Deeplearning_conf.paper-youhaverequested.pdf

International Conferences Computer Graphics, Visualization, Computer Vision and Image Processing 2017 and Big Data Analytics, Data Mining and Computational Intelligence 2017

DEEP LEARNING IN MEDICAL IMAGE ANALYSIS: RECENT ADVANCES AND FUTURE TRENDS 1

Evgin Goceri1 and Numan Goceri2 Akdeniz University, Engineering Faculty, Computer Engineering Department Dumlupinar Boulevard, Antalya, 07058, Turkey 2 Evosoft GmbH, Business Function Information Technology Solutions Marienbergstr. 78-80, Nuremberg, 90411, Germany

ABSTRACT Deep Learning (DL) methods are a set of algorithms in Machine Learning (ML), which provides an effective way to analysis medical images automatically for diagnosis/assessment of a disease. DL enables higher level of abstraction and provides better prediction from datasets. Therefore, DL has a great impact and become popular in recent years. In this work, we present advances and future researches on DL based medical image analysis. KEYWORDS Deep Learning, Medical Images, Image Analysis, Automated Segmentation, Machine Learning

1. INTRODUCTION ML based approaches are very popular and forms the basis of several medical image analysis systems commercially available. Computerized methods decide the optimal decision boundaries in a high-dimensional feature space. The crucial step to develop such a computerized system is feature extraction, which is still done by manually, from images. The next step is ML, which lets computers learning the extracted features representing the data. This procedure is used in many DL algorithms, which models (i.e., networks) many layers to transform inputs to output data by learning higher level features. The term deep refers to the layered non-linearities in a learning system, which enables the model to represent a function by less parameters and increases efficiency in the learning (Bengio, 2009). In this survey, a comprehensive review has been performed on methods applied for medical image analysis with DL. It has been observed that most of the recent works in the literature for medical image analysis are based on DL, particularly in 2016 (Figure 1).

2. DL TECHNIQUES The DL techniques applied with different medical images have been reviewed in this section. Activation of a neuron in a DL based architecture (mostly based on neural networks) is provided by inputs (x) and learned parameters (w,b) and an element-wise non-linearity

a

wT x b

Neural networks are constructed by layers (L) of neurons,

(1) wTL

wTL 1....

bL . A network with many

layers is known Types of neural networks can be grouped as 1) AEs, 2) RBMs, 3) CNNs, 4) RNNs. AEs are trained to reconstruct an input x upon an output layer x0 with a hidden layer (h). Two weight matrices (Wx,h and W ) and biases (bx,h and b ) are used in AEs. This type of networks simply learns the identity function, when the hidden layer and the input has the same size.

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However, there is an important feature, which is to apply a non-linear activation function ro calculate h wx ,h x bx ,h .

(a)

(b)

Figure 1. (a) The number of papers with DL in medical image analysis (CNN: Convolutional Neural Network, RBM: Restricted Boltzmann Machine, RNN: Recurrent Neural Network, AE: Auto Encoder); (b) Numbers of papers and imaging modalities used with deep learning based methods

Constraints on regularizations can be employed to obtain better structures. RBMs construct an input layer x ( x1 , x2 ,.... xN ) and a hidden layer h (h1 , h2 ,...., hN ) , which representsries latent features (Hinton, 2010). The latent feature representation h can be obtained with a given input vector x. Also, an input vector can be obtained with a given latent feature. Therefore, the connection of nodes is bidirectional in this type of neural networks. In an RBMs, an energy function of input and hidden units can be defined as,

E (x, h) hTWx cT x bT h

(2)

(where c and b are bias terms) for a particular state (x,h). Each layer in RBMs is trained as unsupervised. In CNNs, weight values can be shared so that they result in a convolution operation. The input image is convolved at every layer by using K kernels and biases are incorporated to generate a new feature map Xk. The set of features are used in a non-linear transformation with (.) function and the operation is applied at each other layer. Therefore, the number of weights does not depend on the input image the amount of the parameters that need to be learned is reduced. In CNNs, convolutional layers are changed with pooling layers, where pixel values are added with the mean or maximum operations. RNNs usually construct a hidden (or latent) state h at time t as,

P Y

y | x1 , x2 ,.....xT ;

softmax(hT ;Wout , bout )

(3)

3. DL IN MEDICAL IMAGE ANALYSIS In image classification, multiple images or only one image is used as input and a single diagnostic variable (for instance, to show that a disease is present or not) is produced as output. Lesion, tumor or object classification refers to the classification of a tiny region in the image into two or more classes. However, both global and local information is required for an accurate classification of these structures and it is not possible in a generic DL architecture. To solve this main drawback, multi-stream architectures have been proposed (Shen et al. 2015, Kawahara and Hamarneh 2016). For instance, Shen et al. applied 3 CNNs. At a different

