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Yefeng Zheng

Publications and source records attributed to Yefeng Zheng.

At least 145 records · Page 8Linked to original sources
arXiv2023

CSS: A Large-scale Cross-schema Chinese Text-to-SQL Medical Dataset

The cross-domain text-to-SQL task aims to build a system that can parse user questions into SQL on complete unseen databases, and the single-domain text-to-SQL task evaluates the performance on identical databases. Both of these setups confront unavoidable difficulties in real-world applications. To this end, we introduce the cross-schema text-to-SQL task, where the databases of evaluation data are different from that in the training data but come from the same domain. Furthermore, we present CSS, a large-scale CrosS-Schema Chinese text-to-SQL dataset, to carry on corresponding studies. CSS originally consisted of 4,340 question/SQL pairs across 2 databases. In order to generalize models to different medical systems, we extend CSS and create 19 new databases along with 29,280 corresponding dataset examples. Moreover, CSS is also a large corpus for single-domain Chinese text-to-SQL studies. We present the data collection approach and a series of analyses of the data statistics. To show the potential and usefulness of CSS, benchmarking baselines have been conducted and reported. Our dataset is publicly available at \url{https://huggingface.co/datasets/zhanghanchong/css}.

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arXiv2023

Exploring Social Media for Early Detection of Depression in COVID-19 Patients

The COVID-19 pandemic has caused substantial damage to global health. Even though three years have passed, the world continues to struggle with the virus. Concerns are growing about the impact of COVID-19 on the mental health of infected individuals, who are more likely to experience depression, which can have long-lasting consequences for both the affected individuals and the world. Detection and intervention at an early stage can reduce the risk of depression in COVID-19 patients. In this paper, we investigated the relationship between COVID-19 infection and depression through social media analysis. Firstly, we managed a dataset of COVID-19 patients that contains information about their social media activity both before and after infection. Secondly,We conducted an extensive analysis of this dataset to investigate the characteristic of COVID-19 patients with a higher risk of depression. Thirdly, we proposed a deep neural network for early prediction of depression risk. This model considers daily mood swings as a psychiatric signal and incorporates textual and emotional characteristics via knowledge distillation. Experimental results demonstrate that our proposed framework outperforms baselines in detecting depression risk, with an AUROC of 0.9317 and an AUPRC of 0.8116. Our model has the potential to enable public health organizations to initiate prompt intervention with high-risk patients

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arXiv2023

FedMed-GAN: Federated Domain Translation on Unsupervised Cross-Modality Brain Image Synthesis

Utilizing multi-modal neuroimaging data has been proved to be effective to investigate human cognitive activities and certain pathologies. However, it is not practical to obtain the full set of paired neuroimaging data centrally since the collection faces several constraints, e.g., high examination cost, long acquisition time, and image corruption. In addition, these data are dispersed into different medical institutions and thus cannot be aggregated for centralized training considering the privacy issues. There is a clear need to launch a federated learning and facilitate the integration of the dispersed data from different institutions. In this paper, we propose a new benchmark for federated domain translation on unsupervised brain image synthesis (termed as FedMed-GAN) to bridge the gap between federated learning and medical GAN. FedMed-GAN mitigates the mode collapse without sacrificing the performance of generators, and is widely applied to different proportions of unpaired and paired data with variation adaptation property. We treat the gradient penalties by federally averaging algorithm and then leveraging differential privacy gradient descent to regularize the training dynamics. A comprehensive evaluation is provided for comparing FedMed-GAN and other centralized methods, which shows the new state-of-the-art performance by our FedMed-GAN. Our code has been released on the website: https://github.com/M-3LAB/FedMed-GAN

