Medical Image Analysis using Convolutional Neural Networks: A Review
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paper_title: Imagenet classification with deep convolutional neural networks

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We trained a large, deep convolutional neural network to classify the 1.2 million high-resolution images in the ImageNet LSVRC-2010 contest into the 1000 different classes. On the test data, we achieved top-1 and top-5 error rates of 37.5% and 17.0% which is considerably better than the previous state-of-the-art. The neural network, which has 60 million parameters and 650,000 neurons, consists of five convolutional layers, some of which are followed by max-pooling layers, and three fully-connected layers with a final 1000-way softmax. To make training faster, we used non-saturating neurons and a very efficient GPU implementation of the convolution operation. To reduce overriding in the fully-connected layers we employed a recently-developed regularization method called "dropout" that proved to be very effective. We also entered a variant of this model in the ILSVRC-2012 competition and achieved a winning top-5 test error rate of 15.3%, compared to 26.2% achieved by the second-best entry.
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paper_title: Guest Editorial Deep Learning in Medical Imaging: Overview and Future Promise of an Exciting New Technique

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The papers in this special section focus on the technology and applications supported by deep learning. Deep learning is a growing trend in general data analysis and has been termed one of the 10 breakthrough technologies of 2013. Deep learning is an improvement of artificial neural networks, consisting of more layers that permit higher levels of abstraction and improved predictions from data. To date, it is emerging as the leading machine-learning tool in the general imaging and computer vision domains. In particular, convolutional neural networks (CNNs) have proven to be powerful tools for a broad range of computer vision tasks. Deep CNNs automatically learn mid-level and high-level abstractions obtained from raw data (e.g., images). Recent results indicate that the generic descriptors extracted from CNNs are extremely effective in object recognition and localization in natural images. Medical image analysis groups across the world are quickly entering the field and applying CNNs and other deep learning methodologies to a wide variety of applications.
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paper_title: Multimodal Segmentation of Optic Disc and Cup From SD-OCT and Color Fundus Photographs Using a Machine-Learning Graph-Based Approach

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In this work, a multimodal approach is proposed to use the complementary information from fundus photographs and spectral domain optical coherence tomography (SD-OCT) volumes in order to segment the optic disc and cup boundaries. The problem is formulated as an optimization problem where the optimal solution is obtained using a machine-learning theoretical graph-based method. In particular, first the fundus photograph is registered to the 2D projection of the SD-OCT volume. Three in-region cost functions are designed using a random forest classifier corresponding to three regions of cup, rim, and background. Next, the volumes are resampled to create radial scans in which the Bruch's Membrane Opening (BMO) endpoints are easier to detect. Similar to in-region cost function design, the disc-boundary cost function is designed using a random forest classifier for which the features are created by applying the Haar Stationary Wavelet Transform (SWT) to the radial projection image. A multisurface graph-based approach utilizes the in-region and disc-boundary cost images to segment the boundaries of optic disc and cup under feasibility constraints. The approach is evaluated on 25 multimodal image pairs from 25 subjects in a leave-one-out fashion (by subject). The performances of the graph-theoretic approach using three sets of cost functions are compared: 1) using unimodal (OCT only) in-region costs, 2) using multimodal in-region costs, and 3) using multimodal in-region and disc-boundary costs. Results show that the multimodal approaches outperform the unimodal approach in segmenting the optic disc and cup.
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paper_title: Incremental Learning With Selective Memory (ILSM): Towards Fast Prostate Localization for Image Guided Radiotherapy

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Image-guided radiotherapy (IGRT) requires fast and accurate localization of the prostate in 3-D treatment-guided radiotherapy, which is challenging due to low tissue contrast and large anatomical variation across patients. On the other hand, the IGRT workflow involves collecting a series of computed tomography (CT) images from the same patient under treatment. These images contain valuable patient-specific information yet are often neglected by previous works. In this paper, we propose a novel learning framework, namely incremental learning with selective memory (ILSM), to effectively learn the patient-specific appearance characteristics from these patient-specific images. Specifically, starting with a population-based discriminative appearance model, ILSM aims to "personalize" the model to fit patient-specific appearance characteristics. The model is personalized with two steps: backward pruning that discards obsolete population-based knowledge and forward learning that incorporates patient-specific characteristics. By effectively combining the patient-specific characteristics with the general population statistics, the incrementally learned appearance model can localize the prostate of a specific patient much more accurately. This work has three contributions: 1) the proposed incremental learning framework can capture patient-specific characteristics more effectively, compared to traditional learning schemes, such as pure patient-specific learning, population-based learning, and mixture learning with patient-specific and population data; 2) this learning framework does not have any parametric model assumption, hence, allowing the adoption of any discriminative classifier; and 3) using ILSM, we can localize the prostate in treatment CTs accurately (DSC ∼ 0.89 ) and fast ( ∼ 4 s), which satisfies the real-world clinical requirements of IGRT.
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paper_title: Autoencoding the retrieval relevance of medical images

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Content-based image retrieval (CBIR) of medical images is a crucial task that can contribute to a more reliable diagnosis if applied to big data. Recent advances in feature extraction and classification have enormously improved CBIR results for digital images. However, considering the increasing accessibility of big data in medical imaging, we are still in need of reducing both memory requirements and computational expenses of image retrieval systems. This work proposes to exclude the features of image blocks that exhibit a low encoding error when learned by a $n/p/n$ autoencoder ($p\!<\!n$). We examine the histogram of autoendcoding errors of image blocks for each image class to facilitate the decision which image regions, or roughly what percentage of an image perhaps, shall be declared relevant for the retrieval task. This leads to reduction of feature dimensionality and speeds up the retrieval process. To validate the proposed scheme, we employ local binary patterns (LBP) and support vector machines (SVM) which are both well-established approaches in CBIR research community. As well, we use IRMA dataset with 14,410 x-ray images as test data. The results show that the dimensionality of annotated feature vectors can be reduced by up to 50% resulting in speedups greater than 27% at expense of less than 1% decrease in the accuracy of retrieval when validating the precision and recall of the top 20 hits.
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paper_title: Robust Learning-Based Parsing and Annotation of Medical Radiographs

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In this paper, we propose a learning-based algorithm for automatic medical image annotation based on robust aggregation of learned local appearance cues, achieving high accuracy and robustness against severe diseases, imaging artifacts, occlusion, or missing data. The algorithm starts with a number of landmark detectors to collect local appearance cues throughout the image, which are subsequently verified by a group of learned sparse spatial configuration models. In most cases, a decision could already be made at this stage by simply aggregating the verified detections. For the remaining cases, an additional global appearance filtering step is employed to provide complementary information to make the final decision. This approach is evaluated on a large-scale chest radiograph view identification task, demonstrating a very high accuracy ( >; 99.9%) for a posteroanterior/anteroposterior (PA-AP) and lateral view position identification task, compared with the recently reported large-scale result of only 98.2% (Luo, , 2006). Our approach also achieved the best accuracies for a three-class and a multiclass radiograph annotation task, when compared with other state of the art algorithms. Our algorithm was used to enhance advanced image visualization workflows by enabling content-sensitive hanging-protocols and auto-invocation of a computer aided detection algorithm for identified PA-AP chest images. Finally, we show that the same methodology could be utilized for several image parsing applications including anatomy/organ region of interest prediction and optimized image visualization.
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paper_title: Medical image retrieval with probabilistic multi-class support vector machine classifiers and adaptive similarity fusion

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Abstract We present a content-based image retrieval framework for diverse collections of medical images of different modalities, anatomical regions, acquisition views, and biological systems. For the image representation, the probabilistic output from multi-class support vector machines (SVMs) with low-level features as inputs are represented as a vector of confidence or membership scores of pre-defined image categories. The outputs are combined for feature-level fusion and retrieval based on the combination rules that are derived by following Bayes’ theorem. We also propose an adaptive similarity fusion approach based on a linear combination of individual feature level similarities. The feature weights are calculated by considering both the precision and the rank order information of top retrieved relevant images as predicted by SVMs. The weights are dynamically updated by the system for each individual search to produce effective results. The experiments and analysis of the results are based on a diverse medical image collection of 11,000 images of 116 categories. The performances of the classification and retrieval algorithms are evaluated both in terms of error rate and precision–recall. Our results demonstrate the effectiveness of the proposed framework as compared to the commonly used approaches based on low-level feature descriptors.
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paper_title: Machine Learning Methods for Binary and Multiclass Classification of Melanoma Thickness From Dermoscopic Images

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Thickness of the melanoma is the most important factor associated with survival in patients with melanoma. It is most commonly reported as a measurement of depth given in millimeters (mm) and computed by means of pathological examination after a biopsy of the suspected lesion. In order to avoid the use of an invasive method in the estimation of the thickness of melanoma before surgery, we propose a computational image analysis system from dermoscopic images. The proposed feature extraction is based on the clinical findings that correlate certain characteristics present in dermoscopic images and tumor depth. Two supervised classification schemes are proposed: a binary classification in which melanomas are classified into thin or thick, and a three-class scheme (thin, intermediate, and thick). The performance of several nominal classification methods, including a recent interpretable method combining logistic regression with artificial neural networks (Logistic regression using Initial variables and Product Units, LIPU), is compared. For the three-class problem, a set of ordinal classification methods (considering ordering relation between the three classes) is included. For the binary case, LIPU outperforms all the other methods with an accuracy of 77.6%, while, for the second scheme, although LIPU reports the highest overall accuracy, the ordinal classification methods achieve a better balance between the performances of all classes.
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paper_title: Modern Approach of Diagnosis and Management of Acute Flank Pain: Review of All Imaging Modalities

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Abstract Acute flank pain is a common and complex clinical problem which might be caused by a variety of urinary and extraurinary abnormalities among which ureterolithiasis being the most frequent cause. Plain abdominal radiographs combined with intravenous urography (IVU) have been the standard imaging procedures of choice for the evaluation of acute flank pain over the last decades. Direct detection of even small ureteral calculi is achieved in 40–60%, whereas using indirect signs such as ureteral and renal pelvic dilatation stone detection is possible in up to 80–90% of all cases. However, IVU might be hampered by poor quality due to lack of bowel preparation, by nephrotoxicity of contrast agents, by serious allergic and anaphylactic reactions in 10% and 1% of the patients, respectively, and by significant radiation exposure. The use of ultrasonography (US) in the management of acute flank pain has been growing and when combining the findings of pyeloureteral dilatation, direct visualization of stones, and the absence of ureteral ejaculation, the sensitivity to detect ureteral dilatation can be as high as 96%. Recently, unenhanced helical CT (UHCT) has been introduced as imaging modality with a high sensitivity and specificity for the evaluation of acute flank pain. UHCT has been demonstrated to be superior since (1) it detects ureteral stones with a sensitivity and specificity from 98% to 100% regardless of size, location and chemical composition, (2) it identifies extraurinary causes of flank pain in about one third of all patients presenting with acute flank pain, (3) it does not need contrast agent, and (4) it is a time saving imaging technique being performed within 5min. Based on the data published, one can predict that UHCT will become the imaging procedure of choice for evaluation of acute flank pain within the next years. The purpose of this review is to critically evaluate the role all imaging modalities available for a modern approach of diagnosis and management of acute flank pain with regard to their sensitivity, specificity, positive and negative predictive values and their complications, toxicicty and morbidity.
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paper_title: Tsallis entropy based multilevel thresholding for colored satellite image segmentation using evolutionary algorithms

