paper2
paper2
Received May 4, 2019, accepted May 16, 2019, date of publication May 27, 2019, date of current version July 3, 2019.
Digital Object Identifier 10.1109/ACCESS.2019.2919385
Corresponding authors: Xin Hong ([email protected], [email protected]), Chenhui Yang ([email protected]), Nianyin Zeng
([email protected])
This work was supported by the International Science and Technology Cooperation Project of Fujian Province of China under Grant
2019I0003, the Science and Technology Planning Project of Quanzhou under Grant 2017G01, the Online Course Supporting Project of
Fujian under Grant 612-52418005 and 612-50117024, and the Fundamental Research Funds for the Central Universities under Grant
20720190009.
ABSTRACT Alzheimer’s Disease (AD) is a chronic neurodegenerative disease. Early diagnosis will
considerably decrease the risk of further deterioration. Unfortunately, current studies mainly focus on
classifying the states of disease in its current stage, instead of predicting the possible development of the
disease. Long short-term memory (LSTM) is a special kind of recurrent neural network, which might be
able to connect previous information to the present task. Noticing that the temporal data for a patient are
potentially meaningful for predicting the development of the disease, we propose a predicting model based
on LSTM. Therefore an LSTM network, with fully connected layer and activation layers, is built to encode
the temporal relation between features and the next stage of Alzheimer’s Disease. The Experiments show
that our model outperforms most of the existing models.
INDEX TERMS Alzheimer’s Disease, Prediction, LSTM, Time Sequence, Magnetic Resonance Imaging
Then, we compare the efficiency of our algorithm with recent data serialization. Then, an LSTM model is built to perform
state-of-art algorithms. Furthermore, we test our algorithm’s the prediction. As shown in the experiments of Table 2, our
stability in different data size and evaluate our algorithm’s approach demonstrates better performance than the existing
sensibility on different features. approaches on time sequence data.
converted classes as independent classes. Usually, the last according to the stages of the disease (AD, NC, and MCI).
stage of converted classes is one of the following three stages: Besides, linear interpolation is adapted to fill the missing
AD, NC, and MCI. In our experiment, following this con- feature data. The pre-processed data are further re-scaled into
vention, eight categories are reclassified into three categories the range of [0, 1], and the data are serialized after the object
following the time step. Although some of the objects are an LSTM [27] network, with fully connected and activation
collected more than ten years, most of the objects have one layers, is built to encode the temporal relation between fea-
or two records (one record for every six months). Considering tures and the next stage of AD.
the data distribution, we reformat the data series in two time LSTM, with the chain of repeating neural network mod-
steps. ules, is designed to avoid the long-term dependency problem.
In Figure. 2, data interpolation shows one example of a There are four interacting layers in an LSTM neural network,
subject, for whom all the data are in the table. Each row such as ‘‘forget gate’’, ‘‘input gate’’, ‘‘update gate’’, and ‘‘out-
indicates the features, and each column indicates the time put gate’’. The decision whether the information is thrown
intervals. The column is designated as ‘‘M’’ for the month; away from the cell state is made by the ‘‘forget gate’’, shown
e.g., ‘‘M00’’ refers to the first month; ‘‘M06’’ refers to the in Eq. 4. The ‘‘input gate’’ with a sigmoid layer and a tanh
sixth month. Features are denoted by ‘‘F’’, where ‘‘F1’’ refers layer decides which values will be updated. The equation is
to the first feature, ‘‘F2’’ refers to the second feature, etc. shown in Eq. 5 and Eq. 6. The ‘‘update gate’’ in equation
Each subject is scanned multiple times when the maximum Eq. 7. updates the old cell state with the value from the ‘‘input
of months is 120 months. gate’’. Finally, the ‘‘output gate’’ in equation Eq. 8 and Eq. 9
In data interpolation, for a particular subject, as not all the decides which value is to be output from the layer.