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arXiv2023

Combating Mode Collapse in GANs via Manifold Entropy Estimation

Generative Adversarial Networks (GANs) have shown compelling results in various tasks and applications in recent years. However, mode collapse remains a critical problem in GANs. In this paper, we propose a novel training pipeline to address the mode collapse issue of GANs. Different from existing methods, we propose to generalize the discriminator as feature embedding and maximize the entropy of distributions in the embedding space learned by the discriminator. Specifically, two regularization terms, i.e., Deep Local Linear Embedding (DLLE) and Deep Isometric feature Mapping (DIsoMap), are designed to encourage the discriminator to learn the structural information embedded in the data, such that the embedding space learned by the discriminator can be well-formed. Based on the well-learned embedding space supported by the discriminator, a non-parametric entropy estimator is designed to efficiently maximize the entropy of embedding vectors, playing as an approximation of maximizing the entropy of the generated distribution. By improving the discriminator and maximizing the distance of the most similar samples in the embedding space, our pipeline effectively reduces the mode collapse without sacrificing the quality of generated samples. Extensive experimental results show the effectiveness of our method, which outperforms the GAN baseline, MaF-GAN on CelebA (9.13 vs. 12.43 in FID) and surpasses the recent state-of-the-art energy-based model on the ANIME-FACE dataset (2.80 vs. 2.26 in Inception score). The code is available at https://github.com/HaozheLiu-ST/MEE

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arXiv2023

Improving GAN Training via Feature Space Shrinkage

Due to the outstanding capability for data generation, Generative Adversarial Networks (GANs) have attracted considerable attention in unsupervised learning. However, training GANs is difficult, since the training distribution is dynamic for the discriminator, leading to unstable image representation. In this paper, we address the problem of training GANs from a novel perspective, \emph{i.e.,} robust image classification. Motivated by studies on robust image representation, we propose a simple yet effective module, namely AdaptiveMix, for GANs, which shrinks the regions of training data in the image representation space of the discriminator. Considering it is intractable to directly bound feature space, we propose to construct hard samples and narrow down the feature distance between hard and easy samples. The hard samples are constructed by mixing a pair of training images. We evaluate the effectiveness of our AdaptiveMix with widely-used and state-of-the-art GAN architectures. The evaluation results demonstrate that our AdaptiveMix can facilitate the training of GANs and effectively improve the image quality of generated samples. We also show that our AdaptiveMix can be further applied to image classification and Out-Of-Distribution (OOD) detection tasks, by equipping it with state-of-the-art methods. Extensive experiments on seven publicly available datasets show that our method effectively boosts the performance of baselines. The code is publicly available at https://github.com/WentianZhang-ML/AdaptiveMix.

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arXiv2023

M3AE: Multimodal Representation Learning for Brain Tumor Segmentation with Missing Modalities

Multimodal magnetic resonance imaging (MRI) provides complementary information for sub-region analysis of brain tumors. Plenty of methods have been proposed for automatic brain tumor segmentation using four common MRI modalities and achieved remarkable performance. In practice, however, it is common to have one or more modalities missing due to image corruption, artifacts, acquisition protocols, allergy to contrast agents, or simply cost. In this work, we propose a novel two-stage framework for brain tumor segmentation with missing modalities. In the first stage, a multimodal masked autoencoder (M3AE) is proposed, where both random modalities (i.e., modality dropout) and random patches of the remaining modalities are masked for a reconstruction task, for self-supervised learning of robust multimodal representations against missing modalities. To this end, we name our framework M3AE. Meanwhile, we employ model inversion to optimize a representative full-modal image at marginal extra cost, which will be used to substitute for the missing modalities and boost performance during inference. Then in the second stage, a memory-efficient self distillation is proposed to distill knowledge between heterogenous missing-modal situations while fine-tuning the model for supervised segmentation. Our M3AE belongs to the 'catch-all' genre where a single model can be applied to all possible subsets of modalities, thus is economic for both training and deployment. Extensive experiments on BraTS 2018 and 2020 datasets demonstrate its superior performance to existing state-of-the-art methods with missing modalities, as well as the efficacy of its components. Our code is available at: https://github.com/ccarliu/m3ae.

