arXiv subjects

Le Lu

Publications and source records attributed to Le Lu.

At least 145 records · Page 8Linked to original sources

arXiv2018

Accurate Weakly-Supervised Deep Lesion Segmentation using Large-Scale Clinical Annotations: Slice-Propagated 3D Mask Generation from 2D RECIST

Volumetric lesion segmentation from computed tomography (CT) images is a powerful means to precisely assess multiple time-point lesion/tumor changes. However, because manual 3D segmentation is prohibitively time consuming, current practices rely on an imprecise surrogate called response evaluation criteria in solid tumors (RECIST). Despite their coarseness, RECIST markers are commonly found in current hospital picture and archiving systems (PACS), meaning they can provide a potentially powerful, yet extraordinarily challenging, source of weak supervision for full 3D segmentation. Toward this end, we introduce a convolutional neural network (CNN) based weakly supervised slice-propagated segmentation (WSSS) method to 1) generate the initial lesion segmentation on the axial RECIST-slice; 2) learn the data distribution on RECIST-slices; 3) extrapolate to segment the whole lesion slice by slice to finally obtain a volumetric segmentation. To validate the proposed method, we first test its performance on a fully annotated lymph node dataset, where WSSS performs comparably to its fully supervised counterparts. We then test on a comprehensive lesion dataset with 32,735 RECIST marks, where we report a mean Dice score of 92% on RECIST-marked slices and 76% on the entire 3D volumes.

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arXiv2018

Pancreas Segmentation in CT and MRI Images via Domain Specific Network Designing and Recurrent Neural Contextual Learning

Automatic pancreas segmentation in radiology images, eg., computed tomography (CT) and magnetic resonance imaging (MRI), is frequently required by computer-aided screening, diagnosis, and quantitative assessment. Yet pancreas is a challenging abdominal organ to segment due to the high inter-patient anatomical variability in both shape and volume metrics. Recently, convolutional neural networks (CNNs) have demonstrated promising performance on accurate segmentation of pancreas. However, the CNN-based method often suffers from segmentation discontinuity for reasons such as noisy image quality and blurry pancreatic boundary. From this point, we propose to introduce recurrent neural networks (RNNs) to address the problem of spatial non-smoothness of inter-slice pancreas segmentation across adjacent image slices. To inference initial segmentation, we first train a 2D CNN sub-network, where we modify its network architecture with deep-supervision and multi-scale feature map aggregation so that it can be trained from scratch with small-sized training data and presents superior performance than transferred models. Thereafter, the successive CNN outputs are processed by another RNN sub-network, which refines the consistency of segmented shapes. More specifically, the RNN sub-network consists convolutional long short-term memory (CLSTM) units in both top-down and bottom-up directions, which regularizes the segmentation of an image by integrating predictions of its neighboring slices. We train the stacked CNN-RNN model end-to-end and perform quantitative evaluations on both CT and MRI images.

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arXiv2018

Unsupervised Body Part Regression via Spatially Self-ordering Convolutional Neural Networks

Automatic body part recognition for CT slices can benefit various medical image applications. Recent deep learning methods demonstrate promising performance, with the requirement of large amounts of labeled images for training. The intrinsic structural or superior-inferior slice ordering information in CT volumes is not fully exploited. In this paper, we propose a convolutional neural network (CNN) based Unsupervised Body part Regression (UBR) algorithm to address this problem. A novel unsupervised learning method and two inter-sample CNN loss functions are presented. Distinct from previous work, UBR builds a coordinate system for the human body and outputs a continuous score for each axial slice, representing the normalized position of the body part in the slice. The training process of UBR resembles a self-organization process: slice scores are learned from inter-slice relationships. The training samples are unlabeled CT volumes that are abundant, thus no extra annotation effort is needed. UBR is simple, fast, and accurate. Quantitative and qualitative experiments validate its effectiveness. In addition, we show two applications of UBR in network initialization and anomaly detection.

