How to see failed machine learning records - machine-learning

I am using the following code to create my machine learning model. The accuracy of the model is 0.76. I am just curious to know which records from my test data failed? Is there a way I can see those data?
// 1. Load the dataset for training and testing
var trainData = ctx.Data.LoadFromTextFile<SentimentData>(trainDataPath, hasHeader: true);
var testData = ctx.Data.LoadFromTextFile<SentimentData>(testDataPath, hasHeader: true);
// 2. Build a tranformer/estimator to transform input data so that Machine Learning algorithm can understand
IEstimator<ITransformer> estimator = ctx.Transforms.Text.FeaturizeText("Features", nameof(SentimentData.Text));
// 3. - set the training algorithm and create the pipeline for model builder
var trainer = ctx.BinaryClassification.Trainers.SdcaLogisticRegression();
var trainingPipeline = estimator.Append(trainer);
// 4. - Train the model
var trainedModel = trainingPipeline.Fit(trainData);
// 5. - Perform the preditions on the test data
var predictions = trainedModel.Transform(testData);
// 6. - Evalute the model
var metrics = ctx.BinaryClassification.Evaluate(data: predictions);

By using the GetColumn and CreateEnumerable methods, you can find the data that the model didn't predict correctly.
After you the metrics, use the GetColumn method on the predictions that were from the test data set to get the original label values. Then, use the CreateEnuemrable method to get the predictions that will hold the predicted values. Optionally, you can get the sentiment text as well.
var originalLabels = predictions.GetColumn<bool>("Label").ToArray();
var sentimentText = predictions.GetColumn<string>(nameof(SentimentData.SentimentText)).ToArray();
var predictedLabels = context.Data.CreateEnumerable<SentimentPrediction>(predictions, reuseRowObject: false).ToArray();
After getting the data, just loop through one of them (I did a count of the original labels) and you can access the data at each iteration. From there you can check if the actual label doesn't equal the predicted value to only print out the values that the model didn't get correctly.
for (int i = 0; i < originalLabels.Count(); i++)
{
string outputText = String.Empty;
if (originalLabels[i] != predictedLabels[i].Prediction)
{
outputText = $"Text - {sentimentText[i]} | ";
outputText += $"Original - {originalLabels[i]} | ";
outputText += $"Predicted - {predictedLabels[i].Prediction}";
Console.WriteLine(outputText);
}
}
With that you have the data that you need. :)
Hope that helps!

From your comment, I believe the method you are looking for can be found in the keras library. The method should be keras.models.predict_classes as found on their documentation page.
This will provide you with an array of predicted outputs, which you can then compare to the ground truths. Visit the documentation to see the parameters.
Hope this helps!

Related

R: Error in predict.xgboost: Feature names stored in `object` and `newdata` are different

