Journal of Ambient Intelligence and Humanized Computing (2023) 14:4675–4683

https://doi.org/10.1007/s12652-022-04368-w

ORIGINAL RESEARCH

A new framework for multi‑scale CNN‑based malignancy classification

of pulmonary lung nodules
Sakshiwala1 · Maheshwari Prasad Singh1

Received: 2 November 2021 / Accepted: 30 July 2022 / Published online: 18 September 2022
© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2022

Abstract
Lung cancer has the highest mortality rate among all types of cancers. Early detection of lung cancer may improve survival
rates. The two categories of pulmonary lung nodules have high visual similarities. So, distinguishing them is a challenging
task for radiologists. The main purpose of this work is to use convolutional neural network to perform binary classification
of pulmonary nodules in CT images. This paper proposes a new multi-scale (64 × 64, 32 × 32 and 16 × 16) convolutional
neural network architecture for benign and malignant nodules classification. In addition, transfer learning method is used
to initialize the weights of multi-scale architecture. Experimental results on the dataset LIDC-IDRI demonstrate that the
proposed method achieved accuracy of 93.88%, sensitivity of 93.36% and specificity of 93.26% on nodule malignancy
classification. The proposed method also outperforms the other state-of-the-art methods explicitly designed for malignancy
classification of pulmonary lung nodules.

Keywords Transfer learning · Benign · Malignant · LIDC-IDRI · CT scan · Lung cancer

1 Introduction (CAD) systems can be used to reduce these variations. CAD

Lung cancer is the most lethal form of cancerous disease.
It is uncontrolled growth of cells in the lung tissues. Every
year it affects 12.9% of the world’s population. In less devel-
oped countries there is 58% of lung cancer cases (Abid et al.
2021). Typically symptoms of this disease appear only when
it is at an advanced stage. So in order to avoid spread in
the body (Chen et al. 2020; Attique et al. 2020; Zhao et al.
2018a), lung cancer should be treated at an early stage.
Lung cancer diagnosis by analysing CT scans is clini-
cally intensive task for radiologists. It takes ten minutes for
the radiologist to give a thorough inspection of a CT scan.
Moreover, there is considerable variation among radiologists
in identifying nodules. However, this process is influenced
by the emotion and experience of the respective doctors.
The overall error rate is reported to be 7.6% for every 53
patients (Venugopal et al. 2020). Computer-aided diagnosis
* Sakshiwala
sakshiwala.phd19.cs@nitp.ac.in
Maheshwari Prasad Singh
mps@nitp.ac.in
1
National Institute of Technology Patna, Patna, Bihar 800005,
India
systems are able to provide the accurate, quick, and cost-
effective solutions and thus have a clear clinical importance.
In recent years, deep neural network based methods have
shown good performance in image based medical diagno-
sis, and thus has an important role in the design of CAD
systems.
Doctors predict nodule malignancy risk on the basis of
shape and density of the nodules and the other pathology
information. Qualitatively, compared to the benign nodules,
the malignant often has irregular shape, higher volumes, lob-
ulated and spiculated margin. Some images of pulmonary
lung nodules are shown in Fig. 1. To overcome the prob-
lems mentioned above, this paper proposes a new frame-
work using multi-scale convolutional neural network (CNN)
architecture with transfer learning approach. The proposed
method adopts a transfer learning approach to preserve the
learned features using multiple filters with different sizes.
Contributions of this paper can be summarized as follows:
– A new framework for multi-scale CNN-based architec-
ture is proposed to classify the lung nodules into benign
and malignant classes. A 64 × 64 pixels input based
model is first trained.

