DeepLearning_in_R/mxnet.R

# installation 
cran <- getOption("repos")
cran["dmlc"] <- "https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/GPU/cu92"
options(repos = cran)
install.packages("mxnet")


require(mxnet)



# load data and split 
df <-
  structure(list(name = c("acebutolol", "acebutolol_ester", "acetylsalic_acid", 
                          "acyclovir", "alprenolol", "alprenolol ester", "aminopyrin", 
                          "artemisinin", "artesunate", "atenolol", "betazolol ester", "betazolol_", 
                          "bremazocine", "caffeine", "chloramphenicol", "chlorothiazide", 
                          "chlorpromazine", "cimetidine", "clonidine", "corticosterone", 
                          "desiprarnine", "dexamethas", "dexamethas_beta_D_glucoside", 
                          "dexamethas_beta_D_glucuronide", "diazepam", "dopamine", "doxorubici", 
                          "erythromycin", "estradiol", "felodipine", "ganciclovir", "griseofulvin", 
                          "hydrochlorothiazide", "hydrocortisone", "ibuprophen", "imipramine", 
                          "indomethacin", "labetalol", "mannitol", "meloxicam", "methanol", 
                          "methotrexate", "methylscopolamine", "metoprolol", "nadolol", 
                          "naproxen", "nevirapine", "nicotine", "olsalazine", "oxprenolol", 
                          "oxprenolol ester", "phencyclidine", "Phenytoin", "pindolol", 
                          "pirenzepine", "piroxicam", "pnu200603", "practolol", "prazocin", 
                          "progesterone", "propranolol", "propranolo_ester", "quinidine", 
                          "ranitidine", "salicylic acid", "scopolamine", "sucrose", "sulfasalazine", 
                          "telmisartan", "terbutaline", "tesosterone", "timolol", "timolol_ester", 
                          "uracil", "urea", "warfarine", "zidovudine"), log_P_eff_exp = c(-5.83, 
                                                                                          -4.61, -5.06, -6.15, -4.62, -4.47, -4.44, -4.52, -5.4, -6.44, 
                                                                                          -4.81, -4.52, -5.1, -4.41, -4.69, -6.72, -4.7, -5.89, -4.59, 
                                                                                          -4.47, -4.67, -4.75, -6.54, -6.12, -4.32, -5.03, -6.8, -5.43, 
                                                                                          -4.77, -4.64, -6.27, -4.44, -6.06, -4.66, -4.28, -4.85, -4.69, 
                                                                                          -5.03, -6.21, -4.71, -4.58, -5.92, -6.16, -4.59, -5.41, -4.83, 
                                                                                          -4.52, -4.71, -6.96, -4.68, -4.51, -4.61, -4.57, -4.78, -6.36, 
                                                                                          -4.45, -6.25, -6.05, -4.36, -4.37, -4.58, -4.48, -4.69, -6.31, 
                                                                                          -4.79, -4.93, -5.77, -6.33, -4.82, -6.38, -4.34, -4.85, -4.6, 
                                                                                          -5.37, -5.34, -4.68, -5.16), log_D = c(-0.09, 1.59, -2.25, -1.8, 
                                                                                                                                 1.38, 2.78, 0.63, 2.22, -0.88, -1.81, 0.28, 0.63, 1.66, 0.02, 
                                                                                                                                 1.14, -1.15, 1.86, -0.36, 0.78, 1.78, 1.57, 1.89, 0.58, -1.59, 
                                                                                                                                 2.58, -0.8, -0.16, 1.26, 2.24, 3.48, -0.87, 2.47, -0.12, 1.48, 
                                                                                                                                 0.68, 2.52, 1, 1.24, -2.65, 0.03, -0.7, -2.53, -1.14, 0.51, 0.68, 
                                                                                                                                 0.42, 1.81, 0.41, -4.5, 0.45, 1.98, 1.31, 2.26, 0.19, -0.46, 
                                                                                                                                 -0.07, -4, -1.4, 1.88, 3.48, 1.55, 3.02, 2.04, -0.12, -1.44, 
                                                                                                                                 0.21, -3.34, -0.42, 2.41, -1.07, 3.11, 0.03, 1.74, -1.11, -1.64, 
                                                                                                                                 0.64, -0.58), rgyr = c(4.64, 5.12, 3.41, 3.37, 3.68, 3.84, 2.97, 
                                                                                                                                                        2.75, 4.02, 4.58, 5.41, 5.64, 3.43, 2.47, 3.75, 3.11, 3.74, 4.26, 
                                                                                                                                                        2.79, 3.68, 3.4, 3.6, 5.67, 5.75, 3.28, 2.67, 4.85, 4.99, 3.44, 
                                                                                                                                                        3.39, 3.7, 3.37, 3.11, 3.72, 3.45, 3.44, 4.16, 4.61, 2.48, 3.34, 
                                                                                                                                                        0.84, 5.33, 3.67, 4.59, 4.37, 3.38, 2.94, 2.5, 4.62, 3.63, 3.87, 
                                                                                                                                                        2.91, 2.97, 3.71, 3.55, 3.17, 3.89, 4.02, 4.96, 3.58, 3.63, 4.13, 
                                                                                                                                                        3.25, 5.13, 2.14, 3.63, 3.49, 5.68, 5.29, 3.15, 3.33, 4.02, 3.98, 
                                                                                                                                                        1.84, 1.23, 3.45, 3.14), rgyr_d = c(4.51, 5.03, 3.24, 3.23, 3.69, 
                                                                                                                                                                                            3.88, 2.97, 2.75, 3.62, 4.52, 5.27, 5.39, 3.38, 2.47, 3.73, 3.11, 
                                                                                                                                                                                            3.69, 4.24, 2.79, 3.71, 3.42, 3.66, 5.28, 5.23, 3.28, 2.68, 4.9, 
                                                                                                                                                                                            5.01, 3.44, 3.48, 3.48, 3.37, 3.11, 3.79, 3.36, 3.45, 3.16, 4.46, 
                                                                                                                                                                                            2.59, 3.36, 0.84, 5.18, 3.74, 4.53, 4.1, 3.43, 2.94, 2.5, 4.37, 
