arXiv subjects

Ke Yan

Publications and source records attributed to Ke Yan.

At least 91 records · Page 5Linked to original sources

arXiv2022

A New Probabilistic V-Net Model with Hierarchical Spatial Feature Transform for Efficient Abdominal Multi-Organ Segmentation

Accurate and robust abdominal multi-organ segmentation from CT imaging of different modalities is a challenging task due to complex inter- and intra-organ shape and appearance variations among abdominal organs. In this paper, we propose a probabilistic multi-organ segmentation network with hierarchical spatial-wise feature modulation to capture flexible organ semantic variants and inject the learnt variants into different scales of feature maps for guiding segmentation. More specifically, we design an input decomposition module via a conditional variational auto-encoder to learn organ-specific distributions on the low dimensional latent space and model richer organ semantic variations that is conditioned on input images.Then by integrating these learned variations into the V-Net decoder hierarchically via spatial feature transformation, which has the ability to convert the variations into conditional Affine transformation parameters for spatial-wise feature maps modulating and guiding the fine-scale segmentation. The proposed method is trained on the publicly available AbdomenCT-1K dataset and evaluated on two other open datasets, i.e., 100 challenging/pathological testing patient cases from AbdomenCT-1K fully-supervised abdominal organ segmentation benchmark and 90 cases from TCIA+&BTCV dataset. Highly competitive or superior quantitative segmentation results have been achieved using these datasets for four abdominal organs of liver, kidney, spleen and pancreas with reported Dice scores improved by 7.3% for kidneys and 9.7% for pancreas, while being ~7 times faster than two strong baseline segmentation methods(nnUNet and CoTr).

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arXiv2022

Location-free Human Pose Estimation

Human pose estimation (HPE) usually requires large-scale training data to reach high performance. However, it is rather time-consuming to collect high-quality and fine-grained annotations for human body. To alleviate this issue, we revisit HPE and propose a location-free framework without supervision of keypoint locations. We reformulate the regression-based HPE from the perspective of classification. Inspired by the CAM-based weakly-supervised object localization, we observe that the coarse keypoint locations can be acquired through the part-aware CAMs but unsatisfactory due to the gap between the fine-grained HPE and the object-level localization. To this end, we propose a customized transformer framework to mine the fine-grained representation of human context, equipped with the structural relation to capture subtle differences among keypoints. Concretely, we design a Multi-scale Spatial-guided Context Encoder to fully capture the global human context while focusing on the part-aware regions and a Relation-encoded Pose Prototype Generation module to encode the structural relations. All these works together for strengthening the weak supervision from image-level category labels on locations. Our model achieves competitive performance on three datasets when only supervised at a category-level and importantly, it can achieve comparable results with fully-supervised methods with only 25\% location labels on MS-COCO and MPII.

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arXiv2022

Expanding Low-Density Latent Regions for Open-Set Object Detection

Modern object detectors have achieved impressive progress under the close-set setup. However, open-set object detection (OSOD) remains challenging since objects of unknown categories are often misclassified to existing known classes. In this work, we propose to identify unknown objects by separating high/low-density regions in the latent space, based on the consensus that unknown objects are usually distributed in low-density latent regions. As traditional threshold-based methods only maintain limited low-density regions, which cannot cover all unknown objects, we present a novel Open-set Detector (OpenDet) with expanded low-density regions. To this aim, we equip OpenDet with two learners, Contrastive Feature Learner (CFL) and Unknown Probability Learner (UPL). CFL performs instance-level contrastive learning to encourage compact features of known classes, leaving more low-density regions for unknown classes; UPL optimizes unknown probability based on the uncertainty of predictions, which further divides more low-density regions around the cluster of known classes. Thus, unknown objects in low-density regions can be easily identified with the learned unknown probability. Extensive experiments demonstrate that our method can significantly improve the OSOD performance, e.g., OpenDet reduces the Absolute Open-Set Errors by 25%-35% on six OSOD benchmarks. Code is available at: https://github.com/csuhan/opendet2.

