arXiv subjects

Ke Yan

Publications and source records attributed to Ke Yan.

At least 109 records · Page 6Linked to original sources

arXiv2020

Harvesting, Detecting, and Characterizing Liver Lesions from Large-scale Multi-phase CT Data via Deep Dynamic Texture Learning

Non-invasive radiological-based lesion characterization and identification, e.g., to differentiate cancer subtypes, has long been a major aim to enhance oncological diagnosis and treatment procedures. Here we study a specific population of human subjects, with the hope of reducing the need for invasive surgical biopsies of liver cancer patients, which can cause many harmful side-effects. To this end, we propose a fully-automated and multi-stage liver tumor characterization framework designed for dynamic contrast computed tomography (CT). Our system comprises four sequential processes of tumor proposal detection, tumor harvesting, primary tumor site selection, and deep texture-based tumor characterization. Our main contributions are that, (1) we propose a 3D non-isotropic anchor-free detection method for liver lesions; (2) we present and validate spatially adaptivedeep texture (SaDT) learning, which allows for more precise characterization of liver lesions; (3) using a semi-automatic process, we bootstrap off of 200 gold standard annotations to curate another 1001 patients. Experimental evaluations demonstrate that our new data curation strategy, combined with the SaDT deep dynamic texture analysis, can effectively improve the mean F1 scores by >8.6% compared with baselines, in differentiating four major liver lesion types. Our F1 score of (hepatocellular carcinoma versus remaining subclasses) is 0.763, which is higher than reported human observer performance using dynamic CT and comparable to an advanced magnetic resonance imagery protocol. Apart from demonstrating the benefits of our data curation approach and physician-inspired workflow, these results also indicate that analyzing texture features, instead of standard object-based analysis, is a promising strategy for lesion differentiation.

cs.CV↗

arXiv2020

Deep Volumetric Universal Lesion Detection using Light-Weight Pseudo 3D Convolution and Surface Point Regression

Identifying, measuring and reporting lesions accurately and comprehensively from patient CT scans are important yet time-consuming procedures for physicians. Computer-aided lesion/significant-findings detection techniques are at the core of medical imaging, which remain very challenging due to the tremendously large variability of lesion appearance, location and size distributions in 3D imaging. In this work, we propose a novel deep anchor-free one-stage VULD framework that incorporates (1) P3DC operators to recycle the architectural configurations and pre-trained weights from the off-the-shelf 2D networks, especially ones with large capacities to cope with data variance, and (2) a new SPR method to effectively regress the 3D lesion spatial extents by pinpointing their representative key points on lesion surfaces. Experimental validations are first conducted on the public large-scale NIH DeepLesion dataset where our proposed method delivers new state-of-the-art quantitative performance. We also test VULD on our in-house dataset for liver tumor detection. VULD generalizes well in both large-scale and small-sized tumor datasets in CT imaging.

cs.CV↗

arXiv2020

Lymph Node Gross Tumor Volume Detection in Oncology Imaging via Relationship Learning Using Graph Neural Network

Determining the spread of GTV$_{LN}$ is essential in defining the respective resection or irradiating regions for the downstream workflows of surgical resection and radiotherapy for many cancers. Different from the more common enlarged lymph node (LN), GTV$_{LN}$ also includes smaller ones if associated with high positron emission tomography signals and/or any metastasis signs in CT. This is a daunting task. In this work, we propose a unified LN appearance and inter-LN relationship learning framework to detect the true GTV$_{LN}$. This is motivated by the prior clinical knowledge that LNs form a connected lymphatic system, and the spread of cancer cells among LNs often follows certain pathways. Specifically, we first utilize a 3D convolutional neural network with ROI-pooling to extract the GTV$_{LN}$'s instance-wise appearance features. Next, we introduce a graph neural network to further model the inter-LN relationships where the global LN-tumor spatial priors are included in the learning process. This leads to an end-to-end trainable network to detect by classifying GTV$_{LN}$. We operate our model on a set of GTV$_{LN}$ candidates generated by a preliminary 1st-stage method, which has a sensitivity of $>85\%$ at the cost of high false positive (FP) ($>15$ FPs per patient). We validate our approach on a radiotherapy dataset with 142 paired PET/RTCT scans containing the chest and upper abdominal body parts. The proposed method significantly improves over the state-of-the-art (SOTA) LN classification method by $5.5\%$ and $13.1\%$ in F1 score and the averaged sensitivity value at $2, 3, 4, 6$ FPs per patient, respectively.