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arXiv2018

Self-Learning to Detect and Segment Cysts in Lung CT Images without Manual Annotation

Image segmentation is a fundamental problem in medical image analysis. In recent years, deep neural networks achieve impressive performances on many medical image segmentation tasks by supervised learning on large manually annotated data. However, expert annotations on big medical datasets are tedious, expensive or sometimes unavailable. Weakly supervised learning could reduce the effort for annotation but still required certain amounts of expertise. Recently, deep learning shows a potential to produce more accurate predictions than the original erroneous labels. Inspired by this, we introduce a very weakly supervised learning method, for cystic lesion detection and segmentation in lung CT images, without any manual annotation. Our method works in a self-learning manner, where segmentation generated in previous steps (first by unsupervised segmentation then by neural networks) is used as ground truth for the next level of network learning. Experiments on a cystic lung lesion dataset show that the deep learning could perform better than the initial unsupervised annotation, and progressively improve itself after self-learning.

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arXiv2018

Deep LOGISMOS: Deep Learning Graph-based 3D Segmentation of Pancreatic Tumors on CT scans

This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.

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arXiv2018

Accurate Weakly Supervised Deep Lesion Segmentation on CT Scans: Self-Paced 3D Mask Generation from RECIST

Volumetric lesion segmentation via medical imaging is a powerful means to precisely assess multiple time-point lesion/tumor changes. Because manual 3D segmentation is prohibitively time consuming and requires radiological experience, current practices rely on an imprecise surrogate called response evaluation criteria in solid tumors (RECIST). Despite their coarseness, RECIST marks are commonly found in current hospital picture and archiving systems (PACS), meaning they can provide a potentially powerful, yet extraordinarily challenging, source of weak supervision for full 3D segmentation. Toward this end, we introduce a convolutional neural network based weakly supervised self-paced segmentation (WSSS) method to 1) generate the initial lesion segmentation on the axial RECIST-slice; 2) learn the data distribution on RECIST-slices; 3) adapt to segment the whole volume slice by slice to finally obtain a volumetric segmentation. In addition, we explore how super-resolution images (2~5 times beyond the physical CT imaging), generated from a proposed stacked generative adversarial network, can aid the WSSS performance. We employ the DeepLesion dataset, a comprehensive CT-image lesion dataset of 32,735 PACS-bookmarked findings, which include lesions, tumors, and lymph nodes of varying sizes, categories, body regions and surrounding contexts. These are drawn from 10,594 studies of 4,459 patients. We also validate on a lymph-node dataset, where 3D ground truth masks are available for all images. For the DeepLesion dataset, we report mean Dice coefficients of 93% on RECIST-slices and 76% in 3D lesion volumes. We further validate using a subjective user study, where an experienced radiologist accepted our WSSS-generated lesion segmentation results with a high probability of 92.4%.

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arXiv2018

DeepPap: Deep Convolutional Networks for Cervical Cell Classification

Automation-assisted cervical screening via Pap smear or liquid-based cytology (LBC) is a highly effective cell imaging based cancer detection tool, where cells are partitioned into "abnormal" and "normal" categories. However, the success of most traditional classification methods relies on the presence of accurate cell segmentations. Despite sixty years of research in this field, accurate segmentation remains a challenge in the presence of cell clusters and pathologies. Moreover, previous classification methods are only built upon the extraction of hand-crafted features, such as morphology and texture. This paper addresses these limitations by proposing a method to directly classify cervical cells - without prior segmentation - based on deep features, using convolutional neural networks (ConvNets). First, the ConvNet is pre-trained on a natural image dataset. It is subsequently fine-tuned on a cervical cell dataset consisting of adaptively re-sampled image patches coarsely centered on the nuclei. In the testing phase, aggregation is used to average the prediction scores of a similar set of image patches. The proposed method is evaluated on both Pap smear and LBC datasets. Results show that our method outperforms previous algorithms in classification accuracy (98.3%), area under the curve (AUC) (0.99) values, and especially specificity (98.3%), when applied to the Herlev benchmark Pap smear dataset and evaluated using five-fold cross-validation. Similar superior performances are also achieved on the HEMLBC (H&E stained manual LBC) dataset. Our method is promising for the development of automation-assisted reading systems in primary cervical screening.

