Prediction of Idiopathic Recurrent Spontaneous
Miscarriage using Machine Learning
2023 International Conference on Computer, Electrical & Communication Engineering (ICCECE) | 978-1-6654-5251-9/23/$31.00 ©2023 IEEE | DOI: 10.1109/ICCECE51049.2023.10085363
Dadoma Sherpa Rajwade Dhruva Abhijit
School of Medical Science and Department of
Technology Biotechnology
Indian Institute of Technology Indian Institute of
Kharagpur Technology Kharagpur
Kharagpur, India Kharagpur, India
domasherpa27@gmail.com rajwadedhruva@gmail.com
Sunita Sharma Pratip Chakraborty
Institute of Reproductive Institute of Reproductive
Medicine, Kolkata Medicine, Kolkata
sunitapalchaudhuri@yahoo.com pratip_2011@yahoo.com
Abstract— Recurrent spontaneous miscarriage (RSM) is
defined as the spontaneous loss of two or more clinically
diagnosed pregnancies within 20 weeks of gestation. Despite
extensive research, etiology remains undefined in 50% of RSM
cases, and are classified as idiopathic. Thus, further study is
warranted to understand molecular mechanism associated with
the disease pathogenesis. In the present study, we aim to
identify Raman fingerprints in endometrial/uterine tissues of
women with history of idiopathic recurrent spontaneous
miscarriage (IRSM) and controls by performing Raman
spectroscopy with chemometric analysis and spectral
classification models. Unsupervised analysis such as principal
component analysis (PCA), hierarchical cluster analysis (HCA)
and supervised analysis such as orthogonal projections to latent
structures discriminant analysis (OPLS-DA) showed a distinct
separation between IRSM and controls. The principal
component loading plots indicated that proteins, amino acids,
cholesterol and glutamate were responsible for the separation
between the two groups. The pre-processed Raman spectral
data were subjected to eight different machine learning (ML)
classifiers with hyperparameter optimization to develop
prediction models. Comparing the various algorithms, support
vector machine (SVM), decision tree (DT), Extreme Gradient
Boosting (XGBoost), convolutional neural network (CNN),
and artificial neural network (ANN) outperform the other
models based on accuracy (< 85%). Next, grid search and
Bayesian optimization was used for tuning the hyperparameters
of all methods. Further, 10-fold cross-validation was done to
validate the model performances.
The present findings confirm the feasibility of using Raman
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Imon Mitra Dhruba Dhar
School of Medical Science and School of Medical Science
Technology and Technology
Indian Institute of Technology Indian Institute of Technology
Kharagpur Kharagpur
Kharagpur, India Kharagpur, India
imonmitra.sp@gmail.com dhruba.dhar2009@gmail.com
Koel Chaudhury*
School of Medical Science and
*Corresponding author Technology
Indian Institute of Technology
Kharagpur
Kharagpur, India
koel@smst.iitkgp.ac.in
spectroscopy combined with ML algorithm may facilitate a
better understanding of this pathology.
Keywords— IRSM, Raman spectroscopy, machine learning, SVM,
DT, XGBoost, CNN, AdaBoost, RF, GB, ANN, PCA, OPLS-DA
I. INTRODUCTION
Recurrent spontaneous miscarriage (RSM) is defined as the
spontaneous loss of two or more clinically diagnosed
pregnancies within 20 weeks of gestation [1]. Various causative
factors such as endocrine, genetic, immunological, anatomic,
infectious, thrombophilic, environmental, and metabolic are
known to be responsible for RSM [2]. Despite extensive
research in the past few decades, there is no underlying cause
and half of the patients will remain without a diagnosis. The
condition of these patients is known as idiopathic. Thus, further
research is warranted to understand the mechanism of
idiopathic recurrent spontaneous miscarriage (IRSM).
Recently, there has been considerable interest to explore the
pathophysiology of complex diseases using powerful label-free
vibrational techniques [3-5]. Raman spectroscopy, based on
inelastic scattering of light that gives information about
vibrational modes of molecular bonds, is one such technique
which is totally non-invasive in nature and is increasingly
gaining popularity to obtain an insight into the characteristics
of proteins, carbohydrates, lipids and nucleic acids [6-7].
Various diseases lead to structural and chemical changes in
tissues at a molecular level which are reflected through intrinsic
Raman fingerprints and can be effectively used as sensitive
phenotypic markers of the disease.
 Recently, the development of artificial intelligence
(AI) has emerged rapidly into healthcare; it has established
marked potential in disease diagnostics and treatment. Machine
learning (ML) is a subset of AI and is currently being explored
in various areas of reproductive health. ML has been used for
the development of models for prediction of endometriosis,
polycystic ovary syndrome (PCOS) and preeclampsia [8-10].
ML algorithms help to interpret rapidly and efficiently the vast
