cpi_model: Deep learning model fitting and prediction for...

In dongminjung/DeepPINCS: Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

Description

The model for compound-protein interactions (CPI) takes the pair of SMILES strings of compounds and amino acid sequences (one letter amino acid code) of proteins as input. They are fed into the compound and protein encoders, respectively, and then these encoders are concatenated. Due to the combination of compound and protein encoders, there are many kinds of CPI models. However, the graph neural network such as the graph concolutional network (GCN) is only available for compounds. We need to select one of types of compounds. For graph and fingerprint, the SMILES sequences are not used for encoders, because the information of graph or fingerprint is extracted from the SMILES sequenes and then it is fed into encoders. For sequence, the unigram is used as default, but the n-gram is available only for proteins. Since the CPI model needs some arguments of encoders, we may have to match the names of such arguments.

Usage

fit_cpi(smiles = NULL, AAseq = NULL, outcome,
        convert_canonical_smiles = TRUE,
        compound_type = NULL, compound_max_atoms,
        compound_length_seq, protein_length_seq,
        compound_embedding_dim, protein_embedding_dim,
        protein_ngram_max = 1, protein_ngram_min = 1,
        smiles_val = NULL, AAseq_val = NULL, outcome_val = NULL,
        net_args = list(
            compound,
            compound_args,
            protein,
            protein_args,
            fc_units = c(1),
            fc_activation = c("linear"), ...),
        net_names = list(
            name_compound_max_atoms = NULL,
            name_compound_feature_dim = NULL,
            name_compound_fingerprint_size = NULL,
            name_compound_embedding_layer = NULL,
            name_compound_length_seq = NULL,
            name_compound_num_tokens = NULL,
            name_compound_embedding_dim = NULL,
            name_protein_length_seq = NULL,
            name_protein_num_tokens = NULL,
            name_protein_embedding_dim = NULL),
        preprocessor_only = FALSE,
        preprocessing = list(
            outcome = NULL,
            outcome_val = NULL,
            convert_canonical_smiles = NULL,
            canonical_smiles = NULL,
            compound_type = NULL,
            compound_max_atoms = NULL,
            compound_A_pad = NULL,
            compound_X_pad = NULL,
            compound_A_pad_val = NULL,
            compound_X_pad_val = NULL,
            compound_fingerprint = NULL,
            compound_fingerprint_val = NULL,
            smiles_encode_pad = NULL,
            smiles_val_encode_pad = NULL,
            compound_lenc = NULL,
            compound_length_seq = NULL,
            compound_num_tokens = NULL,
            compound_embedding_dim = NULL,
            AAseq_encode_pad = NULL,
            AAseq_val_encode_pad = NULL,
            protein_lenc = NULL,
            protein_length_seq = NULL,
            protein_num_tokens = NULL,
            protein_embedding_dim = NULL,
            protein_ngram_max = NULL,
            protein_ngram_min = NULL),
        batch_size, use_generator = FALSE,
        validation_split = 0, ...)

predict_cpi(modelRes, smiles = NULL, AAseq = NULL,
            preprocessing = list(
                canonical_smiles = NULL,
                compound_A_pad = NULL,
                compound_X_pad = NULL,
                compound_fingerprint = NULL,
                smiles_encode_pad = NULL,
                AAseq_encode_pad = NULL),
            use_generator = FALSE,
            batch_size = NULL)