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arXiv2018

Convolutional Invasion and Expansion Networks for Tumor Growth Prediction

Tumor growth is associated with cell invasion and mass-effect, which are traditionally formulated by mathematical models, namely reaction-diffusion equations and biomechanics. Such models can be personalized based on clinical measurements to build the predictive models for tumor growth. In this paper, we investigate the possibility of using deep convolutional neural networks (ConvNets) to directly represent and learn the cell invasion and mass-effect, and to predict the subsequent involvement regions of a tumor. The invasion network learns the cell invasion from information related to metabolic rate, cell density and tumor boundary derived from multimodal imaging data. The expansion network models the mass-effect from the growing motion of tumor mass. We also study different architectures that fuse the invasion and expansion networks, in order to exploit the inherent correlations among them. Our network can easily be trained on population data and personalized to a target patient, unlike most previous mathematical modeling methods that fail to incorporate population data. Quantitative experiments on a pancreatic tumor data set show that the proposed method substantially outperforms a state-of-the-art mathematical model-based approach in both accuracy and efficiency, and that the information captured by each of the two subnetworks are complementary.

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arXiv2018

TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-rays

Chest X-rays are one of the most common radiological examinations in daily clinical routines. Reporting thorax diseases using chest X-rays is often an entry-level task for radiologist trainees. Yet, reading a chest X-ray image remains a challenging job for learning-oriented machine intelligence, due to (1) shortage of large-scale machine-learnable medical image datasets, and (2) lack of techniques that can mimic the high-level reasoning of human radiologists that requires years of knowledge accumulation and professional training. In this paper, we show the clinical free-text radiological reports can be utilized as a priori knowledge for tackling these two key problems. We propose a novel Text-Image Embedding network (TieNet) for extracting the distinctive image and text representations. Multi-level attention models are integrated into an end-to-end trainable CNN-RNN architecture for highlighting the meaningful text words and image regions. We first apply TieNet to classify the chest X-rays by using both image features and text embeddings extracted from associated reports. The proposed auto-annotation framework achieves high accuracy (over 0.9 on average in AUCs) in assigning disease labels for our hand-label evaluation dataset. Furthermore, we transform the TieNet into a chest X-ray reporting system. It simulates the reporting process and can output disease classification and a preliminary report together. The classification results are significantly improved (6% increase on average in AUCs) compared to the state-of-the-art baseline on an unseen and hand-labeled dataset (OpenI).

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arXiv2017

Unsupervised Joint Mining of Deep Features and Image Labels for Large-scale Radiology Image Categorization and Scene Recognition

The recent rapid and tremendous success of deep convolutional neural networks (CNN) on many challenging computer vision tasks largely derives from the accessibility of the well-annotated ImageNet and PASCAL VOC datasets. Nevertheless, unsupervised image categorization (i.e., without the ground-truth labeling) is much less investigated, yet critically important and difficult when annotations are extremely hard to obtain in the conventional way of "Google Search" and crowd sourcing. We address this problem by presenting a looped deep pseudo-task optimization (LDPO) framework for joint mining of deep CNN features and image labels. Our method is conceptually simple and rests upon the hypothesized "convergence" of better labels leading to better trained CNN models which in turn feed more discriminative image representations to facilitate more meaningful clusters/labels. Our proposed method is validated in tackling two important applications: 1) Large-scale medical image annotation has always been a prohibitively expensive and easily-biased task even for well-trained radiologists. Significantly better image categorization results are achieved via our proposed approach compared to the previous state-of-the-art method. 2) Unsupervised scene recognition on representative and publicly available datasets with our proposed technique is examined. The LDPO achieves excellent quantitative scene classification results. On the MIT indoor scene dataset, it attains a clustering accuracy of 75.3%, compared to the state-of-the-art supervised classification accuracy of 81.0% (when both are based on the VGG-VD model).

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arXiv2017

NegBio: a high-performance tool for negation and uncertainty detection in radiology reports

Negative and uncertain medical findings are frequent in radiology reports, but discriminating them from positive findings remains challenging for information extraction. Here, we propose a new algorithm, NegBio, to detect negative and uncertain findings in radiology reports. Unlike previous rule-based methods, NegBio utilizes patterns on universal dependencies to identify the scope of triggers that are indicative of negation or uncertainty. We evaluated NegBio on four datasets, including two public benchmarking corpora of radiology reports, a new radiology corpus that we annotated for this work, and a public corpus of general clinical texts. Evaluation on these datasets demonstrates that NegBio is highly accurate for detecting negative and uncertain findings and compares favorably to a widely-used state-of-the-art system NegEx (an average of 9.5% improvement in precision and 5.1% in F1-score).