                                                                                                                                                                                            3.56, 3.9, 2.91, 2.97, 3.71, 3.4, 3.26, 3.79, 4.09, 4.99, 3.62, 
                                                                                                                                                                                            3.53, 4.06, 3.3, 4.57, 2.14, 3.49, 3.54, 5.53, 5.01, 3.15, 3.33, 
                                                                                                                                                                                            4.01, 4.13, 1.84, 1.23, 3.5, 3.13), HCPSA = c(82.88, 77.08, 79.38, 
                                                                                                                                                                                                                                          120.63, 38.92, 35.53, 20.81, 54.27, 102.05, 86.82, 43.02, 47.14, 
                                                                                                                                                                                                                                          49.56, 45.55, 113.73, 138.76, 4.6, 105.44, 30.03, 75.95, 13.8, 
                                                                                                                                                                                                                                          90.74, 163.95, 186.88, 25.93, 75.13, 186.78, 138.69, 44.34, 50.34, 
                                                                                                                                                                                                                                          139.45, 67.55, 142.85, 93.37, 39.86, 3.56, 67.13, 93.29, 127.46, 
                                                                                                                                                                                                                                          93.21, 25.64, 204.96, 51.29, 44.88, 86.73, 76.98, 36.68, 15.1, 
                                                                                                                                                                                                                                          144.08, 48.62, 49.58, 1.49, 65.63, 52.8, 59.71, 99.19, 69.89, 
                                                                                                                                                                                                                                          64.79, 86.76, 38.1, 40.42, 36.21, 43.77, 105.15, 61.71, 57.35, 
                                                                                                                                                                                                                                          187.69, 133.67, 55.48, 79.52, 42.35, 100.74, 96.25, 66.72, 82.72, 
                                                                                                                                                                                                                                          59.47, 96.33), TPSA = c(87.66, 93.73, 89.9, 114.76, 41.49, 47.56, 
                                                                                                                                                                                                                                                                  26.79, 53.99, 100.52, 84.58, 50.72, 56.79, 43.7, 58.44, 115.38, 
                                                                                                                                                                                                                                                                  118.69, 6.48, 88.89, 36.42, 74.6, 15.27, 94.83, 173.98, 191.05, 
                                                                                                                                                                                                                                                                  32.67, 66.48, 206.07, 193.91, 40.46, 64.63, 134.99, 71.06, 118.36, 
                                                                                                                                                                                                                                                                  94.83, 37.3, 6.48, 68.53, 95.58, 121.38, 99.6, 20.23, 210.54, 
                                                                                                                                                                                                                                                                  59.06, 50.72, 81.95, 46.53, 58.12, 16.13, 139.78, 50.72, 56.79, 
                                                                                                                                                                                                                                                                  3.24, 58.2, 57.28, 68.78, 99.6, 91.44, 70.59, 106.95, 34.14, 
                                                                                                                                                                                                                                                                  41.49, 47.56, 45.59, 86.26, 57.53, 62.3, 189.53, 141.31, 72.94, 
                                                                                                                                                                                                                                                                  72.72, 37.3, 79.74, 85.81, 58.2, 69.11, 63.6, 103.59), N_rotb = c(0.31, 
                                                                                                                                                                                                                                                                                                                                    0.29, 0.23, 0.21, 0.29, 0.27, 0.17, 0.07, 0.16, 0.29, 0.27, 0.26, 
                                                                                                                                                                                                                                                                                                                                    0.15, 0.12, 0.28, 0.08, 0.14, 0.33, 0.08, 0.1, 0.11, 0.13, 0.17, 
                                                                                                                                                                                                                                                                                                                                    0.17, 0.06, 0.23, 0.18, 0.21, 0.06, 0.22, 0.25, 0.16, 0.08, 0.12, 