amount of complex biomedical data in terms of valuable feature
information. Therefore, ML is recognized as a promising
method for the identification of patterns and has been
extensively applied to understand disease mechanisms,
reducing inevitable errors in diagnosis, treatment and clinical
decision-making [11-12]. According to our knowledge, this is
the first study where Raman spectroscopy combined with ML
is used to understand disease mechanism of IRSM, a common
women’s health issue. We aim to identify the best performing
algorithm by hyperparameter tuning and develop predictive
models for understanding the disease pathophysiology of
IRSM.
II. METHODOLOGY
This study employed recruitment of women with history of
IRSM (n=15) and controls (n=15) as per inclusion criteria at the
Assisted Reproduction Unit, Institute of Reproductive
Medicine, Salt Lake, Kolkata. Endometrial tissue samples
(lining of the uterine cavity where the embryo implants) were
collected from both the groups during a favourable period of
the menstrual cycle, known as the window of implantation
(WOI). All tissue samples were fixed in 4% formalin and
embedded in paraffin for Raman spectroscopy. All spectra were
acquired in the spectral range of 400-1800 cm−1 (the fingerprint
region) and intensity measured. This region provides complete
information about the biomolecules such as lipids,
carbohydrates, proteins and nucleic acids. Further, Raman
spectral data were evaluated by ML algorithms including
Extreme Gradient Boosting (XGBoost), decision tree (DT),
support vector machine (SVM), Adaptive Boosting
(AdaBoost), random forest (RF), gradient boosting (GB)
convolutional neural network (CNN) and artificial neural
network (ANN). The overall workflow of the study design is
shown in Figure 1.
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Fig. 1 Workflow of the study plan
Data processing
All spectra obtained was smoothed using Savitzky–Golay
method and baseline corrected to remove noise and
fluorescence background using ORIGIN PRO 8.5 (Origin Lab
Corporation, Northampton, MA, USA). The band position of
each biomolecules was determined using the peak analyzer
algorithm of Origin Pro software (Northampton, MA, USA).
Data preprocessing enabled clear spectral peaks and improved
spectral quality considerably. The Raman peaks were assigned
based on earlier published articles and literature [13-15]. The
processed Raman data were further taken for chemometric
analysis.
Chemometric analysis
Principal component analysis (PCA) was conducted to gain
information related to the spectral differences between the type
of samples. Moreover, to obtain information about similarity
between the samples, hierarchical cluster analysis (HCA) was
performed with Euclidean distance matrix.
Euclidean Distance (x, y)= ∑ni=1(yi-xi)2  
HCA allows visualization of the overall grouping and
accordingly sub-groups the spectra based on their similarities
[16]. HCA and PCA were performed using the ChemoSpec
package of R. We also obtain the weight (loading plot) from
linear transformation, which contains new variables, and
indicates the molecular vibrational modes that explained most
of the variance. Supervised classification models such as
OPLS-DA (orthogonal partial least squares discriminant
analysis) was applied to visualize class separation using
SIMCA 13.0.1 (Umetrics, Sweden). OPLS-DA augment class
segregation by eliminating variability that is not relevant to
class separation.
Machine learning algorithms
Following spectral preprocessing, Raman spectral data was
subjected to ML in python using scikit-learn library. The
spectral data were divided randomly into training set and
validation set in a ratio of 70:30. The training set was used to
train a classification model and the validation set used to
evaluate the model performance.
Several ML algorithms, including SVM, AdaBoost, XGBoost,
DT, RF, GB, CNN and ANN were used to build the prediction
models for IRSM. We also implemented neural networks to
improve upon ML methodologies. The performance of each
classifier algorithm was measured independently.
A. Support Vector Machine
SVM is a classifier which divides the datasets by defining a
hyperplane, known as a maximum margin hyperplane. This
hyperplane minimizes the distance between the nearest points converted to a single dimension using the flatten layer. The
in each class [17]. This algorithm achieves high discriminative output layers consisted of a dense layer, and a sigmoid
power by using special nonlinear functions (polynomial activation function, which added the final classification
kernels) to transform the input space into a multidimensional label(predicted) to the output. The flowchart of the CNN model
space. SVM has the advantages of increasing separation of class is shown in Figure 2.
and reducing predictable error. Additionally, SVM is used for
both non-linear and linear discriminatory analyses. The
equation of polynomial kernels is given as
K (x, y) = tanh (ϒ.xT y + r)d, ϒ > 0 (2)