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Cuckoo search based multi-level thresholding is presented by maximizing the Tsallis entropy.Different optimization algorithms are exploited with Tsallis entropy method.Cuckoo based Tsallis entropy was found to be more accurate for colored satellite image segmentation.The feasibility of the proposed approach has been tested on 10 different colored satellite images. In this paper, a new technique for color image segmentation using CS algorithm supported by Tsallis entropy for multilevel thresholding has been proposed toward the effective colored segmentation of satellite images. The nonextensive entropy is a new expansion in statistical mechanics, and it is a recent formalism in which a real quantity q was introduced as parameter for physical systems that presents the long range interactions, long time memories and fractal-type structures. The feasibility of the proposed cuckoo search and Tsallis entropy based approach was tested on 10 different satellite images and benchmarked with differential evolution, wind driven optimization, particle swarm optimization and artificial bee colony algorithm for solving the multilevel colored image thresholding problems. Experiments have been conducted on a variety of satellite images. Several measurements are used to evaluate the performance of proposed method which clearly illustrates the effectiveness and robustness of the proposed algorithm. The experimental results qualitative and quantitative both demonstrate that the proposed method selects the threshold values effectively and properly.
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paper_title: Segmentation of Glioma Tumors in Brain Using Deep Convolutional Neural Network

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Detection of brain tumor using a segmentation based approach is critical in cases, where survival of a subject depends on an accurate and timely clinical diagnosis. Gliomas are the most commonly found tumors having irregular shape and ambiguous boundaries, making them one of the hardest tumors to detect. The automation of brain tumor segmentation remains a challenging problem mainly due to significant variations in its structure. An automated brain tumor segmentation algorithm using deep convolutional neural network (DCNN) is presented in this paper. A patch based approach along with an inception module is used for training the deep network by extracting two co-centric patches of different sizes from the input images. Recent developments in deep neural networks such as drop-out, batch normalization, non-linear activation and inception module are used to build a new ILinear nexus architecture. The module overcomes the over-fitting problem arising due to scarcity of data using drop-out regularizer. Images are normalized and bias field corrected in the pre-processing step and then extracted patches are passed through a DCNN, which assigns an output label to the central pixel of each patch. Morphological operators are used for post-processing to remove small false positives around the edges. A two-phase weighted training method is introduced and evaluated using BRATS 2013 and BRATS 2015 datasets, where it improves the performance parameters of state-of-the-art techniques under similar settings.
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paper_title: Improving Iris Recognition Performance Using Segmentation, Quality Enhancement, Match Score Fusion, and Indexing

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This paper proposes algorithms for iris segmentation, quality enhancement, match score fusion, and indexing to improve both the accuracy and the speed of iris recognition. A curve evolution approach is proposed to effectively segment a nonideal iris image using the modified Mumford-Shah functional. Different enhancement algorithms are concurrently applied on the segmented iris image to produce multiple enhanced versions of the iris image. A support-vector-machine-based learning algorithm selects locally enhanced regions from each globally enhanced image and combines these good-quality regions to create a single high-quality iris image. Two distinct features are extracted from the high-quality iris image. The global textural feature is extracted using the 1-D log polar Gabor transform, and the local topological feature is extracted using Euler numbers. An intelligent fusion algorithm combines the textural and topological matching scores to further improve the iris recognition performance and reduce the false rejection rate, whereas an indexing algorithm enables fast and accurate iris identification. The verification and identification performance of the proposed algorithms is validated and compared with other algorithms using the CASIA Version 3, ICE 2005, and UBIRIS iris databases.
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paper_title: Seeded region growing

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We present here a new algorithm for segmentation of intensity images which is robust, rapid, and free of tuning parameters. The method, however, requires the input of a number of seeds, either individual pixels or regions, which will control the formation of regions into which the image will be segmented. In this correspondence, we present the algorithm, discuss briefly its properties, and suggest two ways in which it can be employed, namely, by using manual seed selection or by automated procedures. >
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paper_title: Modified artificial bee colony based computationally efficient multilevel thresholding for satellite image segmentation using Kapur's, Otsu and Tsallis functions

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A modified ABC algorithm based fast satellite image segmentation has been presented.ABC, PSO and GA methods are compared with this proposed method.The experimental results demonstrate better performance of MABC based technique.The proposed MABC based approach is much faster (CPU time is less).The validity of the proposed technique is reported both qualitatively and quantitatively. In this paper, a modified artificial bee colony (MABC) algorithm based satellite image segmentation using different objective function has been presented to find the optimal multilevel thresholds. Three different methods are compared with this proposed method such as ABC, particle swarm optimization (PSO) and genetic algorithm (GA) using Kapur's, Otsu and Tsallis objective function for optimal multilevel thresholding. The experimental results demonstrate that the proposed MABC algorithm based segmentation can efficiently and accurately search multilevel thresholds, which are very close to optimal ones examined by the exhaustive search method. In MABC algorithm, an improved solution search equation is used which is based on the bee's search only around the best solution of previous iteration to improve exploitation. In addition, to improve global convergence when generating initial population, both chaotic system and opposition-based learning method are employed. Compared to other thresholding methods, segmentation results of the proposed MABC algorithm is most promising, and the computational time is also minimized.
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paper_title: A novel fast image segmentation algorithm for large topographic maps

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Image segmentation for topographic maps is challenging due to their low quality, high degrees of mixed and false coloring. Besides, many pixels cannot be explicitly separated from each other because of the fuzziness of their colors. Therefore the algorithms based on fuzzy theory are suitable to process such images utilizing their ability to deal with the blurring effect. However, there are still some problems of large-scale data, high time complexity and inaccurate classification. In order to overcome these problems, we propose a novel algorithm for segmenting large topographic maps based on the ideas of fuzzy theory, randomized sampling and multilevel image fusion. In this algorithm, the large topographic map is randomly sampled first. Then the optimal clustering centers are acquired by fuzzy C-means (FCM) clustering. Further, the map is segmented with the fuzzy classification method. Finally, multilevel image fusion is used to fuse the segmented images into the final segmentation maps. Randomized sampling is used to reduce the amount of data, and improve the efficiency of image segmentation. Multilevel fusion can make the final segmentation maps more accurate. The experiments show that our method has higher efficiency and accuracy than the traditional ones. It provides a reliable image segmentation method for large topographic maps.
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paper_title: An unsupervised learning method with a clustering approach for tumor identification and tissue segmentation in magnetic resonance brain images

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Novel SOM based FKM algorithm for tissue segmentation and tumor identification in magnetic resonance brain images (T1-w, T2-w, FLAIR and MPR sequences) is proposed through this work.Exact demarcation between tumor and edema region is characterized.Validation of the segmented results by an experienced radiologist.Cross comparison with FCM, SOM, FKM and other hybrid clustering algorithms using ten standard comparison parameters. Malignant and benign types of tumor infiltrated in human brain are diagnosed with the help of an MRI scanner. With the slice images obtained using an MRI scanner, certain image processing techniques are utilized to have a clear anatomy of brain tissues. One such image processing technique is hybrid self-organizing map (SOM) with fuzzy K means (FKM) algorithm, which offers successful identification of tumor and good segmentation of tissue regions present inside the tissues of brain. The proposed algorithm is efficient in terms of Jaccard Index, Dice Overlap Index (DOI), sensitivity, specificity, peak signal to noise ratio (PSNR), mean square error (MSE), computational time and memory requirement. The algorithm proposed through this paper has better data handling capacities and it also performs efficient processing upon the input magnetic resonance (MR) brain images. Automatic detection of tumor region in MR (magnetic resonance) brain images has a high impact in helping the radio surgeons assess the size of the tumor present inside the tissues of brain and it also supports in identifying the exact topographical location of tumor region. The proposed hybrid SOM-FKM algorithm assists the radio surgeon by providing an automated tissue segmentation and tumor identification, thus enhancing radio therapeutic procedures. The efficiency of the proposed technique is verified using the clinical images obtained from four patients, along with the images taken from Harvard Brain Repository.
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paper_title: Object recognition using segmentation for feature detection

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A new method is presented to learn object categories from unlabeled and unsegmented images for generic object recognition. We assume that each object can be characterized by a set of typical regions, and use a new segmentation method - "similarity-measure segmentation" - to split the images into regions of interest. This approach may also deliver segments, which are split into several disconnected parts, which turn out to be a powerful description of local similarities. Several textural features are calculated for each region, which are used to learn object categories with boosting. We demonstrate the flexibility and power of our method by excellent results on various datasets. In comparison, our recognition results are significantly higher than the results published in related work.
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paper_title: Fuzzy image segmentation based upon hierarchical clustering

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In this paper we introduce the concept of Fuzzy Image Segmentation, providing an algorithm to build fuzzy boundaries based on the existing relations between the fuzzy boundary set problem and the (crisp) hierarchical image segmentation problem. In particular, since a crisp image segmentation can be characterized in terms of the set of edges that separates the adjacent regions of the segmentation, from these edges we introduce the concept of fuzzy image segmentation. Hence, each fuzzy image segmentation is characterized by means of a fuzzy set over the set of edges, which can be then understood as the fuzzy boundary of the image. Some computational experiences are included in order to show the obtained fuzzy boundaries of some digital images.
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paper_title: A multilevel color image thresholding scheme based on minimum cross entropy and differential evolution

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Abstract We propose a novel multi-level thresholding method for unsupervised separation between objects and background from a natural color image using the concept of the minimum cross entropy (MCE). MCE based thresholding techniques are widely popular for segmenting grayscale images. Color image segmentation is still a challenging field as it involves 3-D histogram unlike the 1-D histogram of grayscale images. Effectiveness of entropy based multi-level thresholding for color image is yet to be explored and this paper presents a humble contribution in this context. We have used differential evolution (DE), a simple yet efficient evolutionary algorithm of current interest, to improve the computation time and robustness of the proposed algorithm. The performance of DE is also investigated extensively through comparison with other well-known nature inspired global optimization techniques like genetic algorithm (GA), particle swarm optimization (PSO), and artificial bee colony (ABC). The proposed method is evaluated by comparing it with seven other prominent algorithms both qualitatively and quantitatively using a well known benchmark suite – the Barkley Segmentation Dataset (BSDS300) with 300 distinct images. Such comparison reflects the efficiency of our algorithm
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paper_title: Medical image segmentation on GPUs - A comprehensive review

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Abstract Segmentation of anatomical structures, from modalities like computed tomography (CT), magnetic resonance imaging (MRI) and ultrasound, is a key enabling technology for medical applications such as diagnostics, planning and guidance. More efficient implementations are necessary, as most segmentation methods are computationally expensive, and the amount of medical imaging data is growing. The increased programmability of graphic processing units (GPUs) in recent years have enabled their use in several areas. GPUs can solve large data parallel problems at a higher speed than the traditional CPU, while being more affordable and energy efficient than distributed systems. Furthermore, using a GPU enables concurrent visualization and interactive segmentation, where the user can help the algorithm to achieve a satisfactory result. This review investigates the use of GPUs to accelerate medical image segmentation methods. A set of criteria for efficient use of GPUs are defined and each segmentation method is rated accordingly. In addition, references to relevant GPU implementations and insight into GPU optimization are provided and discussed. The review concludes that most segmentation methods may benefit from GPU processing due to the methods’ data parallel structure and high thread count. However, factors such as synchronization, branch divergence and memory usage can limit the speedup.
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paper_title: Image Segmentation Based on 3-D Maximum Between-Cluster Variance

