConv method)
(molgraph.layers.GNNLayer method)
(molgraph.layers.GraphSageConv method)
(molgraph.layers.GTConv method)
(molgraph.layers.LaplacianPositionalEncoding method)
(molgraph.layers.MPNNConv method)
(molgraph.layers.NodeReadout method)
(molgraph.layers.SegmentPoolingReadout method)
(molgraph.layers.SetGatherReadout method)
(molgraph.layers.TransformerEncoderReadout method)
compute_output_signature() (molgraph.layers.AttentiveFPConv method)
(molgraph.layers.GNNLayer method)
ConformerGenerator (class in molgraph.chemistry)
Conjugated (class in molgraph.chemistry.features)
CrippenLogPContribution (class in molgraph.chemistry.features)
CrippenMolarRefractivityContribution (class in molgraph.chemistry.features)
D
data (molgraph.tensors.graph_tensor.GraphTensor property)
DatasetFactory (class in molgraph.chemistry.benchmark.datasets)
Degree (class in molgraph.chemistry.features)
DMPNN (class in molgraph.models)
DotProductIncident (class in molgraph.layers)
DTNNConv (class in molgraph.layers)
dtype (molgraph.tensors.graph_tensor.GraphTensor property)
E
EdgeConv (class in molgraph.layers)
EdgeDropout (class in molgraph.layers)
EmbeddingLookup (class in molgraph.layers)
evaluate() (molgraph.models.GraphAutoEncoder method)
(molgraph.models.GraphMasking method)
(molgraph.models.GraphVariationalAutoEncoder method)
ExtractField (class in molgraph.layers)
F
Feature (class in molgraph.chemistry)
FeatureMasking (class in molgraph.layers)
FeatureProjection (class in molgraph.layers)
Featurizer (class in molgraph.chemistry)
fit() (molgraph.models.GraphAutoEncoder method)
(molgraph.models.GraphMasking method)
(molgraph.models.GraphVariationalAutoEncoder method)
FormalCharge (class in molgraph.chemistry.features)
from_config() (molgraph.layers.AttentiveFPConv class method)
(molgraph.layers.AttentiveFPReadout class method)
(molgraph.layers.CenterScaling class method)
(molgraph.layers.DotProductIncident class method)
(molgraph.layers.DTNNConv class method)
(molgraph.layers.EdgeConv class method)
(molgraph.layers.EdgeDropout class method)
(molgraph.layers.EmbeddingLookup class method)
(molgraph.layers.ExtractField class method)
(molgraph.layers.FeatureMasking class method)
(molgraph.layers.FeatureProjection class method)
(molgraph.layers.GATConv class method)
(molgraph.layers.GatedGCNConv class method)
(molgraph.layers.GatherIncident class method)
(molgraph.layers.GATv2Conv class method)
(molgraph.layers.GCFConv class method)
(molgraph.layers.GCNConv class method)
(molgraph.layers.GCNIIConv class method)
(molgraph.layers.GINConv class method)
(molgraph.layers.GMMConv class method)
(molgraph.layers.GraphSageConv class method)
(molgraph.layers.GTConv class method)
(molgraph.layers.LaplacianPositionalEncoding class method)
(molgraph.layers.MinMaxScaling class method)
(molgraph.layers.MPNNConv class method)
(molgraph.layers.NodeDropout class method)
(molgraph.layers.NodeReadout method)
(molgraph.layers.SegmentPoolingReadout class method)
(molgraph.layers.SetGatherReadout class method)
(molgraph.layers.StandardScaling class method)
(molgraph.layers.TransformerEncoderReadout class method)
(molgraph.layers.VarianceThreshold class method)
(molgraph.models.DMPNN class method)
(molgraph.models.GIN class method)
(molgraph.models.GraphAutoEncoder class method)
(molgraph.models.GraphMasking class method)
(molgraph.models.GraphVariationalAutoEncoder class method)
(molgraph.models.MPNN class method)
G
GasteigerCharge (class in molgraph.chemistry.features)
GATConv (class in molgraph.layers)
GatedGCNConv (class in molgraph.layers)
GatherIncident (class in molgraph.layers)
GATv2Conv (class in molgraph.layers)
GCFConv (class in molgraph.layers)
GCNConv (class in molgraph.layers)
GCNIIConv (class in molgraph.layers)
get() (molgraph.chemistry.benchmark.datasets.DatasetFactory method)
get_bias() (molgraph.layers.GNNLayer method)
get_config() (molgraph.chemistry.benchmark.datasets.DatasetFactory method)
(molgraph.layers.AttentiveFPConv method)
(molgraph.layers.AttentiveFPReadout method)
(molgraph.layers.CenterScaling method)
(molgraph.layers.DotProductIncident method)
(molgraph.layers.DTNNConv method)
(molgraph.layers.EdgeConv method)
(molgraph.layers.EdgeDropout method)
(molgraph.layers.EmbeddingLookup method)
(molgraph.layers.ExtractField method)
(molgraph.layers.FeatureMasking method)
(molgraph.layers.FeatureProjection method)
(molgraph.layers.GATConv method)
(molgraph.layers.GatedGCNConv method)
