[return to overview page]

In this section, I will build a neural network model to make truth and lie predictions on our statements. Such methods have seen a recent explosion in popularity, partly due to increases in the computational capacity of computers and the wider availability of massive amounts of data on which these models can more successfully be “trained” (Thompson, 2018). In their widely used textbook, The Elements of Statistical Learning, Hastie, Tibshirani, & Friedman (2009, p. 392) point out that despite the “hype” about neural networks, which can make them seem “magical and mysterious”, they are just another type of nonlinear statistical model. The caret and nnet packages in R make the implementation of at least basic neural networks very easy (Kuhn, 2008; Ripley & Venables, 2016) – so easy, in fact, that charlatans, like me, who have no business using them, are nevertheless able to do so. So, out of reckless curiousity and simply because it is possible, I thought it would be interesting to give this type of modeling a shot.

Because it is possible to build a neural network in R without really understanding how they work or what they are doing and because this is exactly what I will do below, it was important to me that I somehow be punished for this. Thus, I begin by attempting to explain and provide a brief overview of neural networks. I apologize to the reader for what they will have to suffer through in the next few paragraphs, but the process of writing them out proved so humiliating and infuriating that it felt like a partially sufficient punishment.

In broad terms, neural networks draw their inspiration from some basic features of the brain. They seek to provide mathematical and algorithmic descriptions of how sets of (abstracted) neurons in the brain could coalesce to perform tasks like binary classification and image recognition. The fundamental units of neural networks are “nodes” (which can be thought of as representing individual neurons), arranged into different “layers”. These layers are are sequentially connected through links between their constituent nodes (each of these connections can be though of as a synapse). An initial layer of input nodes eventually leads to a final layer of output nodes (with possible layers of nodes in between). Through some process of updating the weights attached to these links between nodes (which emulate the process of updating and changing the strength of synaptic connections; Hebb, 1949), learning of simple and sophisticated relationships can be simulated. The heart of neural network research is in exploring different processes for how these synaptic connections may be updated to lead to successful learning.

Historically, the origin of research on neural network models is often attributed to Warren McCullough and Walter Pitts (1943), for their paper “A logical calculus of the ideas immanent in nervous activity”. A next major innovation came from Frank Rosenblatt (1958) (of Cornell), in his paper on “the perceptron”. As I understand it (which is to say, not well), perceptrons provided a simple model of how a single layer of inputs neurons linked to an output neuron can be trained to perform basic tasks like binary classification, through various threshold functions which emulate the “activation” or non-activation of neurons. In 1969, Marvin Minsky and Seymour Papert, published a book Perceptrons: an introduction to computational geometry, which showed the limitations of such basic perceptron models (and then went on to describe how these limitations could be overcome by linking together multiple perceptrons). Thus, later research expanded into networks with greater numbers of intermediary layers. An important innovation came in the 1980s from Rumelhart, Hinton, & Williams (1986), who developed a technique (back-propogation) which used methods in calculus (“gradient descent”) to allow for a computationally tractable method of “learning” and updating in multilayer networks. Recent research focuses on “deep” networks (i.e. networks with many layers) and networks where information can flow in multiple directions, rather than just forward, making “loops” between different layers in the process of learning and updating (these types of networks are referred to as recurrent neural networks).

Here, we will implement a very simple type of neural network, enabled by the nnet package – a “feed-forward”, neural network with a single hidden layer. Hastie, Tibshirani, & Friedman (2009, p. 392) refer to this as the “the most widely used ‘vanilla’ neural net”. Because vanilla is delicious, I have no problem with this.

