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Yefeng Zheng

Publications and source records attributed to Yefeng Zheng.

At least 127 records · Page 7Linked to original sources
arXiv2023

Simultaneous Alignment and Surface Regression Using Hybrid 2D-3D Networks for 3D Coherent Layer Segmentation of Retinal OCT Images with Full and Sparse Annotations

Layer segmentation is important to quantitative analysis of retinal optical coherence tomography (OCT). Recently, deep learning based methods have been developed to automate this task and yield remarkable performance. However, due to the large spatial gap and potential mismatch between the B-scans of an OCT volume, all of them were based on 2D segmentation of individual B-scans, which may lose the continuity and diagnostic information of the retinal layers in 3D space. Besides, most of these methods required dense annotation of the OCT volumes, which is labor-intensive and expertise-demanding. This work presents a novel framework based on hybrid 2D-3D convolutional neural networks (CNNs) to obtain continuous 3D retinal layer surfaces from OCT volumes, which works well with both full and sparse annotations. The 2D features of individual B-scans are extracted by an encoder consisting of 2D convolutions. These 2D features are then used to produce the alignment displacement vectors and layer segmentation by two 3D decoders coupled via a spatial transformer module. Two losses are proposed to utilize the retinal layers' natural property of being smooth for B-scan alignment and layer segmentation, respectively, and are the key to the semi-supervised learning with sparse annotation. The entire framework is trained end-to-end. To the best of our knowledge, this is the first work that attempts 3D retinal layer segmentation in volumetric OCT images based on CNNs. Experiments on a synthetic dataset and three public clinical datasets show that our framework can effectively align the B-scans for potential motion correction, and achieves superior performance to state-of-the-art 2D deep learning methods in terms of both layer segmentation accuracy and cross-B-scan 3D continuity in both fully and semi-supervised settings, thus offering more clinical values than previous works.

eess.IV↗
arXiv2023

Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural Network with Biomedical Network

Accurately predicting drug-drug interactions (DDI) for emerging drugs, which offer possibilities for treating and alleviating diseases, with computational methods can improve patient care and contribute to efficient drug development. However, many existing computational methods require large amounts of known DDI information, which is scarce for emerging drugs. In this paper, we propose EmerGNN, a graph neural network (GNN) that can effectively predict interactions for emerging drugs by leveraging the rich information in biomedical networks. EmerGNN learns pairwise representations of drugs by extracting the paths between drug pairs, propagating information from one drug to the other, and incorporating the relevant biomedical concepts on the paths. The different edges on the biomedical network are weighted to indicate the relevance for the target DDI prediction. Overall, EmerGNN has higher accuracy than existing approaches in predicting interactions for emerging drugs and can identify the most relevant information on the biomedical network.

q-bio.QM↗
arXiv2023

Relation-aware Ensemble Learning for Knowledge Graph Embedding

Knowledge graph (KG) embedding is a fundamental task in natural language processing, and various methods have been proposed to explore semantic patterns in distinctive ways. In this paper, we propose to learn an ensemble by leveraging existing methods in a relation-aware manner. However, exploring these semantics using relation-aware ensemble leads to a much larger search space than general ensemble methods. To address this issue, we propose a divide-search-combine algorithm RelEns-DSC that searches the relation-wise ensemble weights independently. This algorithm has the same computation cost as general ensemble methods but with much better performance. Experimental results on benchmark datasets demonstrate the effectiveness of the proposed method in efficiently searching relation-aware ensemble weights and achieving state-of-the-art embedding performance. The code is public at https://github.com/LARS-research/RelEns.

cs.LG↗
arXiv2023

Automatic view plane prescription for cardiac magnetic resonance imaging via supervision by spatial relationship between views