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4676
(a) Benign nodules
(b) Malignant nodules
Fig. 1  Pulmonary lung nodule sample images
– Then the transfer learning method is used to train the 32
× 32 pixels and 16 × 16 pixels input based models.
The paper is organized as follows: Sect. 2 describes the
Related Work. Section 3 describes the proposed methodol-
ogy. Section 4 demonstrates experimental results and discus-
sion. Section 5 concludes the paper.
2 Related work
Various studies are present in the literature that have the aim
of detection and classification of lung cancer nodules using
both the deep learning and conventional machine learning
approaches. Early developed CAD systems use low level fea-
tures of medical imaging, which represent the global struc-
tures in the images such as shape and size. These methods
are useful to classify pulmonary nodules because it has dif-
ferent sizes and shapes.
However, visual representations may be different for dif-
ferent types of the nodules and needs to be differentiated
with both global and local structures. The high-level fea-
tures of nodules may be extracted by unsupervised feature
learning methods. It may achieve better classification per-
formance compared to the low-level based feature extractors.
Kuang et al. (2020) train the network to learn features of
anomalous benign images. And tests the network using non-
anomalous images. The method requires manual estimation
of the malignancy scoring threshold. Xie et al. (2019) sug-
gests a multi-view knowledge-based semi-supervised adver-
sarial classification model. It is the extension of the work
proposed in Xie et al. (2018a). The network uses semi-super-
vised reconstruction network trained on labelled and unla-
belled data. The features extracted from each convolution
13
Sakshiwala, M. P. Singh
and identity blocks of the encoder are passed to each respec-
tive layers of classification network.
Yu et al. (2018) propose a density-based spatial clustering
of applications with noise algorithm. The advantage is that
one can choose the best scale combination from multi-scale
according to the need. The method is not able to detect all
types of nodules.
In Hussein et al. (2019), the model uses weights pre-
trained on sports dataset. It is multi-task learning on visual
attributes. K-means clustering and proportion-SVM. The
unsupervised learning methods like GANs and autoencod-
ers are more promising. However, unsupervised learning
schemes require manual feature extractions, so it is complex
to find the optimal feature combinations.
The most popular architecture of DNN is CNN. CNN
and many of its variants are based on supervised learning
methods. From raw input images, CNN is capable to extract
high-level features without any manual intervention. Thus, it
is expected to perform better in classification of pulmonary
nodules.
Pritam Mukherjee et al. (2020) develop LungNet, a shal-
low convolutional neural network. It has two CNNs, the
survival prediction and the malignancy prediction network.
The weights of the survival prediction network is shared by
transfer learning with the malignancy prediction network.
They demonstrated the use of transfer learning. However, the
method extract features by single-scale filter. However, due
to variation in nodule sizes, analyzing nodule images using
multi-scale filters could generate more effective nodule fea-
tures. It has better accuracy compared to the conventional
feature extraction methods. In Zhao et al. (2018b) combines
the benefits of LeNet layer settings and AlexNet parameter
settings. Since LeNet and AlexNet are originally designed
for coloured images, this affects the performance because
the medical images are gray coloured images.
Zhang et al. (2019) develop a meta-learning method,
where the output of the primary learners is input dataset to
the secondary learners. The eight variants of CNN predict
the malignancy value for each patch. The predicted values
for each patch are then used as a new dataset for the ten
ensemble learners. The computational cost involved in this
method might be very high.
To fulfill the need of an accurate and robust pulmonary
nodule classification, in this paper, a novel convolutional
neural network baesd architecture is proposed. The proposed
method adopts a multi-scale feature extraction scheme while
using the benefits of transfer learning approach. The multi-
scale feature have better performance along with multiple
learners. The transfer learning scheme shows promising
results for the nodules classification.
A new framework for multi‑scale CNN‑based malignancy classification of pulmonary lung nodules 4677
3 Methods
This section describes the database and preprocessing meth-
ods used in this paper. The method and the architectural
details of the proposed model are discussed.
3.1 Dataset description and preperation
The Lung Image Database Consortium image collection
(LIDC-IDRI) (Samuel et al. 2004), initiated by the National
Cancer Institute, is used to train and test the proposed
method. Total of 1012 chest CT scans were considered for
this study. Each CT scan has an xml annotation file attached,
which contains information of nodules marked by four expe-
rienced annotated radiologists. Depending on the diameter
of the nodules, the radiologist categorised the nodules into
three categories: nodules > 3 mm, nodules < 3 mm and non-
nodule >= 3 mm.
The original CT images of 512 × 512 pixels in .dcm
format is converted into .png images for faster training.
Since the nodules size is very small compared to the whole
image size, it is required to extract the particular region of
interest of nodules. According to the requirement, first, we
segment the lung parenchyma from CT images to remove
the irrelevant information. Then using threshold probabil-
ity map algorithm, the 64 × 64 pixels rectangular region
is intercepted with the pulmonary nodules. The location
information of nodules (Kuang et al. 2020) is obtained by
Fig. 2  Illustrations of preprocessing
reading the corresponding xml file. The four radiologists
have independently annotated each nodule, and has given
malignancy score that range from 0 to 5. The mean value of
these scores is taken as the final malignant score value for
that particular nodule. This is phrased as mean malignancy
label of a nodule. The nodules with mean malignancy label
equal to 3 were removed from this study. The nodules are
further categorized using mean malignancy label. Finally, a
total of 829 malignant nodules and 1262 benign nodules are
extracted. Figure 2 illustrates the described preprocessing.
3.2 Proposed model
Below mentioned subsections provide the description of the
various layers used in the proposed framework and the pro-
posed multi-scale architecture.
2D convolution layer: Convolution layer performs linear
convolution operation on the input. The convolution opera-
tion involves multiplication of an array of input data with
a filter of weights. Mathematically, convolution is a feature
derived from two given functions by integration which
expresses how one function transforms the shape of other.
Figure 3 shows a 2D convolution operation. In order to get
multiple convolved images, various kind of feature detectors
are applied on input image to extract different features.
Maxpooling layer: Max pooling operation is applied on
each patch of each feature map seperately. It pools out the
maximum values and form a set of same number of feature
maps. While it reduces the size of each feature map. Pooling
helps to downsample the feature maps. It is important that
it preserves the original feature and still able to reduce the
spatial size and thus computation in the network. An sample
of max pooling operation is shown in Fig. 4. The benefit of
Fig. 3  Convolution layer operation
Fig. 4  Maxpooling operation
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4678 Sakshiwala, M. P. Singh