B. Adaptive Boosting

AdaBoost aims to merged many weak learners into a strong

learner to improve the performance of the predictive model
[18]. AdaBoost repeatedly calls a given weak learning
algorithm, where at each step the weights of inaccurately
classified instances are increased such that the weak learner
focusses more on difficult cases. In simple words, weak
learners are transformed into strong ones.

C. Extreme Gradient Boosting

XGBoost is a gradient boosting algorithm that combines the

regression tree by sequentially adding predictors and correcting
Fig. 2 Architecture of CNN
the previous models [19].

D. Decision Tree
DT is a powerful ML model that builds a decision tree from the
set of class labeled training samples [20]. The tree can be
explained by two entities, namely leaves and decision nodes.
The leaves are the decisions or the final outcomes, and the
decision nodes are where the data is split.
E. Random Forest
RF is an ensemble method that operates by construction of
multitude of decision trees by random selection of features with
controlled variance [21].
F. Gradient Boosting
GB is an ensemble technique which creates the model
consisting of weaker prediction models, mostly decision trees
and weak basic classifiers gradually become better than
previous weak classifiers [22].
H. Artificial Neural Network
An artificial neural network was implemented using the
PyTorch library. Initially, linear layers were added, which takes
an input as input dimension, and the number of hidden
dimensions (128), which are the output unit of layers. A ReLU
activation function was added next, and another linear layers
were added. Further, sigmoid activation function was added for
the final output layer. A forward step function was defined,
which activates a forward pass of the network. Next, a
backpropagation pass was used to update the weights using
Adam optimizer. Further the loss was calculated using the
output of forward pass and backpropagation was initialized. An
optimizer. step() function was called, which updates the
model’s parameters using the gradients that were calculated
during the backpropagation step, and defined optimizer with a
learning rate α=0.01. The architecture of ANN model is shown
in Figure 4.

G. Convolutional Neural Network

CNN is a class of neural networks that consists of several The equation for ReLU activation function is given as
hidden layers performing convolution to extract high level of R (z) = max (0, z) (3)
features of input data [23]. The networks consist of convolution
layers, pooling layers, and full connection layers and was
implemented using TensorFlow library. Initially, convolution
block was added to the input with the rectified linear unit The equation for sigmoid activation function is given as
(ReLU) activation function. A dense layer and a global max 1
pooling step were further added. The output of this layer was σ(z) = (4)
1+ e-z