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A method for image segmentation based on 3 D maximum between cluster variance (3 DMBV) is proposed.It constructs 3D observation space using not only gray distribution information of pixels,but also relevant information of neighboring pixels.Based on the competitioo,redundancy and complementation of all information,it can obtain better performance than 1 DMBV methods through efficient fusion.Theoretical analysis and experiments prove that it performs well even on ground target image with low SNR and low contrast.We also propose a recursive algorithm to implement the 3 DMBV method,which can reduce the computation time and necessary storage space.
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paper_title: Brain tumor segmentation using cascaded deep convolutional neural network

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Gliomas are the most common and threatening brain tumors with little to no survival rate. Accurate detection of such tumors is crucial for survival of the subject. Naturally, tumors have irregular shape and can be spatially located anywhere in the brain, which makes it a challenging task to segment them accurately enough for clinical purposes. In this paper, an automated segmentation algorithm for brain tumor using deep convolutional neural networks (DCNN) is proposed. Deep networks tend to have a lot of parameters thus over-fitting is almost always an issue especially when data are sparse. Max-out and drop-out layers are used to reduce the chances of over-fitting since data are scant. Patch based training method is used for the model where two types of patches sized 37×37 and 19×19 with same center pixel are selected. The proposed algorithm includes preprocessing in which images are normalized and bias field corrected, and post processing where small false positives are removed using morphological operators. BRATS 2013 dataset is used for evaluation of the proposed method, where it outperforms state-of-the-art methods with similar settings in key performance indicators.
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paper_title: Supervised Variational Model With Statistical Inference and Its Application in Medical Image Segmentation

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Automated and general medical image segmentation can be challenging because the foreground and the background may have complicated and overlapping density distributions in medical imaging. Conventional region-based level set algorithms often assume piecewise constant or piecewise smooth for segments, which are implausible for general medical image segmentation. Furthermore, low contrast and noise make identification of the boundaries between foreground and background difficult for edge-based level set algorithms. Thus, to address these problems, we suggest a supervised variational level set segmentation model to harness the statistical region energy functional with a weighted probability approximation. Our approach models the region density distributions by using the mixture-of-mixtures Gaussian model to better approximate real intensity distributions and distinguish statistical intensity differences between foreground and background. The region-based statistical model in our algorithm can intuitively provide better performance on noisy images. We constructed a weighted probability map on graphs to incorporate spatial indications from user input with a contextual constraint based on the minimization of contextual graphs energy functional. We measured the performance of our approach on ten noisy synthetic images and 58 medical datasets with heterogeneous intensities and ill-defined boundaries and compared our technique to the Chan-Vese region-based level set model, the geodesic active contour model with distance regularization, and the random walker model. Our method consistently achieved the highest Dice similarity coefficient when compared to the other methods.
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paper_title: Comparative Local Quality Assessment of 3D Medical Image Segmentations with Focus on Statistical Shape Model-Based Algorithms

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The quality of automatic 3D medical segmentation algorithms needs to be assessed on test datasets comprising several 3D images (i.e., instances of an organ). The experts need to compare the segmentation quality across the dataset in order to detect systematic segmentation problems. However, such comparative evaluation is not supported well by current methods. We present a novel system for assessing and comparing segmentation quality in a dataset with multiple 3D images. The data is analyzed and visualized in several views. We detect and show regions with systematic segmentation quality characteristics. For this purpose, we extended a hierarchical clustering algorithm with a connectivity criterion. We combine quality values across the dataset for determining regions with characteristic segmentation quality across instances. Using our system, the experts can also identify 3D segmentations with extraordinary quality characteristics. While we focus on algorithms based on statistical shape models, our approach can also be applied to cases, where landmark correspondences among instances can be established. We applied our approach to three real datasets: liver, cochlea and facial nerve. The segmentation experts were able to identify organ regions with systematic segmentation characteristics as well as to detect outlier instances.
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paper_title: A Computational Approach to Edge Detection

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This paper describes a computational approach to edge detection. The success of the approach depends on the definition of a comprehensive set of goals for the computation of edge points. These goals must be precise enough to delimit the desired behavior of the detector while making minimal assumptions about the form of the solution. We define detection and localization criteria for a class of edges, and present mathematical forms for these criteria as functionals on the operator impulse response. A third criterion is then added to ensure that the detector has only one response to a single edge. We use the criteria in numerical optimization to derive detectors for several common image features, including step edges. On specializing the analysis to step edges, we find that there is a natural uncertainty principle between detection and localization performance, which are the two main goals. With this principle we derive a single operator shape which is optimal at any scale. The optimal detector has a simple approximate implementation in which edges are marked at maxima in gradient magnitude of a Gaussian-smoothed image. We extend this simple detector using operators of several widths to cope with different signal-to-noise ratios in the image. We present a general method, called feature synthesis, for the fine-to-coarse integration of information from operators at different scales. Finally we show that step edge detector performance improves considerably as the operator point spread function is extended along the edge.
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paper_title: Comparative study of image segmentation techniques and object matching using segmentation

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Several general-purpose algorithms and techniques have been developed for image segmentation. Since there is no general solution to the image segmentation problem, these techniques often have to be combined with domain knowledge in order to effectively solve an image segmentation problem for a problem domain. This paper presents a comparative study of the basic image segmentation techniques i.e. Edge-Based, K-Means Clustering, Thresholding and Region-Based techniques, using a number of test images. The objects extracted after image enhancement and image segmentation as compared to the objects desired, whether the region boundaries are closed or disconnected and the Mean Weighted Distance measure of the segmented objects with respect to the original image form the criteria to perform the comparative study. Image segmentation is further used for object matching between two images. Correlation between the objects being matched in the two images is used as a measure of similarity between the two objects. The first principal component axis, determined by Principal Component Analysis (PCA), of the objects being matched are aligned with the x-axis to take into account the different orientation of an object in different images.
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paper_title: Multi-scale improves boundary detection in natural images

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In this work we empirically study the multi-scale boundary detection problem in natural images. We utilize local boundary cues including contrast, localization and relative contrast, and train a classifier to integrate them across scales. Our approach successfully combines strengths from both large-scale detection (robust but poor localization) and small-scale detection (detail-preserving but sensitive to clutter). We carry out quantitative evaluations on a variety of boundary and object datasets with human-marked groundtruth. We show that multi-scale boundary detection offers large improvements, ranging from 20% to 50%, over single-scale approaches. This is the first time that multi-scale is demonstrated to improve boundary detection on large datasets of natural images.
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paper_title: A hybrid edge-based segmentation approach for ultrasound medical images

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Abstract Ultrasound imaging is one of the most widely used and the cheapest diagnostic tools of medical imaging modalities. In this paper, a hybrid approach for accurate segmentation of the ultrasound medical images is presented that utilizes both the features of kernel fuzzy clustering with spatial constraints and edge based active contour method using distance regularized level set (DRLS) function. The result obtained from the kernel fuzzy clustering is utilized not only to initialize the curve that spreads to identify the estimated region or object boundaries, but also helps to estimate the optimal parameters, which are responsible for controlling the level set evolution. The DRLS formulation also increase the processing speed by removing the need of re-initialization of the level set function. The performance of the proposed method is evaluated by conducting the several experiments on both the synthetic and real ultrasound images. Experimental results show that the proposed method improves the segmentation accuracy and also produces better results by successfully segmenting the object boundaries compared to others.
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paper_title: Fast and robust fuzzy c-means clustering algorithms incorporating local information for image segmentation

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Fuzzy c-means (FCM) algorithms with spatial constraints (FCM_S) have been proven effective for image segmentation. However, they still have the following disadvantages: (1) although the introduction of local spatial information to the corresponding objective functions enhances their insensitiveness to noise to some extent, they still lack enough robustness to noise and outliers, especially in absence of prior knowledge of the noise; (2) in their objective functions, there exists a crucial parameter @a used to balance between robustness to noise and effectiveness of preserving the details of the image, it is selected generally through experience; and (3) the time of segmenting an image is dependent on the image size, and hence the larger the size of the image, the more the segmentation time. In this paper, by incorporating local spatial and gray information together, a novel fast and robust FCM framework for image segmentation, i.e., fast generalized fuzzy c-means (FGFCM) clustering algorithms, is proposed. FGFCM can mitigate the disadvantages of FCM_S and at the same time enhances the clustering performance. Furthermore, FGFCM not only includes many existing algorithms, such as fast FCM and enhanced FCM as its special cases, but also can derive other new algorithms such as FGFCM_S1 and FGFCM_S2 proposed in the rest of this paper. The major characteristics of FGFCM are: (1) to use a new factor S"i"j as a local (both spatial and gray) similarity measure aiming to guarantee both noise-immunity and detail-preserving for image, and meanwhile remove the empirically-adjusted parameter @a; (2) fast clustering or segmenting image, the segmenting time is only dependent on the number of the gray-levels q rather than the size N(@?q) of the image, and consequently its computational complexity is reduced from O(NcI"1) to O(qcI"2), where c is the number of the clusters, I"1 and I"2(
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paper_title: Mean shift: A robust approach toward feature space analysis

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A general non-parametric technique is proposed for the analysis of a complex multimodal feature space and to delineate arbitrarily shaped clusters in it. The basic computational module of the technique is an old pattern recognition procedure: the mean shift. For discrete data, we prove the convergence of a recursive mean shift procedure to the nearest stationary point of the underlying density function and, thus, its utility in detecting the modes of the density. The relation of the mean shift procedure to the Nadaraya-Watson estimator from kernel regression and the robust M-estimators; of location is also established. Algorithms for two low-level vision tasks discontinuity-preserving smoothing and image segmentation - are described as applications. In these algorithms, the only user-set parameter is the resolution of the analysis, and either gray-level or color images are accepted as input. Extensive experimental results illustrate their excellent performance.
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paper_title: Normalized cuts and image segmentation

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We propose a novel approach for solving the perceptual grouping problem in vision. Rather than focusing on local features and their consistencies in the image data, our approach aims at extracting the global impression of an image. We treat image segmentation as a graph partitioning problem and propose a novel global criterion, the normalized cut, for segmenting the graph. The normalized cut criterion measures both the total dissimilarity between the different groups as well as the total similarity within the groups. We show that an efficient computational technique based on a generalized eigenvalue problem can be used to optimize this criterion. We have applied this approach to segmenting static images and found results very encouraging.
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paper_title: A Bayesian Network Model for Automatic and Interactive Image Segmentation