maxpooling is that it pools out that feature from the feature
map which is most present.
LeakyReLU operation: In order to get the desired
results, activation functions is used to make decision on
whether to activate or deactivate a neuron. It helps model to
learn non-linear transformations.
LeakyReLU turns all negative input values to a value near
to zero. The idea is to let some gradient flow during training.
While all positive values remain same.
Flatten and the dense layer: Flatten layer translates the
multi-dimensional tensor into a single long feature vector.
Dense layers are the fully connected layers. Unlike convolu-
tion layers where a neuron is connected to local area of input
neurons, in the dense layer each neuron has a path to every
other neuron to next layer. Figure 5 illustrates the flatten and
dense layer.

3.2.1 Architecture details of the proposed framework

The framework of the proposed model is shown in Fig. 6b.

The proposed method has three models that perform multi-
scale feature extraction. The first model takes input of size
64 × 64 pixels. The second model takes input of size 32 ×
32 pixels and third model takes 16 × 16 pixels. Each of the
model has the same architectural details. The first layer uses
filters of size 5 × 5 to perform the convolution operation on
the input image and generates 64 output feature maps. The
second, third and fourth convolution layer uses 3 × 3, 5 ×
Fig. 5  Flatten and dense layer 5 and 3 × 3 sized filters to perform convolution operations