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arXiv2017

ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

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arXiv2017

DeepLesion: Automated Deep Mining, Categorization and Detection of Significant Radiology Image Findings using Large-Scale Clinical Lesion Annotations

Extracting, harvesting and building large-scale annotated radiological image datasets is a greatly important yet challenging problem. It is also the bottleneck to designing more effective data-hungry computing paradigms (e.g., deep learning) for medical image analysis. Yet, vast amounts of clinical annotations (usually associated with disease image findings and marked using arrows, lines, lesion diameters, segmentation, etc.) have been collected over several decades and stored in hospitals' Picture Archiving and Communication Systems. In this paper, we mine and harvest one major type of clinical annotation data - lesion diameters annotated on bookmarked images - to learn an effective multi-class lesion detector via unsupervised and supervised deep Convolutional Neural Networks (CNN). Our dataset is composed of 33,688 bookmarked radiology images from 10,825 studies of 4,477 unique patients. For every bookmarked image, a bounding box is created to cover the target lesion based on its measured diameters. We categorize the collection of lesions using an unsupervised deep mining scheme to generate clustered pseudo lesion labels. Next, we adopt a regional-CNN method to detect lesions of multiple categories, regardless of missing annotations (normally only one lesion is annotated, despite the presence of multiple co-existing findings). Our integrated mining, categorization and detection framework is validated with promising empirical results, as a scalable, universal or multi-purpose CAD paradigm built upon abundant retrospective medical data. Furthermore, we demonstrate that detection accuracy can be significantly improved by incorporating pseudo lesion labels (e.g., Liver lesion/tumor, Lung nodule/tumor, Abdomen lesions, Chest lymph node and others). This dataset will be made publicly available (under the open science initiative).

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arXiv2017

Improving Deep Pancreas Segmentation in CT and MRI Images via Recurrent Neural Contextual Learning and Direct Loss Function

Deep neural networks have demonstrated very promising performance on accurate segmentation of challenging organs (e.g., pancreas) in abdominal CT and MRI scans. The current deep learning approaches conduct pancreas segmentation by processing sequences of 2D image slices independently through deep, dense per-pixel masking for each image, without explicitly enforcing spatial consistency constraint on segmentation of successive slices. We propose a new convolutional/recurrent neural network architecture to address the contextual learning and segmentation consistency problem. A deep convolutional sub-network is first designed and pre-trained from scratch. The output layer of this network module is then connected to recurrent layers and can be fine-tuned for contextual learning, in an end-to-end manner. Our recurrent sub-network is a type of Long short-term memory (LSTM) network that performs segmentation on an image by integrating its neighboring slice segmentation predictions, in the form of a dependent sequence processing. Additionally, a novel segmentation-direct loss function (named Jaccard Loss) is proposed and deep networks are trained to optimize Jaccard Index (JI) directly. Extensive experiments are conducted to validate our proposed deep models, on quantitative pancreas segmentation using both CT and MRI scans. Our method outperforms the state-of-the-art work on CT [11] and MRI pancreas segmentation [1], respectively.

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arXiv2017

Progressive and Multi-Path Holistically Nested Neural Networks for Pathological Lung Segmentation from CT Images

Pathological lung segmentation (PLS) is an important, yet challenging, medical image application due to the wide variability of pathological lung appearance and shape. Because PLS is often a pre-requisite for other imaging analytics, methodological simplicity and generality are key factors in usability. Along those lines, we present a bottom-up deep-learning based approach that is expressive enough to handle variations in appearance, while remaining unaffected by any variations in shape. We incorporate the deeply supervised learning framework, but enhance it with a simple, yet effective, progressive multi-path scheme, which more reliably merges outputs from different network stages. The result is a deep model able to produce finer detailed masks, which we call progressive holistically-nested networks (P-HNNs). Using extensive cross-validation, our method is tested on multi-institutional datasets comprising 929 CT scans (848 publicly available), of pathological lungs, reporting mean dice scores of 0.985 and demonstrating significant qualitative and quantitative improvements over state-of-the art approaches.