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arXiv2023

RECIST Weakly Supervised Lesion Segmentation via Label-Space Co-Training

As an essential indicator for cancer progression and treatment response, tumor size is often measured following the response evaluation criteria in solid tumors (RECIST) guideline in CT slices. By marking each lesion with its longest axis and the longest perpendicular one, laborious pixel-wise manual annotation can be avoided. However, such a coarse substitute cannot provide a rich and accurate base to allow versatile quantitative analysis of lesions. To this end, we propose a novel weakly supervised framework to exploit the existing rich RECIST annotations for pixel-wise lesion segmentation. Specifically, a pair of under- and over-segmenting masks are constructed for each lesion based on its RECIST annotation and served as the label for co-training a pair of subnets, respectively, along with the proposed label-space perturbation induced consistency loss to bridge the gap between the two subnets and enable effective co-training. Extensive experiments are conducted on a public dataset to demonstrate the superiority of the proposed framework regarding the RECIST-based weakly supervised segmentation task and its universal applicability to various backbone networks.

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arXiv2023

Interactive Segmentation as Gaussian Process Classification

Click-based interactive segmentation (IS) aims to extract the target objects under user interaction. For this task, most of the current deep learning (DL)-based methods mainly follow the general pipelines of semantic segmentation. Albeit achieving promising performance, they do not fully and explicitly utilize and propagate the click information, inevitably leading to unsatisfactory segmentation results, even at clicked points. Against this issue, in this paper, we propose to formulate the IS task as a Gaussian process (GP)-based pixel-wise binary classification model on each image. To solve this model, we utilize amortized variational inference to approximate the intractable GP posterior in a data-driven manner and then decouple the approximated GP posterior into double space forms for efficient sampling with linear complexity. Then, we correspondingly construct a GP classification framework, named GPCIS, which is integrated with the deep kernel learning mechanism for more flexibility. The main specificities of the proposed GPCIS lie in: 1) Under the explicit guidance of the derived GP posterior, the information contained in clicks can be finely propagated to the entire image and then boost the segmentation; 2) The accuracy of predictions at clicks has good theoretical support. These merits of GPCIS as well as its good generality and high efficiency are substantiated by comprehensive experiments on several benchmarks, as compared with representative methods both quantitatively and qualitatively.

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arXiv2023

Deep-Learning Tool for Early Identifying Non-Traumatic Intracranial Hemorrhage Etiology based on CT Scan

Background: To develop an artificial intelligence system that can accurately identify acute non-traumatic intracranial hemorrhage (ICH) etiology based on non-contrast CT (NCCT) scans and investigate whether clinicians can benefit from it in a diagnostic setting. Materials and Methods: The deep learning model was developed with 1868 eligible NCCT scans with non-traumatic ICH collected between January 2011 and April 2018. We tested the model on two independent datasets (TT200 and SD 98) collected after April 2018. The model's diagnostic performance was compared with clinicians's performance. We further designed a simulated study to compare the clinicians's performance with and without the deep learning system augmentation. Results: The proposed deep learning system achieved area under the receiver operating curve of 0.986 (95% CI 0.967-1.000) on aneurysms, 0.952 (0.917-0.987) on hypertensive hemorrhage, 0.950 (0.860-1.000) on arteriovenous malformation (AVM), 0.749 (0.586-0.912) on Moyamoya disease (MMD), 0.837 (0.704-0.969) on cavernous malformation (CM), and 0.839 (0.722-0.959) on other causes in TT200 dataset. Given a 90% specificity level, the sensitivities of our model were 97.1% and 90.9% for aneurysm and AVM diagnosis, respectively. The model also shows an impressive generalizability in an independent dataset SD98. The clinicians achieve significant improvements in the sensitivity, specificity, and accuracy of diagnoses of certain hemorrhage etiologies with proposed system augmentation. Conclusions: The proposed deep learning algorithms can be an effective tool for early identification of hemorrhage etiologies based on NCCT scans. It may also provide more information for clinicians for triage and further imaging examination selection.