(a) training (b) testing

Fig. 6  Proposed model

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A new framework for multi‑scale CNN‑based malignancy classification of pulmonary lung nodules 4679
respectively. The LeakyReLU activation function is used
after every convolutional layer. It helps the model to con-
verge faster and is easy to implement.
Then, this is followed by a max-pooling layer. This layer
reduces the spatial resolution and helps in learning the more
complex features from the input. Further two dense layers
are used. The flattened output feature maps are then passed
to a dense layer of 512 neurons. After this, LeakyReLU
activation function is used. The last fully connected layer
has two neurons which classifies the nodules as benign and
malignant. The outputs from the last fully-connected layer
is normalized using softmax. The fully-connected layers
often lead to overfitting. The problem of overfitting can be
resolved using dropout. A dropout of 0.5 is used to avoid
the overfitting. A sparse categorical crossentropy loss (L)
function is used. It is defined as:
2
∑ framework. Some parameters depend on the outcome of the
L=- log(p(i))t(i), (1)
x=1
where p(i) is the predicted probability, t(i) is the true prob-
ability, ‘x’ is the class label and ‘i’ is the sample training
data. Smaller value of loss function implies that the pre-
dicted probability is closer to the true probability.
3.2.2 Multi‑scale feature extraction and transfer learning
The purpose of multi-scale feature extraction is to learn dif-
ferent patterns in images using different filter sizes. Differ-
ent filter sizes can focus on the context information of the
candidate nodules in different scale images and the features
extracted from the different streams can also complement
each other. Therefore, more effective features can be learnt
through different scale images. The method uses transfer
learning concept to transfer the weights learned by convo-
lutional layer of 64 × 64 pixels input based model to the
respective layers of 32 × 32 pixels input based model. The
layers are then trained. The weights after training of 32 ×
32 pixels input based model is transferred to the 16 × 16
pixels input based model. Figure 6b shows the described
framework.
4 Results and discussion
4.1 Experimental environment
This work uses dataset having 2091 images. To increase the
randomness data augmentation techniques are employed.
Such as rotation by 90°, 180°and 270° angle. The nodule
images were cropped and flipped. The nodules are aug-
mented by translating the nodules images by x axis and
y axis ± 2 pixels. Data augmentation techniques helps to
generalize the model. Adam optimizer with learning rate of
0.001 is used.
All experiments in this paper were performed on Python
programming language using Keras library. The net-
works were trained on 32 GB RAM with a single NVIDIA
QUADRO M2000, Windows 10 operating system. Results
are given below with discussions.
4.2 Performance metrics
Different evaluation parameters, including accuracy, preci-
sion, recall (sensitivity or True positive rate), F1-score, spec-
ificity, false positive rate are used to evaluate the proposed
confusion matrix true positive (TP), false negative (FN), true
negative (TN) and false positive (FP). TP is the number of
correctly predicted malignant nodules. TN is the number
of correctly predicted benign nodules. FP is the number of
actual benign nodules that are predicted malignant. FN is the
actual malignant nodules that are predicted benign.
The statistical parameters are expressed as follows:
TP + TN
Accuracy = (2)
TP + FP + TN + FN
TP
Precision = (3)
TP + FP
TP
Recall = (4)
TP + FN
TN
Specificity = (5)
TN + FP
FP
FPR = . (6)
TN + FP
4.3 Tuning of hyperparameters
A series of experiments is carried out to justify the choices:
the number of convolutional layers, maxpooling layers, fully
connected layers, size and number of filters, increasing or
decreasing the batch size, initializing convolutional layer
weights. Table 1 shows accuracies obtained by different sets
of hyperparameters.
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4680 Sakshiwala, M. P. Singh

Table 1  Tuning of hyperparameters of the proposed model

Input scale Conv layers Fully con- Filter size Dropout ratio Batch size Weight initialization Accuracy
nected layer

64 × 64 4 2 5 × 5, 3 × 3 0.5 96 Random 92.27

64 × 64 4 2 5 × 5, 3 × 3 0.5 128 Random 92.55
64 × 64 4 3 5 × 5, 3 × 3 0.5 224 Random 92.65
64 × 64 3 2 5 × 5, 3 × 3 0.5 224 Random 93.21
64 × 64 4 2 5 × 5, 3 × 3 0.5 224 Random 93.88

(a) Conv1

Fig. 7  Illustration of filters in Conv1 layer of 64 × 64 input size

model

4.4 Effectiveness of multi‑scale features

and usefulness of transfer learning approach

Figure 7 illustrates 64 filters used in the first convolution

layer of a 64 × 64 pixels input based model. These filters
slide over the input image to learn different portions of an
input image. Figures 8a, b, 9a, b represents the output feature
(b) Conv2
maps obtained from first and second convolution layers. As
64 filters are used in first convolution layer, so 64 output fea-
Fig. 8  Representing the hidden layer output activation maps of a 64 ×
ture maps are generated. While 32 filters are used in second 64 benign nodule image
convolution layer, so 32 output feature maps are generated.
Figure 10a–c show the training and validation accuracy
graph of the model on respective input sizes. From the the training, validation and test datasets. In order to avoid
graph, it can be concluded that the model is best trained. the overfitting, patience parameter is used as early stopping
Table 2 shows the classification accuracies of the different criteria during training.
input sizes of the model. The results shown in Table 2 are In Table 3, the accuracy of the model is shown under
when the convolutional layers of 32 × 32 model are initial- the following conditions: by using the transfer learning
ized by the weights of 64 × 64 pixels input based model. approach, the weights learned by filters of first convolutional
The convolutional layers of 16 × 16 model are initialized layer of input size 64 × 64 model is transferred to the 32 ×
by the weights of 32 × 32 pixels input based model. Table 2 32 model. The weights learned by filters of first and second
shows the classification accuracy of the proposed method on

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A new framework for multi‑scale CNN‑based malignancy classification of pulmonary lung nodules 4681

Table 2  Classification Input size Train Val Test

accuracies of the proposed
model with transfer learning, 64 × 64 0.95 0.94 0.93
non-trainable layers in 16 × 16
32 × 32 0.93 0.93 0.93
input based model is conv1
16 × 16 0.92 0.92 0.92