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Fig. 3 (A) Graph of ReLU function (B) Sigmoid function
Fig. 4 Architecture of ANN
Hyperparameter Tuning
When building ML models, the hyperparameters must be tuned
and fixed to defined values to improve the model performances.
Herein, for optimizing the parameters and to improve model
performance, grid search method was implemented in python
using the scikit-learn package [24]. This method searches
through different values of model hyperparameters and selects
a single subset that provides the best performance on a given
dataset and is used to configure a model.
Four key parameters, i.e. C, degree, gamma and kernel were
used for SVM. For AdaBoost, parameters such as algorithm,
learning_rate, and n_estimators were used for tuning purposes.
We have tuned four parameters, including colsample_bytree,
gamma, max_depth, min_child_weight for XGBoost. For DT,
the parameters max_depth, max_features, ccp_alpha and
criterion were tuned. For RT, four parameters, i.e. criterion,
max_depth, max_features and n_estimators were used.
Parameters such as criterion, learning_rate, loss, max_features
were tuned for GB. Bayesian optimization (Keras tuner) was
used for hyperparameter tuning in the layers for CNN and ANN.
A grid search also includes an inbuilt K-fold cross validation
(CV) loop which cross validates the best fit model. All models
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were cross validated using GridSearchCV; separate cross
validation for each model was also conducted for additional
verification. After tuning the hyperparameters, K-fold (CV)
(k=10) was performed for each set of hyperparameter values and
the performance measured by assessing the area under receiver
operating characteristic (ROC) curve (AUC). The
hyperparameters that showed the highest accuracy were chosen
further for all ML algorithms.
Cross -Validation
K-fold CV was used to validate model performances. We
applied the 10-fold CV method to the dataset. In this approach,
each sample is used the same number of times for training and
the metrices in 10 iterations. The performance of each metrices
such as sensitivity, accuracy, and specificity, where TN, TP, FN
and FP, represent the number of true negatives, true positives,
false negatives and false positives, respectively.
Accuracy = TP +TN/ TP +TN + FP + FN (5)
Sensitivity = TP/TP + FN (6)
Specificity = TN/ TN + FP (7)
In order to access model performance, area under ROC curves
and F1 scores were also generated. AUC close to 1 indicates
that the model has good predictive performance. In addition,
learning curves were also generated which are diagnostic tools
that assess the algorithm performances, with different sizes of
training data. The curves also indicate changes in learning
performances and can effectively identify overfitting,
underfitting and good fitting in models [25]. We obtained
learning curves from seven different algorithms to diagnose the
ML model performances.
III. RESULTS AND DISCUSSION
Raman spectra were generated using endometrial tissues of
women with and without history of IRSM and the vibrational
modes of biomolecules in the spectral range of 400-1800cm-1
were analyzed. A significant peak shift originating from amide
I, amide III, CH2 bending mode of proteins and lipids, glutamate
and cholesterol were observed in IRSM when compared with
controls. Moreover, the intensity of the assigned peaks were
observed to be reduced in the IRSM group. The assigned Raman
peaks and their respective shifts are presented in Table 1. The
differences in the intensity of these characteristic peaks are
responsible for subsequent discrimination between the two
groups. Further, chemometric analysis was applied to classify
the spectral datasets and identify the biochemical differences
between IRSM and controls.
 Table 1. Raman shifts and assignment of peak The study was carried a step further to examine the performance
S. No IRSM Controls Vibrations
of the ML algorithms on Raman spectral data. For this purpose,
eight different models i.e. XGBoost, DT, SVM, AdaBoost, RF
1. 1650 1665 Amide I
GB, CNN and ANN were developed. To improve the model
2. 1446 1451 CH2 bending mode of proteins and
lipids performances, grid-search method and Bayesian optimization
3. 1254 1249 Amide III was used to perform hyperparameter tuning of all classifiers.
4. 1090 1096 Glutamate The best parameters selected with fixed defined values are
5. 550 548 Cholesterol shown in Figure 7 and Table 2.

After tuning the hyperparameters, K-fold cross-validation (CV)

(k=10) was performed for each set of hyperparameter values
Further, PCA was performed to detect differences between the
two groups (IRSM vs. controls). PCA analysis demonstrated and AUC performance measured. SVM, XGBoost, DT, CNN
that Raman spectra of the IRSM group differed from that of the and ANN were found to outperform all other models based on
control group. Also, PCA plot demonstrated considerable accuracy and AUC values.
overlapping; this may be attributed to intra-class variability due Table 2. Parameters of different classifiers
to the use of patient samples. We also conducted an analysis of Models Selected values of parameters
variance (ANOVA) to examine the variance by setting a Support vector C = 10, degree = 3, gamma = 0.001, kernel =
threshold of 0.05 for the chi-square test. However, the variance machine linear
was found to be statistically insignificant (p value < 0.05). Random forest criterion = gini, max_depth = 8, max_features =
sqrt, n_estimators = 500
Further, OPLS-DA analysis showed optimized class separation Adaptive Algorithm = SAMME.R, learning_rate = 0.97,
between IRSM and controls ((R2Y= 0.992 and Q2=0.899). Boosting n_estimators = 2
Furthermore, HCA analysis of almost all Raman spectra of the Decision tree ccp_alpha = 0.1, criterion = entropy, max_depth =
control group exhibited a distinct similarity, while spectra of 8, max_features = log2
Extreme Gradient colsample_bytree = 1, gamma = 2, max_depth =
IRSM tissues showed similarity between themselves, thereby Boosting 5, min_child _weight = 1
clearly forming two different clusters. The loading plots of PC1 Gradient boosting criterion = Friedman_msc, learning _rate = 0.5,
and PC2 represent the spectral bands that contribute most to the loss = logloss, max_features = sqrt
variance described by the principal component (Figure 5). The
strong contribution was observed from peaks 1665 cm-1, 1451
cm-1, 1245 cm-1, 1096 cm-1 and 548 cm-1. These results indicate The confusion matrix of the classifiers SVM, XGBoost, DT,
that amide I, CH2 bending mode of proteins and lipids, amide and CNN were also generated. Since confusion matrices are a
III, cholesterol and glutamate are responsible for separation useful way to assess the classifier, each row represents the
between IRSM and controls. actual target values while each column displays those values
predicted by the ML models. The confusion matrix of
classifiers are shown in Figure 6.