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We propose a new Bayesian network (BN) model for both automatic and interactive image segmentation. A multilayer BN is constructed from an oversegmentation to model the statistical dependencies among superpixel regions, edge segments, vertices, and their measurements. The BN also incorporates various local constraints to further restrain the relationships among these image entities. Given the BN model and various image measurements, belief propagation is performed to update the probability of each node. Image segmentation is generated by the most probable explanation inference of the true states of both region and edge nodes from the updated BN. Besides the automatic image segmentation, the proposed model can also be used for interactive image segmentation. While existing interactive segmentation (IS) approaches often passively depend on the user to provide exact intervention, we propose a new active input selection approach to provide suggestions for the user's intervention. Such intervention can be conveniently incorporated into the BN model to perform actively IS. We evaluate the proposed model on both the Weizmann dataset and VOC2006 cow images. The results demonstrate that the BN model can be used for automatic segmentation, and more importantly, for actively IS. The experiments also show that the IS with active input selection can improve both the overall segmentation accuracy and efficiency over the IS with passive intervention.
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paper_title: A multi-scale 3D Otsu thresholding algorithm for medical image segmentation

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Abstract Thresholding technique is one of the most imperative practices to accomplish image segmentation. In this paper, a novel thresholding algorithm based on 3D Otsu and multi-scale image representation is proposed for medical image segmentation. Considering the high time complexity of 3D Otsu algorithm, an acceleration variant is invented using dimension decomposition rule. In order to reduce the effects of noises and weak edges, multi-scale image representation is brought into the segmentation algorithm. The whole segmentation algorithm is designed as an iteration procedure. In each iteration, the image is segmented by the efficient 3D Otsu, and then it is filtered by a fast local Laplacian filtering to get a smoothed image which will be input into the next iteration. Finally, the segmentation results are pooled to get a final segmentation using majority voting rules. The attractive features of the algorithm are that its segmentation results are stable, it is robust to noises and it holds for both bi-level and multi-level thresholding cases. Experiments on medical MR brain images are conducted to demonstrate the effectiveness of the proposed method. The experimental results indicate that the proposed algorithm is superior to the other multilevel thresholding algorithms consistently.
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paper_title: Snakes: Active contour models

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A snake is an energy-minimizing spline guided by external constraint forces and influenced by image forces that pull it toward features such as lines and edges. Snakes are active contour models: they lock onto nearby edges, localizing them accurately. Scale-space continuation can be used to enlarge the capture region surrounding a feature. Snakes provide a unified account of a number of visual problems, including detection of edges, lines, and subjective contours; motion tracking; and stereo matching. We have used snakes successfully for interactive interpretation, in which user-imposed constraint forces guide the snake near features of interest.
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paper_title: Adaptive latent fingerprint segmentation using feature selection and random decision forest classification

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Abstract Latent fingerprints are important evidences used by law enforcement agencies. However, current state-of-the-art for automatic latent fingerprint recognition is not as reliable as live-scan fingerprints and advancements are required in every step of the recognition pipeline. This research focuses on automatically segmenting latent fingerprints to distinguish between ridge and non-ridge patterns. There are three major contributions of this research: (i) a machine learning algorithm for combining five different categories of features for automatic latent fingerprint segmentation, (ii) a feature selection technique using modified RELIEF formulation for analyzing the influence of multiple category features on latent fingerprint segmentation, and (iii) a novel SIVV based metric to measure the effect of the segmentation algorithm without the requirement to perform the entire matching process. The image is tessellated into local patches and saliency based features along with image, gradient, ridge, and quality based features are extracted. Feature selection is performed to study the contribution of the various category features towards foreground ridge pattern representation. Using these selected features, a trained Random Decision Forest based algorithm classifies the local patches as background or foreground. The results on three publicly available databases demonstrate the efficacy of the proposed algorithm.
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paper_title: MRI segmentation fusion for brain tumor detection

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Abstract The process of manually generating precise segmentations of brain tumors from magnetic resonance images (MRI) is time-consuming and error-prone. We present a new algorithm, Potential Field Segmentation (PFS), and propose the use of ensemble approaches that combine the results generated by PFS and other methods to achieve a fused segmentation. For the PFS method, we build on our recently proposed clustering algorithm, Potential Field Clustering, which is based on an analogy with the concept of potential field in Physics. We view the intensity of a pixel in an MRI as a “mass” that creates a potential field. Specifically, for each pixel in the MRI, the potential field is computed and, if smaller than an adaptive potential threshold, the pixel is associated with the tumor region. This “small potential” segmentation criterion is intuitively valid because tumor pixels have larger “mass” and thus the potential of surrounding regions is also much larger than in other regions of smaller or no “mass”. We evaluate the performance of the different methods, including the ensemble approaches, on the publicly available Brain Tumor Image Segmentation (BRATS) MRI benchmark database.
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paper_title: A CAD System for the Detection of Abnormalities in the Mammograms Using the Metaheuristic Algorithm Particle Swarm Optimization (PSO)

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The discovery of a malignant mass in the breast is considered one of the most devastating and depressing health issue women can face. However an early detection can be so helpful and could bring hope to control the disease and even cure it. Nowadays In spite the fact that Digital mammograms have proven to be an efficient tool for the screening of breast cancer, an accurate detection of the abnormalities remains a challenging task for radiologists. In this paper, we propose an effective method for the detection and classification of the suspicious regions. In our proposed approach, we use Entropy thresholding for pectoral muscle removal, and we extract the region of interest (ROI) using the Metaheuristic algorithm Particle Swarm Optimization (PSO). Then we extract Shape and texture features from the abnormalities using Fourier transform and Gray Level Co-Occurrence Matrix (GLCM) respectively. The classification of the detected abnormalities is carried out through the Support Vector Machine, which classifies the segmented region into normal and abnormal based on the extracted features.
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paper_title: Artificial intelligence based smart diagnosis of alzheimer's disease and mild cognitive impairment

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Modern pattern recognition and artificial intelligence systems can help in providing better health care and medical solutions. The performance of human diagnosis degrades due to fatigue, cognitive biases, systems faults, and distractions. However, artificial intelligence based diagnosis systems are less error prone and give safe support to clinicians in detection and decision making. This work presents a smart and reliable way of diagnosing Alzheimer's disease (AD) and its possible early stage i.e., mild cognitive impairment. Alzheimer's is a neurodegenerative disease and leads to severe memory loss and inability to cope with daily life tasks. The diagnosis of AD from structural images requires great skill and is challenging for human diagnostics. The presented framework is based on deep learning and detects Alzheimer's and its initial stages accurately from structural MRI scans. The framework analyzes four different classes simultaneously in a single setup. The testing accuracy of diagnosis obtained by the method is 98.88%. Experiments are also performed on binary data and transfer learning is applied for multiclass classification achieving 99.7% accuracy. Once a good trained model is obtained, the decision for an unseen test scan is given within a few seconds. These models are free from the factors that are responsible for causing human diagnostic errors. Therefore, these models are dependable and can provide much faster diagnosis.
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paper_title: Detection of left ventricular regional dysfunction and myocardial abnormalities using complementary cardiac magnetic resonance imaging in patients with systemic sclerosis without cardiac symptoms

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Background In patients with systemic sclerosis (SSc), myocardial involvement is common, may have serious consequences, and may lead to a poor prognosis. We aimed to detect LV regional dysfunction and myocardial abnormalities in SSc patients without cardiac symptoms using a cardiac magnetic resonance (CMR) imaging approach. Methods Consecutive patients with SSc without cardiac symptoms and healthy controls underwent CMR. Peak systolic regional circumferential and radial strain (Ecc and Err, %) were calculated using a feature tracking analysis on mid-left ventricular slices obtained with cine MRI in six segments. Furthermore, perfusion defect (PD) under pharmacological stress and late gadolinium enhancement (LGE) were obtained for the assessment of myocardial abnormalities. We compared the patients and controls in terms of prevalence of CMR abnormalities, and explored possible associations between CMR abnormalities and SSc disease characteristics. Results We compared 14 SSc patients with 10 healthy controls. No statistically significant differences were observed in baseline characteristics between the patients and healthy controls. The mean peak Ecc of all segments was significantly reduced in the patients compared with the controls (p = 0.004). The mean peak Err was significantly lower in the patients than the controls (p = 0.013). Five patients with LGE (28.6%) and 11 patients with PD (50.0%) were observed. The mean peak Ecc and Err in the patients with LGE was reduced compared to those without LGE, but not significant difference (p = 0.056, p = 0.077, respectively). The mean peak Ecc and Err in the patients with PD tended to be reduced compared to those without PD, but not significant difference (p = 0.250, p = 0.523, respectively). PD was significantly associated with history of digital ulcer (p = 0.005). Conclusions Subclinical myocardial involvement, as detected by CMR, was prevalent in the SSc patients without cardiac symptoms.
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paper_title: Computer-Aided Prostate Cancer Diagnosis From Digitized Histopathology: A Review on Texture-Based Systems

paper_content:

Prostate cancer (PCa) is currently diagnosed by microscopic evaluation of biopsy samples. Since tissue assessment heavily relies on the pathologists level of expertise and interpretation criteria, it is still a subjective process with high intra- and interobserver variabilities. Computer-aided diagnosis (CAD) may have a major impact on detection and grading of PCa by reducing the pathologists reading time, and increasing the accuracy and reproducibility of diagnosis outcomes. However, the complexity of the prostatic tissue and the large volumes of data generated by biopsy procedures make the development of CAD systems for PCa a challenging task. The problem of automated diagnosis of prostatic carcinoma from histopathology has received a lot of attention. As a result, a number of CAD systems, have been proposed for quantitative image analysis and classification. This review aims at providing a detailed description of selected literature in the field of CAD of PCa, emphasizing the role of texture analysis methods in tissue description. It includes a review of image analysis tools for image preprocessing, feature extraction, classification, and validation techniques used in PCa detection and grading, as well as future directions in pursuit of better texture-based CAD systems.
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paper_title: CASDES: A Computer-Aided System to Support Dry Eye Diagnosis Based on Tear Film Maps

paper_content:

Dry eye syndrome is recognized as a growing health problem, and one of the most frequent reasons for seeking eye care. Its etiology and management challenge clinicians and researchers alike, and several clinical tests can be used to diagnose it. One of the most frequently used tests is the evaluation of the interference patterns of the tear film lipid layer. Based on this clinical test, this paper presents CASDES, a computer-aided system to support the diagnosis of dry eye syndrome. Furthermore, CASDES is also useful to support the diagnosis of other eye diseases, such as meibomian gland dysfunction, since it provides a tear film map with highly useful information for eye practitioners. Experiments demonstrate the robustness of this novel tool, which outperforms the previous attempts to create tear film maps and provides reliable results in comparison with the clinicians’ annotations. Note that the processing time is noticeably reduced with the proposed method, which will help to promote its clinical use in the diagnosis and treatment of dry eye.
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paper_title: A Review of Computer Vision Methods for Purpose on Computer-Aided Diagnosis