I wrote a script using xgboost to predict soil class for a certain area using data from field and satellite images. The script as below:
`
rm(list=ls())
library(xgboost)
library(caret)
library(raster)
library(sp)
library(rgeos)
library(ggplot2)
setwd("G:/DATA")
data <- read.csv('96PointsClay02finalone.csv')
head(data)
summary(data)
dim(data)
ras <- stack("Allindices04TIFF.tif")
names(ras) <- c("b1", "b2", "b3", "b4", "b5", "b6", "b7", "b10", "b11","DEM",
"R1011", "SCI", "SAVI", "NDVI", "NDSI", "NDSandI", "MBSI",
"GSI", "GSAVI", "EVI", "DryBSI", "BIL", "BI","SRCI")
set.seed(27) # set seed for generating random data.
# createDataPartition() function from the caret package to split the original dataset into a training and testing set and split data into training (80%) and testing set (20%)
parts = createDataPartition(data$Clay, p = .8, list = F)
train = data[parts, ]
test = data[-parts, ]
#define predictor and response variables in training set
train_x = data.matrix(train[, -1])
train_y = train[,1]
#define predictor and response variables in testing set
test_x = data.matrix(test[, -1])
test_y = test[, 1]
#define final training and testing sets
xgb_train = xgb.DMatrix(data = train_x, label = train_y)
xgb_test = xgb.DMatrix(data = test_x, label = test_y)
#defining a watchlist
watchlist = list(train=xgb_train, test=xgb_test)
#fit XGBoost model and display training and testing data at each iteartion
model = xgb.train(data = xgb_train, max.depth = 3, watchlist=watchlist, nrounds = 100)
#define final model
model_xgboost = xgboost(data = xgb_train, max.depth = 3, nrounds = 86, verbose = 0)
summary(model_xgboost)
#use model to make predictions on test data
pred_y = predict(model_xgboost, xgb_test)
# performance metrics on the test data
mean((test_y - pred_y)^2) #mse - Mean Squared Error
caret::RMSE(test_y, pred_y) #rmse - Root Mean Squared Error
y_test_mean = mean(test_y)
rmseE<- function(error)
{
sqrt(mean(error^2))
}
y = test_y
yhat = pred_y
rmseresult=rmseE(y-yhat)
(r2 = R2(yhat , y, form = "traditional"))
cat('The R-square of the test data is ', round(r2,4), ' and the RMSE is ', round(rmseresult,4), '\n')
#use model to make predictions on satellite image
result <- predict(model_xgboost, ras[1:(nrow(ras)*ncol(ras))])
#create a result raster
res <- raster(ras)
#fill in results and add a "1" to them (to get back to initial class numbering! - see above "Prepare data" for more information)
res <- setValues(res,result+1)
#Save the output .tif file into saved directory
writeRaster(res, "xgbmodel_output", format = "GTiff", overwrite=T)
`
The script works well till it reachs
result <- predict(model_xgboost, ras[1:(nrow(ras)*ncol(ras))])
it takes some time then gives this error:
Error in predict.xgb.Booster(model_xgboost, ras[1:(nrow(ras) * ncol(ras))]) :
Feature names stored in `object` and `newdata` are different!
I realize that I am doing something wrong in that line. However, I do not know how to apply the xgboost model to a raster image that represents my study area.
It would be highly appreciated if someone give a hand, enlightened me, and helped me solve this problem....
My data as csv and raster image can be found here.
Finally, I got the reason for this error.
It was my mistake as the number of columns in the traning data was not the same as in the number of layers in the satellite image.