(molgraph.layers.GatherIncident method)
(molgraph.layers.GATv2Conv method)
(molgraph.layers.GCFConv method)
(molgraph.layers.GCNConv method)
(molgraph.layers.GCNIIConv method)
(molgraph.layers.GINConv method)
(molgraph.layers.GMMConv method)
(molgraph.layers.GraphSageConv method)
(molgraph.layers.GTConv method)
(molgraph.layers.LaplacianPositionalEncoding method)
(molgraph.layers.MinMaxScaling method)
(molgraph.layers.MPNNConv method)
(molgraph.layers.NodeDropout method)
(molgraph.layers.NodeReadout method)
(molgraph.layers.SegmentPoolingReadout method)
(molgraph.layers.SetGatherReadout method)
(molgraph.layers.StandardScaling method)
(molgraph.layers.TransformerEncoderReadout method)
(molgraph.layers.VarianceThreshold method)
(molgraph.models.DMPNN method)
(molgraph.models.GIN method)
(molgraph.models.GraphAutoEncoder method)
(molgraph.models.GraphMasking method)
(molgraph.models.GraphVariationalAutoEncoder method)
(molgraph.models.MPNN method)
get_dense() (molgraph.layers.GNNLayer method)
get_einsum_dense() (molgraph.layers.GNNLayer method)
get_kernel() (molgraph.layers.GNNLayer method)
GIN (class in molgraph.models)
GINConv (class in molgraph.layers)
GMMConv (class in molgraph.layers)
GNNLayer (class in molgraph.layers)
GradientActivationMapping (class in molgraph.models)
GraphAutoEncoder (class in molgraph.models)
GraphMasking (class in molgraph.models)
GraphSageConv (class in molgraph.layers)
GraphTensor (class in molgraph.tensors.graph_tensor)
GraphVariationalAutoEncoder (class in molgraph.models)
GTConv (class in molgraph.layers)
H
Hetero (class in molgraph.chemistry.features)
Hybridization (class in molgraph.chemistry.features)
HydrogenAcceptor (class in molgraph.chemistry.features)
HydrogenDonor (class in molgraph.chemistry.features)
I
IntegratedSaliencyMapping (class in molgraph.models)
is_ragged() (molgraph.tensors.graph_tensor.GraphTensor method)
is_scalar() (molgraph.tensors.graph_tensor.GraphTensor method)
L
LabuteASAContribution (class in molgraph.chemistry.features)
LaplacianPositionalEncoding (class in molgraph.layers)
load() (in module molgraph.chemistry.benchmark.tf_records)
M
merge() (molgraph.tensors.graph_tensor.GraphTensor method)
MinMaxScaling (class in molgraph.layers)
module
molgraph.chemistry.benchmark.tf_records
molgraph.chemistry.ops
molgraph.layers.gnn_ops
MolecularGraphEncoder (class in molgraph.chemistry)
MolecularGraphEncoder3D (class in molgraph.chemistry)
molecule_from_string() (in module molgraph.chemistry.ops)
molgraph.chemistry.benchmark.tf_records
module
molgraph.chemistry.ops
module
molgraph.layers.gnn_ops
module
MPNN (class in molgraph.models)
MPNNConv (class in molgraph.layers)
N
NodeDropout (class in molgraph.layers)
NodeReadout (class in molgraph.layers)
NumRadicalElectrons (class in molgraph.chemistry.features)
P
predict() (molgraph.models.GraphAutoEncoder method)
(molgraph.models.GraphMasking method)
(molgraph.models.GraphVariationalAutoEncoder method)
propagate() (molgraph.tensors.graph_tensor.GraphTensor method)
propagate_node_features() (in module molgraph.layers.gnn_ops)
R
rank (molgraph.tensors.graph_tensor.GraphTensor property)
reduce_features() (in module molgraph.layers.gnn_ops)
registered_datasets (molgraph.chemistry.benchmark.datasets.DatasetFactory property)
remove() (molgraph.tensors.graph_tensor.GraphTensor method)
Ring (class in molgraph.chemistry.features)
RingSize (class in molgraph.chemistry.features)
Rotatable (class in molgraph.chemistry.features)
S
SaliencyMapping (class in molgraph.models)
SegmentPoolingReadout (class in molgraph.layers)
separate() (molgraph.tensors.graph_tensor.GraphTensor method)
SetGatherReadout (class in molgraph.layers)
shape (molgraph.tensors.graph_tensor.GraphTensor property)
SmoothGradSaliencyMapping (class in molgraph.models)
softmax_edge_weights() (in module molgraph.layers.gnn_ops)
spec (molgraph.tensors.graph_tensor.GraphTensor property)
StandardScaling (class in molgraph.layers)
Stereo (class in molgraph.chemistry.features)
Symbol (class in molgraph.chemistry.features)
T
Tokenizer (class in molgraph.chemistry)
TotalNumHs (class in molgraph.chemistry.features)
TotalValence (class in molgraph.chemistry.features)
TPSAContribution (class in molgraph.chemistry.features)
TransformerEncoderReadout (class in molgraph.layers)
U
update() (molgraph.tensors.graph_tensor.GraphTensor method)
V
VarianceThreshold (class in molgraph.layers)
W
write() (in module molgraph.chemistry.benchmark.tf_records)