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Medical imaging devices such as X-ray, CT and MRI provide information such as disease, abnormality and anatomic land-mark of inside of human body which cannot be seen directly. This information can be used for diagnosis or surgical planning. Since there are hundreds of slices to examine for CT and MRI data, it is time-consuming to examine all slices. Also, some noises inherent in these devices disturb the diagnosis process. For an efficient and clear Computer Aided Diagnosis, it is im-portant to process the images in order to remove the degrada-tion and to extract meaningful information from slices. This is the reason why the computer vision algorithms are essential for the Computer Aided Diagnosis.In the Computer Aided Diagnosis, extracting surgical infor-mation from image is processed through pattern recognition algorithms. In the pattern recognition procedure, image pro-cessing method is applied to eliminate possible noises from the imaging device and to enhance the image quality such as image contrast and sharpness. After that, the structural information of vessel, bone, organs is extracted via a segmentation method. Segmentation is the process which separates an image into seg -ments based on its pixel information. Each segment should rep-resent a region of human body on the image. Finally, the pattern
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paper_title: A Computer-Aided Diagnosis Scheme For Detection Of Fatty Liver In Vivo Based On Ultrasound Kurtosis Imaging

paper_content:

Fatty liver disease is a common disease caused by alcoholism, obesity, and diabetes, resulting in triglyceride accumulation in hepatocytes. Kurtosis coefficient, a measure of the peakedness of the probability distribution, has been applied to the analysis of backscattered statistics for characterizing fatty liver. This study proposed ultrasound kurtosis imaging as a computer-aided diagnosis (CAD) method to visually and quantitatively stage the fatty liver. A total of 107 patients were recruited to participate in the experiments. The livers were scanned using a clinical ultrasound scanner with a 3.5-MHz curved transducer to acquire the raw ultrasound backscattered signals for kurtosis imaging. The kurtosis image was constructed using the sliding window technique. Experimental results showed that kurtosis imaging has the ability to visualize and quantify the variation of backscattered statistics caused by fatty infiltration. The kurtosis coefficient corresponding to liver parenchyma decreased from 5.41 ± 0.89 to 3.68 ± 0.12 with increasing the score of fatty liver from 0 (normal) to 3 (severe), indicating that fatty liver reduces the degree of peakedness of backscattered statistics. The best performance of kurtosis imaging was found when discriminating between normal and fatty livers with scores ?1: the area under the curve (AUC) is 0.92 at a cutoff value of 4.36 (diagnostic accuracy =86.9 %, sensitivity =86.7 %, specificity =87.0 %). The current findings suggest that kurtosis imaging may be useful in designing CAD tools to assist in physicians in early detection of fatty liver.
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paper_title: The adaptive computer‐aided diagnosis system based on tumor sizes for the classification of breast tumors detected at screening ultrasound

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Screening ultrasound (US) is increasingly used as a supplement to mammography in women with dense breasts, and more than 80% of cancers detected by US alone are 1cm or smaller. An adaptive computer-aided diagnosis (CAD) system based on tumor size was proposed to classify breast tumors detected at screening US images using quantitative morphological and textural features. In the present study, a database containing 156 tumors (78 benign and 78 malignant) was separated into two subsets of different tumor sizes (<1cm and ⩾1cm) to explore the improvement in the performance of the CAD system. After adaptation, the accuracies, sensitivities, specificities and Az values of the CAD for the entire database increased from 73.1% (114/156), 73.1% (57/78), 73.1% (57/78), and 0.790 to 81.4% (127/156), 83.3% (65/78), 79.5% (62/78), and 0.852, respectively. In the data subset of tumors larger than 1cm, the performance improved from 66.2% (51/77), 68.3% (28/41), 63.9% (23/36), and 0.703 to 81.8% (63/77), 85.4% (35/41), 77.8% (28/36), and 0.855, respectively. The proposed CAD system can be helpful to classify breast tumors detected at screening US.
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paper_title: Complex wavelet algorithm for computer-aided diagnosis of Alzheimer's disease

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Electroencephalography signals are used for computer-aided diagnosis of Alzheimer's disease. Therefore, extracting critical features that belong to Alzheimer's signals are useful and tedious for neural network classification due to the high-frequency non-stationary components. For this purpose, time-frequency analysis and the multi-resolution capability of wavelets represent an attractive choice. However, fluctuations of the transformed coefficients and the absence of phase information make the process less accurate in certain scenarios. Because of this, complex wavelet transform has been selected to handle Alzheimer's signals. Moreover, the importance of calculating an optimal threshold value has been highlighted, usually by means of Shannon entropy as a helpful threshold identifier of the complex wavelet transform used to produce significant results. The effectiveness of Tsallis entropy instead of Shannon entropy in handling Alzheimer's signals is evaluated, the former giving place to better features for neural network classification. As a result, accuracy has been improved from 90 to 95% using Tsallis entropy. Hence, this new proposal boosts the opportunity to reduce mortality rates by detecting the disease accurately.
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paper_title: Computer-aided diagnosis of breast cancer using cytological images: A systematic review

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Abstract Cytological evaluation by microscopic image-based characterization [imprint cytology (IC) and fine needle aspiration cytology (FNAC)] plays an integral role in primary screening/detection of breast cancer. The sensitivity of IC and FNAC as a screening tool is dependent on the image quality and the pathologist’s level of expertise. Computer-aided diagnosis (CAD) is used to assists the pathologists by developing various machine learning and image processing algorithms. This study reviews the various manual and computer-aided techniques used so far in breast cytology. Diagnostic applications were studied to estimate the role of CAD in breast cancer diagnosis. This paper presents an overview of image processing and pattern recognition techniques that have been used to address several issues in breast cytology-based CAD including slide preparation, staining, microscopic imaging, pre-processing, segmentation, feature extraction and diagnostic classification. This review provides better insights to readers regarding the state of the art the knowledge on CAD-based breast cancer diagnosis to date.
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paper_title: Multiple instance learning for computer aided detection and diagnosis of gastric cancer with dual-energy CT imaging

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Display Omitted A multiple instance learning algorithm-based CAD scheme is proposed.Identify tumor invasion depth of gastric cancer with dual-energy CT imaging.We extract two-level features, bag-level features and instance-level features.We propose weighted distance Citation-KNN algorithm for classification. Multiple instance learning algorithms have been increasingly utilized in computer aided detection and diagnosis field. In this study, we propose a novel multiple instance learning method for the identification of tumor invasion depth of gastric cancer with dual-energy CT imaging. In the proposed scheme, two level features, bag-level features and instance-level features are extracted for subsequent processing and classification work. For instance-level features, there is some ambiguity in assigning labels to selected patches. An improved Citation-KNN method is presented to solve this problem. Compared with benchmarking state-of-the-art multiple instance learning algorithms using the same clinical dataset, the proposed algorithm can achieve improved results. The experimental evaluation is performed using leave-one-out cross validation with the total accuracy of 0.7692. The proposed multiple instance learning algorithm serves as an alternative method for computer aided diagnosis and identification of tumor invasion depth of gastric cancer with dual-energy CT imaging techniques.
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paper_title: Medical Image Retrieval: Past and Present

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With the widespread dissemination of picture archiving and communication systems (PACSs) in hospitals, the amount of imaging data is rapidly increasing. Effective image retrieval systems are required to manage these complex and large image databases. The authors reviewed the past development and the present state of medical image retrieval systems including text-based and content-based systems. In order to provide a more effective image retrieval service, the intelligent content-based retrieval systems combined with semantic systems are required.
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paper_title: Content-based image retrieval in dermatology using intelligent technique

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This study proposes a content-based image retrieval system for skin lesion images as a diagnostic aid. Effectiveness is measured by the rate of correct retrieval of images from skin lesions. The proposed architecture is used to retrieve digital images and the name of the disease category from an image data repository by the contents in the image, such as shape, texture and colour that is extracted from the image. The author's proposed algorithm used feature vector, classification and regression tree to retrieve comprehensive reference sources for diagnostic purpose. The results proved using a receiver operating characteristic curve that the proposed architecture has high contribute to computer-aided diagnosis of skin lesions. Experiments on a set of 1210 images yielded a specificity of 97.25% and a sensitivity of 91.24%. Their empirical evaluation has a superior retrieval and diagnosis performance when compared to the performance of other works. The authors present explicit combinations of feature vectors corresponding to healthy and lesion skin.
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paper_title: A Learning-Based Similarity Fusion and Filtering Approach for Biomedical Image Retrieval Using SVM Classification and Relevance Feedback

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This paper presents a classification-driven biomedical image retrieval framework based on image filtering and similarity fusion by employing supervised learning techniques. In this framework, the probabilistic outputs of a multiclass support vector machine (SVM) classifier as category prediction of query and database images are exploited at first to filter out irrelevant images, thereby reducing the search space for similarity matching. Images are classified at a global level according to their modalities based on different low-level, concept, and keypoint-based features. It is difficult to find a unique feature to compare images effectively for all types of queries. Hence, a query-specific adaptive linear combination of similarity matching approach is proposed by relying on the image classification and feedback information from users. Based on the prediction of a query image category, individual precomputed weights of different features are adjusted online. The prediction of the classifier may be inaccurate in some cases and a user might have a different semantic interpretation about retrieved images. Hence, the weights are finally determined by considering both precision and rank order information of each individual feature representation by considering top retrieved relevant images as judged by the users. As a result, the system can adapt itself to individual searches to produce query-specific results. Experiment is performed in a diverse collection of 5 000 biomedical images of different modalities, body parts, and orientations. It demonstrates the efficiency (about half computation time compared to search on entire collection) and effectiveness (about 10%-15% improvement in precision at each recall level) of the retrieval approach.
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paper_title: Query-by-Pictorial-Example

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Query-by-Pictorial-Example is a relational query language introduced for manipulating queries regarding pictorial relations as well as conventional relations. In addition to the manipulating capabilities of the conventional query languages, queries can also be expressed in terms of pictorial examples through a display tenninal. Example queries are used to illustrate the language facilities.
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paper_title: Feature-based brain MRI retrieval for Alzheimer disease diagnosis

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In this paper we consider the application of the feature-based approach to medical image retrieval, particularly brain MRI scans for early Alzheimer's disease diagnosis. The key idea is to provide the doctor with the images which have similar visual properties and have full case record, giving the ability to make more informed decision in the prodromal phase of the disease. With regard to the state-of-the art SIFT features in a Bag-of-Visual-Words approach we propose to use the Laguerre Circular Harmonic Functions coefficients as feature vectors. An additional pre-classification step based on estimation of Alzheimer's disease early image abnormalities is proposed to improve overall precision.
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paper_title: Fast wavelet based image characterization for content based medical image retrieval

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A large collection of medical images surrounds health care centers and hospitals. Medical images produced by different modalities like magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), and X-rays have increased incredibly with the advent of latest technologies for image acquisition. Retrieving clinical images of interest from these large data sets is a thought-provoking and demanding task. In this paper, a fast wavelet based medical image retrieval system is proposed that can aid physicians in the identification or analysis of medical images. The image signature is calculated using kurtosis and standard deviation as features. A possible use case is when the radiologist has some suspicion on diagnosis and wants further case histories, the acquired clinical images are sent (e.g. MRI images of brain) as a query to the content based medical image retrieval system. The system is tuned to retrieve the top most relevant images to the query. The proposed system is computationally efficient and more accurate in terms of the quality of retrieved images.
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paper_title: Improving CBIR systems by integrating semantic features