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arXiv2023

A New Perspective to Boost Vision Transformer for Medical Image Classification

Transformer has achieved impressive successes for various computer vision tasks. However, most of existing studies require to pretrain the Transformer backbone on a large-scale labeled dataset (e.g., ImageNet) for achieving satisfactory performance, which is usually unavailable for medical images. Additionally, due to the gap between medical and natural images, the improvement generated by the ImageNet pretrained weights significantly degrades while transferring the weights to medical image processing tasks. In this paper, we propose Bootstrap Own Latent of Transformer (BOLT), a self-supervised learning approach specifically for medical image classification with the Transformer backbone. Our BOLT consists of two networks, namely online and target branches, for self-supervised representation learning. Concretely, the online network is trained to predict the target network representation of the same patch embedding tokens with a different perturbation. To maximally excavate the impact of Transformer from limited medical data, we propose an auxiliary difficulty ranking task. The Transformer is enforced to identify which branch (i.e., online/target) is processing the more difficult perturbed tokens. Overall, the Transformer endeavours itself to distill the transformation-invariant features from the perturbed tokens to simultaneously achieve difficulty measurement and maintain the consistency of self-supervised representations. The proposed BOLT is evaluated on three medical image processing tasks, i.e., skin lesion classification, knee fatigue fracture grading and diabetic retinopathy grading. The experimental results validate the superiority of our BOLT for medical image classification, compared to ImageNet pretrained weights and state-of-the-art self-supervised learning approaches.

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arXiv2022

RCDNet: An Interpretable Rain Convolutional Dictionary Network for Single Image Deraining

As a common weather, rain streaks adversely degrade the image quality. Hence, removing rains from an image has become an important issue in the field. To handle such an ill-posed single image deraining task, in this paper, we specifically build a novel deep architecture, called rain convolutional dictionary network (RCDNet), which embeds the intrinsic priors of rain streaks and has clear interpretability. In specific, we first establish a RCD model for representing rain streaks and utilize the proximal gradient descent technique to design an iterative algorithm only containing simple operators for solving the model. By unfolding it, we then build the RCDNet in which every network module has clear physical meanings and corresponds to each operation involved in the algorithm. This good interpretability greatly facilitates an easy visualization and analysis on what happens inside the network and why it works well in inference process. Moreover, taking into account the domain gap issue in real scenarios, we further design a novel dynamic RCDNet, where the rain kernels can be dynamically inferred corresponding to input rainy images and then help shrink the space for rain layer estimation with few rain maps so as to ensure a fine generalization performance in the inconsistent scenarios of rain types between training and testing data. By end-to-end training such an interpretable network, all involved rain kernels and proximal operators can be automatically extracted, faithfully characterizing the features of both rain and clean background layers, and thus naturally lead to better deraining performance. Comprehensive experiments substantiate the superiority of our method, especially on its well generality to diverse testing scenarios and good interpretability for all its modules. Code is available in \emph{\url{https://github.com/hongwang01/DRCDNet}}.

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arXiv2022

Orientation-Shared Convolution Representation for CT Metal Artifact Learning

During X-ray computed tomography (CT) scanning, metallic implants carrying with patients often lead to adverse artifacts in the captured CT images and then impair the clinical treatment. Against this metal artifact reduction (MAR) task, the existing deep-learning-based methods have gained promising reconstruction performance. Nevertheless, there is still some room for further improvement of MAR performance and generalization ability, since some important prior knowledge underlying this specific task has not been fully exploited. Hereby, in this paper, we carefully analyze the characteristics of metal artifacts and propose an orientation-shared convolution representation strategy to adapt the physical prior structures of artifacts, i.e., rotationally symmetrical streaking patterns. The proposed method rationally adopts Fourier-series-expansion-based filter parametrization in artifact modeling, which can better separate artifacts from anatomical tissues and boost the model generalizability. Comprehensive experiments executed on synthesized and clinical datasets show the superiority of our method in detail preservation beyond the current representative MAR methods. Code will be available at \url{https://github.com/hongwang01/OSCNet}

