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Title: Zero-Shot Medical Image Artifact Reduction

Paper content:
Medical images may contain various types of artifacts with different patterns and mixtures, which depend on many factors such as scan setting, machine condition, patients’ characteristics, surrounding environment, etc.
However, existing deep learning based artifact reduction methods are restricted by their training set with specific predetermined artifact type and pattern.
As such, they have limited clinical adoption.
In this paper, we introduce a “Zero-Shot” medical image Artifact Reduction (ZSAR) framework, which leverages the power of deep learning but without using general pre-trained networks or any clean image reference.
Specifically, we utilize the low internal visual entropy of an image and train a light-weight image-specific artifact reduction network to reduce artifacts in an image at test-time.
We use Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) as vehicles to show that ZSAR can reduce artifacts better than state-of-the-art both qualitatively and quantitatively, while using shorter execution time.
To the best of our knowledge, this is the first deep learning framework that reduces artifacts in medical images without using a priori training set.
Deep learning has demonstrated its great power in artifact reduction, a fundamental task in medical image analysis to produce clean images for clinical diagnosis, decision making, and accurate quantitative image analysis.
Existing deep learning based frameworks Jiang et al., 2018; Yuan et al., 2019; Yi & Babyn, 2018) use training data sets that contain paired images (same images with and without artifacts) to learn the artifact features.
Simulations are often needed to generate the data set for these methods, which may be different from clinical situations and lead to biased learning Veraart et al., 2016) .
To address this issue, Kang et al. (2018) used cycle-consistent adversarial denoising network (CCADN) which no longer requires paired data.
However, all these methods still suffer from two mainstays: First, they require clean image references, which can be hard to obtain clinically.
For example, motion artifacts in Magnetic Resonance Imaging (MRI) are almost always present due to the lengthy acquisition process (Zaitsev et al., 2015) .
In such situations, simulation is still the only way to generate the data set.
Second, although the trained networks outperform non-learning based algorithms such as Block Matching 3D (BM3D) (Dabov et al., 2007) , they can only be applied to scenarios where the artifacts resemble what are in the training set, lacking the versatility that non-learning based methods can offer.
To attain the performance of deep learning based methods and the versatility of non-learning based ones, we introduce a "Zero-Shot" image-specific artifact reduction network (ZSAR), which builds upon deep learning yet does not require any clean image reference or a priori training data.
Based on the key observation that most medical images have areas that contain artifacts on a relatively uniform background and that the internal visual entropy of an image is much lower than that among images (Zontak & Irani, 2011) .
At test-time, ZSAR extracts an artifact pattern directly and synthesizes paired image patches from input image to iteratively train a light-weight image-specific autoencoder for artifact reduction.
Experimental results on clinical CT and MRI data with a variety of artifacts show that it outperforms the state-of-the-art methods both qualitatively and quantitatively, using shorter execution time.
To the best of our knowledge, ZSAR is the first deep learning based method that reduces artifacts in medical images without a priori training data.
We limit our discussion to CT and MRI as they are the vehicles to demonstrate the efficacy of our method.
For CT, artifacts can be classified into patient-based (e.g., motion artifact), physics-based (e.g., noise, metal artifact), and helical and multi-channel artifacts (e.g., cone beam effect) according to the underlying cause (Boas & Fleischmann, 2012) .
For MRI, the types include truncation artifacts, motion artifacts, aliasing artifacts, Gibbs ringing artifacts, and others (Krupa & Bekiesińska-Figatowska, 2015) .
These artifacts are influenced by a number of factors, including scan setting, machine condition, patient size and age, surrounding environment, etc.
These artifacts may occur at random places in an image.
In addition, an image can contain multiple artifacts and mixture simultaneously.
We also limit our discussion to medical image specific deep learning based methods only, although some general-purpose denoising methods such as Deep image prior (DIP) Ulyanov et al. (2018) and non deep-learning based methods such as BM3D can also be readily applied but inferior in this problem.
For noise and artifacts reduction, Chen et al. (2017) proposed a convolution neural network (CNN) to denoise low-dose CT images and reconstruct the corresponding routine-dose CT images.
Kang et al. (2017) proposed a directional wavelet transform on the CNN to suppress CT-specific noise.
Wolterink et al. (2017) designed a generative adversarial network (GAN) with CNN.
adopted Wasserstein distance and perceptual loss to ensure the similarity between input and the generated image.