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arXiv2022

SIOD: Single Instance Annotated Per Category Per Image for Object Detection

Object detection under imperfect data receives great attention recently. Weakly supervised object detection (WSOD) suffers from severe localization issues due to the lack of instance-level annotation, while semi-supervised object detection (SSOD) remains challenging led by the inter-image discrepancy between labeled and unlabeled data. In this study, we propose the Single Instance annotated Object Detection (SIOD), requiring only one instance annotation for each existing category in an image. Degraded from inter-task (WSOD) or inter-image (SSOD) discrepancies to the intra-image discrepancy, SIOD provides more reliable and rich prior knowledge for mining the rest of unlabeled instances and trades off the annotation cost and performance. Under the SIOD setting, we propose a simple yet effective framework, termed Dual-Mining (DMiner), which consists of a Similarity-based Pseudo Label Generating module (SPLG) and a Pixel-level Group Contrastive Learning module (PGCL). SPLG firstly mines latent instances from feature representation space to alleviate the annotation missing problem. To avoid being misled by inaccurate pseudo labels, we propose PGCL to boost the tolerance to false pseudo labels. Extensive experiments on MS COCO verify the feasibility of the SIOD setting and the superiority of the proposed method, which obtains consistent and significant improvements compared to baseline methods and achieves comparable results with fully supervised object detection (FSOD) methods with only 40% instances annotated.

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arXiv2021

Learning from Subjective Ratings Using Auto-Decoded Deep Latent Embeddings

Depending on the application, radiological diagnoses can be associated with high inter- and intra-rater variabilities. Most computer-aided diagnosis (CAD) solutions treat such data as incontrovertible, exposing learning algorithms to considerable and possibly contradictory label noise and biases. Thus, managing subjectivity in labels is a fundamental problem in medical imaging analysis. To address this challenge, we introduce auto-decoded deep latent embeddings (ADDLE), which explicitly models the tendencies of each rater using an auto-decoder framework. After a simple linear transformation, the latent variables can be injected into any backbone at any and multiple points, allowing the model to account for rater-specific effects on the diagnosis. Importantly, ADDLE does not expect multiple raters per image in training, meaning it can readily learn from data mined from hospital archives. Moreover, the complexity of training ADDLE does not increase as more raters are added. During inference each rater can be simulated and a 'mean' or 'greedy' virtual rating can be produced. We test ADDLE on the problem of liver steatosis diagnosis from 2D ultrasound (US) by collecting 46 084 studies along with clinical US diagnoses originating from 65 different raters. We evaluated diagnostic performance using a separate dataset with gold-standard biopsy diagnoses. ADDLE can improve the partial areas under the curve (AUCs) for diagnosing severe steatosis by 10.5% over standard classifiers while outperforming other annotator-noise approaches, including those requiring 65 times the parameters.

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arXiv2021

Transformer-based Dual Relation Graph for Multi-label Image Recognition

The simultaneous recognition of multiple objects in one image remains a challenging task, spanning multiple events in the recognition field such as various object scales, inconsistent appearances, and confused inter-class relationships. Recent research efforts mainly resort to the statistic label co-occurrences and linguistic word embedding to enhance the unclear semantics. Different from these researches, in this paper, we propose a novel Transformer-based Dual Relation learning framework, constructing complementary relationships by exploring two aspects of correlation, i.e., structural relation graph and semantic relation graph. The structural relation graph aims to capture long-range correlations from object context, by developing a cross-scale transformer-based architecture. The semantic graph dynamically models the semantic meanings of image objects with explicit semantic-aware constraints. In addition, we also incorporate the learnt structural relationship into the semantic graph, constructing a joint relation graph for robust representations. With the collaborative learning of these two effective relation graphs, our approach achieves new state-of-the-art on two popular multi-label recognition benchmarks, i.e., MS-COCO and VOC 2007 dataset.

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arXiv2021

Accurate and Generalizable Quantitative Scoring of Liver Steatosis from Ultrasound Images via Scalable Deep Learning

Background & Aims: Hepatic steatosis is a major cause of chronic liver disease. 2D ultrasound is the most widely used non-invasive tool for screening and monitoring, but associated diagnoses are highly subjective. We developed a scalable deep learning (DL) algorithm for quantitative scoring of liver steatosis from 2D ultrasound images. Approach & Results: Using retrospectively collected multi-view ultrasound data from 3,310 patients, 19,513 studies, and 228,075 images, we trained a DL algorithm to diagnose steatosis stages (healthy, mild, moderate, or severe) from ultrasound diagnoses. Performance was validated on two multi-scanner unblinded and blinded (initially to DL developer) histology-proven cohorts (147 and 112 patients) with histopathology fatty cell percentage diagnoses, and a subset with FibroScan diagnoses. We also quantified reliability across scanners and viewpoints. Results were evaluated using Bland-Altman and receiver operating characteristic (ROC) analysis. The DL algorithm demonstrates repeatable measurements with a moderate number of images (3 for each viewpoint) and high agreement across 3 premium ultrasound scanners. High diagnostic performance was observed across all viewpoints: area under the curves of the ROC to classify >=mild, >=moderate, =severe steatosis grades were 0.85, 0.90, and 0.93, respectively. The DL algorithm outperformed or performed at least comparably to FibroScan with statistically significant improvements for all levels on the unblinded histology-proven cohort, and for =severe steatosis on the blinded histology-proven cohort. Conclusions: The DL algorithm provides a reliable quantitative steatosis assessment across view and scanners on two multi-scanner cohorts. Diagnostic performance was high with comparable or better performance than FibroScan.