Table 3  Classification Input size Train Val Test

accuracies of the proposed
Model with transfer learning, 64 × 64 0.94 0.92 0.93
non-trainable layers in 32 × 32
32 × 32 0.93 0.92 0.94
is conv1 and 16 × 16 are conv1
and conv2 16 × 16 0.91 0.91 0.92
(a) Conv1

4.5 Effectiveness of the proposed model

A contingency table called confusion matrix shown in

Fig. 11 depicts how many nodules are correctly classified
and how many were not correctly predicted. 774 nodules
were actually malignant and are correctly predicted as
malignant. 1177 nodule images are actually benign and
are correctly predicted as benign. While 55 nodules were
actually malignant but are wrongly predicted as benign. 85
benign nodules are predicted as malignant.
(b) Conv2
The confusion matrix enteries (TP, TN, FP, FN) are not
meaningful independently, so it is interpreted relative to each
Fig. 9  Representing the hidden layer output activation maps of a 64 ×
other. So we plot ROC curve in Fig. 12. It is the plot between
64 malignant nodule image sensitivity (true positive rate) and 1-specificity (false posi-
tive rate). It shows that the model achieves area under curve
(AUC) of 93.315%. Table 4 shows the precision, recall and
convolution layers of 32 × 32 model is transferred to respec- F1-score of respective classification categories.
tive layers of 16 × 16 model.
4.6 Comparison with previous work

To illustrate the effectiveness of the proposed method,

Table 5 provides the comparison of the proposed method

(a) 64*64 input model (b) 32*32 input model (c) 16*16 input model

Fig. 10  Training graph of model

13
4682 Sakshiwala, M. P. Singh

with other deep learning based methods. All the models

use LIDC-IDRI database for experiments. The number of
data used in Xie et al. (2018b) and Ren et al. (2020) is
relatively small, so the final accuracy rate is lower than
the other studies. Xie et al. (2019) is a semi-supervised
learning approach based on both labeled and unlabeled
data. In addition, it can be seen from Table 4 that the
proposed model has a significant improvement in clas-
sification performance.

5 Conclusion
Fig. 11  Confusion matrix (label ‘0’: benign, label ‘1’: malignant)
In this paper, a new framework of multi-scale CNN-
based architecture is proposed for malignancy classifi-
cation of lung nodules on chest CT scans. The proposed
method adopts a transfer learning based multi-scale fea-
ture extraction method. In this method first a size of 64
× 64 pixels input images is fed as an input to the network
and trained. Then the learned weights are transferred to
the 32 × 32 pixels input based model of same architec-
ture and is then trained. The weights learned by convolu-
tional layers of 32 × 32 pixels input size based model is
initialized to the respective layers of 16 × 16 pixels input
based models and is then trained. Finally, the model
is evaluated on LIDC-IDRI dataset. The experimental
results showed that the proposed model is efficient for
Fig. 12  ROC curve malignancy classification of lung nodules in chest CT
scans.
In this work only 2D image of a single nodule is used
for cancer prediction. While in reality, the oncologists
Table 4  Performance of the proposed model
consider 3D view of CT scans. The current study does not
consider scores of attributes related to malignancy. For
Category Precision Recall F1-score the future work, in order to avoid human cropped nodule
Benign 0.96 0.93 0.94 regions, deep learning based malignancy classification
Malignant 0.90 0.93 0.92 method along with the method of nodule detection may
be added.

Table 5  Comparison with previous models

References Method Database (number) Accuracy Sensitivity Specificity AUC​

Xie et al. (2018b) Fuse-TSD LIDC-IDRI (1972) 89.53 84.19 92.02 96.65
Ren et al. (2020) Manifold regularized CNN LIDC-IDRI (1226) 90 81 95 -
Xie et al. (2019) Semi-supervised adversarial classification LIDC-IDRI (2557) 92.53 84.94 96.28 95.81
Proposed method Multi-scale CNN + transfer learning LIDC-IDRI (2091) 93.88 93.36 93.26 93.31

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A new framework for multi‑scale CNN‑based malignancy classification of pulmonary lung nodules 4683
Data availibility statement The datasets used in the current study are
available in the below https://​wiki.​cance​rimag​ingar​chive.​net/​displ​ay/​
Public/​LIDC-​IDRI.
Declarations
Conflict of interest The authors have no conflict of interest.
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