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Layers

Deep learning models are often said to be made up of "layers". Intuitively, a "layer" is a function which transforms some tensor into another tensor. DeepChem maintains an extensive collection of layers which perform various useful scientific transformations. For now, most layers are Keras only but over time we expect this support to expand to other types of models and layers.

Keras Layers

deepchem.models.layers.InteratomicL2Distances

deepchem.models.layers.GraphConv

deepchem.models.layers.GraphPool

deepchem.models.layers.GraphGather

deepchem.models.layers.MolGANConvolutionLayer

deepchem.models.layers.MolGANAggregationLayer

deepchem.models.layers.MolGANMultiConvolutionLayer

deepchem.models.layers.MolGANEncoderLayer

deepchem.models.layers.LSTMStep

deepchem.models.layers.AttnLSTMEmbedding

deepchem.models.layers.IterRefLSTMEmbedding

deepchem.models.layers.SwitchedDropout

deepchem.models.layers.WeightedLinearCombo

deepchem.models.layers.CombineMeanStd

deepchem.models.layers.Stack

deepchem.models.layers.VinaFreeEnergy

deepchem.models.layers.NeighborList

deepchem.models.layers.AtomicConvolution

deepchem.models.layers.AlphaShareLayer

deepchem.models.layers.SluiceLoss

deepchem.models.layers.BetaShare

deepchem.models.layers.ANIFeat

deepchem.models.layers.GraphEmbedPoolLayer

deepchem.models.layers.GraphCNN

deepchem.models.layers.Highway

deepchem.models.layers.WeaveLayer

deepchem.models.layers.WeaveGather

deepchem.models.layers.DTNNEmbedding

deepchem.models.layers.DTNNStep

deepchem.models.layers.DTNNGather

deepchem.models.layers.DAGLayer

deepchem.models.layers.DAGGather

deepchem.models.layers.MessagePassing

deepchem.models.layers.EdgeNetwork

deepchem.models.layers.GatedRecurrentUnit

deepchem.models.layers.SetGather

Torch Layers

deepchem.models.torch_models.layers.MultilayerPerceptron

deepchem.models.torch_models.layers.CNNModule

deepchem.models.torch_models.layers.ScaleNorm

deepchem.models.torch_models.layers.MATEncoderLayer

deepchem.models.torch_models.layers.MultiHeadedMATAttention

deepchem.models.torch_models.layers.SublayerConnection

deepchem.models.torch_models.layers.PositionwiseFeedForward

deepchem.models.torch_models.layers.MATEmbedding

deepchem.models.torch_models.layers.MATGenerator

deepchem.models.layers.cosine_dist

deepchem.models.torch_models.layers.GraphNetwork

deepchem.models.torch_models.layers.Affine

deepchem.models.torch_models.layers.RealNVPLayer

deepchem.models.torch_models.layers.DMPNNEncoderLayer

deepchem.models.torch_models.InfoGraphEncoder

deepchem.models.torch_models.GINEncoder

deepchem.models.torch_models.layers.SetGather

deepchem.models.torch_models.gnn.GNN

deepchem.models.torch_models.gnn.GNNHead

deepchem.models.torch_models.gnn.LocalGlobalDiscriminator

deepchem.models.torch_models.pna_gnn.AtomEncoder

deepchem.models.torch_models.pna_gnn.BondEncoder

deepchem.models.torch_models.pna_gnn.PNALayer

deepchem.models.torch_models.pna_gnn.PNAGNN

deepchem.models.torch_models.PNA

deepchem.models.torch_models.gnn3d.Net3DLayer

deepchem.models.torch_models.gnn3d.Net3D

deepchem.models.torch_models.layers.DTNNEmbedding

deepchem.models.torch_models.layers.EdgeNetwork

Grover Layers

The following layers are used for implementing GROVER model as described in the paper <Self-Supervised Graph Transformer on Large-Scale Molecular Data <https://drug.ai.tencent.com/publications/GROVER.pdf>_

deepchem.models.torch_models.grover_layers.GroverMPNEncoder

deepchem.models.torch_models.grover_layers.GroverAttentionHead

deepchem.models.torch_models.grover_layers.GroverMTBlock

deepchem.models.torch_models.grover_layers.GroverTransEncoder

deepchem.models.torch_models.grover_layers.GroverEmbedding

deepchem.models.torch_models.grover_layers.GroverEmbedding

deepchem.models.torch_models.grover_layers.GroverAtomVocabPredictor

deepchem.models.torch_models.grover_layers.GroverBondVocabPredictor

deepchem.models.torch_models.grover_layers.GroverFunctionalGroupPredictor

deepchem.models.torch_models.grover.GroverPretrain

deepchem.models.torch_models.grover.GroverFinetune

Attention Layers

deepchem.models.torch_models.attention.ScaledDotProductAttention

deepchem.models.torch_models.attention.SelfAttention

Readout Layers

deepchem.models.torch_models.readout.GroverReadout

Jax Layers

deepchem.models.jax_models.layers.Linear

Density Functional Theory Layers

deepchem.models.dft.nnxc.BaseNNXC

deepchem.models.dft.nnxc.NNLDA

deepchem.models.dft.nnxc.HybridXC

deepchem.models.dft.scf.XCNNSCF

deepchem.models.dft.dftxc.DFTXC