MSclassifR (version 0.4.0)

LogReg: Estimation of a multinomial regression to predict the category to which a mass spectrum belongs

Description

This function estimates a multinomial regression using cross-validation to predict the category (species, phenotypes...) to which a mass spectrum belongs from a set of shortlisted mass-to-charge values corresponding to discriminant peaks. Two main kinds of models can be estimated: linear or nonlinear (with neural networks, random forests, support vector machines with linear kernel, or eXtreme Gradient Boosting). Hyperparameters are randomly searched, except for the eXtreme Gradient Boosting where a grid search is performed.

Usage

LogReg(X,
       moz,
       Y,
       number = 2,
       repeats = 2,
       Metric = c("Kappa", "Accuracy", "F1", "AdjRankIndex", "MatthewsCorrelation"),
       kind="linear",
       Sampling = c("no", "up", "down", "smote"))

Value

Returns a list with four items:

train_mod

a list corresponding to the output of the train function of the caret R package containing the multinomial regression model estimated using repeated cross-validation.

conf_mat

a confusion matrix containing percentages classes of predicted categories in function of actual categories, resulting from repeated cross-validation.

stats_global

a data frame containing the mean and standard deviation values of the "Accuracy"" and "Kappa" parameters computed for each cross-validation.

boxplot

a ggplot object (see ggplot2 R package). This is a graphical representation of the Metric parameters of stats_global using boxplots.

Arguments

X

matrix corresponding to a library of mass spectra. Each row of X is the intensities of a mass spectrum measured on the moz values. The columns should be represented by mass-to-charge values.

moz

vector with shortlisted mass-to-charge values.

Y

factor with a length equal to the number of rows in X and containing the categories of each mass spectrum in X.

number

integer corresponding to the number of folds or number of resampling iterations. See arguments of the trainControl function of the caret R package.

Metric

a character indicating metric to select the optimal model. The possibles metrics are the "Kappa" coefficient,"Accuracy", the "F1" score, "AdjRankIndex" for the Adjusted Rand Index or "MatthewsCorrelation" for the Matthews Correlation Coefficient.

repeats

integer corresponding to the number of complete sets of folds to compute. See trainControl function of the caret R package for more details.

kind

If kind="nnet", then a nonlinear multinomial logistic regression is estimated via neural networks. If kind="rf", then it is estimated via random forests. If kind="svm", then it is estimated via support vector machines with linear kernel. If kind="xgb", then it is estimated via eXtreme gradient boosting. Else a linear multinomial logistic regression is performed (by default).

Sampling

a character indicating an optional subsampling method to handle imbalanced datasets: subsampling methods are either "no" (no subsampling), "up", "down" or "smote". "no" by default.

Details

This function estimates a model from a library of mass spectra for which we already know the category to which they belong (ex.: species, etc). This model can next be used to predict the category of a new coming spectrum for which the category is unknown (see PredictLogReg).

The estimation is performed using the train function of the caret R package. For each kind of model, random parameters are tested to find a model according to the best metric. The formulas for the metric are as follows:

$$Accuracy = Number Of Correct Predictions/Total Number Of Predictions$$ $$Kappa coefficient = (Observed Agreement-Chance Agreement)/(1-Chance Agreement)$$ $$F1 = True Positive/(True Positive + 1/2 (False Positive + False Negative))$$

The adjusted Rand index ("AdjRankIndex") is defined as the corrected-for-chance version of the Rand index which allows comparing two groups (see mclust package and adjustedRandIndex() function for more details). The Matthews correlation coefficient ("MatthewsCorrelation") is estimated using mcc function in the mltools R package.

The Sampling methods available for imbalanced data are: "up" to the up-sampling method which consists of random sampling (with replacement) so that the minority class is the same size as the majority class; "down" to the down-sampling method which consists of random sampling (without replacement) of the majority class so that their class frequencies match the minority class; "smote" to the Synthetic Minority Over sampling Technique (SMOTE) algorithm for data augmentation which consists of creating new data from minority class using the K Nearest Neighbor algorithm.

Godmer et al. (2025) presents a comparison of different pipelines using LogReg that can help you to optimize your workflow. For a comprehensive guide, additional applications, and detailed examples of using this package, please visit our GitHub repository: here.

References

Kuhn, M. (2008). Building predictive models in R using the caret package. Journal of statistical software, 28(1), 1-26.

L. Hubert and P. Arabie (1985) Comparing Partitions, Journal of the Classification, 2, pp. 193-218.

Scrucca L, Fop M, Murphy TB, Raftery AE (2016). mclust 5: clustering, classification and density estimation using Gaussian finite mixture models. The R Journal.

Nitesh V. Chawla, Kevin W. Bowyer, Lawrence O. Hall, and W. Philip Kegelmeyer. 2002. SMOTE: synthetic minority over-sampling technique. J. Artif. Int. Res. 16, 1.

Matthews, B. W. (1975). "Comparison of the predicted and observed secondary structure of T4 phage lysozyme". Biochimica et Biophysica Acta (BBA) - Protein Structure. PMID 1180967.