Different predictions for the same data

I use Deeplearning4j to classify equipment names. I marked ~ 50,000 items with 495 classes, and I use this data to train the neural network.
That is, as input, I provide a set of vectors (50,000) consisting of 0 and 1, and the expected class for each vector (0 to 494).
I use the IrisClassifier example as a basis for the code.
I saved the trained model to a file, and now I can use it to predict the class of equipment.
As an example, I tried to use for prediction the same data (50,000 items) that I used for training, and compare the prediction with my markup of this data.
The result turned out to be very good, the error of the neural network is ~ 1%.
After that, I tried to use for prediction the first 100 vectors from these 50,000 records, and removed the rest 49900.
And for these 100 vectors, the prediction is different when compared with the prediction for the same 100 vectors in the composition of 50,000.
That is, the less data we provide to the trained model, the greater the prediction error.
Even for exactly the same vectors.
Why does this happen?
My code.
Training:
//First: get the dataset using the record reader. CSVRecordReader handles loading/parsing
int numLinesToSkip = 0;
char delimiter = ',';
RecordReader recordReader = new CSVRecordReader(numLinesToSkip,delimiter);
recordReader.initialize(new FileSplit(new File(args[0])));
//Second: the RecordReaderDataSetIterator handles conversion to DataSet objects, ready for use in neural network
int labelIndex = 3331;
int numClasses = 495;
int batchSize = 4000;
// DataSetIterator iterator = new RecordReaderDataSetIterator(recordReader,batchSize,labelIndex,numClasses);
DataSetIterator iterator = new RecordReaderDataSetIterator.Builder(recordReader, batchSize).classification(labelIndex, numClasses).build();
List<DataSet> trainingData = new ArrayList<>();
List<DataSet> testData = new ArrayList<>();
while (iterator.hasNext()) {
DataSet allData = iterator.next();
allData.shuffle();
SplitTestAndTrain testAndTrain = allData.splitTestAndTrain(0.8); //Use 80% of data for training
trainingData.add(testAndTrain.getTrain());
testData.add(testAndTrain.getTest());
}
DataSet allTrainingData = DataSet.merge(trainingData);
DataSet allTestData = DataSet.merge(testData);
//We need to normalize our data. We'll use NormalizeStandardize (which gives us mean 0, unit variance):
DataNormalization normalizer = new NormalizerStandardize();
normalizer.fit(allTrainingData); //Collect the statistics (mean/stdev) from the training data. This does not modify the input data
normalizer.transform(allTrainingData); //Apply normalization to the training data
normalizer.transform(allTestData); //Apply normalization to the test data. This is using statistics calculated from the *training* set
long seed = 6;
int firstHiddenLayerSize = labelIndex/6;
int secondHiddenLayerSize = firstHiddenLayerSize/4;
//log.info("Build model....");
MultiLayerConfiguration conf = new NeuralNetConfiguration.Builder()
.seed(seed)
.activation(Activation.TANH)
.weightInit(WeightInit.XAVIER)
.updater(new Sgd(0.1))
.l2(1e-4)
.list()
.layer(new DenseLayer.Builder().nIn(labelIndex).nOut(firstHiddenLayerSize)
.build())
.layer(new DenseLayer.Builder().nIn(firstHiddenLayerSize).nOut(secondHiddenLayerSize)
.build())
.layer( new OutputLayer.Builder(LossFunctions.LossFunction.NEGATIVELOGLIKELIHOOD)
.activation(Activation.SOFTMAX) //Override the global TANH activation with softmax for this layer
.nIn(secondHiddenLayerSize).nOut(numClasses).build())
.build();
//run the model
MultiLayerNetwork model = new MultiLayerNetwork(conf);
model.init();
//record score once every 100 iterations
model.setListeners(new ScoreIterationListener(100));
for(int i=0; i<5000; i++ ) {
model.fit(allTrainingData);
}
//evaluate the model on the test set
Evaluation eval = new Evaluation(numClasses);
INDArray output = model.output(allTestData.getFeatures());
eval.eval(allTestData.getLabels(), output);
log.info(eval.stats());
// Save the Model
File locationToSave = new File(args[1]);
model.save(locationToSave, false);
Prediction:
// Open the network file
File locationToLoad = new File(args[0]);
MultiLayerNetwork model = MultiLayerNetwork.load(locationToLoad, false);
model.init();
// First: get the dataset using the record reader. CSVRecordReader handles loading/parsing
int numLinesToSkip = 0;
char delimiter = ',';
// Data to predict
CSVRecordReader recordReader = new CSVRecordReader(numLinesToSkip, delimiter); //skip no lines at the top - i.e. no header
recordReader.initialize(new FileSplit(new File(args[1])));
//Second: the RecordReaderDataSetIterator handles conversion to DataSet objects, ready for use in neural network
int batchSize = 4000;
DataSetIterator iterator = new RecordReaderDataSetIterator.Builder(recordReader, batchSize).build();
List<DataSet> dataSetList = new ArrayList<>();
while (iterator.hasNext()) {
DataSet allData = iterator.next();
dataSetList.add(allData);
}
DataSet dataSet = DataSet.merge(dataSetList);
DataNormalization normalizer = new NormalizerStandardize();
normalizer.fit(dataSet);
normalizer.transform(dataSet);
// Now use it to classify some data
INDArray output = model.output(dataSet.getFeatures());
// Save result
BufferedWriter writer = new BufferedWriter(new FileWriter(args[2], true));
for (int i=0; i<output.rows(); i++) {
writer
.append(output.getRow(i).argMax().toString())
.append(" ")
.append(String.valueOf(i))
.append(" ")
.append(output.getRow(i).toString())
.append('\n');
}
writer.close();
Ensure you save the normalizer as follows alongside the model:
import org.nd4j.linalg.dataset.api.preprocessor.serializer.NormalizerSerializer;
NormalizerSerializer SUT = NormalizerSerializer.getDefault();
SUT.write(normalizer,new File("outputFile.bin"));
NormalizeStandardize restored = SUT.restore(new File("outputFile.bin");
You need to use the same normalizer data for both training and prediction. Otherwise it will use wrong statistics when transforming your data.
The way you are currently doing it, results in data that looks very different from the training data, that is why you get such a different result.