Background: View planning for the acquisition of cardiac magnetic resonance (CMR) imaging remains a demanding task in clinical practice. Purpose: Existing approaches to its automation relied either on an additional volumetric image not typically acquired in clinic routine, or on laborious manual annotations of cardiac structural landmarks. This work presents a clinic-compatible, annotation-free system for automatic CMR view planning. Methods: The system mines the spatial relationship, more specifically, locates the intersecting lines, between the target planes and source views, and trains deep networks to regress heatmaps defined by distances from the intersecting lines. The intersection lines are the prescription lines prescribed by the technologists at the time of image acquisition using cardiac landmarks, and retrospectively identified from the spatial relationship. As the spatial relationship is self-contained in properly stored data, the need for additional manual annotation is eliminated. In addition, the interplay of multiple target planes predicted in a source view is utilized in a stacked hourglass architecture to gradually improve the regression. Then, a multi-view planning strategy is proposed to aggregate information from the predicted heatmaps for all the source views of a target plane, for a globally optimal prescription, mimicking the similar strategy practiced by skilled human prescribers. Results: The experiments include 181 CMR exams. Our system yields the mean angular difference and point-to-plane distance of 5.68 degrees and 3.12 mm, respectively. It not only achieves superior accuracy to existing approaches including conventional atlas-based and newer deep-learning-based in prescribing the four standard CMR planes but also demonstrates prescription of the first cardiac-anatomy-oriented plane(s) from the body-oriented scout.

eess.IV↗
arXiv2023

Cross-Modality Neuroimage Synthesis: A Survey

Multi-modality imaging improves disease diagnosis and reveals distinct deviations in tissues with anatomical properties. The existence of completely aligned and paired multi-modality neuroimaging data has proved its effectiveness in brain research. However, collecting fully aligned and paired data is expensive or even impractical, since it faces many difficulties, including high cost, long acquisition time, image corruption, and privacy issues. An alternative solution is to explore unsupervised or weakly supervised learning methods to synthesize the absent neuroimaging data. In this paper, we provide a comprehensive review of cross-modality synthesis for neuroimages, from the perspectives of weakly supervised and unsupervised settings, loss functions, evaluation metrics, imaging modalities, datasets, and downstream applications based on synthesis. We begin by highlighting several opening challenges for cross-modality neuroimage synthesis. Then, we discuss representative architectures of cross-modality synthesis methods under different supervisions. This is followed by a stepwise in-depth analysis to evaluate how cross-modality neuroimage synthesis improves the performance of its downstream tasks. Finally, we summarize the existing research findings and point out future research directions. All resources are available at https://github.com/M-3LAB/awesome-multimodal-brain-image-systhesis

eess.IV↗
arXiv2023

JoTR: A Joint Transformer and Reinforcement Learning Framework for Dialog Policy Learning

Dialogue policy learning (DPL) is a crucial component of dialogue modelling. Its primary role is to determine the appropriate abstract response, commonly referred to as the "dialogue action". Traditional DPL methodologies have treated this as a sequential decision problem, using pre-defined action candidates extracted from a corpus. However, these incomplete candidates can significantly limit the diversity of responses and pose challenges when dealing with edge cases, which are scenarios that occur only at extreme operating parameters. To address these limitations, we introduce a novel framework, JoTR. This framework is unique as it leverages a text-to-text Transformer-based model to generate flexible dialogue actions. Unlike traditional methods, JoTR formulates a word-level policy that allows for a more dynamic and adaptable dialogue action generation, without the need for any action templates. This setting enhances the diversity of responses and improves the system's ability to handle edge cases effectively. In addition, JoTR employs reinforcement learning with a reward-shaping mechanism to efficiently finetune the word-level dialogue policy, which allows the model to learn from its interactions, improving its performance over time. We conducted an extensive evaluation of JoTR to assess its effectiveness. Our extensive evaluation shows that JoTR achieves state-of-the-art performance on two benchmark dialogue modelling tasks, as assessed by both user simulators and human evaluators.

