Traditional survival models such as the Cox proportional hazards model are typically based on scalar or categorical clinical features. With the advent of increasingly large image datasets, it has become feasible to incorporate quantitative image features into survival prediction. So far, this kind of analysis is mostly based on radiomics features, i.e. a fixed set of features that is mathematically defined a priori. To capture highly abstract information, it is desirable to learn the feature extraction using convolutional neural networks. However, for tomographic medical images, model training is difficult because on the one hand, only few samples of 3D image data fit into one batch at once and on the other hand, survival loss functions are essentially ordering measures that require large batch sizes. In this work, we show that by simplifying survival analysis to median survival classification, convolutional neural networks can be trained with small batch sizes and learn features that predict survival equally well as end-to-end hazard prediction networks. Our approach outperforms the previous state of the art in a publicly available lung cancer dataset.
We aim to address this issue by transferring features learned by a classification problem to survival analysis without losing performance. Moreover, we propose a method to combine radiomics and learned CNN features that enforce the CNN to learn features that are both discriminative and not covered by the radiomics feature set. All methods are evaluated on a publicly available dataset of computed tomography (CT) images of non-small-cell lung cancer (NSCLC) patients and corresponding survival labels. We show that our method can outperform the previous state-of-the-art presented in @cite_3 .
@cite_3
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Human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. Radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. Here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. We find that a large number of radiomic features have prognostic power in independent data sets of lung and head-and-neck cancer patients, many of which were not identified as significant before. Radiogenomics analysis reveals that a prognostic radiomic signature, capturing intratumour heterogeneity, is associated with underlying gene-expression patterns. These data suggest that radiomics identifies a general prognostic phenotype existing in both lung and head-and-neck cancer. This may have a clinical impact as imaging is routinely used in clinical practice, providing an unprecedented opportunity to improve decision-support in cancer treatment at low cost. Convolutional Neural Networks (CNN) are state-of-the-art models for many image classification tasks. However, to recognize cancer subtypes automatically, training a CNN on gigapixel resolution Whole Slide Tissue Images (WSI) is currently computationally impossible. The differentiation of cancer subtypes is based on cellular-level visual features observed on image patch scale. Therefore, we argue that in this situation, training a patch-level classifier on image patches will perform better than or similar to an image-level classifier. The challenge becomes how to intelligently combine patch-level classification results and model the fact that not all patches will be discriminative. We propose to train a decision fusion model to aggregate patch-level predictions given by patch-level CNNs, which to the best of our knowledge has not been shown before. Furthermore, we formulate a novel Expectation-Maximization (EM) based method that automatically locates discriminative patches robustly by utilizing the spatial relationships of patches. We apply our method to the classification of glioma and non-small-cell lung carcinoma cases into subtypes. The classification accuracy of our method is similar to the inter-observer agreement between pathologists. Although it is impossible to train CNNs on WSIs, we experimentally demonstrate using a comparable non-cancer dataset of smaller images that a patch-based CNN can outperform an image-based CNN. Deep learning is considered as a popular and powerful method in pattern recognition and classification. However, there are not many deep structured applications used in medical imaging diagnosis area, because large dataset is not always available for medical images. In this study we tested the feasibility of using deep learning algorithms for lung cancer diagnosis with the cases from Lung Image Database Consortium (LIDC) database. The nodules on each computed tomography (CT) slice were segmented according to marks provided by the radiologists. After down sampling and rotating we acquired 174412 samples with 52 by 52 pixel each and the corresponding truth files. Three deep learning algorithms were designed and implemented, including Convolutional Neural Network (CNN), Deep Belief Networks (DBNs), Stacked Denoising Autoencoder (SDAE). To compare the performance of deep learning algorithms with traditional computer aided diagnosis (CADx) system, we designed a scheme with 28 image features and support vector machine. The accuracies of CNN, DBNs, and SDAE are 0.7976, 0.8119, and 0.7929, respectively; the accuracy of our designed traditional CADx is 0.7940, which is slightly lower than CNN and DBNs. We also noticed that the mislabeled nodules using DBNs are 4 larger than using traditional CADx, this might be resulting from down sampling process lost some size information of the nodules. 