cs.CV↗

arXiv2020

Lymph Node Gross Tumor Volume Detection and Segmentation via Distance-based Gating using 3D CT/PET Imaging in Radiotherapy

Finding, identifying and segmenting suspicious cancer metastasized lymph nodes from 3D multi-modality imaging is a clinical task of paramount importance. In radiotherapy, they are referred to as Lymph Node Gross Tumor Volume (GTVLN). Determining and delineating the spread of GTVLN is essential in defining the corresponding resection and irradiating regions for the downstream workflows of surgical resection and radiotherapy of various cancers. In this work, we propose an effective distance-based gating approach to simulate and simplify the high-level reasoning protocols conducted by radiation oncologists, in a divide-and-conquer manner. GTVLN is divided into two subgroups of tumor-proximal and tumor-distal, respectively, by means of binary or soft distance gating. This is motivated by the observation that each category can have distinct though overlapping distributions of appearance, size and other LN characteristics. A novel multi-branch detection-by-segmentation network is trained with each branch specializing on learning one GTVLN category features, and outputs from multi-branch are fused in inference. The proposed method is evaluated on an in-house dataset of $141$ esophageal cancer patients with both PET and CT imaging modalities. Our results validate significant improvements on the mean recall from $72.5\%$ to $78.2\%$, as compared to previous state-of-the-art work. The highest achieved GTVLN recall of $82.5\%$ at $20\%$ precision is clinically relevant and valuable since human observers tend to have low sensitivity (around $80\%$ for the most experienced radiation oncologists, as reported by literature).

eess.IV↗

arXiv2020

CFAD: Coarse-to-Fine Action Detector for Spatiotemporal Action Localization

Most current pipelines for spatio-temporal action localization connect frame-wise or clip-wise detection results to generate action proposals, where only local information is exploited and the efficiency is hindered by dense per-frame localization. In this paper, we propose Coarse-to-Fine Action Detector (CFAD),an original end-to-end trainable framework for efficient spatio-temporal action localization. The CFAD introduces a new paradigm that first estimates coarse spatio-temporal action tubes from video streams, and then refines the tubes' location based on key timestamps. This concept is implemented by two key components, the Coarse and Refine Modules in our framework. The parameterized modeling of long temporal information in the Coarse Module helps obtain accurate initial tube estimation, while the Refine Module selectively adjusts the tube location under the guidance of key timestamps. Against other methods, theproposed CFAD achieves competitive results on action detection benchmarks of UCF101-24, UCFSports and JHMDB-21 with inference speed that is 3.3x faster than the nearest competitors.

cs.CV↗

arXiv2020

Reliable Liver Fibrosis Assessment from Ultrasound using Global Hetero-Image Fusion and View-Specific Parameterization

Ultrasound (US) is a critical modality for diagnosing liver fibrosis. Unfortunately, assessment is very subjective, motivating automated approaches. We introduce a principled deep convolutional neural network (CNN) workflow that incorporates several innovations. First, to avoid overfitting on non-relevant image features, we force the network to focus on a clinical region of interest (ROI), encompassing the liver parenchyma and upper border. Second, we introduce global heteroimage fusion (GHIF), which allows the CNN to fuse features from any arbitrary number of images in a study, increasing its versatility and flexibility. Finally, we use 'style'-based view-specific parameterization (VSP) to tailor the CNN processing for different viewpoints of the liver, while keeping the majority of parameters the same across views. Experiments on a dataset of 610 patient studies (6979 images) demonstrate that our pipeline can contribute roughly 7% and 22% improvements in partial area under the curve and recall at 90% precision, respectively, over conventional classifiers, validating our approach to this crucial problem.