cs.CL↗
arXiv2023

BoxDiff: Text-to-Image Synthesis with Training-Free Box-Constrained Diffusion

Recent text-to-image diffusion models have demonstrated an astonishing capacity to generate high-quality images. However, researchers mainly studied the way of synthesizing images with only text prompts. While some works have explored using other modalities as conditions, considerable paired data, e.g., box/mask-image pairs, and fine-tuning time are required for nurturing models. As such paired data is time-consuming and labor-intensive to acquire and restricted to a closed set, this potentially becomes the bottleneck for applications in an open world. This paper focuses on the simplest form of user-provided conditions, e.g., box or scribble. To mitigate the aforementioned problem, we propose a training-free method to control objects and contexts in the synthesized images adhering to the given spatial conditions. Specifically, three spatial constraints, i.e., Inner-Box, Outer-Box, and Corner Constraints, are designed and seamlessly integrated into the denoising step of diffusion models, requiring no additional training and massive annotated layout data. Extensive experimental results demonstrate that the proposed constraints can control what and where to present in the images while retaining the ability of Diffusion models to synthesize with high fidelity and diverse concept coverage. The code is publicly available at https://github.com/showlab/BoxDiff.

cs.CV↗
arXiv2023

Nuclei Segmentation with Point Annotations from Pathology Images via Self-Supervised Learning and Co-Training

Nuclei segmentation is a crucial task for whole slide image analysis in digital pathology. Generally, the segmentation performance of fully-supervised learning heavily depends on the amount and quality of the annotated data. However, it is time-consuming and expensive for professional pathologists to provide accurate pixel-level ground truth, while it is much easier to get coarse labels such as point annotations. In this paper, we propose a weakly-supervised learning method for nuclei segmentation that only requires point annotations for training. First, coarse pixel-level labels are derived from the point annotations based on the Voronoi diagram and the k-means clustering method to avoid overfitting. Second, a co-training strategy with an exponential moving average method is designed to refine the incomplete supervision of the coarse labels. Third, a self-supervised visual representation learning method is tailored for nuclei segmentation of pathology images that transforms the hematoxylin component images into the H&E stained images to gain better understanding of the relationship between the nuclei and cytoplasm. We comprehensively evaluate the proposed method using two public datasets. Both visual and quantitative results demonstrate the superiority of our method to the state-of-the-art methods, and its competitive performance compared to the fully-supervised methods. Code: https://github.com/hust-linyi/SC-Net

eess.IV↗
arXiv2023

DS-Depth: Dynamic and Static Depth Estimation via a Fusion Cost Volume

Self-supervised monocular depth estimation methods typically rely on the reprojection error to capture geometric relationships between successive frames in static environments. However, this assumption does not hold in dynamic objects in scenarios, leading to errors during the view synthesis stage, such as feature mismatch and occlusion, which can significantly reduce the accuracy of the generated depth maps. To address this problem, we propose a novel dynamic cost volume that exploits residual optical flow to describe moving objects, improving incorrectly occluded regions in static cost volumes used in previous work. Nevertheless, the dynamic cost volume inevitably generates extra occlusions and noise, thus we alleviate this by designing a fusion module that makes static and dynamic cost volumes compensate for each other. In other words, occlusion from the static volume is refined by the dynamic volume, and incorrect information from the dynamic volume is eliminated by the static volume. Furthermore, we propose a pyramid distillation loss to reduce photometric error inaccuracy at low resolutions and an adaptive photometric error loss to alleviate the flow direction of the large gradient in the occlusion regions. We conducted extensive experiments on the KITTI and Cityscapes datasets, and the results demonstrate that our model outperforms previously published baselines for self-supervised monocular depth estimation.