Manjón & Coupe (2018) proposed a simple CNN network for 2D MRI artifact reduction and Jiang et al. (2018) explored multi-channel CNN for 3D MRI.
The use of deep learning to reduce other artifacts has also been explored (Gjesteby et al., 2017; .
For these methods, simulations are often used to generate the paired data, which may lead to biased learning when simulated artifacts differ from the real ones (Kang et al., 2018) .
To address this issue, Kang et al. (2018) ; You et al. (2018) used cycle-consistent adversarial denoising network that learns the mapping between the low and routine dose cardiac phase without matched image pairs.
Yet this method still requires clean image reference, which may be hard to obtain in some situations. .
Note that we treat the original input image as the output of "0 th " iteration.
The main motivation of our work lies behind the fact that it is almost always possible to identify small regions of interests where significant artifacts exist over a relatively uniform background in any medical images.
As such, it is possible to synthesize the paired dirty-clean patches from the exact image with artifacts to be reduced.
The overall framework of the proposed ZSAR is shown in Fig. 1 , which is an iterative process.
The framework works with 2D images, so 3D volumes are sliced first, similar to many existing works .
For clarity, we call the phase where the model is trained to obtain the weights as "training", and the phase that applies the trained model to the input image to reduce artifacts as "test".
Note that both phases are done on the spot for each specific input image and no pre-training is conducted.
For every iteration, ZSAR first extracts artifact patterns and synthesizes the paired dirty and clean images using the patterns (the details will be explained in Section 3.2).
Note that the artifact pattern extraction in the 1 st iteration is different from those in the subsequent (i + 1) th iterations (i ≥ 1).
Later, the synthesized image is then used to train a light-weight artifact reduction network (ARN), which is used to reduce the artifact in input image (the details will be explained in Section 3.3).
We terminate the iterative process when the artifact level doesn't decrease.
Our experiments show that the number of iteration needed is usally not more than four (the details will be explained in Section 4.3).
For a 3D volume, we only perform the above training process for one 2D slice of it.
Since the artifacts are usually similar across all slices in the same 3D volume, the remaining slices can directly use the trained ARNs to iteratively reduce the artifact (by following the test path only in Fig. 1 ).
For the 1 st iteration, since no clean reference image is provided, we extract the artifact pattern from the input image itself through an unsupervised approach.
This is made possible based on the fact that for most artifacts in medical images, we can always identify areas where only artifacts exist (Boas & Fleischmann, 2012; Krupa & Bekiesińska-Figatowska, 2015) .
As such, we need to identify areas where the background is relatively uniform yet significant artifacts are present.
Towards this, we first crop the input image into patches with size 32×32.
After that, an unsupervised clustering method, K-means (Fahim et al., 2006 ) is applied.
The main idea is to classify the patches into two clusters, one containing patches without structure boundaries (i.e., relatively uniform background), and the other containing patches with structure boundaries.
Such a classification is possible as the patches in these two clusters will exhibit significant differences in terms of standard distributions of the pixel values: when structure boundaries are present, significant mean shift and large yet localized variations in pixel values can be observed.
The feature of each patch is thus extracted as follows: the overall standard deviation of all the pixel values in the patch, and the mean value of all standard deviations extracted by a 8×8 sliding window.
Fig. 2 shows an example of the clustering process.
It can be clearly seen that one of the clusters contains patches with only uniform backgrounds (either with or without artifacts), while the other one contains all the patches with structure boundaries.
As the patches in the former cluster always contain relatively uniform background, a zero-mean artifact pattern can be extracted by subtracting the mean pixel value of each patch.
Note that in the patches without artifacts, the pattern extracted will just be empty.
On the other hand, as long as some of the patches contain artifacts, our framework can utilize them to further synthesize the training data, which will be discussed later.
In the subsequent (i + 1) th iteration (i ≥ 1), we observed that the difference between the clean image and the output image of (i) th iteration can be seen as the reduced artifact.
The zero-mean artifact pattern is again generated by subtracting the mean pixel value of the difference.
To reflect artifacts of different intensities, we randomly scale each pattern following standard normal distribution.
Those scaled artifact patterns are then superposed to random areas in the input image to form dirty images, and we use the input image as the corresponding clean image so that paired dirty-clean data set is formed.
Note that this synthesis process is conducted in every iteration.
Convolution + ReLU Deconvolution + ReLU After the paired data is synthesized, it can be used to train any existing neural networks for artifact reduction.
Considering the need of test-time training, we design a compacted network as shown in Fig. 3 , which is formed by a 11-layer contextual autoencoder to reduce artifacts and restore the structural information.