                                                                                                                                                                                                                                                                                                                                    0.24, 0.13, 0.19, 0.24, 0.44, 0.16, 0.2, 0.26, 0.16, 0.3, 0.24, 
                                                                                                                                                                                                                                                                                                                                    0.19, 0.05, 0.07, 0.27, 0.31, 0.29, 0.04, 0.06, 0.23, 0.08, 0.13, 
                                                                                                                                                                                                                                                                                                                                    0.15, 0.29, 0.15, 0.07, 0.22, 0.22, 0.14, 0.33, 0.19, 0.15, 0.28, 
                                                                                                                                                                                                                                                                                                                                    0.2, 0.15, 0.29, 0.06, 0.24, 0.23, 0, 0.29, 0.15, 0.18), log_P_eff_calc = c(-5.3, 
                                                                                                                                                                                                                                                                                                                                                                                                                -4.89, -5.77, -5.91, -4.58, -4.39, -4.63, -4.47, -5.64, -5.85, 
                                                                                                                                                                                                                                                                                                                                                                                                                -5.2, -5.13, -4.57, -4.89, -5.11, -5.87, -4.38, -5.55, -4.69, 
                                                                                                                                                                                                                                                                                                                                                                                                                -4.78, -4.46, -4.77, -5.83, -6.55, -4.45, -5.27, -6, -5.13, -4.57, 
                                                                                                                                                                                                                                                                                                                                                                                                                -4.44, -5.79, -4.59, -5.62, -4.94, -4.78, -4.28, -5, -5.09, -5.87, 
                                                                                                                                                                                                                                                                                                                                                                                                                -5.27, -4.67, -6.79, -5.37, -4.99, -5.15, -5.09, -4.49, -4.65, 
                                                                                                                                                                                                                                                                                                                                                                                                                -6.97, -4.84, -4.45, -4.42, -4.6, -5.02, -5.3, -5.31, -6.37, 
                                                                                                                                                                                                                                                                                                                                                                                                                -5.5, -5.05, -4.54, -4.57, -4.5, -4.46, -5.6, -5.29, -5.07, -6.56, 
                                                                                                                                                                                                                                                                                                                                                                                                                -6.06, -4.85, -5.36, -4.53, -5.35, -4.82, -5.23, -5.29, -4.95, 
                                                                                                                                                                                                                                                                                                                                                                                                                -5.43), residuals = c(-0.53, 0.28, 0.71, -0.24, -0.04, -0.08, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      0.19, -0.05, 0.24, -0.59, 0.39, 0.61, -0.53, 0.48, 0.42, -0.85, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      -0.32, -0.34, 0.1, 0.31, -0.21, 0.02, -0.71, 0.43, 0.13, 0.24, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      -0.8, -0.3, -0.2, -0.2, -0.48, 0.15, -0.44, 0.28, 0.5, -0.57, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      0.31, 0.06, -0.34, 0.56, 0.09, 0.87, -0.79, 0.4, -0.26, 0.26, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      -0.03, -0.06, 0.01, 0.16, -0.06, -0.19, 0.03, 0.24, -1.06, 0.86, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      0.12, -0.55, 0.69, 0.17, -0.01, 0.02, -0.23, -0.71, 0.5, 0.14, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      0.79, -0.27, 0.03, -1.02, 0.19, 0.5, 0.22, -0.14, -0.05, 0.27, 
                                                                                                                                                                                                                                                                                                                                                                                                                                      0.27)), row.names = c(NA, -77L), class = c("tbl_df", "tbl", "data.frame"
                                                                                                                                                                                                                                                                                                                                                                                                                                      ))