Fig. 5 (A) Principal component analysis (PCA) shows separation between

IRSM and controls (B) Loading plot of PC1 and PC2 show distinct peak
separation between IRSM and controls (C) OPLS-DA models shows optimized
separation between the two groups (D) Hierarchical cluster analysis (HCA) of
Raman spectra of endometrial tissue obtained from women with IRSM (n=15,
red) and controls (n=15, black)
Fig.6 Confusion matrix of (A) support vector machine (SVM) (B) Extreme
Gradient Boosting (XGBoost) (C) decision tree (DT) and (D) convolutional
neural network (CNN)

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 Fig. 7 Hyperparameter tuning of classifiers (A) Support vector machine (SVM) (B) Random forest (RF) (C) Adaptive Boosting (AdaBoost) (D)
Decision tree (DT) (E) Extreme Gradient Boosting (XGBoost) (F) Gradient boosting (GB)

The performance of the applied classification models was Fig. 8 Receiver operating characteristic (ROC) curve of different
determined in terms of sensitivity, specificity, accuracy, F1 models (A) Support vector machine (SVM) (B) Extreme Gradient
Boosting (XGBoost) and (C) Decision tree (DT) (D) Convolutional
scores and AUC values. Sensitivity and specificity are neural network (CNN)
measures of classification success in predicting the presence or
absence of a disease. Additionally, accuracy is the most
Table 3. Comparison of machine learning algorithms
common performance metric for classification algorithms. F1
score specifies the harmonic mean of sensitivity and precision.
Models Sensitivity Specificity Accurac AUC F1
Further, K-fold CV (k=10) was used to validate model y score
performances using grid search. Comparing all the algorithms, SVM 100% 81% 90% 0.91 90%
SVM, XGBoost, DT classifiers demonstrated best performance XGBoost 88% 81% 85% 0.85 84%
and achieved the classification accuracy of 90% 85%, and 85% DT 88% 81% 85% 0.85 84%
respectively. (Table 3). The proposed neural network CNN and CNN 100% 82% 90% 0.91 90%
ANN 100% 88% 92% 0.94 89%
ANN model also showed very good results in terms of
accuracy. The 1D CNN, showed a mean accuracy of 90% while
ANN model attained a mean accuracy of 92%. The ROC curves
of classifiers are presented in Figure 8.
In addition, learning curves were also generated to measure the
algorithm learning performances with different training data
sizes over time. The learning curves of classifiers are shown in
Figure 9.

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 macromolecules such as lipids, glutamate, proteins etc. was
observed in the endometrial tissue microenvironment of IRSM
cases. It is concluded that Raman spectroscopy in conjunction
with ML approach helped identify biomolecular fingerprints in
endometrium of women with history of IRSM. This approach
paves way for better understanding of the endometrial
impairment at a molecular level in women undergoing IRSM.

ACKNOWLEDGMENT
The authors thankfully acknowledge the financial support
provided by MHRD, India, from Indian Institute of Technology,
Kharagpur.

Fig. 9 Learning curves of different models (A) Support vector machine (SVM)
(B)Extreme Gradient Boosting (XGBoost) and (C) decision tree (DT)
Among all models generated, SVM, DT, XGBoost, CNN and
ANN exhibited highest classification model accuracy on
Raman spectral data. These findings confirm the feasibility of
using Raman spectroscopy in combination with the ML
algorithm for understanding disease pathophysiology of IRSM.
IV. CONCLUSION
We present a novel throughput strategy using Raman
spectroscopy to understand the altered biochemical signatures
in endometrial tissue of IRSM women. Raman spectral analysis
showed a significant decrease in the expression of proteins,
lipids, glutamate and cholesterol in IRSM as compared with
controls. Additionally, we performed PCA, HCA combined
with OPLS-DA for automated classification of data. We further
applied eight ML algorithms including SVM, AdaBoost,
XGBoost, DT, RF, GB, CNN and ANN and evaluated the
models using five different evaluation metrics, namely
accuracy, sensitivity, specificity, F1-score, and ROC metrics.
Grid search and Bayesian optimization was used for
hyperparameter optimization to obtain the best combination of
parameters. We observed that SVM, DT, XGBoost, CNN and
ANN performed better than other models in term of accuracy.
This study has considerable clinical utility since the
endometrium i.e., the lining of the uterus where the embryo
implants in women with IRSM remains poorly understood. A
significant downregulation of various biological
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