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 @math 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 ( @math ) 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. Early diagnosis of interstitial lung diseases is crucial for their treatment, but even experienced physicians find it difficult, as their clinical manifestations are similar. In order to assist with the diagnosis, computer-aided diagnosis (CAD) systems have been developed. These commonly rely on a fixed scale classifier that scans CT images, recognizes textural lung patterns and generates a map of pathologies. In a previous study, we proposed a method for classifying lung tissue patterns using a deep convolutional neural network (CNN), with an architecture designed for the specific problem. In this study, we present an improved method for training the proposed network by transferring knowledge from the similar domain of general texture classification. Six publicly available texture databases are used to pretrain networks with the proposed architecture, which are then fine-tuned on the lung tissue data. The resulting CNNs are combined in an ensemble and their fused knowledge is compressed back to a network with the original architecture. The proposed approach resulted in an absolute increase of about 2 in the performance of the proposed CNN. The results demonstrate the potential of transfer learning in the field of medical image analysis, indicate the textural nature of the problem and show that the method used for training a network can be as important as designing its architecture. 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. Early detection of Ground Glass Nodule (GGN) in lung Computed Tomography (CT) images is important for lung cancer prognosis. Due to its indistinct boundaries, manual detection and segmentation of GGN is labor-intensive and problematic. In this paper, we propose a novel multi-level learning-based framework for automatic detection and segmentation of GGN in lung CT images. Our main contributions are: firstly, a multi-level statistical learning-based approach that seamlessly integrates segmentation and detection to improve the overall accuracy for GGN detection (in a subvolume). The classification is done at two levels, both voxel-level and object-level. The algorithm starts with a three-phase voxel-level classification step, using volumetric features computed per voxel to generate a GGN class-conditional probability map. GGN candidates are then extracted from this probability map by integrating prior knowledge of shape and location, and the GGN object-level classifier is used to determine the occurrence of the GGN. Secondly, an extensive set of volumetric features are used to capture the GGN appearance. Finally, to our best knowledge, the GGN dataset used for experiments is an order of magnitude larger than previous work. The effectiveness of our method is demonstrated on a dataset of 1100 subvolumes (100 containing GGNs) extracted from about 200 subjects. Thanks to the powerful feature representations obtained through deep convolutional neural network (CNN), the performance of object detection has recently been substantially boosted. Despite the remarkable success, the problems of object rotation, within-class variability, and between-class similarity remain several major challenges. To address these problems, this paper proposes a novel and effective method to learn a rotation-invariant and Fisher discriminative CNN (RIFD-CNN) model. This is achieved by introducing and learning a rotation-invariant layer and a Fisher discriminative layer, respectively, on the basis of the existing high-capacity CNN architectures. Specifically, the rotation-invariant layer is trained by imposing an explicit regularization constraint on the objective function that enforces invariance on the CNN features before and after rotating. The Fisher discriminative layer is trained by imposing the Fisher discrimination criterion on the CNN features so that they have small within-class scatter but large between-class separation. In the experiments, we comprehensively evaluate the proposed method for object detection task on a public available aerial image dataset and the PASCAL VOC 2007 dataset. State-of-the-art results are achieved compared with the existing baseline methods. Unlabeled high-dimensional text-image web news data are produced every day, presenting new challenges to unsupervised feature selection on multi-view data. State-of-the-art multi-view unsupervised feature selection methods learn pseudo class labels by spectral analysis, which is sensitive to the choice of similarity metric for each view. For text-image data, the raw text itself contains more discriminative information than similarity graph which loses information during construction, and thus the text feature can be directly used for label learning, avoiding information loss as in spectral analysis. We propose a new multi-view unsupervised feature selection method in which image local learning