Kuhn & Johnson (2013, p. 334) provide a graphical depiction of the basic structure of a feedforward single hidden layer neural network. As we can see, there are three fundamental components in this neural network:

When implementing a neural network to model our lie and truth data, the nodes of our input layer will consist of the 90 predictor features we extracted earlier. The output layer will consist of two nodes, one for of the classes our statements can fall into (lies and truths). Linking these two together will be a hidden layer. The number of nodes in our hidden layer is a free parameter that we will have to select a value for as before. (As with our support vector machines models, this will be done through a process of model tuning.) The values of the nodes in the hidden layer will be determined as linear combinations of the nodes (features) in the input layer (as the authors depict, for example, a sigmoid function can be used as the basis of this transformation). And likewise, the final classes will be predicted as a linear combination of the nodes in the hidden layer (Kuhn & Johnson, 2013; p. 333). The modeling process will begin by assigning random weights to the connections between nodes, which are then iteratively updated as predictions are checked against reality and error is back-propagated. In part because this back-propogation process does not provide a “global solution” as other modeling techniques can be proven to do, such models are susceptible to over-fitting. In attempt to deal with this, another free parameter, weight decay, applies penalties in order to limit such overfitting (Kuhn & Johnson, 2013; p. 143). This, along with the number of nodes in the hidden layer is another parameter that we will have to tune in our modeling. Lets now get to it.


Let’s make sure to load all the relevant packages.

# before knitting: message = FALSE, warning = FALSE
library(tidyverse) # cleaning and visualization
library(caret) # modeling
library(nnet) # for neural networks specifically (caret "nnet" wraps these functions)

Load Data

Next, I will again load the pre-processed data, which we created earlier (see Data Cleaning & Pre-Processing). As a reminder, this dataset has a row for each of 5,004 statements, a column indicating whether that particular statement was a truth or a lie, and 90 possible predictor variables for each statement, which comes from the textual features we extracted earlier.

# load pre-processed df's

# For rendering, I'm going to cheat here and load results created when this model was first run
# For some reason, chunks that were supposed to be caches when originally run are rerunning
results <- results_neural # change the specific named (renamed at end), back to generic name

EXAMPLE (Neural Network)

As usual, let’s begin with an example. We will conduct one training-testing split and create and assess the performance of of one resultant support vector machine model, with a radial basis kernel function.

Split Sample Into Training and Testing Sets

As with our logistic regression models, we will conduct a 50-50 training-testing split, randomly allocating one half of the statements to the training set, and the other half to the testing set using the createDataPartition function in the caret package (Kuhn, 2008).

# set seed, so that statistics don't keep changing for every analysis

# partition data in 50-50 lgocv split (create index for test set)
index_train_ex <- 
  createDataPartition(y = stats_proc$stat_id,
                      p = 0.50,
                      times = 1,
                      list = FALSE)

# actually create data frame with training set (predictors and outcome together)
train_set_ex <- stats_proc[index_train_ex, ]

# actualy create data frame with test set (predictors and outcome together)
test_set_ex <- stats_proc[-index_train_ex, ]

Build Model (on Training Set)

Now that the data are split, we can train a neural network on our training data. This is made almost trivially easy by the “train” function in the the caret package (Kuhn, 2008; Kuhn, 2019), which allows us to model our data using a single hidden layer feedforward neural network by selecting the “nnet” model (a wrapper on the nnet function in the nnet package from (Ripley & Venables, 2016)).

As mentioned earlierr and as with with our support vector machine model, we have two free tuning parameters, which need to be set. These are (1) the number of nodes in the hidden layer and the (2) the value of the “weight decay” parameter. (Note that weight decay is not the same as the “learning rate”, which is a parameter in earlier, simpler neural network models. It is my understanding that in neural network models such as the one here the gradient descent method obviates the need to select a “learning rate”; see discussion here).

I will cycle through these number of hidden layer nodes: 1, 2, 3, 4, 5, and 10. (The computational complexity of our model and the time it takes to run increases massively as we add more layers; thus I will not explore models with large numbers, like dozens and dozens, of hidden layer nodes). And I will cycle through decay rates of: 0, 0.05, 0.1, 1, and 2 (which are the range of values that Kuhn & Johnson (2013, p. 361) cycle through in their implementations of similar models). Thus, we will have cycle through 30 different combinations of parameter values (6 different hidden layer candidate values times 5 different decay rate values).

As with our support vector machine model, we will select tuning parameter values through a process of training and testing within our training set (again, using a 50-50 split, with 3 resamples for each of the 30 parameter combinations). (See the “Build Model (on Training Set)” of the SMV page for a more in depth discussion of how we implement this process.)