Alexandre Godmer, Yahia Benzerara, Emmanuelle Varon, Nicolas Veziris, Karen Druart, Renaud Mozet, Mariette Matondo, Alexandra Aubry, Quentin Giai Gianetto, MSclassifR: An R package for supervised classification of mass spectra with machine learning methods, Expert Systems with Applications, Volume 294, 2025, 128796, ISSN 0957-4174, tools:::Rd_expr_doi("10.1016/j.eswa.2025.128796").

Examples

# \donttest{
library("MSclassifR")
library("MALDIquant")

###############################################################################
## 1. Pre-processing of mass spectra

# load mass spectra and their metadata
data("CitrobacterRKIspectra","CitrobacterRKImetadata", package = "MSclassifR")
# standard pre-processing of mass spectra
spectra <- SignalProcessing(CitrobacterRKIspectra)
# detection of peaks in pre-processed mass spectra
peaks <- MSclassifR::PeakDetection(x = spectra, averageMassSpec=FALSE)
# matrix with intensities of peaks arranged in rows (each column is a mass-to-charge value)
IntMat <- MALDIquant::intensityMatrix(peaks)
rownames(IntMat) <- paste(CitrobacterRKImetadata$Strain_name_spot)
# remove missing values in the matrix
IntMat[is.na(IntMat)] <- 0
# normalize peaks according to the maximum intensity value for each mass spectrum
IntMat <- apply(IntMat,1,function(x) x/(max(x)))
# transpose the matrix for statistical analysis
X <- t(IntMat)
# define the known categories of mass spectra for the classification
Y <- factor(CitrobacterRKImetadata$Species)

###############################################################################
## 2. Selection of discriminant mass-to-charge values using RFERF
# with 5 to 10 variables,
# up sampling method and
# trained with the Accuracy coefficient metric

a <- MSclassifR::SelectionVar(X,
                              Y,
                              MethodSelection = c("RFERF"),
                              MethodValidation = c("cv"),
                              PreProcessing = c("center","scale","nzv","corr"),
                              NumberCV = 2,
                              Metric = "Accuracy",
                              Sizes = c(2:5),
                              Sampling = "up")

sel_moz=a$sel_moz

###############################################################################
## 3. Perform LogReg from shortlisted discriminant mass-to-charge values

# linear multinomial regression
# without sampling mehod
# and trained with the Kappa coefficient metric

model_lm=MSclassifR::LogReg(X=X,
                            moz=sel_moz,
                            Y=factor(Y),
                            number=2,
                            repeats=2,
                            Metric = "Kappa")
# Estimated model:
model_lm

# nonlinear multinomial regression using neural networks
# with up-sampling method and
# trained with the Kappa coefficient metric

model_nn=MSclassifR::LogReg(X=X,
                            moz=sel_moz,
                            Y=factor(Y),
                            number=2,
                            repeats=2,
                            kind="nnet",
                            Metric = "Kappa",
                            Sampling = "up")
# Estimated model:
model_nn

# nonlinear multinomial regression using random forests
# without down-sampling method and
# trained with the Kappa coefficient metric

model_rf=MSclassifR::LogReg(X=X,
                            moz=sel_moz,
                            Y=factor(Y),
                            number=2,
                            repeats=2,
                            kind="rf",
                            Metric = "Kappa",
                            Sampling = "down")

# Estimated model:
model_rf

# nonlinear multinomial regression using xgboost
# with down-sampling method and
# trained with the Kappa coefficient metric

model_xgb=MSclassifR::LogReg(X=X,
                             moz=sel_moz,
                             Y=factor(Y),
                             number=2,
                             repeats=2,
                             kind="xgb",
                             Metric = "Kappa",
                             Sampling = "down")
# Estimated model:
model_xgb

# nonlinear multinomial regression using svm
# with down-sampling method and
# trained with the Kappa coefficient metric

model_svm=MSclassifR::LogReg(X=X,
                             moz=sel_moz,
                             Y=factor(Y),
                             number=2,
                             repeats=2,
                             kind="svm",
                             Metric = "Kappa",
                             Sampling = "down")
# Estimated model:
model_svm

##########
# Of note, step 3 can be performed several times
# to find optimal models
# because of random hyperparameter search

###############################################################################
## 4. Select best models in term of average Kappa and saving it for reuse

Kappa_model=c(model_lm$stats_global[1,2],model_nn$stats_global[1,2],
              model_rf$stats_global[1,2],model_xgb$stats_global[1,2],model_svm$stats_global[1,2])
names(Kappa_model)=c("lm","nn","rf","xgb","svm")
#Best models in term of accuracy
Kappa_model[which(Kappa_model==max(Kappa_model))]

#save best models for reuse
#models=list(model_lm$train_mod,model_nn$train_mod,model_rf$train_mod,
#model_xgb$train_mod,model_svm$train_mod)
#models_best=models[which(Kappa_model==max(Kappa_model))]
#for (i in 1:length(models_best)){
#save(models_best[[i]], file = paste0("model_best_",i,".rda",collapse="")
#}

#load a saved model
#load("model_best_1.rda")

###############################################################################
## 5. Try other metrics to select the best model

# linear multinomial regression
# with up-sampling method and
# trained with the Adjusted Rank index metric

model_lm=MSclassifR::LogReg(X=X,
                            moz=sel_moz,
                            Y=factor(Y),
                            number=2,
                            repeats=3,
                            Metric = "AdjRankIndex",
                            Sampling = "up")

# }