eess.IV↗

arXiv2020

One Click Lesion RECIST Measurement and Segmentation on CT Scans

In clinical trials, one of the radiologists' routine work is to measure tumor sizes on medical images using the RECIST criteria (Response Evaluation Criteria In Solid Tumors). However, manual measurement is tedious and subject to inter-observer variability. We propose a unified framework named SEENet for semi-automatic lesion \textit{SE}gmentation and RECIST \textit{E}stimation on a variety of lesions over the entire human body. The user is only required to provide simple guidance by clicking once near the lesion. SEENet consists of two main parts. The first one extracts the lesion of interest with the one-click guidance, roughly segments the lesion, and estimates its RECIST measurement. Based on the results of the first network, the second one refines the lesion segmentation and RECIST estimation. SEENet achieves state-of-the-art performance in lesion segmentation and RECIST estimation on the large-scale public DeepLesion dataset. It offers a practical tool for radiologists to generate reliable lesion measurements (i.e. segmentation mask and RECIST) with minimal human effort and greatly reduced time.

eess.IV↗

arXiv2020

Universal Lesion Detection by Learning from Multiple Heterogeneously Labeled Datasets

Lesion detection is an important problem within medical imaging analysis. Most previous work focuses on detecting and segmenting a specialized category of lesions (e.g., lung nodules). However, in clinical practice, radiologists are responsible for finding all possible types of anomalies. The task of universal lesion detection (ULD) was proposed to address this challenge by detecting a large variety of lesions from the whole body. There are multiple heterogeneously labeled datasets with varying label completeness: DeepLesion, the largest dataset of 32,735 annotated lesions of various types, but with even more missing annotation instances; and several fully-labeled single-type lesion datasets, such as LUNA for lung nodules and LiTS for liver tumors. In this work, we propose a novel framework to leverage all these datasets together to improve the performance of ULD. First, we learn a multi-head multi-task lesion detector using all datasets and generate lesion proposals on DeepLesion. Second, missing annotations in DeepLesion are retrieved by a new method of embedding matching that exploits clinical prior knowledge. Last, we discover suspicious but unannotated lesions using knowledge transfer from single-type lesion detectors. In this way, reliable positive and negative regions are obtained from partially-labeled and unlabeled images, which are effectively utilized to train ULD. To assess the clinically realistic protocol of 3D volumetric ULD, we fully annotated 1071 CT sub-volumes in DeepLesion. Our method outperforms the current state-of-the-art approach by 29% in the metric of average sensitivity.

cs.CV↗

arXiv2020

Detecting Scatteredly-Distributed, Small, andCritically Important Objects in 3D OncologyImaging via Decision Stratification

Finding and identifying scatteredly-distributed, small, and critically important objects in 3D oncology images is very challenging. We focus on the detection and segmentation of oncology-significant (or suspicious cancer metastasized) lymph nodes (OSLNs), which has not been studied before as a computational task. Determining and delineating the spread of OSLNs is essential in defining the corresponding resection/irradiating regions for the downstream workflows of surgical resection and radiotherapy of various cancers. For patients who are treated with radiotherapy, this task is performed by experienced radiation oncologists that involves high-level reasoning on whether LNs are metastasized, which is subject to high inter-observer variations. In this work, we propose a divide-and-conquer decision stratification approach that divides OSLNs into tumor-proximal and tumor-distal categories. This is motivated by the observation that each category has its own different underlying distributions in appearance, size and other characteristics. Two separate detection-by-segmentation networks are trained per category and fused. To further reduce false positives (FP), we present a novel global-local network (GLNet) that combines high-level lesion characteristics with features learned from localized 3D image patches. Our method is evaluated on a dataset of 141 esophageal cancer patients with PET and CT modalities (the largest to-date). Our results significantly improve the recall from $45\%$ to $67\%$ at $3$ FPs per patient as compared to previous state-of-the-art methods. The highest achieved OSLN recall of $0.828$ is clinically relevant and valuable.

cs.CV↗

arXiv2020

Some geometric correspondences for homothetic navigation

In this paper, we provide conceptional explanations for the geodesic and Jacobi field correspondences for homothetic navigation, and then let them guide us to the shortcuts to some well known flag curvature and S-curvature formulas. They also help us directly see the local correspondence between isoparametric functions or isoparametric hypersurfaces, which generalizes the classification works of Q. He and her coworkers for isoparametric hypersurfaces in Randers space forms and Funk spaces.

math.DG↗

arXiv2019

Integrating high-quality dielectrics with one-nanometer equivalent oxide thickness on two-dimensional electronic devices

