Drug/Target Encoder

Drug encoding

Drug Encodings Description
Morgan Extended-Connectivity Fingerprints
Pubchem Pubchem Substructure-based Fingerprints
Daylight Daylight-type fingerprints
rdkit_2d_normalized Normalized Descriptastorus
CNN Convolutional Neural Network on SMILES
CNN_RNN A GRU/LSTM on top of a CNN on SMILES
Transformer Transformer Encoder on ESPF
MPNN Message-passing neural network

Target encoding

Target Encodings Description
AAC Amino acid composition up to 3-mers
PseudoAAC Pseudo amino acid composition
Conjoint_triad Conjoint triad features
Quasi-seq Quasi-sequence order descriptor
CNN Convolutional Neural Network on target seq
CNN_RNN A GRU/LSTM on top of a CNN on target seq
Transformer Transformer Encoder on ESPF

Encoder Model

Encoder Model Description
CNN Convolutional Neural Network on SMILES
CNN_RNN A GRU/LSTM on top of a CNN on SMILES
Transformer Transformer Encoder on SMILES
MPNN Message Passing Neural Network on Molecular Graph
MLP MultiLayer Perceptron on fix-dim feature vector

Technical Details

First, we describe the common modules we import in DeepPurpose.

import torch
from torch.autograd import Variable
import torch.nn.functional as F
from torch import nn
import numpy as np
import pandas as pd

Links of details of various encoders