Arguments

smiles	SMILES strings, each column for the element of a pair (default: NULL)
AAseq	amino acid sequences, each column for the element of a pair (default: NULL)
outcome	a variable that indicates how strong two molecules interact with each other or whether there is an interaction between them
convert_canonical_smiles	SMILES strings are converted to canonical SMILES strings if TRUE (default: TRUE)
compound_type	"graph", "fingerprint" or "sequence"
compound_max_atoms	maximum number of atoms for compounds
compound_length_seq	length of compound sequence
protein_length_seq	length of protein sequence
compound_embedding_dim	dimension of the dense embedding for compounds
protein_embedding_dim	dimension of the dense embedding for proteins
protein_ngram_max	maximum size of an n-gram for protein sequences (default: 1)
protein_ngram_min	minimum size of an n-gram for protein sequences (default: 1)
smiles_val	SMILES strings for validation (default: NULL)
AAseq_val	amino acid sequences for validation (default: NULL)
outcome_val	outcome for validation (default: NULL)
net_args	list of arguments for compound and protein encoder networks and for fully connected layer compound : encoder network for compounds compound_args : arguments of compound encoder protein : encoder network for proteins protein_args : arguments of protein encoder fc_units : dimensionality of the output space in the fully connected layer (default: 1) fc_activation : activation of the fully connected layer (default: "linear") ... : arguments of "keras::compile" but for object
net_names	list of names of arguments used in both the CPI model and encoder networks, names are set to NULL as default name_compound_max_atoms : corresponding name for the maximum number of atoms in the compound encoder, "max_atoms" if NULL name_compound_feature_dim : corresponding name for the dimension of node features in the compound encoder, "feature_dim" if NULL name_compound_fingerprint_size : corresponding name for the length of a fingerprint in the compound encoder, "fingerprint_size" if NULL name_compound_embedding_layer : corresponding name for the use of the embedding layer in the compound encoder, "embedding_layer" if NULL name_compound_length_seq : corresponding name for the length of sequences in the compound encoder, "length_seq" if NULL name_compound_num_tokens : corresponding name for the total number of distinct strings in the compound encoder, "num_tokens" if NULL name_compound_embedding_dim : corresponding name for dimension of the dense embedding in the compound encoder, "embedding_dim" if NULL name_protein_length_seq : corresponding name for the length of sequences in the protein encoder, "length_seq" if NULL name_protein_num_tokens : corresponding name for the total number of distinct strings in the protein encoder, "num_tokens" if NULL name_protein_embedding_dim : corresponding name for dimension of the dense embedding in the protein encoder, "embedding_dim" if NULL
preprocessor_only	model is not fitted after preprocessing if TRUE (default: FALSE)
preprocessing	list of preprocessed results for "fit_cpi" or "predict_cpi", they are set to NULL as default outcome : outcome variable outcome_val : outcome variable for validation convert_canonical_smiles : canonical representation used for preprocessing if TRUE canonical_smiles : canonical representation of SMILES compound_type : "graph", "fingerprint" or "sequence" compound_max_atoms : maximum number of atoms for compounds compound_A_pad : padded or turncated adjacency matrix of compounds compound_X_pad : padded or turncated node features of compounds compound_A_pad_val : padded or turncated adjacency matrix for validation compound_X_pad_val : padded or turncated node features for validation compound_fingerprint : fingerprint of compounds compound_fingerprint_val : fingerprint for validation smiles_encode_pad : encoded SMILES sequence which is padded or truncated smiles_val_encode_pad : encoded SMILES sequence for validation compound_lenc : encoded labels for characters of SMILES strings compound_length_seq : length of compound sequence compound_num_tokens : total number of characters of compounds compound_embedding_dim : dimension of the dense embedding for compounds AAseq_encode_pad : encoded amino acid sequence which is padded or truncated AAseq_val_encode_pad : encoded amino acid sequence for validation protein_lenc : encoded labels for characters of amino acid sequenes protein_length_seq : length of protein sequence protein_num_tokens : total number of characters of proteins protein_embedding_dim : dimension of the dense embedding for proteins protein_ngram_max : maximum size of an n-gram for protein sequences protein_ngram_min : minimum size of an n-gram for protein sequences removed_smiles : index for removed smiles while checking removed_AAseq : index for removed AAseq while checking removed_smiles_val : index for removed smiles of validation removed_AAseq_val : index for removed AAseq of validation
batch_size	batch size
use_generator	use data generator if TRUE (default: FALSE)
validation_split	proportion of validation data, it is ignored when there is a validation set (default: 0)
modelRes	result of the "fit_cpi"
...	additional parameters for the "keras::fit" or "keras::fit_generator"

Value

model

Author(s)

Dongmin Jung

See Also

keras::compile, keras::fit, keras::fit_generator, keras::layer_dense, keras::keras_model, purrr::pluck, webchem::is.smiles

Examples

compound_max_atoms <- 50
protein_embedding_dim <- 16
protein_length_seq <- 100
gcn_cnn_cpi <- fit_cpi(
    smiles = example_cpi[1:100, 1],
    AAseq = example_cpi[1:100, 2],
    outcome = example_cpi[1:100, 3],
    compound_type = "graph",
    compound_max_atoms = compound_max_atoms,
    protein_length_seq = protein_length_seq,
    protein_embedding_dim = protein_embedding_dim,
    net_args = list(
        compound = "gcn_in_out",
        compound_args = list(
            gcn_units = c(128, 64),
            gcn_activation = c("relu", "relu"),
            fc_units = c(10),
            fc_activation = c("relu")),
        protein = "cnn_in_out",
        protein_args = list(
            cnn_filters = c(32),
            cnn_kernel_size = c(3),
            cnn_activation = c("relu"),
            fc_units = c(10),
            fc_activation = c("relu")),
        fc_units = c(1),
        fc_activation = c("sigmoid"),
        loss = "binary_crossentropy",
        optimizer = keras::optimizer_adam(),
        metrics = "accuracy"),
    epochs = 2, batch_size = 16)
pred <- predict_cpi(gcn_cnn_cpi, example_cpi[101:110, 1], example_cpi[101:110, 2])

gcn_cnn_cpi2 <- fit_cpi(
    preprocessing = gcn_cnn_cpi$preprocessing,
    net_args = list(
        compound = "gcn_in_out",
        compound_args = list(
            gcn_units = c(128, 64),
            gcn_activation = c("relu", "relu"),
            fc_units = c(10),
            fc_activation = c("relu")),
        protein = "cnn_in_out",
        protein_args = list(
            cnn_filters = c(32),
            cnn_kernel_size = c(3),
            cnn_activation = c("relu"),
            fc_units = c(10),
            fc_activation = c("relu")),
        fc_units = c(1),
        fc_activation = c("sigmoid"),
        loss = "binary_crossentropy",
        optimizer = keras::optimizer_adam(),
        metrics = "accuracy"),
    epochs = 2, batch_size = 16)
pred <- predict_cpi(gcn_cnn_cpi2, preprocessing = pred$preprocessing)

dongminjung/DeepPINCS documentation built on Dec. 20, 2021, 12:13 a.m.