Thismodel tuning process is completed below, followed by a summary of our results. As we can see in the textual output, the parameters that led to the best results were a model with only one single node in the hidden layer, and a decay rate value of 2 (which together led to an average accuracy rate of 59.7%). Thus, the neural network we will use will have its tuning parameters set to: number of nodes = 1, and decay rate = 2.

# note: these setting chunks are separated for reuse later

# set seed, so that statistics don't keep changing for every analysis

# -----------------------------------------------------------------------------

# part a: set range of tuning parameters (layer size and weight decay)
tune_grid_neural <- expand.grid(size = c(1:5, 10),
                                decay = c(0, 0.05, 0.1, 1, 2))

# part b: set some other consrains to be imposed on network (to keep computation manageable)
# see: p. 361 of Kuhn & Johnson (2013, 
max_size_neaural <- max(tune_grid_neural$size)
max_weights_neural <- max_size_neaural*(nrow(train_set_ex) + 1) + max_size_neaural + 1

# -----------------------------------------------------------------------------
# set up train control object, which specifies training/testing technique
train_control_neural <- trainControl(method = "LGOCV",
                                     number = 3,
                                     p = 0.50)
# set seed, so that statistics don't keep changing for every analysis
# (applies for models which might have random parameters)

# start timer
start_time <- Sys.time()

# -----------------------------------------------------------------------------

# use caret "train" function to train svm
model_ex <- 
  train(form = grd_truth ~ . - stat_id,
        data = train_set_ex,
        method = "nnet",
        tuneGrid = tune_grid_neural,
        trControl = train_control_neural,
        metric = "Accuracy", # how to select among models
        trace = FALSE,
        maxit = 100,
        MaxNWts = max_weights_neural) # don't print output along the way

# end timer
total_time <- Sys.time() - start_time
# print out overall summary for tuning process
## Neural Network 
## 2504 samples
##   91 predictor
##    2 classes: 'lie', 'truth' 
## No pre-processing
## Resampling: Repeated Train/Test Splits Estimated (3 reps, 50%) 
## Summary of sample sizes: 1252, 1252, 1252 
## Resampling results across tuning parameters:
##   size  decay  Accuracy   Kappa     
##    1    0.00   0.5702875  0.14057508
##    1    0.05   0.5681576  0.13631523
##    1    0.10   0.5774760  0.15495208
##    1    1.00   0.5897231  0.17944622
##    1    2.00   0.5969116  0.19382322
##    2    0.00   0.5535144  0.10702875
##    2    0.05   0.5497870  0.09957401
##    2    0.10   0.5615016  0.12300319
##    2    1.00   0.5665602  0.13312034
##    2    2.00   0.5851970  0.17039404
##    3    0.00   0.5905218  0.18104366
##    3    0.05   0.5646965  0.12939297
##    3    0.10   0.5644302  0.12886049
##    3    1.00   0.5612354  0.12247071
##    3    2.00   0.5918530  0.18370607
##    4    0.00   0.5471246  0.09424920
##    4    0.05   0.5575080  0.11501597
##    4    0.10   0.5676251  0.13525027
##    4    1.00   0.5758786  0.15175719
##    4    2.00   0.5782748  0.15654952
##    5    0.00   0.5607029  0.12140575
##    5    0.05   0.5625666  0.12513312
##    5    0.10   0.5524494  0.10489883
##    5    1.00   0.5543131  0.10862620
##    5    2.00   0.5753461  0.15069223
##   10    0.00   0.5386049  0.07720980
##   10    0.05   0.5769436  0.15388711
##   10    0.10   0.5646965  0.12939297
##   10    1.00   0.5774760  0.15495208
##   10    2.00   0.5724175  0.14483493
## Accuracy was used to select the optimal model using the largest value.
## The final values used for the model were size = 1 and decay = 2.

Evaluate Model (on Testing Set)

Now that we have selected values for our two tuning parameters (number of nodes = 1, and decay rate = 2), let’s build our full model and evaluate its peformance. (Note again that that while we built and evaluated a model with these tuning parameters earler, these were only built on subsets (i.e of ~1250 entries) of the training dataset and evaluated on diferent subsets of that same training dataset (also of ~1250 entries). Now that we have selected our tuning parameters, we want to build a model with those parameters on the full training dataset (i.e. ~2500 entries) and evaluate its performance on the original training set we put aside at the beginning (also of ~2500 entries)).