cs.CV↗
arXiv2023

FemtoDet: An Object Detection Baseline for Energy Versus Performance Tradeoffs

Efficient detectors for edge devices are often optimized for parameters or speed count metrics, which remain in weak correlation with the energy of detectors. However, some vision applications of convolutional neural networks, such as always-on surveillance cameras, are critical for energy constraints. This paper aims to serve as a baseline by designing detectors to reach tradeoffs between energy and performance from two perspectives: 1) We extensively analyze various CNNs to identify low-energy architectures, including selecting activation functions, convolutions operators, and feature fusion structures on necks. These underappreciated details in past work seriously affect the energy consumption of detectors; 2) To break through the dilemmatic energy-performance problem, we propose a balanced detector driven by energy using discovered low-energy components named \textit{FemtoDet}. In addition to the novel construction, we improve FemtoDet by considering convolutions and training strategy optimizations. Specifically, we develop a new instance boundary enhancement (IBE) module for convolution optimization to overcome the contradiction between the limited capacity of CNNs and detection tasks in diverse spatial representations, and propose a recursive warm-restart (RecWR) for optimizing training strategy to escape the sub-optimization of light-weight detectors by considering the data shift produced in popular augmentations. As a result, FemtoDet with only 68.77k parameters achieves a competitive score of 46.3 AP50 on PASCAL VOC and 1.11 W $\&$ 64.47 FPS on Qualcomm Snapdragon 865 CPU platforms. Extensive experiments on COCO and TJU-DHD datasets indicate that the proposed method achieves competitive results in diverse scenes.

cs.CV↗
arXiv2023

Relational Experience Replay: Continual Learning by Adaptively Tuning Task-wise Relationship

Continual learning is a promising machine learning paradigm to learn new tasks while retaining previously learned knowledge over streaming training data. Till now, rehearsal-based methods, keeping a small part of data from old tasks as a memory buffer, have shown good performance in mitigating catastrophic forgetting for previously learned knowledge. However, most of these methods typically treat each new task equally, which may not adequately consider the relationship or similarity between old and new tasks. Furthermore, these methods commonly neglect sample importance in the continual training process and result in sub-optimal performance on certain tasks. To address this challenging problem, we propose Relational Experience Replay (RER), a bi-level learning framework, to adaptively tune task-wise relationships and sample importance within each task to achieve a better `stability' and `plasticity' trade-off. As such, the proposed method is capable of accumulating new knowledge while consolidating previously learned old knowledge during continual learning. Extensive experiments conducted on three publicly available datasets (i.e., CIFAR-10, CIFAR-100, and Tiny ImageNet) show that the proposed method can consistently improve the performance of all baselines and surpass current state-of-the-art methods.

cs.LG↗
arXiv2023

Gait Cycle-Inspired Learning Strategy for Continuous Prediction of Knee Joint Trajectory from sEMG

Predicting lower limb motion intent is vital for controlling exoskeleton robots and prosthetic limbs. Surface electromyography (sEMG) attracts increasing attention in recent years as it enables ahead-of-time prediction of motion intentions before actual movement. However, the estimation performance of human joint trajectory remains a challenging problem due to the inter- and intra-subject variations. The former is related to physiological differences (such as height and weight) and preferred walking patterns of individuals, while the latter is mainly caused by irregular and gait-irrelevant muscle activity. This paper proposes a model integrating two gait cycle-inspired learning strategies to mitigate the challenge for predicting human knee joint trajectory. The first strategy is to decouple knee joint angles into motion patterns and amplitudes former exhibit low variability while latter show high variability among individuals. By learning through separate network entities, the model manages to capture both the common and personalized gait features. In the second, muscle principal activation masks are extracted from gait cycles in a prolonged walk. These masks are used to filter out components unrelated to walking from raw sEMG and provide auxiliary guidance to capture more gait-related features. Experimental results indicate that our model could predict knee angles with the average root mean square error (RMSE) of 3.03(0.49) degrees and 50ms ahead of time. To our knowledge this is the best performance in relevant literatures that has been reported, with reduced RMSE by at least 9.5%.

cs.RO↗
arXiv2023

You've Got Two Teachers: Co-evolutionary Image and Report Distillation for Semi-supervised Anatomical Abnormality Detection in Chest X-ray