set.seed(42)


#transform and split train on x and y
train_ind <- sample(1:77, 60)
x_train <- as.matrix(df[train_ind, 2:8])
y_train <- unlist(df[train_ind, 9])
x_val <- as.matrix(df[-train_ind, 2:8])
y_val <- unlist(df[-train_ind, 9])


# define model
data <- mx.symbol.Variable("data")

fc1 <- mx.symbol.FullyConnected(data, 
                                num_hidden = 1)
linreg <- mx.symbol.LinearRegressionOutput(fc1)

# define initializer
initializer <- mx.init.normal(sd = 0.1)

# define optimizer algorythm to update weigths
optimizer <- mx.opt.create("sgd", 
                           learning.rate = 1e-6,
                           momentum = 0.9)

# define logger where we will keep updates
logger <- mx.metric.logger()
epoch.end.callback <- mx.callback.log.train.metric(
  period = 4, # число батчей, после которого оценивается метрика
  logger = logger)

n_epoch <- 20

# plot our model
graph.viz(linreg)

# train model with parameters
model <- mx.model.FeedForward.create(
  symbol = linreg, 
  X = x_train, 
  y = y_train,
  ctx = mx.cpu(), 
  num.round = n_epoch, 
  initializer = initializer, 
  optimizer = optimizer,
  eval.data = list(data = x_val, label = y_val),
  eval.metric = mx.metric.rmse,
  array.batch.size = 15,
  epoch.end.callback = epoch.end.callback)

# plot train loss curve and eval
rmse_log <- data.frame(RMSE = c(logger$train, logger$eval),
                       dataset = c(rep("train", 
                                       length(logger$train)), 
                                   rep("val", 
                                       length(logger$eval))),
                       epoch = 1:n_epoch)

library(ggplot2)
ggplot(rmse_log, aes(epoch, RMSE, 
                     group = dataset,
                     colour = dataset)) +
  geom_point() +
  geom_line()