Refactoring gridCvDeep (#104)

R/Estimator.R

@@ -58,11 +58,9 @@ setEstimator <- function(learningRate = "auto",
 ) {
 
   checkIsClass(learningRate, c("numeric", "character"))
-  if (inherits(learningRate, "character")) {
-    if (learningRate != "auto") {
-      stop(paste0('Learning rate should be either a numeric or "auto", 
-                  you provided: ', learningRate))
-    }
+  if (inherits(learningRate, "character") && learningRate != "auto") {
+    stop(paste0('Learning rate should be either a numeric or "auto", 
+                you provided: ', learningRate))
   }
   checkIsClass(weightDecay, "numeric")
   checkHigherEqual(weightDecay, 0.0)
@@ -113,23 +111,7 @@ setEstimator <- function(learningRate = "auto",
                                          class(estimatorSettings$device))
   }
 
-  paramsToTune <- list()
-  for (name in names(estimatorSettings)) {
-    param <- estimatorSettings[[name]]
-    if (length(param) > 1 && is.atomic(param)) {
-      paramsToTune[[paste0("estimator.", name)]] <- param
-    }
-    if ("params" %in% names(param)) {
-      for (name2 in names(param[["params"]])) {
-        param2 <- param[["params"]][[name2]]
-        if (length(param2) > 1) {
-          paramsToTune[[paste0("estimator.", name, ".", name2)]] <- param2
-        }
-      }
-    }
-  }
-  estimatorSettings$paramsToTune <- paramsToTune
-
+  estimatorSettings$paramsToTune <- extractParamsToTune(estimatorSettings)
   return(estimatorSettings)
 }
 
@@ -342,14 +324,10 @@ gridCvDeep <- function(mappedData,
       currentModelParams <- paramSearch[[gridId]][modelSettings$modelParamNames]
 
       currentEstimatorSettings <-
-        fillEstimatorSettings(modelSettings$estimatorSettings, fitParams,
+        fillEstimatorSettings(modelSettings$estimatorSettings,
+                              fitParams,
                               paramSearch[[gridId]])
-
-      # initiate prediction
-      prediction <- NULL
-
-      fold <- labels$index
-      ParallelLogger::logInfo(paste0("Max fold: ", max(fold)))
+      currentEstimatorSettings$modelType <- modelSettings$modelType
       currentModelParams$catFeatures <- dataset$get_cat_features()$shape[[1]]
       currentModelParams$numFeatures <-
         dataset$get_numerical_features()$shape[[1]]
@@ -363,63 +341,35 @@ gridCvDeep <- function(mappedData,
         currentEstimatorSettings$learningRate <- lr
       }
 