time intervals have values, subsequent data is required for a
full record. (1) In the case of the missing data in row F1, where ft = σ (Wf · [ht−1 , xt ] + bf ) (4)
there is only one value for all the procedures, we assign this where Wf is the weight matrix; bf is the bias vector; and ft is
feature value to all the time intervals. (2) Linear interpolation a number between 0 and 1, where 0 represents the forget and
is applied to the incomplete data at M36 in row F2. (3) In the 1 represents the keep.
case of row F4 (where all the values are missing), we fill the
average feature value for the same classification. it = σ (Wi · [ht−1 , xt ] + bi ) (5)
As AD is a smooth progression of brain atrophy in et = tanh(WC · [ht−1 , xt ] + bC )
C (6)
time series, the missing interval data in case (2) is inter-
polated in linear. We define the feature as {(xi , ti ); i = where Wi and WC are the weight matrices; bi and bC are the
1, · · · , n}, where xi refers to the i-th feature value and ti bias vectors; and it , C
et are the outputs of these two equations.
refers to the i-th time step. Feature sequence is formatted as
{(x0 , t0 ),(xi , ti ), · · · , (xn , tn )}. Suppose (xm , tm ) is the missing Ct = ft ∗ Ct−1 + it ∗ C
et (7)
value to be interpolated, (xi , ti ) and (xj , tj ) are the feature where ft decides which information is to be forgotten, and
values in time step i and j. it ∗ Cet chooses how many values are to be updated for the
When i < m < j, we interpolate xm as follows: cell.
(xj − xi )(tm − ti )
xm = xi +
tj − ti
(1) io = σ (Wo · [ht−1 , xt ] + bo ) (8)
ht = ot ∗ tanh(Ct ) (9)
When xi is the first not null feature value in time step i and
0 < m < i, we interpolate xm as follows: where the value of io in Equation 8 decides which part of the
(xi+1 − xi )(ti − tm ) cell state will be the output. The new cell state Ct multiplied
xm = xi − (2) by ot , and function tanh have selected, to obtain ht in Equa-
ti+1 − ti
tion 9, which is the output of the parts io .
When xj is the last not null feature value in time step j and As Long Short-Term Memory (LSTM) is capable of learn-
j < m < n, we interpolate xm as follows: ing long-term dependencies, a model based on LSTM is built
(xj − xj−1 )(tm − tj ) to express the progression of AD. In this paper, we create
xm = xj + (3)
tj − tj−1 a model that processes the time series data to make the
six months’ prediction of AD. The proposed model, shown
in Figure. 3, involves three layers: the Pre-Fully Connected
IV. AD PREDICTION MODEL AND EVALUATION Layer, Cells Layer, and Post-Fully Connected Layer. The
Studies have demonstrated that brain changes associated with Pre-Fully Connected layer consists of one fully connected
AD may begin more than twenty years before symptoms layer and a ReLU function; the Cells layer consists of one
appear [23]–[26]. MRI is a technique used to image the LSTM layer and a Dropout Wrapper; the Post-Fully Con-
anatomy of the brain. Between two scans, atrophy can be nected layer consists of one fully connected layer and a
measured by the loss of volume in a particular brain region. softmax layer.
It stands to the reason that different brain Regions Of Inter- During the model training, preprocess sequential data with
est (ROIs) have different disease prediction abilities under time steps are fed to the model, and the state of the next six
the sequence-dependent temporal context. LSTM is a special months is predicted by the model. For example, in Figure. 3,
kind of recurrent neural network, which might be able to the first two steps of O1 (subject O1) time sequential data
connect previous information to the present task. Therefore, from the 6-th month to the 12-th month, are fed to the model.
The state of the 18-th month, six months after the 12-th month where N is the number of classes; and AUC(c ˆ i , cj ) is the
is predicted by the model as ‘‘AD’’. average AUC(ci , cj ) for classes i and j.