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arXiv2017

Personalized Pancreatic Tumor Growth Prediction via Group Learning

Tumor growth prediction, a highly challenging task, has long been viewed as a mathematical modeling problem, where the tumor growth pattern is personalized based on imaging and clinical data of a target patient. Though mathematical models yield promising results, their prediction accuracy may be limited by the absence of population trend data and personalized clinical characteristics. In this paper, we propose a statistical group learning approach to predict the tumor growth pattern that incorporates both the population trend and personalized data, in order to discover high-level features from multimodal imaging data. A deep convolutional neural network approach is developed to model the voxel-wise spatio-temporal tumor progression. The deep features are combined with the time intervals and the clinical factors to feed a process of feature selection. Our predictive model is pretrained on a group data set and personalized on the target patient data to estimate the future spatio-temporal progression of the patient's tumor. Multimodal imaging data at multiple time points are used in the learning, personalization and inference stages. Our method achieves a Dice coefficient of 86.8% +- 3.6% and RVD of 7.9% +- 5.4% on a pancreatic tumor data set, outperforming the DSC of 84.4% +- 4.0% and RVD 13.9% +- 9.8% obtained by a previous state-of-the-art model-based method.

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arXiv2017

Spatial Aggregation of Holistically-Nested Convolutional Neural Networks for Automated Pancreas Localization and Segmentation

Accurate and automatic organ segmentation from 3D radiological scans is an important yet challenging problem for medical image analysis. Specifically, the pancreas demonstrates very high inter-patient anatomical variability in both its shape and volume. In this paper, we present an automated system using 3D computed tomography (CT) volumes via a two-stage cascaded approach: pancreas localization and segmentation. For the first step, we localize the pancreas from the entire 3D CT scan, providing a reliable bounding box for the more refined segmentation step. We introduce a fully deep-learning approach, based on an efficient application of holistically-nested convolutional networks (HNNs) on the three orthogonal axial, sagittal, and coronal views. The resulting HNN per-pixel probability maps are then fused using pooling to reliably produce a 3D bounding box of the pancreas that maximizes the recall. We show that our introduced localizer compares favorably to both a conventional non-deep-learning method and a recent hybrid approach based on spatial aggregation of superpixels using random forest classification. The second, segmentation, phase operates within the computed bounding box and integrates semantic mid-level cues of deeply-learned organ interior and boundary maps, obtained by two additional and separate realizations of HNNs. By integrating these two mid-level cues, our method is capable of generating boundary-preserving pixel-wise class label maps that result in the final pancreas segmentation. Quantitative evaluation is performed on a publicly available dataset of 82 patient CT scans using 4-fold cross-validation (CV). We achieve a Dice similarity coefficient (DSC) of 81.27+/-6.27% in validation, which significantly outperforms previous state-of-the art methods that report DSCs of 71.80+/-10.70% and 78.01+/-8.20%, respectively, using the same dataset.

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arXiv2017

Holistic Interstitial Lung Disease Detection using Deep Convolutional Neural Networks: Multi-label Learning and Unordered Pooling

Accurately predicting and detecting interstitial lung disease (ILD) patterns given any computed tomography (CT) slice without any pre-processing prerequisites, such as manually delineated regions of interest (ROIs), is a clinically desirable, yet challenging goal. The majority of existing work relies on manually-provided ILD ROIs to extract sampled 2D image patches from CT slices and, from there, performs patch-based ILD categorization. Acquiring manual ROIs is labor intensive and serves as a bottleneck towards fully-automated CT imaging ILD screening over large-scale populations. Furthermore, despite the considerable high frequency of more than one ILD pattern on a single CT slice, previous works are only designed to detect one ILD pattern per slice or patch. To tackle these two critical challenges, we present multi-label deep convolutional neural networks (CNNs) for detecting ILDs from holistic CT slices (instead of ROIs or sub-images). Conventional single-labeled CNN models can be augmented to cope with the possible presence of multiple ILD pattern labels, via 1) continuous-valued deep regression based robust norm loss functions or 2) a categorical objective as the sum of element-wise binary logistic losses. Our methods are evaluated and validated using a publicly available database of 658 patient CT scans under five-fold cross-validation, achieving promising performance on detecting four major ILD patterns: Ground Glass, Reticular, Honeycomb, and Emphysema. We also investigate the effectiveness of a CNN activation-based deep-feature encoding scheme using Fisher vector encoding, which treats ILD detection as spatially-unordered deep texture classification.

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