With the skip connection, these decoder layers can capture more contextual information extracted from different encoder layers.
With such a light-weight network structure, it requires only a few epochs to converge.
The pixel-wise mean square error (MSE) is used as the loss function to preserve structural and substance information:
where O and G are the output of the contextual autoencoder and the clean image reference, respectively.
Through experiments, we find that ARN should be initialized and retrained in every iteration, which is more effective than incremental training based on the network from previous iterations.
This is because each iteration is essentially a new artifact reduction procedure and the model only needs to learn the artifact level in the input of the current iteration.
Also, in each iteration, only a single pair of images are used for training due to speed consideration.
Since essentially, the same image is used during training and test, there is no overfitting concern.
Our CT data set is a collection of 48 3D cardiac CT volumes from 24 patients, which consists of 11,616 gray-scale 2D images (512x512) acquired through a wide detector 256-slice multiple detector computed tomography scanner.
The dosages are set between 80 kVp/55 mAs (low-dose) and 100 kVp/651 mAs (routine-dose).
Our MRI data set contains 286 pulse sequences as 17,844 2D MRI images from 11 patients, scanned by a 3T system.
Along with long-axis planes, a stack of short-axis single-shot balanced standard steady-state in free-precession sequence images from apex to basal were collected.
All CT and MRI images are qualitatively evaluated by our radiologists on structural preservation and artifact level.
For quantitative evaluation, due to the lack of ground truth, for CT, we follow existing work (Wolterink et al., 2017; and select the most homogeneous area in regions of interest selected by our radiologists.
The standard deviation (artifact level) of the pixels in the area should be as low as possible, and the mean (substance information) discrepancy after artifact reduction should not be too large to cause information loss.
ZSAR was implemented in Python3 with TensorFlow library.
NVIDIA GeForce GTX 1080 Ti GPU was used to train and test the networks.
For every convolution and deconvolution layer, Xavier initialization (Glorot & Bengio, 2010) was used for the kernels and the filter size is set to 3 and 4, respectively.
Adam optimization (Kingma & Ba, 2014) method was applied to train ARN by setting learning rate as 0.0005.
Training phase was performed by minimizing loss function with the number of epoch set to 1,000.
We compare ZSAR with CCADN, a state-of-the-art deep learning based method for medical image artifact reduction (Kang et al., 2018) , which unlike other deep learning based method does not require paired training data.
We train it with exactly the same settings as used in (Kang et al., 2018) for the data set generated through training data synthesis algorithm (excluding 10% of the images used for test).
We would like to emphasize again that although ZSAR is also based on deep learning, it does not require any prior training data.
We also compare ZSAR with Deep image prior (DIP) (Ulyanov et al., 2018) , a state-of-the-art general-purpose denoising method, and a nonlearning based algorithm BM3D.
For DIP, we follow the setting recommended in the paper.
For each image, we tuned the parameters in BM3D to attain the best quality.
Due to the space limit, in the paper we only present comparisons between the four methods using a limited number of test images.
Additional results can be found in the appendix.
Similar conclusions are drawn there.
We use the input image as shown in Fig. 4 (a) to study the efficiency of the iterative process in ZSAR.
In the image, our radiologists selected the most homogeneous areas inside the regions marked with red and blue rectangles for quantitative evaluation.
The resulting mean (substance information) and standard deviation (artifact level) are shown in Fig. 4 (b) and (c), respectively.
Note that the"0 th " iteration contains the data for the input image in Fig. 4 (a) .
From Fig. 4 (b) we can see that as the number of iterations increase, small fluctuations in mean can be observed for both regions.
On the other hand, in Fig. 4 (c) , the standard deviation of both regions stops to decrease around the 4 th iteration.
This experiment demonstrates the efficiency of the iterative process.
We start our experiments with the ideal scenario where the artifacts in both training set of CCADN and test CT images contain Poisson noise only.
The qualitative results for CCADN, BM3D, DIP, and ZSAR are shown in Fig. 5 (a) .
In the figure, we found CCADN, BM3D, and ZSAR can all preserve structure well, while DIP is oversmoothed visually.
Our radiologists then selected the largest homogeneous areas inside the regions marked with red and blue rectangles for quantitative comparison, and the results are summarized in Table 1.
scenario.
Although DIP seems to reduce artifact the most effectively, it yields over 200% mean discrepancy, which is a critical problem for CT images.