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Nowadays, access to information requires to manage effectively multimedia databases, and among challenges offered to scientific community since last decades, multimedia retrieval techniques (particularly images retrieval) are became an active research direction. Introduced to overcome the main drawbacks encountered by text-based images retrieval, which are the subjective and manual annotation of images, content based images retrieval (CBIR) systems index images according to low-level visual features such as color, texture, shape to retrieve similar images. However, despite the progress achieved in the content based image retrieval, in particular with the relevance feedback approach where the user refine the search via the specification of relevant or not relevant items, the current CBIR systems still have a major difficulty that it has yet to overcome: how to negotiate the "semantic gap"? This problem comes from the mismatch between their capabilities and the needs of users. ::: ::: In this paper, we address the problem of how relate low-level features to high level to bring out semantic concepts from images. Our aim is to combine content-based and metadata-based approaches for image retrieval from a user perspective to yield better results and overcome to the lacks of these techniques when they are taken separately. To represent the semantic content of images, we propose a model which takes account of the interaction between the user and the metadata. In particular, we model the semantic user' preference by analyzing its answers through the Relevance Feedback process. Furthermore, we introduce a new machine learning technique that modify the weights (i.e. relative importance) of metadata representing the semantic content of images.
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paper_title: A reference data set for the evaluation of medical image retrieval systems

paper_content:

Abstract Content-based image retrieval is starting to become an increasingly important factor in medical imaging research and image management systems. Several retrieval systems and methodologies exist and are used in a large variety of applications from automatic labelling of images to diagnostic aid and image classification. Still, it is very hard to compare the performance of these systems as the used databases often contain copyrighted or private images and are thus not interchangeable between research groups, also for patient privacy. Most of the currently used databases for evaluating systems are also fairly small which is partly due to the high cost in obtaining a gold standard or ground truth that is necessary for evaluation. Several large image databases, though without a gold standard, start to be available publicly, for example by the NIH (National Institutes for Health). This article describes the creation of a large medical image database that is used in a teaching file containing more than 8700 varied medical images. The images are anonymised and can be exchanged free of charge and copyright. Ground truth (a gold standard) has been obtained for a set of 26 images being selected as query topics for content-based query by image example. To reduce the time for the generation of ground truth, pooling methods well known from the text or information retrieval field have been used. Such a database is a good starting point for comparing the current image retrieval systems and to measure the retrieval quality, especially within the context of teaching files, image case databases and the support of teaching. For a comparison of retrieval systems for diagnostic aid, specialised image databases, including the diagnosis and a case description will need to be made available, as well, including gold standards for a proper system evaluation. A first evaluation event for image retrieval is foreseen at the 2004 CLEF conference (Cross Language Evaluation Forum) to compare text-and content-based access mechanism to images.
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paper_title: Regional deep learning model for visual tracking

paper_content:

Deep learning has been successfully applied to visual tracking due to its powerful feature learning characteristic. However, existing deep learning trackers rely on single observation model and focus on the holistic representation of the tracking object. When occlusion occurs, the trackers suffer from the contaminated features obtained in occluded areas. In this paper, we propose a regional deep learning tracker that observes the target by multiple sub-regions and each region is observed by a deep learning model. In particular, we devise a stable factor, modeled as a hidden variable of the Factorial Hidden Markov Model, to characterize the stability of these sub-models. The stability indicator not only provides a confidence degree for the response score of each model during inference stage, but also determines the online training criteria for each deep learning model. This online training strategy enables the tracker to achieve more accurate local features compared with those fixed training trackers. In addition, to improve the computational efficiency, we exploit the structurized response property of the customized deep learning model to approximate the final tracking results by the weighted Gaussian Mixture Model under the particle filter framework. Qualitative and quantitative evaluations on the recent public benchmark dataset show that our approach outperforms most state-of-the-art trackers.
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paper_title: Large-Scale Video Classification with Convolutional Neural Networks

paper_content:

Convolutional Neural Networks (CNNs) have been established as a powerful class of models for image recognition problems. Encouraged by these results, we provide an extensive empirical evaluation of CNNs on large-scale video classification using a new dataset of 1 million YouTube videos belonging to 487 classes. We study multiple approaches for extending the connectivity of a CNN in time domain to take advantage of local spatio-temporal information and suggest a multiresolution, foveated architecture as a promising way of speeding up the training. Our best spatio-temporal networks display significant performance improvements compared to strong feature-based baselines (55.3% to 63.9%), but only a surprisingly modest improvement compared to single-frame models (59.3% to 60.9%). We further study the generalization performance of our best model by retraining the top layers on the UCF-101 Action Recognition dataset and observe significant performance improvements compared to the UCF-101 baseline model (63.3% up from 43.9%).
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paper_title: Visualizing and Understanding Convolutional Networks

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Large Convolutional Network models have recently demonstrated impressive classification performance on the ImageNet benchmark Krizhevsky et al. [18]. However there is no clear understanding of why they perform so well, or how they might be improved. In this paper we explore both issues. We introduce a novel visualization technique that gives insight into the function of intermediate feature layers and the operation of the classifier. Used in a diagnostic role, these visualizations allow us to find model architectures that outperform Krizhevsky et al on the ImageNet classification benchmark. We also perform an ablation study to discover the performance contribution from different model layers. We show our ImageNet model generalizes well to other datasets: when the softmax classifier is retrained, it convincingly beats the current state-of-the-art results on Caltech-101 and Caltech-256 datasets.
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paper_title: Imagenet classification with deep convolutional neural networks

paper_content:

We trained a large, deep convolutional neural network to classify the 1.2 million high-resolution images in the ImageNet LSVRC-2010 contest into the 1000 different classes. On the test data, we achieved top-1 and top-5 error rates of 37.5% and 17.0% which is considerably better than the previous state-of-the-art. The neural network, which has 60 million parameters and 650,000 neurons, consists of five convolutional layers, some of which are followed by max-pooling layers, and three fully-connected layers with a final 1000-way softmax. To make training faster, we used non-saturating neurons and a very efficient GPU implementation of the convolution operation. To reduce overriding in the fully-connected layers we employed a recently-developed regularization method called "dropout" that proved to be very effective. We also entered a variant of this model in the ILSVRC-2012 competition and achieved a winning top-5 test error rate of 15.3%, compared to 26.2% achieved by the second-best entry.
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paper_title: Digital selection and analogue amplification coexist in a cortex-inspired silicon circuit

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Digital circuits such as the flip-flop use feedback to achieve multi-stability and nonlinearity to restore signals to logical levels, for example 0 and 1. Analogue feedback circuits are generally designed to operate linearly, so that signals are over a range, and the response is unique. By contrast, the response of cortical circuits to sensory stimulation can be both multistable and graded1,2,3,4. We propose that the neocortex combines digital selection of an active set of neurons with analogue response by dynamically varying the positive feedback inherent in its recurrent connections. Strong positive feedback causes differential instabilities that drive the selection of a set of active neurons under the constraints embedded in the synaptic weights. Once selected, the active neurons generate weaker, stable feedback that provides analogue amplification of the input. Here we present our model of cortical processing as an electronic circuit that emulates this hybrid operation, and so is able to perform computations that are similar to stimulus selection, gain modulation and spatiotemporal pattern generation in the neocortex.
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paper_title: Understanding the difficulty of training deep feedforward neural networks

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Whereas before 2006 it appears that deep multilayer neural networks were not successfully trained, since then several algorithms have been shown to successfully train them, with experimental results showing the superiority of deeper vs less deep architectures. All these experimental results were obtained with new initialization or training mechanisms. Our objective here is to understand better why standard gradient descent from random initialization is doing so poorly with deep neural networks, to better understand these recent relative successes and help design better algorithms in the future. We first observe the influence of the non-linear activations functions. We find that the logistic sigmoid activation is unsuited for deep networks with random initialization because of its mean value, which can drive especially the top hidden layer into saturation. Surprisingly, we find that saturated units can move out of saturation by themselves, albeit slowly, and explaining the plateaus sometimes seen when training neural networks. We find that a new non-linearity that saturates less can often be beneficial. Finally, we study how activations and gradients vary across layers and during training, with the idea that training may be more difficult when the singular values of the Jacobian associated with each layer are far from 1. Based on these considerations, we propose a new initialization scheme that brings substantially faster convergence. 1 Deep Neural Networks Deep learning methods aim at learning feature hierarchies with features from higher levels of the hierarchy formed by the composition of lower level features. They include Appearing in Proceedings of the 13 International Conference on Artificial Intelligence and Statistics (AISTATS) 2010, Chia Laguna Resort, Sardinia, Italy. Volume 9 of JMLR: WC Weston et al., 2008). Much attention has recently been devoted to them (see (Bengio, 2009) for a review), because of their theoretical appeal, inspiration from biology and human cognition, and because of empirical success in vision (Ranzato et al., 2007; Larochelle et al., 2007; Vincent et al., 2008) and natural language processing (NLP) (Collobert & Weston, 2008; Mnih & Hinton, 2009). Theoretical results reviewed and discussed by Bengio (2009), suggest that in order to learn the kind of complicated functions that can represent high-level abstractions (e.g. in vision, language, and other AI-level tasks), one may need deep architectures. Most of the recent experimental results with deep architecture are obtained with models that can be turned into deep supervised neural networks, but with initialization or training schemes different from the classical feedforward neural networks (Rumelhart et al., 1986). Why are these new algorithms working so much better than the standard random initialization and gradient-based optimization of a supervised training criterion? Part of the answer may be found in recent analyses of the effect of unsupervised pretraining (Erhan et al., 2009), showing that it acts as a regularizer that initializes the parameters in a “better” basin of attraction of the optimization procedure, corresponding to an apparent local minimum associated with better generalization. But earlier work (Bengio et al., 2007) had shown that even a purely supervised but greedy layer-wise procedure would give better results. So here instead of focusing on what unsupervised pre-training or semi-supervised criteria bring to deep architectures, we focus on analyzing what may be going wrong with good old (but deep) multilayer neural networks. Our analysis is driven by investigative experiments to monitor activations (watching for saturation of hidden units) and gradients, across layers and across training iterations. We also evaluate the effects on these of choices of activation function (with the idea that it might affect saturation) and initialization procedure (since unsupervised pretraining is a particular form of initialization and it has a drastic impact).
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paper_title: Deep Learning: Methods and Applications

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This monograph provides an overview of general deep learning methodology and its applications to a variety of signal and information processing tasks. The application areas are chosen with the following three criteria in mind: (1) expertise or knowledge of the authors; (2) the application areas that have already been transformed by the successful use of deep learning technology, such as speech recognition and computer vision; and (3) the application areas that have the potential to be impacted significantly by deep learning and that have been experiencing research growth, including natural language and text processing, information retrieval, and multimodal information processing empowered by multi-task deep learning.
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paper_title: Deep Sparse Rectifier Neural Networks

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While logistic sigmoid neurons are more biologically plausible than hyperbolic tangent neurons, the latter work better for training multi-layer neural networks. This paper shows that rectifying neurons are an even better model of biological neurons and yield equal or better performance than hyperbolic tangent networks in spite of the hard non-linearity and non-dierentiabil ity
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paper_title: Active deep learning method for semi-supervised sentiment classification