Getting classification result from mahout

Finally I am able to train mahout classifier , now my problem is how can i get target category for my input document.
What is the process of getting target category for my text documents ?
First, you have to vectorize the text document, RandomAccessSparseVector.
Some sample code for your reference:
Vector vector = new RandomAccessSparseVector(FEATURES);
FeatureExtractor fe = new FeatureExtractor();
HashSet<String> fs = fe.extract(text);
for (String s : fs) {
int index = dictionary.get(s);
vector.setQuick(index, frequency.get(index));
}
Then, use the Classifier.classify(Vector) to get the result.

WEKA classification likelihood of the classes

I would like to know if there is a way in WEKA to output a number of 'best-guesses' for a classification.
My scenario is: I classify the data with cross-validation for instance, then on weka's output I get something like: these are the 3 best-guesses for the classification of this instance. What I want is like, even if an instance isn't correctly classified i get an output of the 3 or 5 best-guesses for that instance.
Example:
Classes: A,B,C,D,E
Instances: 1...10
And output would be:
instance 1 is 90% likely to be class A, 75% likely to be class B, 60% like to be class C..
Thanks.
Weka's API has a method called Classifier.distributionForInstance() tha can be used to get the classification prediction distribution. You can then sort the distribution by decreasing probability to get your top-N predictions.
Below is a function that prints out: (1) the test instance's ground truth label; (2) the predicted label from classifyInstance(); and (3) the prediction distribution from distributionForInstance(). I have used this with J48, but it should work with other classifiers.
The inputs parameters are the serialized model file (which you can create during the model training phase and applying the -d option) and the test file in ARFF format.
public void test(String modelFileSerialized, String testFileARFF)
throws Exception
{
// Deserialize the classifier.
Classifier classifier =
(Classifier) weka.core.SerializationHelper.read(
modelFileSerialized);
// Load the test instances.
Instances testInstances = DataSource.read(testFileARFF);
// Mark the last attribute in each instance as the true class.
testInstances.setClassIndex(testInstances.numAttributes()-1);
int numTestInstances = testInstances.numInstances();
System.out.printf("There are %d test instances\n", numTestInstances);
// Loop over each test instance.
for (int i = 0; i < numTestInstances; i++)
{
// Get the true class label from the instance's own classIndex.
String trueClassLabel =
testInstances.instance(i).toString(testInstances.classIndex());
// Make the prediction here.
double predictionIndex =
classifier.classifyInstance(testInstances.instance(i));
// Get the predicted class label from the predictionIndex.
String predictedClassLabel =
testInstances.classAttribute().value((int) predictionIndex);
// Get the prediction probability distribution.
double[] predictionDistribution =
classifier.distributionForInstance(testInstances.instance(i));
// Print out the true label, predicted label, and the distribution.
System.out.printf("%5d: true=%-10s, predicted=%-10s, distribution=",
i, trueClassLabel, predictedClassLabel);
// Loop over all the prediction labels in the distribution.
for (int predictionDistributionIndex = 0;
predictionDistributionIndex < predictionDistribution.length;
predictionDistributionIndex++)
{
// Get this distribution index's class label.
String predictionDistributionIndexAsClassLabel =
testInstances.classAttribute().value(
predictionDistributionIndex);
// Get the probability.
double predictionProbability =
predictionDistribution[predictionDistributionIndex];
System.out.printf("[%10s : %6.3f]",
predictionDistributionIndexAsClassLabel,
predictionProbability );
}
o.printf("\n");
}
}
I don't know if you can do it natively, but you can just get the probabilities for each class, sorted them and take the first three.
The function you want is distributionForInstance(Instance instance) which returns a double[] giving the probability for each class.
Not in general. The information you want is not available with all classifiers -- in most cases (for example for decision trees), the decision is clear (albeit potentially incorrect) without a confidence value. Your task requires classifiers that can handle uncertainty (such as the naive Bayes classifier).
Technically the easiest thing to do is probably to train the model and then classify an individual instance, for which Weka should give you the desired output. In general you can of course also do it for sets of instances, but I don't think that Weka provides this out of the box. You would probably have to customise the code or use it through an API (for example in R).
when you calculate a probability for the instance, how exactly do you do this?
I have posted my PART rules and data for the new instance here but as far as calculation manually I am not so sure how to do this! Thanks
EDIT: now calculated:
private float[] getProbDist(String split){
// takes in something such as (52/2) meaning 52 instances correctly classified and 2 incorrectly classified.
if(prob_dis.length > 2)
return null;
if(prob_dis.length == 1){
String temp = prob_dis[0];
prob_dis = new String[2];
prob_dis[0] = "1";
prob_dis[1] = temp;
}
float p1 = new Float(prob_dis[0]);
float p2 = new Float(prob_dis[1]);
// assumes two tags
float[] tag_prob = new float[2];
tag_prob[1] = 1 - tag_prob[1];
tag_prob[0] = (float)p2/p1;
// returns double[] as being the probabilities
return tag_prob;
}