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International Conferences Computer Graphics, Visualization, Computer Vision and Image Processing 2017 and Big Data Analytics, Data Mining and Computational Intelligence 2017

scale, every CNN gets a nodule as an input (Shen et al. 2015). Then, a final vector is constructed with the result features obtained as outputs of these CNNs. An other multi-stream architecture was implemented in (Kawahara and Hamarneh 2016) to classify skin lessions by using each stream with different resolution of the image. In addition to local and global information, three dimensional (3D) infromation was used to increase accuracy of multi-stream CNNs in classification of an object/lesion (Setio et al. 2016, Nie et al. 2016b). RBMs (Zhang et al. 2016b, van Tulder and de Bruijne 2016), Convolutional Sparse AEs (CSAEs) (Kallenberg et al. 2016) and SAEs (Cheng et al. 2016) have also been applied to classify lesions/objects in medical images. Among the works with DL in the literature, segmentation from medical images is the most common. Especially, RNNs have bacome important in this area. For instance, Xie et al. proposed to use a clockwork RNN with prior information, which was obtained by column and row predecessors of the current patch, for segmentation of pathological images (Xie et al. 2016). Andermatt et al. implemented an RNN (as 3D) with gated recurrent units for tissue segmentation from MR image slices (Andermatt et al. 2016). In addition to RNNs, U-net (Ronneberger et al. 2015), which takes into account the full context of an image and processesses the network in one forward pass, has been proposed. For instance, in (Cicek et al. 2016), the authors showed that an image segmentation task can be performed as fully 3D by feeding the network with only some 2D slices taken from the same dataset. In another paper (Drozdzal et al. 2016), both short and long skip connections have been used with a U-net. In (Milletari et al. 2016), the U-net architecture was applied with convolutional layers (3D) and the cost function that is based on Dice distance coefficients. Poudel et al. proposed to combine a gated recurrent unit with U-net architecture to achieve 3D segmentation (Poudel et al. 2016). Besides, fCNNs have been proposed for segmentation of vertebral body from MR image data sets (Korez et al. 2016), tissues from brain MR images, coronary arteries in cardiac CT angiography images and muscles in breast MR images (Moeskops et al. 2016b). To solve spurious response problem caused by voxel based classification, fCNN architectures have been combined with Conditional Random Fields (CRFs) (Christ et al. 2016, Gao et al. 2016, Fu et al. 2016, Dou et al. 2016b, Cai et al. 2016) and MRFs (Shakeri et al. 2016, Song et al. 2015). Also, patchtrained neural networks with a sliding window-based classification was applied in (Ciresan et al. 2012). DL based methods proposed for object/lesion detection and organ segmentation have been combined for lesion segmentation. Both local and global information are required to achieve an accurate lesion segmentation. Therefore, a U-net based approach with a single skip connection was used for segmentation of white matter lesions in (Brosch et al. 2016). Also, non-uniformly sampled patches and multi-stream neural networks using different scales was proposed (Kamnitsas et al. 2017, Ghafoorian et al. 2016). In some works (Litjens et al. 2016, Pereira et al. 2016), authors focused on data imbalance (since, usually pixels are from the non-diseased class) in lesion segmentation and proposed to use augmented data to solve the balance problem.

4. APPLICATION AREAS DL in medical image analysis have been applied with different images for different purposes. For instance, analysis of brain images with DL techniques have been performed for disorder classification (Suk et al. 2016, Suk and Shen 2016, Hosseini-Asl et al. 2016, Pinaya et al. 2016, Ortiz et al. 2016, Shi et al. 2017), lesion/tumor segmentation (Andermatt et al. 2016, Brosch et al. 2016, Chen et al. 2016a, Ghafoorian et al. 2016, Havaei et al. 2016, Kamnitsas et al. 2017, Moeskops et al. 2016a, Nie et al. 2016a, Pereira et al. 2016), lesion/tumor detection (Dou et al. 2016b, Ghafoorian et al. 2017) and also for enhancement or construction of brain images (Bahrami et al. 2016, Benou et al. 2016, Golkov et al. 2016, Hoffmann et al. 2016, Sevetlidis et al.2016). Breast image analysis with DL is mostly performed for detection of lesions or mass-like structures and grading of breast cancer risk (Dalmis et al. 2016, Arevalo et al. 2016, Dubrovina et al. 2016, Fotin et al. 2016, Dhungel et al. 2016, Kallenberg et al. 2016, Samala et al. 2016, Zhang et al. 2016b, Wang et al. 2017, Kooi et al. 2017). DL techniques have been applied to for segmentation of ventricles or cardiac structures from MR (Avendi et al. 2016, Poudel et al. 2016, Tran 2016, Zhang et al. 2016a, Ngo et al. 2017), CT (Zreik et al. 2016, Moradi et al. 2016b, Lessmann et al. 2016), or US (Chen et al. 2016b, Ghesu et al. 2016, Moradi et al. 2016a) cardiac images. Most of them use CNN architectures.

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Segmentation of liver (Ben-Cohen et al. 2016, Dou et al. 2016a, Hu et al. 2016b, Lu et al. 2017), kidney (Thong et al. 2016), pancreas (Roth et al. 2016, Cai et al. 2016) and bladder (Cha et al. 2016) with DL based methods has been usually applied with CT images and CNNs. In the literature, there is only one work that proposes segmentation of multiple organs, which are spleen, kidney and liver, by using DL (Hu et al. 2016a).

5. CONCLUSIONS It has been observed that DL based techniques are used effectively in medical image analysis especially in recent years. CNNs are successful models for image analysis. Therefore, mostly, CNN architectures have been prefered and integrated into other techniques such as, SVM and level sets. We expect that DL will become more popular for analysis of medical images and have great impact in this research area.

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