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arXiv2021

SAME: Deformable Image Registration based on Self-supervised Anatomical Embeddings

In this work, we introduce a fast and accurate method for unsupervised 3D medical image registration. This work is built on top of a recent algorithm SAM, which is capable of computing dense anatomical/semantic correspondences between two images at the pixel level. Our method is named SAME, which breaks down image registration into three steps: affine transformation, coarse deformation, and deep deformable registration. Using SAM embeddings, we enhance these steps by finding more coherent correspondences, and providing features and a loss function with better semantic guidance. We collect a multi-phase chest computed tomography dataset with 35 annotated organs for each patient and conduct inter-subject registration for quantitative evaluation. Results show that SAME outperforms widely-used traditional registration techniques (Elastix FFD, ANTs SyN) and learning based VoxelMorph method by at least 4.7% and 2.7% in Dice scores for two separate tasks of within-contrast-phase and across-contrast-phase registration, respectively. SAME achieves the comparable performance to the best traditional registration method, DEEDS (from our evaluation), while being orders of magnitude faster (from 45 seconds to 1.2 seconds).

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arXiv2021

Heterogeneous Relational Complement for Vehicle Re-identification

The crucial problem in vehicle re-identification is to find the same vehicle identity when reviewing this object from cross-view cameras, which sets a higher demand for learning viewpoint-invariant representations. In this paper, we propose to solve this problem from two aspects: constructing robust feature representations and proposing camera-sensitive evaluations. We first propose a novel Heterogeneous Relational Complement Network (HRCN) by incorporating region-specific features and cross-level features as complements for the original high-level output. Considering the distributional differences and semantic misalignment, we propose graph-based relation modules to embed these heterogeneous features into one unified high-dimensional space. On the other hand, considering the deficiencies of cross-camera evaluations in existing measures (i.e., CMC and AP), we then propose a Cross-camera Generalization Measure (CGM) to improve the evaluations by introducing position-sensitivity and cross-camera generalization penalties. We further construct a new benchmark of existing models with our proposed CGM and experimental results reveal that our proposed HRCN model achieves new state-of-the-art in VeRi-776, VehicleID, and VERI-Wild.

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arXiv2021

Discriminator-Free Generative Adversarial Attack

The Deep Neural Networks are vulnerable toadversarial exam-ples(Figure 1), making the DNNs-based systems collapsed byadding the inconspicuous perturbations to the images. Most of the existing works for adversarial attack are gradient-based and suf-fer from the latency efficiencies and the load on GPU memory. Thegenerative-based adversarial attacks can get rid of this limitation,and some relative works propose the approaches based on GAN.However, suffering from the difficulty of the convergence of train-ing a GAN, the adversarial examples have either bad attack abilityor bad visual quality. In this work, we find that the discriminatorcould be not necessary for generative-based adversarial attack, andpropose theSymmetric Saliency-based Auto-Encoder (SSAE)to generate the perturbations, which is composed of the saliencymap module and the angle-norm disentanglement of the featuresmodule. The advantage of our proposed method lies in that it is notdepending on discriminator, and uses the generative saliency map to pay more attention to label-relevant regions. The extensive exper-iments among the various tasks, datasets, and models demonstratethat the adversarial examples generated by SSAE not only make thewidely-used models collapse, but also achieves good visual quality.The code is available at https://github.com/BravoLu/SSAE.

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arXiv2021

Distilling Self-Knowledge From Contrastive Links to Classify Graph Nodes Without Passing Messages

Nowadays, Graph Neural Networks (GNNs) following the Message Passing paradigm become the dominant way to learn on graphic data. Models in this paradigm have to spend extra space to look up adjacent nodes with adjacency matrices and extra time to aggregate multiple messages from adjacent nodes. To address this issue, we develop a method called LinkDist that distils self-knowledge from connected node pairs into a Multi-Layer Perceptron (MLP) without the need to aggregate messages. Experiment with 8 real-world datasets shows the MLP derived from LinkDist can predict the label of a node without knowing its adjacencies but achieve comparable accuracy against GNNs in the contexts of semi- and full-supervised node classification. Moreover, LinkDist benefits from its Non-Message Passing paradigm that we can also distil self-knowledge from arbitrarily sampled node pairs in a contrastive way to further boost the performance of LinkDist.