During the model testing, when the 18-th and 24-th month We evaluate our method by applying it to the MRI data.
features’ data of the subject are fed to the model, the output The goal is to select a compact set of time-sensitive and
is the prediction of the subject’s state in the 30-th month. disease-relevant features while maintaining high predictive
One of the most essential evaluation metrics for check- power. Specifically, when the brain region features are fed to
ing classification model’s performance, the Area Under the model with time series, the most relative combination of
Curve (AUC) is defined as the area under the Receiver features are extracted by Pre-Fully Connected layer. There-
Operating Characteristic (ROC) curve. It measures how after, time-sensitive features are selected by the Cells layer.
true positive rate (recall) and false positive rate trade- When the features are fed to the Post-Fully Connected layer,
off. And multi-class Area Under the receiver operating the combinations of the time-sensitive features are employed
Curve (mAUC), which is independent of the group sizes, to predict AD.
gives an overall measure of classification ability to each With 5-fold cross-validation, based on prediction, follow-
class. Our system is evaluated by using AUC/mAUC, where ing parameters are fixed to adjust the network structure of
binary-class is accounted for by AUC, and the multi-class is our model in the experiments: batch_size as 256, the learn-
accounted for by mAUC [28]. These measures are defined as ing_rate as 1e-4, the type of cell as LSTM Cell, the number
follows: of pre-fully connected cells as 512, the number of post-fully
AUC is the area under the ROC curve, and AUC(ci , cj ) is connected cells as 3 and keep_prob as 0.8. Furthermore,
the AUC of a class ci against the other class cj , defined in to find the best parameters, we tune our model with the
Equation 10 as follows: following parameters: the number of the fully connected
cells, the number of LSTM cells, and the number of LSTM
Ri − ni (n2i +1)
AUC(ci , cj ) = (10) layers. Experiments of three classes prediction on AD vs MCI
ni nj vs NC show that the model achieves the best mAUC when
where ni and nj are the total numbers of points belonging to the number of fully connected cells is 512, and the number
classes i and j, respectively Ri is the sum of the ranks of the of LSTM layers is 2. The results in Table 1 show that our
likelihood belonging to class i. model achieves the best mAUC when the number of LSTM
ˆ
AUC(c i , cj ) [28] is the average AUC(ci , cj ) for classes i and cells is 128.
j, defined as AUC(cˆ i , cj ) = 0.5 ∗ (AUC(ci , cj ) + AUC(cj , ci )).
While the mAUC [28] is multi-class Area Under the ROC V. EXPERIMENT
Curve, defined by Equation 11 as follows: Studies have demonstrated that brain changes associated with
2 XX N i AD may begin more than twenty years before symptoms
mAUC = ˆ
AUC(ci , cj ) (11) appear [23]–[26]. Multiple symptoms reflect the degree of
N (N − 1)
i=2 j=1 damage to neurons in different parts of the brain, where
VI. CONCLUSION
In this paper, a deep learning model is introduced to predict
the development of AD. Noticing that the disease is inher-
ently progressive, the temporal information collected from
the cases is considered in the model. Compared with existing
FIGURE 9. Varying data sizes based on TS feature.
approaches, our model can carry out the future state predic-
tion for the disease, rather than classify the state of a current
TABLE 3. The AUC/mAUC of different features. diagnosis. Experiments show that the performance of our
model is much better than most of the existing approaches.
Besides, our method is table for different data size. At the
same time, the results also show that the Cortical Thickness
Average (TA) feature is a significant feature to predict the
progression of AD.
ACKNOWLEDGMENT
Thickness Standard deviation (TS), cortical Thickness Aver- This work is supported by International Science and
age (TA), WM Parcellation Volume (SV), Surface Area (SA), Technology Cooperation Project of Fujian Province of
and Cortical parcellation Volume (CV). Among those five China under Grant 2019I0003, the Science and Tech-
features, TA is the identification of gross atrophy in the nology Planning Project of Quanzhou under Grant
cerebral cortex and certain subcortical regions. According 2017G01,the Online Course Supporting Project of Fujian
to neuropathology, AD is characterized by loss of neurons under Grant (612-52418005,612-50117024) and the Funda-
and synapses in the cerebral cortex and certain subcortical mental Research Funds for the Central Universities under
regions, resulting in gross atrophy of the affected regions. Grant 20720190009.