Chest X-ray (CXR) anatomical abnormality detection aims at localizing and characterising cardiopulmonary radiological findings in the radiographs, which can expedite clinical workflow and reduce observational oversights. Most existing methods attempted this task in either fully supervised settings which demanded costly mass per-abnormality annotations, or weakly supervised settings which still lagged badly behind fully supervised methods in performance. In this work, we propose a co-evolutionary image and report distillation (CEIRD) framework, which approaches semi-supervised abnormality detection in CXR by grounding the visual detection results with text-classified abnormalities from paired radiology reports, and vice versa. Concretely, based on the classical teacher-student pseudo label distillation (TSD) paradigm, we additionally introduce an auxiliary report classification model, whose prediction is used for report-guided pseudo detection label refinement (RPDLR) in the primary vision detection task. Inversely, we also use the prediction of the vision detection model for abnormality-guided pseudo classification label refinement (APCLR) in the auxiliary report classification task, and propose a co-evolution strategy where the vision and report models mutually promote each other with RPDLR and APCLR performed alternatively. To this end, we effectively incorporate the weak supervision by reports into the semi-supervised TSD pipeline. Besides the cross-modal pseudo label refinement, we further propose an intra-image-modal self-adaptive non-maximum suppression, where the pseudo detection labels generated by the teacher vision model are dynamically rectified by high-confidence predictions by the student. Experimental results on the public MIMIC-CXR benchmark demonstrate CEIRD's superior performance to several up-to-date weakly and semi-supervised methods.

cs.CV↗
arXiv2023

CoAD: Automatic Diagnosis through Symptom and Disease Collaborative Generation

Automatic diagnosis (AD), a critical application of AI in healthcare, employs machine learning techniques to assist doctors in gathering patient symptom information for precise disease diagnosis. The Transformer-based method utilizes an input symptom sequence, predicts itself through auto-regression, and employs the hidden state of the final symptom to determine the disease. Despite its simplicity and superior performance demonstrated, a decline in disease diagnosis accuracy is observed caused by 1) a mismatch between symptoms observed during training and generation, and 2) the effect of different symptom orders on disease prediction. To address the above obstacles, we introduce the CoAD, a novel disease and symptom collaborative generation framework, which incorporates several key innovations to improve AD: 1) aligning sentence-level disease labels with multiple possible symptom inquiry steps to bridge the gap between training and generation; 2) expanding symptom labels for each sub-sequence of symptoms to enhance annotation and eliminate the effect of symptom order; 3) developing a repeated symptom input schema to effectively and efficiently learn the expanded disease and symptom labels. We evaluate the CoAD framework using four datasets, including three public and one private, and demonstrate that it achieves an average 2.3% improvement over previous state-of-the-art results in automatic disease diagnosis. For reproducibility, we release the code and data at https://github.com/KwanWaiChung/coad.

cs.CL↗
arXiv2023

MADAv2: Advanced Multi-Anchor Based Active Domain Adaptation Segmentation

Unsupervised domain adaption has been widely adopted in tasks with scarce annotated data. Unfortunately, mapping the target-domain distribution to the source-domain unconditionally may distort the essential structural information of the target-domain data, leading to inferior performance. To address this issue, we firstly propose to introduce active sample selection to assist domain adaptation regarding the semantic segmentation task. By innovatively adopting multiple anchors instead of a single centroid, both source and target domains can be better characterized as multimodal distributions, in which way more complementary and informative samples are selected from the target domain. With only a little workload to manually annotate these active samples, the distortion of the target-domain distribution can be effectively alleviated, achieving a large performance gain. In addition, a powerful semi-supervised domain adaptation strategy is proposed to alleviate the long-tail distribution problem and further improve the segmentation performance. Extensive experiments are conducted on public datasets, and the results demonstrate that the proposed approach outperforms state-of-the-art methods by large margins and achieves similar performance to the fully-supervised upperbound, i.e., 71.4% mIoU on GTA5 and 71.8% mIoU on SYNTHIA. The effectiveness of each component is also verified by thorough ablation studies.

