metric_concordance_index {DeepPINCS} | R Documentation

## Concordance index

### Description

The concordance index or c-index can be seen as one of the model performance metrics. It represents a good fit of the model.

### Author(s)

Dongmin Jung

### References

Kose, U., & Alzubi, J. (2020). Deep learning for cancer diagnosis. Springer.

### See Also

keras::k_cast, keras::k_equal, keras::k_sum, tensorflow::tf

### Examples

    compound_length_seq <- 50
    compound_embedding_dim <- 16
    protein_embedding_dim <- 16
    protein_length_seq <- 100

    mlp_cnn_cpi <- fit_cpi(
        smiles = example_cpi[1:100, 1],
        AAseq = example_cpi[1:100, 2],
        outcome = example_cpi[1:100, 3],
        compound_type = "sequence",
        compound_length_seq = compound_length_seq,
        compound_embedding_dim = compound_embedding_dim,
        protein_length_seq = protein_length_seq,
        protein_embedding_dim = protein_embedding_dim,
        net_args = list(
        compound = "mlp_in_out",
        compound_args = list(
                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 = custom_metric("concordance_index",
                metric_concordance_index)),
        epochs = 2,
        batch_size = 16)

[Package DeepPINCS version 1.0.2 Index]