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2016. XIN HONG received the B.S. and M.S. degrees
[13] X. Zhu, H.-I. Suk, S.-W. Lee, and D. Shen, ‘‘Discriminative self- in computer science from Hua Qiao University,
representation sparse regression for neuroimaging-based Alzheimer’s dis- China, in 2001 and 2004, respectively. She is cur-
ease diagnosis,’’ Brain Imag. Behav., vol. 13, no. 1, pp. 27–40, 2017.
rently pursuing the Ph.D. degree in computer sci-
[14] N. Zeng, H. Qiu, Z. Wang, W. Liu, H. Zhang, and Y. Li, ‘‘A new
ence with Xiamen University, China. From 2004 to
switching-delayed-PSO-based optimized SVM algorithm for diagno-
sis of Alzheimer’s disease,’’ Neurocomputing, vol. 320, pp. 195–202,
2006, she was a Teaching Assistant with the Col-
Dec. 2018. lege of Computer Science and Technology, Hua
[15] S. H. Nozadi, S. Kadoury, and Alzheimer’s Disease Neuroimaging Initia- Qiao University. From 2006 to 2012, she was a
tive, ‘‘Classification of Alzheimer’s and MCI patients from semantically Lecturer with the College of Computer Science
parcelled PET Images: A comparison between AV45 and FDG-PET,’’ Int. and Technology, Hua Qiao University. Since 2012,
J. Biomed. Imag., vol. 2018, Mar. 2018, Art. no. 1247430. she has been an Associate Professor with the College of Computer Science
[16] H. Choi, K. H. Jin, and Alzheimer’s Disease Neuroimaging Initiative, and Technology, Hua Qiao University. From 2009 to 2010, she was a Visiting
‘‘Predicting cognitive decline with deep learning of brain metabolism Researcher with CAD and CG National Research Lab, Zhe Jian University,
and amyloid imaging,’’ Behav. Brain Res., vol. 344, pp. 103–109, China. From 2012 to 2013, she was a Visiting Researcher with the Faculty of
May 2018. Science and Technology, University of Stavanger, Norway. She is the author
[17] H.-I. Suk and D. Shen, ‘‘Deep learning-based feature representation for of 5 books, 2 inventions and more than 15 articles. Her research interests
AD/MCI classification,’’ in Proc. Int. Conf. Med. Image Comput. Comput.- include medical image, data mining, and pattern recognition.
Assist. Intervent., vol. 16, 2013, pp. 583–590.
[18] F. Li, L. Tran, K. H. Thung, S. Ji, D. Shen, and J. Li, ‘‘A robust deep model
for improved classification of AD/MCI patients,’’ IEEE J. Biomed. Health
Inform., vol. 19, no. 5, pp. 1610–1616, Sep. 2015. RONGJIE LIN was born in Fujian, China, in 1995.
[19] W. Lin, T. Tong, Q. Gao, D. Guo, X. Du, Y. Yang, G. Guo, M. Xiao, M. Du, He received the bachelor’s degree in software engi-
X. Qu, and Alzheimer’s Disease Neuroimaging Initiative, ‘‘Convolutional
neering from Huaqiao University, Xiamen, China,
neural networks-based MRI image analysis for the Alzheimer’s disease
and he is pursuing the master’s degree at Xiamen
prediction from mild cognitive impairment,’’ Frontiers Neurosci., vol. 12,
p. 777, Nov. 2018. University, Xiamen, China, since 2018. His current
[20] N. Amoroso, D. Diacono, A. Fanizzi, M. La Rocca, A. Monaco, research interests include computer vision and pat-