Log likelihood to implement Naive Bayes for Text Classification

I am implementing Naive Bayes algorithm for text classification. I have ~1000 documents for training and 400 documents for testing. I think I've implemented training part correctly, but I am confused in testing part. Here is what I've done briefly:
In my training function:
vocabularySize= GetUniqueTermsInCollection();//get all unique terms in the entire collection
spamModelArray[vocabularySize];
nonspamModelArray[vocabularySize];
for each training_file{
class = GetClassLabel(); // 0 for spam or 1 = non-spam
document = GetDocumentID();
counterTotalTrainingDocs ++;
if(class == 0){
counterTotalSpamTrainingDocs++;
}
for each term in document{
freq = GetTermFrequency; // how many times this term appears in this document?
id = GetTermID; // unique id of the term
if(class = 0){ //SPAM
spamModelArray[id]+= freq;
totalNumberofSpamWords++; // total number of terms marked as spam in the training docs
}else{ // NON-SPAM
nonspamModelArray[id]+= freq;
totalNumberofNonSpamWords++; // total number of terms marked as non-spam in the training docs
}
}//for
for i in vocabularySize{
spamModelArray[i] = spamModelArray[i]/totalNumberofSpamWords;
nonspamModelArray[i] = nonspamModelArray[i]/totalNumberofNonSpamWords;
}//for
priorProb = counterTotalSpamTrainingDocs/counterTotalTrainingDocs;// calculate prior probability of the spam documents
}
I think I understood and implemented training part correctly, but I am not sure I could implemented testing part properly. In here, I am trying to go through each test document and I calculate logP(spam|d) and logP(non-spam|d) for each document. Then I compare these two quantities in order to determine the class (spam/non-spam).
In my testing function:
vocabularySize= GetUniqueTermsInCollection;//get all unique terms in the entire collection
for each testing_file:
document = getDocumentID;
logProbabilityofSpam = 0;
logProbabilityofNonSpam = 0;
for each term in document{
freq = GetTermFrequency; // how many times this term appears in this document?
id = GetTermID; // unique id of the term
// logP(w1w2.. wn) = C(wj)∗logP(wj)
logProbabilityofSpam+= freq*log(spamModelArray[id]);
logProbabilityofNonSpam+= freq*log(nonspamModelArray[id]);
}//for
// Now I am calculating the probability of being spam for this document
if (logProbabilityofNonSpam + log(1-priorProb) > logProbabilityofSpam +log(priorProb)) { // argmax[logP(i|ck) + logP(ck)]
newclass = 1; //not spam
}else{
newclass = 0; // spam
}
}//for
My problem is; I want to return the probability of each class instead of exact 1's and 0's (spam/non-spam). I want to see e.g. newclass = 0.8684212 so I can apply threshold later on. But I am confused here. How can I calculate the probability for each document? Can I use logProbabilities to calculate it?
The probability of the data described by a set of features {F1, F2, ..., Fn} belonging in class C, according to the naïve Bayes probability model, is
P(C|F) = P(C) * (P(F1|C) * P(F2|C) * ... * P(Fn|C)) / P(F1, ..., Fn)
You have all the terms (in logarithmic form), except for the 1 / P( F1, ..., Fn) term since that's not used in the naïve Bayes classifier that you're implementing. (Strictly, the MAP classifier.)
You'd have to collect frequencies of the features as well, and from them calculate
P(F1, ..., Fn) = P(F1) * ... * P(Fn)

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