regularized orthogonal nonnegative matrix factorization is used to learn pseudo labels and simultaneously robust joint @math -norm minimization is performed to select discriminative features. Cross-view consensus on pseudo labels can be obtained as much as possible. We systematically evaluate the proposed method in multi-view text-image web news datasets. Our extensive experiments on web news datasets crawled from two major US media channels: CNN and FOXNews demonstrate the efficacy of the new method over state-of-the-art multi-view and single-view unsupervised feature selection methods. Display Omitted Survival prediction of HCC patients is modeled in a real and high complex scenario.Its complexity is due to a small dataset with heterogeneous and missing input data.We propose a new cluster-based oversampling method to overcome these drawbacks.Neural networks and logistic regression are applied in the classification stage.Experimental results show that our method outperforms previous existing approaches. Liver cancer is the sixth most frequently diagnosed cancer and, particularly, Hepatocellular Carcinoma (HCC) represents more than 90 of primary liver cancers. Clinicians assess each patients treatment on the basis of evidence-based medicine, which may not always apply to a specific patient, given the biological variability among individuals. Over the years, and for the particular case of Hepatocellular Carcinoma, some research studies have been developing strategies for assisting clinicians in decision making, using computational methods (e.g. machine learning techniques) to extract knowledge from the clinical data. However, these studies have some limitations that have not yet been addressed: some do not focus entirely on Hepatocellular Carcinoma patients, others have strict application boundaries, and none considers the heterogeneity between patients nor the presence of missing data, a common drawback in healthcare contexts. In this work, a real complex Hepatocellular Carcinoma database composed of heterogeneous clinical features is studied. We propose a new cluster-based oversampling approach robust to small and imbalanced datasets, which accounts for the heterogeneity of patients with Hepatocellular Carcinoma. The preprocessing procedures of this work are based on data imputation considering appropriate distance metrics for both heterogeneous and missing data (HEOM) and clustering studies to assess the underlying patient groups in the studied dataset (K-means). The final approach is applied in order to diminish the impact of underlying patient profiles with reduced sizes on survival prediction. It is based on K-means clustering and the SMOTE algorithm to build a representative dataset and use it as training example for different machine learning procedures (logistic regression and neural networks). The results are evaluated in terms of survival prediction and compared across baseline approaches that do not consider clustering and or oversampling using the Friedman rank test. Our proposed methodology coupled with neural networks outperformed all others, suggesting an improvement over the classical approaches currently used in Hepatocellular Carcinoma prediction models. Music auto-tagging is often handled in a similar manner to image classification by regarding the two-dimensional audio spectrogram as image data. However, music auto-tagging is distinguished from image classification in that the tags are highly diverse and have different levels of abstraction. Considering this issue, we propose a convolutional neural networks (CNN)-based architecture that embraces multi-level and multi-scaled features. The architecture is trained in three steps. First, we conduct supervised feature learning to capture local audio features using a set of CNNs with different input sizes. Second, we extract audio features from each layer of the pretrained convolutional networks separately and aggregate them altogether giving a long audio clip. Finally, we put them into fully connected networks and make final predictions of the tags. Our experiments show that using the combination of multi-level and multi-scale features is highly effective in music auto-tagging and the proposed method outperforms the previous state-of-the-art methods on the MagnaTagATune dataset and the Million Song Dataset. We further show that the proposed architecture is useful in transfer learning. In this paper, we propose a new classification method for five categories of lung tissues in high-resolution computed tomography (HRCT) images, with feature-based image patch approximation. We design two new feature descriptors for higher feature descriptiveness, namely the rotation-invariant Gabor-local binary patterns (RGLBP) texture descriptor and multi-coordinate histogram of oriented gradients (MCHOG) gradient descriptor. Together with intensity features, each image patch is then labeled based on its feature approximation from reference image patches. And a new patch-adaptive sparse approximation (PASA) method is designed with the following main components: minimum discrepancy criteria for sparse-based classification, patch-specific adaptation for discriminative approximation, and feature-space weighting for distance computation. The patch-wise