We further applied the four methods to MRI motion artifact reduction in the ideal scenario that both training set of CCADN and the test images contain motion artifact pattern only.
The qualitative results are shown in Fig. 6 (a) .
All the methods preserve structures well, and ZSAR leads to the best motion artifact reduction.
The corresponding statistics for the largest homogeneous areas inside the marked regions are reported in Table 3 (a).
From the table, though CCADN has the largest SNR, it suffers from large mean discrepancy, which again can be problematic.
ZSAR achieves up to 50% higher SNR than BM3D.
When comparing with DIP, ZSAR achieves similar SNR but less mean discrepancy.
Next, we studied the non-ideal scenario where different artifact patterns or noise level of artifacts absent from the training set of CCADN appeared in the test image.
For CT denoising, the qualitative results are shown in Fig. 5 (b-c) and the corresponding mean and standard deviation numbers are presented in Table 1 (b-c).
The results for MRI with different artifact patterns are shown in Fig.  6 (b-c) and Table 3 (b-c), respectively.
Qualitatively, we can see that ZSAR outperforms CCADN and BM3D, while all the three methods preserve the structures well.
On the other hand, DIP has oversmoothing issue in all the non-ideal cases of CT images, which causes the disappearance of tissue (region highlighted using yellow circle in case (b)).
Quantitatively, for CT images, ZSAR beats CCADN and BM3D in all the four cases, achieving up to 19% and 25% lower standard deviation, respectively.
For MRI, ZSAR attains up to 77% and 74% higher SNR compared with CCADN and BM3D, respectively.
In addition, since CCADN was trained in different scenario, in the region marked with red in case (c), it obtains SNR even smaller than the input image.
This clearly demonstrates the advantage of ZSAR, which does not rely on and thus is not limited to artifacts in a training set.
Compared with DIP, ZSAR achieves lower SNR on region marked with red in case (b) and region marked with blue in case (c).
However, this is in fact due to the large mean discrepancy in those two cases from DIP, which is not acceptable.
Finally, to show that test-time training is feasible, we compare the average execution time of ZSAR (which include both training and test) with CCADN (which only include test), BM3D, and DIP on the 3D CT and MRI images above.
The results are shown in Table 2 .
From the table, ZSAR requires less time than the other three methods despite the fact that it is trained on the spot for each input image.
The fast speed of ZSAR is brought by two factors: 1) Its training usually converges within four iterations, and with few training data.
Each iteration only takes about 1,000 epochs to converge.
2) It is much simpler than CCADN or DIP in structure and thus takes less time to test each 2D slice of the 3D images.
Table 2 : Execution time comparison between ZSAR and the three methods, CCADN, BM3D, and DIP for 3D cardiac CT (512×512) and MRI images (320×320) (in sec.).
In this paper, we introduced ZSAR, a "Zero-Shot" medical image artifact reduction framework, which exploits the power of deep learning to suppress artifacts in a medical image without using general pre-trained networks.
Unlike previous state-of-the-art methods which are restricted by the training data, our method can be adapted for almost any medical images that contain varying or unknown artifacts.
Experimental results on cardiac CT and MRI images have shown that our framework can reduce noises and motion artifacts qualitatively and quantitatively better than the state-of-the-art, using shorter execution time.
In this section, we expand our results in Section 4 of the paper, and show more comparison between ZSAR and the state-of-the-art deep learning based methods for medical image artifact reduction, CCADN, a general-purpose deep learning based denoising framework, DIP, and the non-learning based method, BM3D.
For CT denoising, the qualitative and quantitative results are shown in Fig. 7 and Table 4 , respectively.
Qualitatively, we can see that ZSAR outperforms CCADN and BM3D, while all the three methods preserve the structures well.
On the other hand, DIP has oversmoothing issue in all those cases of CT images.
Quantitatively, for CT images, ZSAR beats CCADN and BM3D in all the four cases, achieving up to 14% and 22% lower standard deviation, respectively.
For MRI, the results are shown in Fig. 8 and Table 5 , respectively.
From the table, ZSAR attains up to 25% and 52% higher SNR compared with CCADN and BM3D, respectively.
Compared with DIP, ZSAR achieves higher SNR in most cases, except the region marked with red in case (a).
However, in this case, DIP obtains a larger mean discrepancy than ZSAR, which is not acceptable.
Table 5 .

assistant: text: We introduce a “Zero-Shot” medical image Artifact Reduction framework, which leverages the power of deep learning but without using general pre-trained networks or any clean image reference.