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arXiv2021

Memory-Associated Differential Learning

Conventional Supervised Learning approaches focus on the mapping from input features to output labels. After training, the learnt models alone are adapted onto testing features to predict testing labels in isolation, with training data wasted and their associations ignored. To take full advantage of the vast number of training data and their associations, we propose a novel learning paradigm called Memory-Associated Differential (MAD) Learning. We first introduce an additional component called Memory to memorize all the training data. Then we learn the differences of labels as well as the associations of features in the combination of a differential equation and some sampling methods. Finally, in the evaluating phase, we predict unknown labels by inferencing from the memorized facts plus the learnt differences and associations in a geometrically meaningful manner. We gently build this theory in unary situations and apply it on Image Recognition, then extend it into Link Prediction as a binary situation, in which our method outperforms strong state-of-the-art baselines on ogbl-ddi dataset.

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arXiv2021

Lesion Segmentation and RECIST Diameter Prediction via Click-driven Attention and Dual-path Connection

Measuring lesion size is an important step to assess tumor growth and monitor disease progression and therapy response in oncology image analysis. Although it is tedious and highly time-consuming, radiologists have to work on this task by using RECIST criteria (Response Evaluation Criteria In Solid Tumors) routinely and manually. Even though lesion segmentation may be the more accurate and clinically more valuable means, physicians can not manually segment lesions as now since much more heavy laboring will be required. In this paper, we present a prior-guided dual-path network (PDNet) to segment common types of lesions throughout the whole body and predict their RECIST diameters accurately and automatically. Similar to [1], a click guidance from radiologists is the only requirement. There are two key characteristics in PDNet: 1) Learning lesion-specific attention matrices in parallel from the click prior information by the proposed prior encoder, named click-driven attention; 2) Aggregating the extracted multi-scale features comprehensively by introducing top-down and bottom-up connections in the proposed decoder, named dual-path connection. Experiments show the superiority of our proposed PDNet in lesion segmentation and RECIST diameter prediction using the DeepLesion dataset and an external test set. PDNet learns comprehensive and representative deep image features for our tasks and produces more accurate results on both lesion segmentation and RECIST diameter prediction.

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arXiv2021

Weakly-Supervised Universal Lesion Segmentation with Regional Level Set Loss

Accurately segmenting a variety of clinically significant lesions from whole body computed tomography (CT) scans is a critical task on precision oncology imaging, denoted as universal lesion segmentation (ULS). Manual annotation is the current clinical practice, being highly time-consuming and inconsistent on tumor's longitudinal assessment. Effectively training an automatic segmentation model is desirable but relies heavily on a large number of pixel-wise labelled data. Existing weakly-supervised segmentation approaches often struggle with regions nearby the lesion boundaries. In this paper, we present a novel weakly-supervised universal lesion segmentation method by building an attention enhanced model based on the High-Resolution Network (HRNet), named AHRNet, and propose a regional level set (RLS) loss for optimizing lesion boundary delineation. AHRNet provides advanced high-resolution deep image features by involving a decoder, dual-attention and scale attention mechanisms, which are crucial to performing accurate lesion segmentation. RLS can optimize the model reliably and effectively in a weakly-supervised fashion, forcing the segmentation close to lesion boundary. Extensive experimental results demonstrate that our method achieves the best performance on the publicly large-scale DeepLesion dataset and a hold-out test set.

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arXiv2021

Deep Lesion Tracker: Monitoring Lesions in 4D Longitudinal Imaging Studies

Monitoring treatment response in longitudinal studies plays an important role in clinical practice. Accurately identifying lesions across serial imaging follow-up is the core to the monitoring procedure. Typically this incorporates both image and anatomical considerations. However, matching lesions manually is labor-intensive and time-consuming. In this work, we present deep lesion tracker (DLT), a deep learning approach that uses both appearance- and anatomical-based signals. To incorporate anatomical constraints, we propose an anatomical signal encoder, which prevents lesions being matched with visually similar but spurious regions. In addition, we present a new formulation for Siamese networks that avoids the heavy computational loads of 3D cross-correlation. To present our network with greater varieties of images, we also propose a self-supervised learning (SSL) strategy to train trackers with unpaired images, overcoming barriers to data collection. To train and evaluate our tracker, we introduce and release the first lesion tracking benchmark, consisting of 3891 lesion pairs from the public DeepLesion database. The proposed method, DLT, locates lesion centers with a mean error distance of 7 mm. This is 5% better than a leading registration algorithm while running 14 times faster on whole CT volumes. We demonstrate even greater improvements over detector or similarity-learning alternatives. DLT also generalizes well on an external clinical test set of 100 longitudinal studies, achieving 88% accuracy. Finally, we plug DLT into an automatic tumor monitoring workflow where it leads to an accuracy of 85% in assessing lesion treatment responses, which is only 0.46% lower than the accuracy of manual inputs.