cs.CV↗
arXiv2023

MEPNet: A Model-Driven Equivariant Proximal Network for Joint Sparse-View Reconstruction and Metal Artifact Reduction in CT Images

Sparse-view computed tomography (CT) has been adopted as an important technique for speeding up data acquisition and decreasing radiation dose. However, due to the lack of sufficient projection data, the reconstructed CT images often present severe artifacts, which will be further amplified when patients carry metallic implants. For this joint sparse-view reconstruction and metal artifact reduction task, most of the existing methods are generally confronted with two main limitations: 1) They are almost built based on common network modules without fully embedding the physical imaging geometry constraint of this specific task into the dual-domain learning; 2) Some important prior knowledge is not deeply explored and sufficiently utilized. Against these issues, we specifically construct a dual-domain reconstruction model and propose a model-driven equivariant proximal network, called MEPNet. The main characteristics of MEPNet are: 1) It is optimization-inspired and has a clear working mechanism; 2) The involved proximal operator is modeled via a rotation equivariant convolutional neural network, which finely represents the inherent rotational prior underlying the CT scanning that the same organ can be imaged at different angles. Extensive experiments conducted on several datasets comprehensively substantiate that compared with the conventional convolution-based proximal network, such a rotation equivariance mechanism enables our proposed method to achieve better reconstruction performance with fewer network parameters. We will release the code at \url{https://github.com/hongwang01/MEPNet}.

eess.IV↗
arXiv2023

Cross-Modal Vertical Federated Learning for MRI Reconstruction

Federated learning enables multiple hospitals to cooperatively learn a shared model without privacy disclosure. Existing methods often take a common assumption that the data from different hospitals have the same modalities. However, such a setting is difficult to fully satisfy in practical applications, since the imaging guidelines may be different between hospitals, which makes the number of individuals with the same set of modalities limited. To this end, we formulate this practical-yet-challenging cross-modal vertical federated learning task, in which shape data from multiple hospitals have different modalities with a small amount of multi-modality data collected from the same individuals. To tackle such a situation, we develop a novel framework, namely Federated Consistent Regularization constrained Feature Disentanglement (Fed-CRFD), for boosting MRI reconstruction by effectively exploring the overlapping samples (individuals with multi-modalities) and solving the domain shift problem caused by different modalities. Particularly, our Fed-CRFD involves an intra-client feature disentangle scheme to decouple data into modality-invariant and modality-specific features, where the modality-invariant features are leveraged to mitigate the domain shift problem. In addition, a cross-client latent representation consistency constraint is proposed specifically for the overlapping samples to further align the modality-invariant features extracted from different modalities. Hence, our method can fully exploit the multi-source data from hospitals while alleviating the domain shift problem. Extensive experiments on two typical MRI datasets demonstrate that our network clearly outperforms state-of-the-art MRI reconstruction methods. The source code will be publicly released upon the publication of this work.

eess.IV↗
arXiv2023

VisorGPT: Learning Visual Prior via Generative Pre-Training

Various stuff and things in visual data possess specific traits, which can be learned by deep neural networks and are implicitly represented as the visual prior, e.g., object location and shape, in the model. Such prior potentially impacts many vision tasks. For example, in conditional image synthesis, spatial conditions failing to adhere to the prior can result in visually inaccurate synthetic results. This work aims to explicitly learn the visual prior and enable the customization of sampling. Inspired by advances in language modeling, we propose to learn Visual prior via Generative Pre-Training, dubbed VisorGPT. By discretizing visual locations of objects, e.g., bounding boxes, human pose, and instance masks, into sequences, VisorGPT can model visual prior through likelihood maximization. Besides, prompt engineering is investigated to unify various visual locations and enable customized sampling of sequential outputs from the learned prior. Experimental results demonstrate that VisorGPT can effectively model the visual prior, which can be employed for many vision tasks, such as customizing accurate human pose for conditional image synthesis models like ControlNet. Code will be released at https://github.com/Sierkinhane/VisorGPT.

cs.CV↗