When we evaluate the performance of our tuned model on the holdout testing set, we see that it performs well. Its overall accuracy was significantly better than chance: 60.4% [95% CI: 58.5, 62.4%]. And it performed well both in identifying truths (i.e. sensitivity: 61.2%) and identifying lies (i.e. specificity: 59.7%). And when the model made a prediction that a statement was a truth, it was correct more often than not (i.e. precision or positive predictive value: 60.3%). And when it made a prediction that a statement was a lie, it was also correct more often than not (i.e. negative predictive value: 60.6%). (Confidence intervals can easily be generated for these other four statistics as well (i.e. +/- z*(sqrt(p*(1-p)/n), where z = 1.96; I won’t calculate these for this example, but I will do so below in our full analysis.)

# note: https://stats.stackexchange.com/questions/52274/how-to-choose-a-predictive-model-after-k-fold-cross-validation
# which makes clear that we retrain our final model selected after turning on ALL the training data

# make predictions
preds_ex <-
  predict(object = model_ex,
          newdata = test_set_ex,
          type = "raw")
# record model performance
conf_ex <-
  confusionMatrix(data = preds_ex,
                  reference = test_set_ex$grd_truth,
                  positive = "truth")
# print confusion matrix
## Confusion Matrix and Statistics
##           Reference
## Prediction lie truth
##      lie   746   485
##      truth 504   765
##                Accuracy : 0.6044          
##                  95% CI : (0.5849, 0.6236)
##     No Information Rate : 0.5             
##     P-Value [Acc > NIR] : <2e-16          
##                   Kappa : 0.2088          
##  Mcnemar's Test P-Value : 0.5671          
##             Sensitivity : 0.6120          
##             Specificity : 0.5968          
##          Pos Pred Value : 0.6028          
##          Neg Pred Value : 0.6060          
##              Prevalence : 0.5000          
##          Detection Rate : 0.3060          
##    Detection Prevalence : 0.5076          
##       Balanced Accuracy : 0.6044          
##        'Positive' Class : truth           

FULL (Neural Networks)

Let’s now repeated the process from above 10 times, and evaluate the average performance of our neural network model across these 10 iterations.

Run 10 models

Below is the code that runs through this modeling process 10 different times and saves the result from each round.

# -----------------------------------------------------------------------------
# STEP 0: set seed, so that statistics don't keep changing for every analysis

# -----------------------------------------------------------------------------
# STEP 1: decide how many times to run the model
rounds <- 10

# -----------------------------------------------------------------------------
# STEP 2: set up object to store results
# part a: create names of results to store
result_cols <- c("model_type", "round", "accuracy", "accuracy_LL", "accuracy_UL",
                 "sensitivity", "specificity", "precision", "npv", "n")

# part b: create matrix
results <-
  matrix(nrow = rounds,
         ncol = length(result_cols))

# part c: actually name columns in results marix
colnames(results) <- result_cols

# part d: convert to df (so multiple variables of different types can be stored)
results <- data.frame(results)

# -----------------------------------------------------------------------------
# STEP 2: start timer
start_time <- Sys.time()

# -----------------------------------------------------------------------------
# STEP 3: create rounds number of models, and store results each time