Two-dimensional (2D) semiconductors are widely recognized as attractive channel materials for low-power electronics. However, an unresolved challenge is the integration of high-quality, ultrathin high-\k{appa} dielectrics that fully meet the roadmap requirements for low-power applications. With a dangling-bond free surface, the deposition of dielectrics by atomic layer deposition (ALD) on 2D materials is usually characterized with non-uniform nucleation and island formation, producing a highly porous dielectric layer with serious leakage particularly at the small equivalent oxide thickness (EOT) limit. Here, we report the robust ALD of highly uniform high-\k{appa} dielectric on 2D semiconductors by using ~0.3 nm-thick exclusively monolayer molecular crystal as seeding layer. Ultrathin dielectrics down to 1 nm EOT is realized on graphene, MoS2 and WSe2, with considerably reduced roughness, density of interface states, leakage current and improved breakdown field compared to prior methods. Taking advantage of the reduced EOT, we demonstrate graphene RF transistors operating at 60 GHz, as well as MoS2 and WSe2 complementary metal-oxide-semiconductor (CMOS) transistors with Vdd =0.8 V and ideal subthreshold swing (SS) of 60 mV/dec, 20 nm-channel-length MoS2 transistors with on/off ratio over 10^7. These studies highlight that our dielectric integration method is generally applicable for different 2D materials, and compatible with top-down fabrication process on large-area chemical vapor deposited films.

physics.app-ph↗

arXiv2019

MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation

When reading medical images such as a computed tomography (CT) scan, radiologists generally search across the image to find lesions, characterize and measure them, and then describe them in the radiological report. To automate this process, we propose a multitask universal lesion analysis network (MULAN) for joint detection, tagging, and segmentation of lesions in a variety of body parts, which greatly extends existing work of single-task lesion analysis on specific body parts. MULAN is based on an improved Mask R-CNN framework with three head branches and a 3D feature fusion strategy. It achieves the state-of-the-art accuracy in the detection and tagging tasks on the DeepLesion dataset, which contains 32K lesions in the whole body. We also analyze the relationship between the three tasks and show that tag predictions can improve detection accuracy via a score refinement layer.

cs.CV↗

arXiv2019

A self-attention based deep learning method for lesion attribute detection from CT reports

In radiology, radiologists not only detect lesions from the medical image, but also describe them with various attributes such as their type, location, size, shape, and intensity. While these lesion attributes are rich and useful in many downstream clinical applications, how to extract them from the radiology reports is less studied. This paper outlines a novel deep learning method to automatically extract attributes of lesions of interest from the clinical text. Different from classical CNN models, we integrated the multi-head self-attention mechanism to handle the long-distance information in the sentence, and to jointly correlate different portions of sentence representation subspaces in parallel. Evaluation on an in-house corpus demonstrates that our method can achieve high performance with 0.848 in precision, 0.788 in recall, and 0.815 in F-score. The new method and constructed corpus will enable us to build automatic systems with a higher-level understanding of the radiological world.

cs.CL↗

arXiv2019

Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning from Radiology Reports and Label Ontology

In radiologists' routine work, one major task is to read a medical image, e.g., a CT scan, find significant lesions, and describe them in the radiology report. In this paper, we study the lesion description or annotation problem. Given a lesion image, our aim is to predict a comprehensive set of relevant labels, such as the lesion's body part, type, and attributes, which may assist downstream fine-grained diagnosis. To address this task, we first design a deep learning module to extract relevant semantic labels from the radiology reports associated with the lesion images. With the images and text-mined labels, we propose a lesion annotation network (LesaNet) based on a multilabel convolutional neural network (CNN) to learn all labels holistically. Hierarchical relations and mutually exclusive relations between the labels are leveraged to improve the label prediction accuracy. The relations are utilized in a label expansion strategy and a relational hard example mining algorithm. We also attach a simple score propagation layer on LesaNet to enhance recall and explore implicit relation between labels. Multilabel metric learning is combined with classification to enable interpretable prediction. We evaluated LesaNet on the public DeepLesion dataset, which contains over 32K diverse lesion images. Experiments show that LesaNet can precisely annotate the lesions using an ontology of 171 fine-grained labels with an average AUC of 0.9344.