-      learnRates <- list()
-      for (i in 1:max(fold)) {
-        ParallelLogger::logInfo(paste0("Fold ", i))
-        trainDataset <-
-          torch$utils$data$Subset(dataset,
-                                  indices = as.integer(which(fold != i) - 1))
-        # -1 for python 0-based indexing
-        testDataset <-
-          torch$utils$data$Subset(dataset,
-                                  indices = as.integer(which(fold == i) - 1))
-        # -1 for python 0-based indexing
-
-        estimator <- createEstimator(modelType = modelSettings$modelType,
-                                     modelParameters = currentModelParams,
-                                     estimatorSettings =
-                                       currentEstimatorSettings)
-        estimator$fit(trainDataset, testDataset)
-
-        ParallelLogger::logInfo("Calculating predictions on left out 
-                                fold set...")
-
-        prediction <- rbind(
-          prediction,
-          predictDeepEstimator(
-            plpModel = estimator,
-            data = testDataset,
-            cohort = labels[fold == i, ]
-          )
-        )
-        learnRates[[i]] <- list(
-          LRs = estimator$learn_rate_schedule,
-          bestEpoch = estimator$best_epoch
-        )
-      }
+      crossValidationResults <-
+        doCrossvalidation(dataset,
+                          labels = labels,
+                          modelSettings = currentModelParams,
+                          estimatorSettings = currentEstimatorSettings)
+      learnRates <- crossValidationResults$learnRates
+      prediction <- crossValidationResults$prediction
+
+      gridPerformance <-
+        PatientLevelPrediction::computeGridPerformance(prediction,
+                                                       paramSearch[[gridId]])
       maxIndex <- which.max(unlist(sapply(learnRates, `[`, 2)))
       gridSearchPredictons[[gridId]] <- list(
         prediction = prediction,
         param = paramSearch[[gridId]],
-        gridPerformance =
-          PatientLevelPrediction::computeGridPerformance(prediction,
-                                                         paramSearch[[gridId]])
+        gridPerformance = gridPerformance
       )
       gridSearchPredictons[[gridId]]$gridPerformance$hyperSummary$learnRates <-
         rep(list(unlist(learnRates[[maxIndex]]$LRs)),
             nrow(gridSearchPredictons[[gridId]]$gridPerformance$hyperSummary))
       gridSearchPredictons[[gridId]]$param$learnSchedule <-
         learnRates[[maxIndex]]
-
       # remove all predictions that are not the max performance
       indexOfMax <-
         which.max(unlist(lapply(gridSearchPredictons,
                                 function(x) x$gridPerformance$cvPerformance)))
       for (i in seq_along(gridSearchPredictons)) {
-        if (!is.null(gridSearchPredictons[[i]])) {
-          if (i != indexOfMax) {
-            gridSearchPredictons[[i]]$prediction <- list(NULL)
-          }
+        if (!is.null(gridSearchPredictons[[i]]) && i != indexOfMax) {
+          gridSearchPredictons[[i]]$prediction <- list(NULL)
         }
       }
       ParallelLogger::logInfo(paste0("Caching all grid search results and 
@@ -543,3 +493,67 @@ createEstimator <- function(modelType,
                          estimator_settings = estimatorSettings)
   return(estimator)
 }
+
+doCrossvalidation <- function(dataset,
+                              labels,
+                              modelSettings,
+                              estimatorSettings) {
+  fold <- labels$index
+  ParallelLogger::logInfo(paste0("Max fold: ", max(fold)))
+  learnRates <- list()
+  prediction <- NULL
+  for (i in 1:max(fold)) {
+    ParallelLogger::logInfo(paste0("Fold ", i))
+
+    # -1 for python 0-based indexing
+    trainDataset <- torch$utils$data$Subset(dataset,
+                                            indices =
+                                              as.integer(which(fold != i) - 1))
+
+    # -1 for python 0-based indexing
+    testDataset <- torch$utils$data$Subset(dataset,
+                                           indices =
+                                             as.integer(which(fold == i) - 1))
+    estimator <- createEstimator(modelType = estimatorSettings$modelType,
+                                 modelParameters = modelSettings,
+                                 estimatorSettings = estimatorSettings)
+    estimator$fit(trainDataset, testDataset)
+
+    ParallelLogger::logInfo("Calculating predictions on left out fold set...")
+
+    prediction <- rbind(
+      prediction,
+      predictDeepEstimator(
+        plpModel = estimator,
+        data = testDataset,
+        cohort = labels[fold == i, ]
+      )
+    )
+    learnRates[[i]] <- list(
+      LRs = estimator$learn_rate_schedule,
+      bestEpoch = estimator$best_epoch
+    )
+  }
+  return(results = list(prediction = prediction,
+                        learnRates = learnRates))
+
+}
+
+extractParamsToTune <- function(estimatorSettings) {
+  paramsToTune <- list()
+  for (name in names(estimatorSettings)) {
+    param <- estimatorSettings[[name]]
+    if (length(param) > 1 && is.atomic(param)) {
+      paramsToTune[[paste0("estimator.", name)]] <- param
+    }
+    if ("params" %in% names(param)) {
+      for (name2 in names(param[["params"]])) {
+        param2 <- param[["params"]][[name2]]
+        if (length(param2) > 1) {
+          paramsToTune[[paste0("estimator.", name, ".", name2)]] <- param2
+        }
+      }
+    }
+  }
+  return(paramsToTune)
+}