labelings are then accumulated as probabilistic estimations for region-level classification. The proposed method is evaluated on a publicly available ILD database, showing encouraging performance improvements over the state-of-the-arts. We present an adversarial domain adaptation based deep learning approach for automatic tumor segmentation from T2-weighted MRI. Our approach is composed of two steps: (i) a tumor-aware unsupervised cross-domain adaptation (CT to MRI), followed by (ii) semi-supervised tumor segmentation using Unet trained with synthesized and limited number of original MRIs. We introduced a novel target specific loss, called tumor-aware loss, for unsupervised cross-domain adaptation that helps to preserve tumors on synthesized MRIs produced from CT images. In comparison, state-of-the art adversarial networks trained without our tumor-aware loss produced MRIs with ill-preserved or missing tumors. All networks were trained using labeled CT images from 377 patients with non-small cell lung cancer obtained from the Cancer Imaging Archive and unlabeled T2w MRIs from a completely unrelated cohort of 6 patients with pre-treatment and 36 on-treatment scans. Next, we combined 6 labeled pre-treatment MRI scans with the synthesized MRIs to boost tumor segmentation accuracy through semi-supervised learning. Semi-supervised training of cycle-GAN produced a segmentation accuracy of 0.66 computed using Dice Score Coefficient (DSC). Our method trained with only synthesized MRIs produced an accuracy of 0.74 while the same method trained in semi-supervised setting produced the best accuracy of 0.80 on test. Our results show that tumor-aware adversarial domain adaptation helps to achieve reasonably accurate cancer segmentation from limited MRI data by leveraging large CT datasets. This paper presents a new state-of-the-art for document image classification and retrieval, using features learned by deep convolutional neural networks (CNNs). In object and scene analysis, deep neural nets are capable of learning a hierarchical chain of abstraction from pixel inputs to concise and descriptive representations. The current work explores this capacity in the realm of document analysis, and confirms that this representation strategy is superior to a variety of popular hand-crafted alternatives. Experiments also show that (i) features extracted from CNNs are robust to compression, (ii) CNNs trained on non-document images transfer well to document analysis tasks, and (iii) enforcing region-specific feature-learning is unnecessary given sufficient training data. This work also makes available a new labelled subset of the IIT-CDIP collection, containing 400,000 document images across 16 categories, useful for training new CNNs for document analysis. Discriminating lung nodules as malignant or benign is still an underlying challenge. To address this challenge, radiologists need computer aided diagnosis (CAD) systems which can assist in learning discriminative imaging features corresponding to malignant and benign nodules. However, learning highly discriminative imaging features is an open problem. In this paper, our aim is to learn the most discriminative features pertaining to lung nodules by using an adversarial learning methodology. Specifically, we propose to use unsupervised learning with Deep Convolutional-Generative Adversarial Networks (DC-GANs) to generate lung nodule samples realistically. We hypothesize that imaging features of lung nodules will be discriminative if it is hard to differentiate them (fake) from real (true) nodules. To test this hypothesis, we present Visual Turing tests to two radiologists in order to evaluate the quality of the generated (fake) nodules. Extensive comparisons are performed in discerning real, generated, benign, and malignant nodules. This experimental set up allows us to validate the overall quality of the generated nodules, which can then be used to (1) improve diagnostic decisions by mining highly discriminative imaging features, (2) train radiologists for educational purposes, and (3) generate realistic samples to train deep networks with big data. Discriminating lung nodules as malignant or benign is still an underlying challenge. To address this challenge, radiologists need computer aided diagnosis (CAD) systems which can assist in learning discriminative imaging features corresponding to malignant and benign nodules. However, learning highly discriminative imaging features is an open problem. In this paper, our aim is to learn the most discriminative features pertaining to lung nodules by using an adversarial learning methodology. Specifically, we propose to use un-supervised learning with Deep Convolutional-Generative Adversarial Networks (DC-GANs) to generate lung nodule samples realistically. We hypothesize that imaging features of lung nodules will be discriminative if it is hard to differentiate them (fake) from real (true) nodules. To test this hypothesis, we present Visual Turing tests to two radiologists in order to evaluate the quality of the generated (fake) nodules. Extensive comparisons are performed in discerning real, generated, benign, and malignant nodules. This experimental set up allows us to validate the overall quality of the