cs.CV↗

arXiv2019

Fine-grained lesion annotation in CT images with knowledge mined from radiology reports

In radiologists' routine work, one major task is to read a medical image, e.g., a CT scan, find significant lesions, and write sentences in the radiology report to describe them. In this paper, we study the lesion description or annotation problem as an important step of computer-aided diagnosis (CAD). Given a lesion image, our aim is to predict multiple relevant labels, such as the lesion's body part, type, and attributes. To address this problem, we define a set of 145 labels based on RadLex to describe a large variety of lesions in the DeepLesion dataset. We directly mine training labels from the lesion's corresponding sentence in the radiology report, which requires minimal manual effort and is easily generalizable to large data and label sets. A multi-label convolutional neural network is then proposed for images with multi-scale structure and a noise-robust loss. Quantitative and qualitative experiments demonstrate the effectiveness of the framework. The average area under ROC curve on 1,872 test lesions is 0.9083.

cs.CV↗

arXiv2019

Emerging Privacy Issues and Solutions in Cyber-Enabled Sharing Services: From Multiple Perspectives

Fast development of sharing services has become a crucial part of the cyber-enabled world construction process, as sharing services reinvent how people exchange and obtain goods or services. However, privacy leakage or disclosure remains a key concern during the sharing service development process. While significant efforts have been undertaken to address various privacy issues in recent years, there is a surprising lack of review for privacy concerns in the cyber-enabled sharing world. To bridge the gap, in this study, we survey and evaluate existing and emerging privacy issues relating to sharing services from various perspectives. Differing from existing similar works on surveying sharing practices in various fields, our work comprehensively covers six branches of sharing services in the cyber-enabled world and selects solutions mostly from the recent five to six years. We conclude the issues and solutions from three perspectives, namely, from users', platforms' and service providers' perspectives. Hot topics and less discussed topics are identified, which provides hints to researchers for their future studies.

cs.CY↗

arXiv2019

ULDor: A Universal Lesion Detector for CT Scans with Pseudo Masks and Hard Negative Example Mining

Automatic lesion detection from computed tomography (CT) scans is an important task in medical imaging analysis. It is still very challenging due to similar appearances (e.g. intensity and texture) between lesions and other tissues, making it especially difficult to develop a universal lesion detector. Instead of developing a specific-type lesion detector, this work builds a Universal Lesion Detector (ULDor) based on Mask R-CNN, which is able to detect all different kinds of lesions from whole body parts. As a state-of-the-art object detector, Mask R-CNN adds a branch for predicting segmentation masks on each Region of Interest (RoI) to improve the detection performance. However, it is almost impossible to manually annotate a large-scale dataset with pixel-level lesion masks to train the Mask R-CNN for lesion detection. To address this problem, this work constructs a pseudo mask for each lesion region that can be considered as a surrogate of the real mask, based on which the Mask R-CNN is employed for lesion detection. On the other hand, this work proposes a hard negative example mining strategy to reduce the false positives for improving the detection performance. Experimental results on the NIH DeepLesion dataset demonstrate that the ULDor is enhanced using pseudo masks and the proposed hard negative example mining strategy and achieves a sensitivity of 86.21% with five false positives per image.

cs.CV↗

arXiv2018

Attention Driven Person Re-identification

Person re-identification (ReID) is a challenging task due to arbitrary human pose variations, background clutters, etc. It has been studied extensively in recent years, but the multifarious local and global features are still not fully exploited by either ignoring the interplay between whole-body images and body-part images or missing in-depth examination of specific body-part images. In this paper, we propose a novel attention-driven multi-branch network that learns robust and discriminative human representation from global whole-body images and local body-part images simultaneously. Within each branch, an intra-attention network is designed to search for informative and discriminative regions within the whole-body or body-part images, where attention is elegantly decomposed into spatial-wise attention and channel-wise attention for effective and efficient learning. In addition, a novel inter-attention module is designed which fuses the output of intra-attention networks adaptively for optimal person ReID. The proposed technique has been evaluated over three widely used datasets CUHK03, Market-1501 and DukeMTMC-ReID, and experiments demonstrate its superior robustness and effectiveness as compared with the state of the arts.

cs.CV↗