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Abstract In natural language processing community, sentiment classification based on insufficient labeled data is a well-known challenging problem. In this paper, a novel semi-supervised learning algorithm called active deep network (ADN) is proposed to address this problem. First, we propose the semi-supervised learning framework of ADN. ADN is constructed by restricted Boltzmann machines (RBM) with unsupervised learning based on labeled reviews and abundant of unlabeled reviews. Then the constructed structure is fine-tuned by gradient-descent based supervised learning with an exponential loss function. Second, in the semi-supervised learning framework, we apply active learning to identify reviews that should be labeled as training data, then using the selected labeled reviews and all unlabeled reviews to train ADN architecture. Moreover, we combine the information density with ADN, and propose information ADN (IADN) method, which can apply the information density of all unlabeled reviews in choosing the manual labeled reviews. Experiments on five sentiment classification datasets show that ADN and IADN outperform classical semi-supervised learning algorithms, and deep learning techniques applied for sentiment classification.
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paper_title: Gradient-Based Learning Applied to Document Recognition

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Multilayer neural networks trained with the back-propagation algorithm constitute the best example of a successful gradient based learning technique. Given an appropriate network architecture, gradient-based learning algorithms can be used to synthesize a complex decision surface that can classify high-dimensional patterns, such as handwritten characters, with minimal preprocessing. This paper reviews various methods applied to handwritten character recognition and compares them on a standard handwritten digit recognition task. Convolutional neural networks, which are specifically designed to deal with the variability of 2D shapes, are shown to outperform all other techniques. Real-life document recognition systems are composed of multiple modules including field extraction, segmentation recognition, and language modeling. A new learning paradigm, called graph transformer networks (GTN), allows such multimodule systems to be trained globally using gradient-based methods so as to minimize an overall performance measure. Two systems for online handwriting recognition are described. Experiments demonstrate the advantage of global training, and the flexibility of graph transformer networks. A graph transformer network for reading a bank cheque is also described. It uses convolutional neural network character recognizers combined with global training techniques to provide record accuracy on business and personal cheques. It is deployed commercially and reads several million cheques per day.
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paper_title: Improving Computer-aided Detection using Convolutional Neural Networks and Random View Aggregation

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Automated computer-aided detection (CADe) has been an important tool in clinical practice and research. State-of-the-art methods often show high sensitivities at the cost of high false-positives (FP) per patient rates. We design a two-tiered coarse-to-fine cascade framework that first operates a candidate generation system at sensitivities $\sim 100\%$ of but at high FP levels. By leveraging existing CADe systems, coordinates of regions or volumes of interest (ROI or VOI) are generated and function as input for a second tier, which is our focus in this study. In this second stage, we generate 2D (two-dimensional) or 2.5D views via sampling through scale transformations, random translations and rotations. These random views are used to train deep convolutional neural network (ConvNet) classifiers. In testing, the ConvNets assign class (e.g., lesion, pathology) probabilities for a new set of random views that are then averaged to compute a final per-candidate classification probability. This second tier behaves as a highly selective process to reject difficult false positives while preserving high sensitivities. The methods are evaluated on three data sets: 59 patients for sclerotic metastasis detection, 176 patients for lymph node detection, and 1,186 patients for colonic polyp detection. Experimental results show the ability of ConvNets to generalize well to different medical imaging CADe applications and scale elegantly to various data sets. Our proposed methods improve performance markedly in all cases. Sensitivities improved from 57% to 70%, 43% to 77%, and 58% to 75% at 3 FPs per patient for sclerotic metastases, lymph nodes and colonic polyps, respectively.
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paper_title: Multi-Instance Deep Learning: Discover Discriminative Local Anatomies for Bodypart Recognition

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In general image recognition problems, discriminative information often lies in local image patches. For example, most human identity information exists in the image patches containing human faces. The same situation stays in medical images as well. “Bodypart identity” of a transversal slice—which bodypart the slice comes from—is often indicated by local image information, e.g., a cardiac slice and an aorta arch slice are only differentiated by the mediastinum region. In this work, we design a multi-stage deep learning framework for image classification and apply it on bodypart recognition. Specifically, the proposed framework aims at: 1) discover the local regions that are discriminative and non-informative to the image classification problem, and 2) learn a image-level classifier based on these local regions. We achieve these two tasks by the two stages of learning scheme, respectively. In the pre-train stage, a convolutional neural network (CNN) is learned in a multi-instance learning fashion to extract the most discriminative and and non-informative local patches from the training slices. In the boosting stage, the pre-learned CNN is further boosted by these local patches for image classification. The CNN learned by exploiting the discriminative local appearances becomes more accurate than those learned from global image context. The key hallmark of our method is that it automatically discovers the discriminative and non-informative local patches through multi-instance deep learning. Thus, no manual annotation is required. Our method is validated on a synthetic dataset and a large scale CT dataset. It achieves better performances than state-of-the-art approaches, including the standard deep CNN.
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paper_title: Joint Sequence Learning and Cross-Modality Convolution for 3D Biomedical Segmentation

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Deep learning models such as convolutional neural network have been widely used in 3D biomedical segmentation and achieve state-of-the-art performance. However, most of them often adapt a single modality or stack multiple modalities as different input channels, which ignores the correlations among them. To leverage the multi-modalities, we propose a deep convolution encoder-decoder structure with fusion layers to incorporate different modalities of MRI data. In addition, we exploit convolutional LSTM (convLSTM) to model a sequence of 2D slices, and jointly learn the multi-modalities and convLSTM in an end-to-end manner. To avoid converging to the certain labels, we adopt a re-weighting scheme and two phase training to handle the label imbalance. Experimental results on BRATS-2015 [13] show that our method outperforms state-of-the-art biomedical segmentation approaches.
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paper_title: AggNet: Deep Learning From Crowds for Mitosis Detection in Breast Cancer Histology Images

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The lack of publicly available ground-truth data has been identified as the major challenge for transferring recent developments in deep learning to the biomedical imaging domain. Though crowdsourcing has enabled annotation of large scale databases for real world images, its application for biomedical purposes requires a deeper understanding and hence, more precise definition of the actual annotation task. The fact that expert tasks are being outsourced to non-expert users may lead to noisy annotations introducing disagreement between users. Despite being a valuable resource for learning annotation models from crowdsourcing, conventional machine-learning methods may have difficulties dealing with noisy annotations during training. In this manuscript, we present a new concept for learning from crowds that handle data aggregation directly as part of the learning process of the convolutional neural network (CNN) via additional crowdsourcing layer (AggNet). Besides, we present an experimental study on learning from crowds designed to answer the following questions. 1) Can deep CNN be trained with data collected from crowdsourcing? 2) How to adapt the CNN to train on multiple types of annotation datasets (ground truth and crowd-based)? 3) How does the choice of annotation and aggregation affect the accuracy? Our experimental setup involved Annot8, a self-implemented web-platform based on Crowdflower API realizing image annotation tasks for a publicly available biomedical image database. Our results give valuable insights into the functionality of deep CNN learning from crowd annotations and prove the necessity of data aggregation integration.
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paper_title: Deep Feature Learning for Knee Cartilage Segmentation Using a Triplanar Convolutional Neural Network

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Segmentation of anatomical structures in medical images is often based on a voxel/pixel classification approach. Deep learning systems, such as convolutional neural networks (CNNs), can infer a hierarchical representation of images that fosters categorization. We propose a novel system for voxel classification integrating three 2D CNNs, which have a one-to-one association with the xy, yz and zx planes of 3D image, respectively. We applied our method to the segmentation of tibial cartilage in low field knee MRI scans and tested it on 114 unseen scans. Although our method uses only 2D features at a single scale, it performs better than a state-of-the-art method using 3D multi-scale features. In the latter approach, the features and the classifier have been carefully adapted to the problem at hand. That we were able to get better results by a deep learning architecture that autonomously learns the features from the images is the main insight of this study.
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paper_title: Brain tumor segmentation with Deep Neural Networks

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Abstract In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we’ve found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test data-set reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster.
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paper_title: Dermatologist-level classification of skin cancer with deep neural networks

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An artificial intelligence trained to classify images of skin lesions as benign lesions or malignant skin cancers achieves the accuracy of board-certified dermatologists.
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paper_title: Brain Tumor Segmentation Using Convolutional Neural Networks in MRI Images

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Among brain tumors, gliomas are the most common and aggressive, leading to a very short life expectancy in their highest grade. Thus, treatment planning is a key stage to improve the quality of life of oncological patients. Magnetic resonance imaging (MRI) is a widely used imaging technique to assess these tumors, but the large amount of data produced by MRI prevents manual segmentation in a reasonable time, limiting the use of precise quantitative measurements in the clinical practice. So, automatic and reliable segmentation methods are required; however, the large spatial and structural variability among brain tumors make automatic segmentation a challenging problem. In this paper, we propose an automatic segmentation method based on Convolutional Neural Networks (CNN), exploring small 3 $\times$ 3 kernels. The use of small kernels allows designing a deeper architecture, besides having a positive effect against overfitting, given the fewer number of weights in the network. We also investigated the use of intensity normalization as a pre-processing step, which though not common in CNN-based segmentation methods, proved together with data augmentation to be very effective for brain tumor segmentation in MRI images. Our proposal was validated in the Brain Tumor Segmentation Challenge 2013 database (BRATS 2013), obtaining simultaneously the first position for the complete, core, and enhancing regions in Dice Similarity Coefficient metric (0.88, 0.83, 0.77) for the Challenge data set. Also, it obtained the overall first position by the online evaluation platform. We also participated in the on-site BRATS 2015 Challenge using the same model, obtaining the second place, with Dice Similarity Coefficient metric of 0.78, 0.65, and 0.75 for the complete, core, and enhancing regions, respectively.
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paper_title: Combining Generative and Discriminative Representation Learning for Lung CT Analysis With Convolutional Restricted Boltzmann Machines

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The choice of features greatly influences the performance of a tissue classification system. Despite this, many systems are built with standard, predefined filter banks that are not optimized for that particular application. Representation learning methods such as restricted Boltzmann machines may outperform these standard filter banks because they learn a feature description directly from the training data. Like many other representation learning methods, restricted Boltzmann machines are unsupervised and are trained with a generative learning objective; this allows them to learn representations from unlabeled data, but does not necessarily produce features that are optimal for classification. In this paper we propose the convolutional classification restricted Boltzmann machine, which combines a generative and a discriminative learning objective. This allows it to learn filters that are good both for describing the training data and for classification. We present experiments with feature learning for lung texture classification and airway detection in CT images. In both applications, a combination of learning objectives outperformed purely discriminative or generative learning, increasing, for instance, the lung tissue classification accuracy by 1 to 8 percentage points. This shows that discriminative learning can help an otherwise unsupervised feature learner to learn filters that are optimized for classification.
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paper_title: Deep convolutional neural networks for multi-modality isointense infant brain image segmentation.