generated nodules, which can then be used to (1) improve diagnostic decisions by mining highly discriminative imaging features, (2) train radiologists for educational purposes, and (3) generate realistic samples to train deep networks with big data. We propose a method for inferring human attributes (such as gender, hair style, clothes style, expression, action) from images of people under large variation of viewpoint, pose, appearance, articulation and occlusion. Convolutional Neural Nets (CNN) have been shown to perform very well on large scale object recognition problems. In the context of attribute classification, however, the signal is often subtle and it may cover only a small part of the image, while the image is dominated by the effects of pose and viewpoint. Discounting for pose variation would require training on very large labeled datasets which are not presently available. Part-based models, such as poselets [4] and DPM [12] have been shown to perform well for this problem but they are limited by shallow low-level features. We propose a new method which combines part-based models and deep learning by training pose-normalized CNNs. We show substantial improvement vs. state-of-the-art methods on challenging attribute classification tasks in unconstrained settings. Experiments confirm that our method outperforms both the best part-based methods on this problem and conventional CNNs trained on the full bounding box of the person. Automatic localization of the standard plane containing complicated anatomical structures in ultrasound (US) videos remains a challenging problem. In this paper, we present a learning-based approach to locate the fet al abdominal standard plane (FASP) in US videos by constructing a domain transferred deep convolutional neural network (CNN). Compared with previous works based on low-level features, our approach is able to represent the complicated appearance of the FASP and hence achieve better classification performance. More importantly, in order to reduce the overfitting problem caused by the small amount of training samples, we propose a transfer learning strategy, which transfers the knowledge in the low layers of a base CNN trained from a large database of natural images to our task-specific CNN. Extensive experiments demonstrate that our approach outperforms the state-of-the-art method for the FASP localization as well as the CNN only trained on the limited US training samples. The proposed approach can be easily extended to other similar medical image computing problems, which often suffer from the insufficient training samples when exploiting the deep CNN to represent high-level features. In this paper we propose a new technique for learning a discriminative codebook for local feature descriptors, specifically designed for scalable landmark classification. The key contribution lies in exploiting the knowledge of correspondences within sets of feature descriptors during code-book learning. Feature correspondences are obtained using structure from motion (SfM) computation on Internet photo collections which serve as the training data. Our codebook is defined by a random forest that is trained to map corresponding feature descriptors into identical codes. Unlike prior forest-based codebook learning methods, we utilize fine-grained descriptor labels and address the challenge of training a forest with an extremely large number of labels. Our codebook is used with various existing feature encoding schemes and also a variant we propose for importance-weighted aggregation of local features. We evaluate our approach on a public dataset of 25 landmarks and our new dataset of 620 landmarks (614K images). Our approach significantly outperforms the state of the art in landmark classification. Furthermore, our method is memory efficient and scalable. Time-to-event outcomes based data can be modelled using survival regression methods which can predict these outcomes in different censored data applications in diverse fields such as engineering, economics and healthcare. Predictive models are built by inferring from the censored variable in time-to-event data, which differentiates them from other regression methods. Censoring is represented as a binary indicator variable and machine learning methods have been tuned to account for the censored attribute. Active learning from censored data using survival regression methods can make the model query a domain expert for the time-to-event label of the sampled instances. This offers higher advantages in the healthcare domain where a domain expert can interactively refine the model with his feedback. With this motivation, we address this problem by providing an active learning based survival model which uses a novel model discriminative gradient based sampling scheme. We evaluate this framework on electronic health records (EHR), publicly available survival and synthetic censored datasets of varying diversity. Experimental evaluation against state of the art survival regression methods indicates the higher discriminative ability of the proposed approach. We also present the sampling results for the proposed approach in an active learning setting which indicate better learning rates in comparison to other sampling strategies.