A. Lombardi, C. Guaragnella, R. Bellotti, S. Tangaro, and Alzheimer’s tern recognition.
Disease Neuroimaging Initiative, ‘‘Deep learning reveals Alzheimer’s dis-
ease onset in MCI subjects: Results from an international challenge,’’
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[21] K. K. Leung, J. Barnes, M. Modat, G. R. Ridgway, J. W. Bartlett,
N. C. Fox, S. Ourselin, and Alzheimer’s Disease Neuroimaging Initiative,
‘‘Brain MAPS: An automated, accurate and robust brain extraction tech- CHENHUI YANG received the B.S. and M.S.
nique using a template library,’’ NeuroImage, vol. 55, no. 3, pp. 1091–1108, degrees in automatic control department from
2011. the National University of Defense Technol-
[22] M. S. Albert, S. T. DeKosky, D. Dickson, B. Dubois, H. H. Feldman, N. ogy, in 1989 and 1992, respectively, where he
C. Fox, A. Gamst, D. M. Holtzman, W. J. Jagust, R. C. Petersen, P. J. started to conduct research on driverless vehicle.
Snyder, M. C. Carrillo, B. Thies, and C. H. Phelps, ‘‘The diagnosis of
He received the Ph.D. degree in mechanical engi-
mild cognitive impairment due to Alzheimer’s disease: Recommendations
neering from Zhejiang University, in 1995. He had
from the National Institute on Aging-Alzheimer’s Association workgroups
on diagnostic guidelines for Alzheimer’s disease,’’ Alzheimer’s Dementia, been being a Faculty Member in computer science
vol. 7, no. 3, pp. 270–279, 2011. department in Xiamen University, and becoming a
[23] V. L. Villemagne, S. Burnham, P. Bourgeat, B. Brown, K. A. Ellis, Full Professor, in 2005. He was a Visiting Scholar
O. Salvado, C. Szoeke, S. L. Macaulay, R. Martins, P. Maruff, and in Argonne National Laboratory, from 1990 to 2000 and in USC, from
D. Ames, ‘‘Amyloid β deposition, neurodegeneration, and cognitive 2014 to 2015. His research interests include computer vision, graphics and
decline in sporadic Alzheimer’s disease: A prospective cohort study,’’ machine learning, with strong desires to design new products in intelligent
Lancet Neurol., vol. 12, pp. 357–367, Apr. 2013. transportation, medicine and industry.
NIANYIN ZENG received the B.Eng. degree in JIN GOU received the B.E. and M.E. degrees in
electrical engineering and automation, in 2008, computer science and technology from Fuzhou
and the Ph.D. degree in electrical engineer- University, China, in 1999 and 2002, respectively.
ing, in 2013, both from Fuzhou University. He received the Ph.D. degree in computer science
From October 2012 to March 2013, he was a and technology from Zhejiang University, China,
Research Associate in the Department of Elec- in 2006. Currently, he is a Professor with Huaqiao
trical and Electronic Engineering, the Univer- University, China. His research interests include
sity of Hong Kong. From September 2017 to knowledge fusion and artificial intelligence.
August 2018, he was an ISEF Fellow founded by
the Korea Foundation for Advance Studies and
also a Visiting Professor at the Korea Advanced Institute of Science and
Technology. Currently, he is an Associate Professor with the Department
of Instrumental and Electrical Engineering, Xiamen University. His current
research interests include intelligent data analysis, computational intelligent,
time-series modeling, and applications. He is the author or coauthor of
several technical papers including 6 ESI Highly Cited Papers according to the
most recent Clarivate Analytics ESI report and also a very active Reviewer
for many international journals and conferences. He is currently serving
as an Associate Editor for Neurocomputing, Editorial Board members for
Computers in Biology and Medicine, Biomedical Engineering Online, and
also a Guest Editor for Frontiers in Neuroscience. He also serves as a
technical program committee member for ICBEB 2014, an Invited Session
Chair of ICCSE 2017.