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Abstract The segmentation of infant brain tissue images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) plays an important role in studying early brain development in health and disease. In the isointense stage (approximately 6–8 months of age), WM and GM exhibit similar levels of intensity in both T1 and T2 MR images, making the tissue segmentation very challenging. Only a small number of existing methods have been designed for tissue segmentation in this isointense stage; however, they only used a single T1 or T2 images, or the combination of T1 and T2 images. In this paper, we propose to use deep convolutional neural networks (CNNs) for segmenting isointense stage brain tissues using multi-modality MR images. CNNs are a type of deep models in which trainable filters and local neighborhood pooling operations are applied alternatingly on the raw input images, resulting in a hierarchy of increasingly complex features. Specifically, we used multi-modality information from T1, T2, and fractional anisotropy (FA) images as inputs and then generated the segmentation maps as outputs. The multiple intermediate layers applied convolution, pooling, normalization, and other operations to capture the highly nonlinear mappings between inputs and outputs. We compared the performance of our approach with that of the commonly used segmentation methods on a set of manually segmented isointense stage brain images. Results showed that our proposed model significantly outperformed prior methods on infant brain tissue segmentation. In addition, our results indicated that integration of multi-modality images led to significant performance improvement.
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paper_title: Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neural Network

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Automated tissue characterization is one of the most crucial components of a computer aided diagnosis (CAD) system for interstitial lung diseases (ILDs). Although much research has been conducted in this field, the problem remains challenging. Deep learning techniques have recently achieved impressive results in a variety of computer vision problems, raising expectations that they might be applied in other domains, such as medical image analysis. In this paper, we propose and evaluate a convolutional neural network (CNN), designed for the classification of ILD patterns. The proposed network consists of 5 convolutional layers with 2 $\,\times\,$ 2 kernels and LeakyReLU activations, followed by average pooling with size equal to the size of the final feature maps and three dense layers. The last dense layer has 7 outputs, equivalent to the classes considered: healthy, ground glass opacity (GGO), micronodules, consolidation, reticulation, honeycombing and a combination of GGO/reticulation. To train and evaluate the CNN, we used a dataset of 14696 image patches, derived by 120 CT scans from different scanners and hospitals. To the best of our knowledge, this is the first deep CNN designed for the specific problem. A comparative analysis proved the effectiveness of the proposed CNN against previous methods in a challenging dataset. The classification performance ( $\sim 85.5\%$ ) demonstrated the potential of CNNs in analyzing lung patterns. Future work includes, extending the CNN to three-dimensional data provided by CT volume scans and integrating the proposed method into a CAD system that aims to provide differential diagnosis for ILDs as a supportive tool for radiologists.
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paper_title: Efficient multi‐scale 3D CNN with fully connected CRF for accurate brain lesion segmentation

paper_content:

HIGHLIGHTSAn efficient 11‐layers deep, multi‐scale, 3D CNN architecture.A novel training strategy that significantly boosts performance.The first employment of a 3D fully connected CRF for post‐processing.State‐of‐the‐art performance on three challenging lesion segmentation tasks.New insights into the automatically learned intermediate representations. ABSTRACT We propose a dual pathway, 11‐layers deep, three‐dimensional Convolutional Neural Network for the challenging task of brain lesion segmentation. The devised architecture is the result of an in‐depth analysis of the limitations of current networks proposed for similar applications. To overcome the computational burden of processing 3D medical scans, we have devised an efficient and effective dense training scheme which joins the processing of adjacent image patches into one pass through the network while automatically adapting to the inherent class imbalance present in the data. Further, we analyze the development of deeper, thus more discriminative 3D CNNs. In order to incorporate both local and larger contextual information, we employ a dual pathway architecture that processes the input images at multiple scales simultaneously. For post‐processing of the network's soft segmentation, we use a 3D fully connected Conditional Random Field which effectively removes false positives. Our pipeline is extensively evaluated on three challenging tasks of lesion segmentation in multi‐channel MRI patient data with traumatic brain injuries, brain tumours, and ischemic stroke. We improve on the state‐of‐the‐art for all three applications, with top ranking performance on the public benchmarks BRATS 2015 and ISLES 2015. Our method is computationally efficient, which allows its adoption in a variety of research and clinical settings. The source code of our implementation is made publicly available.
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paper_title: Large scale deep learning for computer aided detection of mammographic lesions

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Recent advances in machine learning yielded new techniques to train deep neural networks, which resulted in highly successful applications in many pattern recognition tasks such as object detection and speech recognition. In this paper we provide a head-to-head comparison between a state-of-the art in mammography CAD system, relying on a manually designed feature set and a Convolutional Neural Network (CNN), aiming for a system that can ultimately read mammograms independently. Both systems are trained on a large data set of around 45,000 images and results show the CNN outperforms the traditional CAD system at low sensitivity and performs comparable at high sensitivity. We subsequently investigate to what extent features such as location and patient information and commonly used manual features can still complement the network and see improvements at high specificity over the CNN especially with location and context features, which contain information not available to the CNN. Additionally, a reader study was performed, where the network was compared to certified screening radiologists on a patch level and we found no significant difference between the network and the readers.
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paper_title: Predicting brain age with deep learning from raw imaging data results in a reliable and heritable biomarker

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Abstract Machine learning analysis of neuroimaging data can accurately predict chronological age in healthy people. Deviations from healthy brain ageing have been associated with cognitive impairment and disease. Here we sought to further establish the credentials of ‘brain-predicted age’ as a biomarker of individual differences in the brain ageing process, using a predictive modelling approach based on deep learning, and specifically convolutional neural networks (CNN), and applied to both pre-processed and raw T1-weighted MRI data. Firstly, we aimed to demonstrate the accuracy of CNN brain-predicted age using a large dataset of healthy adults (N = 2001). Next, we sought to establish the heritability of brain-predicted age using a sample of monozygotic and dizygotic female twins (N = 62). Thirdly, we examined the test-retest and multi-centre reliability of brain-predicted age using two samples (within-scanner N = 20; between-scanner N = 11). CNN brain-predicted ages were generated and compared to a Gaussian Process Regression (GPR) approach, on all datasets. Input data were grey matter (GM) or white matter (WM) volumetric maps generated by Statistical Parametric Mapping (SPM) or raw data. CNN accurately predicted chronological age using GM (correlation between brain-predicted age and chronological age r = 0.96, mean absolute error [MAE] = 4.16 years) and raw (r = 0.94, MAE = 4.65 years) data. This was comparable to GPR brain-predicted age using GM data (r = 0.95, MAE = 4.66 years). Brain-predicted age was a heritable phenotype for all models and input data (h 2 ≥ 0.5). Brain-predicted age showed high test-retest reliability (intraclass correlation coefficient [ICC] = 0.90–0.99). Multi-centre reliability was more variable within high ICCs for GM (0.83–0.96) and poor-moderate levels for WM and raw data (0.51–0.77). Brain-predicted age represents an accurate, highly reliable and genetically-influenced phenotype, that has potential to be used as a biomarker of brain ageing. Moreover, age predictions can be accurately generated on raw T1-MRI data, substantially reducing computation time for novel data, bringing the process closer to giving real-time information on brain health in clinical settings.
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paper_title: Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning

paper_content:

Remarkable progress has been made in image recognition, primarily due to the availability of large-scale annotated datasets and deep convolutional neural networks (CNNs). CNNs enable learning data-driven, highly representative, hierarchical image features from sufficient training data. However, obtaining datasets as comprehensively annotated as ImageNet in the medical imaging domain remains a challenge. There are currently three major techniques that successfully employ CNNs to medical image classification: training the CNN from scratch, using off-the-shelf pre-trained CNN features, and conducting unsupervised CNN pre-training with supervised fine-tuning. Another effective method is transfer learning, i.e., fine-tuning CNN models pre-trained from natural image dataset to medical image tasks. In this paper, we exploit three important, but previously understudied factors of employing deep convolutional neural networks to computer-aided detection problems. We first explore and evaluate different CNN architectures. The studied models contain 5 thousand to 160 million parameters, and vary in numbers of layers. We then evaluate the influence of dataset scale and spatial image context on performance. Finally, we examine when and why transfer learning from pre-trained ImageNet (via fine-tuning) can be useful. We study two specific computer-aided detection (CADe) problems, namely thoraco-abdominal lymph node (LN) detection and interstitial lung disease (ILD) classification. We achieve the state-of-the-art performance on the mediastinal LN detection, and report the first five-fold cross-validation classification results on predicting axial CT slices with ILD categories. Our extensive empirical evaluation, CNN model analysis and valuable insights can be extended to the design of high performance CAD systems for other medical imaging tasks.
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paper_title: Locality Sensitive Deep Learning for Detection and Classification of Nuclei in Routine Colon Cancer Histology Images

paper_content:

Detection and classification of cell nuclei in histopathology images of cancerous tissue stained with the standard hematoxylin and eosin stain is a challenging task due to cellular heterogeneity. Deep learning approaches have been shown to produce encouraging results on histopathology images in various studies. In this paper, we propose a Spatially Constrained Convolutional Neural Network (SC-CNN) to perform nucleus detection. SC-CNN regresses the likelihood of a pixel being the center of a nucleus, where high probability values are spatially constrained to locate in the vicinity of the centers of nuclei. For classification of nuclei, we propose a novel Neighboring Ensemble Predictor (NEP) coupled with CNN to more accurately predict the class label of detected cell nuclei. The proposed approaches for detection and classification do not require segmentation of nuclei. We have evaluated them on a large dataset of colorectal adenocarcinoma images, consisting of more than 20,000 annotated nuclei belonging to four different classes. Our results show that the joint detection and classification of the proposed SC-CNN and NEP produces the highest average F1 score as compared to other recently published approaches. Prospectively, the proposed methods could offer benefit to pathology practice in terms of quantitative analysis of tissue constituents in whole-slide images, and potentially lead to a better understanding of cancer.
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Title: Medical Image Analysis using Convolutional Neural Networks: A Review

Section 1: Introduction
Description 1: Introduce the use and importance of deep learning in various research domains, specifically focusing on its impact and applications in medical image analysis.

Section 2: Medical Imaging Modalities
Description 2: Discuss different medical imaging modalities such as CT, MRI, PET, and their significance in diagnosis and medical research.

Section 3: Medical Image Analysis
Description 3: Describe the purpose and processes involved in medical image analysis. Highlight its applications in aiding diagnostic and treatment processes.

Section 4: Segmentation
Description 4: Explain the process of segmentation in medical image analysis, its significance, and various algorithms utilized for this purpose.

Section 5: Detection and Classification of Abnormality
Description 5: Discuss methods and processes involved in detecting abnormalities in medical images, including some specific algorithms and techniques.

Section 6: Computer Aided Diagnosis (CADx)
Description 6: Detail the functionality of Computer Aided Diagnosis systems, their integration with machine learning techniques, and their applications.

Section 7: Medical Image Retrieval
Description 7: Explore the systems and techniques used for medical image retrieval and their importance in facilitating accurate diagnosis and treatment decisions.

Section 8: Evaluation Metrics for Medical Image Analysis System
Description 8: List and describe the key performance measures used to evaluate medical image analysis systems, such as accuracy, F1-score, precision, recall, sensitivity, and specificity.

Section 9: Deep Learning
Description 9: Provide an overview of deep learning, explaining its significance, evolution, and different algorithms used in this domain.

Section 10: Convolutional Neural Network
Description 10: Explain what Convolutional Neural Networks (CNNs) are, their functioning, and their relevance in medical image analysis.

Section 11: Medical Image Analysis using Convolutional Neural Network
Description 11: Present various applications and successes of CNNs in medical image analysis, highlighting notable studies and their outcomes.

Section 12: Conclusion
Description 12: Summarize the review, reiterating the impact of deep learning and CNNs on the field of medical image analysis and suggesting areas for future research.