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arXiv2021

Sequential Learning on Liver Tumor Boundary Semantics and Prognostic Biomarker Mining

The boundary of tumors (hepatocellular carcinoma, or HCC) contains rich semantics: capsular invasion, visibility, smoothness, folding and protuberance, etc. Capsular invasion on tumor boundary has proven to be clinically correlated with the prognostic indicator, microvascular invasion (MVI). Investigating tumor boundary semantics has tremendous clinical values. In this paper, we propose the first and novel computational framework that disentangles the task into two components: spatial vertex localization and sequential semantic classification. (1) A HCC tumor segmentor is built for tumor mask boundary extraction, followed by polar transform representing the boundary with radius and angle. Vertex generator is used to produce fixed-length boundary vertices where vertex features are sampled on the corresponding spatial locations. (2) The sampled deep vertex features with positional embedding are mapped into a sequential space and decoded by a multilayer perceptron (MLP) for semantic classification. Extensive experiments on tumor capsule semantics demonstrate the effectiveness of our framework. Mining the correlation between the boundary semantics and MVI status proves the feasibility to integrate this boundary semantics as a valid HCC prognostic biomarker.

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arXiv2021

Learning from Multiple Datasets with Heterogeneous and Partial Labels for Universal Lesion Detection in CT

Large-scale datasets with high-quality labels are desired for training accurate deep learning models. However, due to the annotation cost, datasets in medical imaging are often either partially-labeled or small. For example, DeepLesion is such a large-scale CT image dataset with lesions of various types, but it also has many unlabeled lesions (missing annotations). When training a lesion detector on a partially-labeled dataset, the missing annotations will generate incorrect negative signals and degrade the performance. Besides DeepLesion, there are several small single-type datasets, such as LUNA for lung nodules and LiTS for liver tumors. These datasets have heterogeneous label scopes, i.e., different lesion types are labeled in different datasets with other types ignored. In this work, we aim to develop a universal lesion detection algorithm to detect a variety of lesions. The problem of heterogeneous and partial labels is tackled. First, we build a simple yet effective lesion detection framework named Lesion ENSemble (LENS). LENS can efficiently learn from multiple heterogeneous lesion datasets in a multi-task fashion and leverage their synergy by proposal fusion. Next, we propose strategies to mine missing annotations from partially-labeled datasets by exploiting clinical prior knowledge and cross-dataset knowledge transfer. Finally, we train our framework on four public lesion datasets and evaluate it on 800 manually-labeled sub-volumes in DeepLesion. Our method brings a relative improvement of 49% compared to the current state-of-the-art approach in the metric of average sensitivity. We have publicly released our manual 3D annotations of DeepLesion in https://github.com/viggin/DeepLesion_manual_test_set.

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arXiv2020

Lesion Harvester: Iteratively Mining Unlabeled Lesions and Hard-Negative Examples at Scale

Acquiring large-scale medical image data, necessary for training machine learning algorithms, is frequently intractable, due to prohibitive expert-driven annotation costs. Recent datasets extracted from hospital archives, e.g., DeepLesion, have begun to address this problem. However, these are often incompletely or noisily labeled, e.g., DeepLesion leaves over 50% of its lesions unlabeled. Thus, effective methods to harvest missing annotations are critical for continued progress in medical image analysis. This is the goal of our work, where we develop a powerful system to harvest missing lesions from the DeepLesion dataset at high precision. Accepting the need for some degree of expert labor to achieve high fidelity, we exploit a small fully-labeled subset of medical image volumes and use it to intelligently mine annotations from the remainder. To do this, we chain together a highly sensitive lesion proposal generator and a very selective lesion proposal classifier. While our framework is generic, we optimize our performance by proposing a 3D contextual lesion proposal generator and by using a multi-view multi-scale lesion proposal classifier. These produce harvested and hard-negative proposals, which we then re-use to finetune our proposal generator by using a novel hard negative suppression loss, continuing this process until no extra lesions are found. Extensive experimental analysis demonstrates that our method can harvest an additional 9,805 lesions while keeping precision above 90%. To demonstrate the benefits of our approach, we show that lesion detectors trained on our harvested lesions can significantly outperform the same variants only trained on the original annotations, with boost of average precision of 7% to 10%. We open source our annotations at https://github.com/JimmyCai91/DeepLesionAnnotation.

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