for (i in 1:rounds){
  # part a: partition data in 50-50 lgocv split (create index for test set)
  index_train <- 
    createDataPartition(y = stats_proc$stat_id,
                        p = 0.50,
                        times = 1,
                        list = FALSE)
  # part b: create testing and training data sets
  train_set <- stats_proc[index_train, ]
  test_set <- stats_proc[-index_train, ]
  # part c: use caret "train" function to train logistic regression model
  model <- 
    train(form = grd_truth ~ . - stat_id,
        data = train_set_ex,
        method = "nnet",
        tuneGrid = tune_grid_neural,
        trControl = train_control_neural,
        metric = "Accuracy", # how to select among models
        trace = FALSE,
        maxit = 100,
        MaxNWts = max_weights_neural) # don't print output along the way
  # part d: make predictions
  preds <-
    predict(object = model,
            newdata = test_set,
            type = "raw")
  # part e: store model performance
  conf_m <-
    confusionMatrix(data = preds,
                    reference = test_set$grd_truth,
                    positive = "truth")
  # part f: store model results
  # model type
  results[i, 1] <- "neural"
  # round
  results[i, 2] <- i
  # accuracy
  results[i, 3] <- conf_m$overall[1]
  # accuracy LL
  results[i, 4] <- conf_m$overall[3]
  # accuracy UL
  results[i, 5] <- conf_m$overall[4]
  # sensitivity
  results[i, 6] <- conf_m$byClass[1]
  # specificity
  results[i, 7] <- conf_m$byClass[2]
  # precision
  results[i, 8] <- conf_m$byClass[3]
  # negative predictive value
  results[i, 9] <- conf_m$byClass[4]
  # sample size (of test set)
  results[i, 10] <- sum(conf_m$table)
  # part g: print round and total elapsed time so far
  cumul_time <- difftime(Sys.time(), start_time, units = "mins")
  print(paste("round #", i, ": cumulative time ", round(cumul_time, 2), " mins",
              sep = ""))


View Results (Tabular)

Below, I’ve displayed a raw tabular summary of the results from each of the 10 models. Unlike with our earlier logistic regression and support vector machine models, we see a great degree of variability from model to model (e.g. our worst fit model has an overall accuracy of 60.0%, while our best fit model has an accuracy that jumps to 75.4%). I believe this greater variability might be a function of the fact tha neural network models do not find provably “global” solutions, and thus may vary more from one model to another through the iterative process whereby the initial random weight values are updated. However, this is only a guess and I would be curious about the explanations of real experts.


View Results (Graphically)

The average neural network performance across our the 10 iterations is plotted below, where our five primary performance statistics are highlighted (accuracy, sensitivity, specificity, precision and negative predictive value). All are significantly above 50% (and the point estimate for our average overall accuracy rate is over 65%).

# calculate average sample size
mean_n <- mean(results$n)

# create df to use for visualization
results_viz <-
  results %>%
  group_by(model_type) %>%
  summarize(accuracy = mean(accuracy),
            sensitivity = mean(sensitivity),
            specificity = mean(specificity),
            precision = mean(precision),
            npv = mean(npv)) %>%
  select(-model_type) %>%
  gather(key = "perf_stat",
         value = "value") %>%
  mutate(value = as.numeric(value))

# actual visualization
ggplot(data = results_viz,
  aes(x = perf_stat,
           y = value)) +
geom_point(size = 2,
           color = "#545EDF") +
geom_errorbar(aes(ymin = (value - 1.96*sqrt(value*(1-value)/mean_n)),
                   ymax = (value + 1.96*sqrt(value*(1-value)/mean_n))),
              color = "#545EDF",
              width = 0.15,
              size = 1.25) +
geom_hline(yintercept = 0.5,
           linetype = "dashed",
           size = 0.5,
           color = "red") +
scale_y_continuous(breaks = seq(from = 0, to = 1, by = 0.05),
                   limits = c(0, 1)) +
scale_x_discrete(limits = rev(c("accuracy", "sensitivity", "specificity", 
                            "precision", "npv"))) + 
coord_flip() +
theme(panel.grid.major.x = element_line(color = "grey",
                                        size = 0.25),
      panel.grid.minor.x = element_blank(),
      panel.grid.major.y = element_blank(),
      panel.background = element_blank(),
      axis.ticks = element_blank(),
      plot.title = element_text(hjust = 0.5),
      axis.title.y = element_text(margin = 
                                    margin(t = 0, r = 10, b = 0, l = 0)),
      axis.title.x = element_text(margin = 
                                    margin(t = 10, r = 00, b = 0, l = 0)),
      axis.text.x = element_text(angle = 90)) +
labs(title = "Performance Statistics (Neural Network)",
     x = "Performance Statistic",
     y = "Proportion (0 to 1)")

Save Results

Finally, we can save our results and we are done.

# rename results df, to be particular to this model type (for disambiguation later)
results_neural <- results

# clear results variable

# save results in Rda file
     file = "results_neural.Rda")


If needed, I can render with rmarkdown::render(“hld_MODEL_svm.Rmd”).