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arXiv2022

InDuDoNet+: A Deep Unfolding Dual Domain Network for Metal Artifact Reduction in CT Images

During the computed tomography (CT) imaging process, metallic implants within patients often cause harmful artifacts, which adversely degrade the visual quality of reconstructed CT images and negatively affect the subsequent clinical diagnosis. For the metal artifact reduction (MAR) task, current deep learning based methods have achieved promising performance. However, most of them share two main common limitations: 1) the CT physical imaging geometry constraint is not comprehensively incorporated into deep network structures; 2) the entire framework has weak interpretability for the specific MAR task; hence, the role of each network module is difficult to be evaluated. To alleviate these issues, in the paper, we construct a novel deep unfolding dual domain network, termed InDuDoNet+, into which CT imaging process is finely embedded. Concretely, we derive a joint spatial and Radon domain reconstruction model and propose an optimization algorithm with only simple operators for solving it. By unfolding the iterative steps involved in the proposed algorithm into the corresponding network modules, we easily build the InDuDoNet+ with clear interpretability. Furthermore, we analyze the CT values among different tissues, and merge the prior observations into a prior network for our InDuDoNet+, which significantly improve its generalization performance.Comprehensive experiments on synthesized data and clinical data substantiate the superiority of the proposed methods as well as the superior generalization performance beyond the current state-of-the-art (SOTA) MAR methods. . Code is available at \url{https://github.com/hongwang01/InDuDoNet_plus}.

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arXiv2022

Lesion Guided Explainable Few Weak-shot Medical Report Generation

Medical images are widely used in clinical practice for diagnosis. Automatically generating interpretable medical reports can reduce radiologists' burden and facilitate timely care. However, most existing approaches to automatic report generation require sufficient labeled data for training. In addition, the learned model can only generate reports for the training classes, lacking the ability to adapt to previously unseen novel diseases. To this end, we propose a lesion guided explainable few weak-shot medical report generation framework that learns correlation between seen and novel classes through visual and semantic feature alignment, aiming to generate medical reports for diseases not observed in training. It integrates a lesion-centric feature extractor and a Transformer-based report generation module. Concretely, the lesion-centric feature extractor detects the abnormal regions and learns correlations between seen and novel classes with multi-view (visual and lexical) embeddings. Then, features of the detected regions and corresponding embeddings are concatenated as multi-view input to the report generation module for explainable report generation, including text descriptions and corresponding abnormal regions detected in the images. We conduct experiments on FFA-IR, a dataset providing explainable annotations, showing that our framework outperforms others on report generation for novel diseases.

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arXiv2022

DeltaNet:Conditional Medical Report Generation for COVID-19 Diagnosis

Fast screening and diagnosis are critical in COVID-19 patient treatment. In addition to the gold standard RT-PCR, radiological imaging like X-ray and CT also works as an important means in patient screening and follow-up. However, due to the excessive number of patients, writing reports becomes a heavy burden for radiologists. To reduce the workload of radiologists, we propose DeltaNet to generate medical reports automatically. Different from typical image captioning approaches that generate reports with an encoder and a decoder, DeltaNet applies a conditional generation process. In particular, given a medical image, DeltaNet employs three steps to generate a report: 1) first retrieving related medical reports, i.e., the historical reports from the same or similar patients; 2) then comparing retrieved images and current image to find the differences; 3) finally generating a new report to accommodate identified differences based on the conditional report. We evaluate DeltaNet on a COVID-19 dataset, where DeltaNet outperforms state-of-the-art approaches. Besides COVID-19, the proposed DeltaNet can be applied to other diseases as well. We validate its generalization capabilities on the public IU-Xray and MIMIC-CXR datasets for chest-related diseases. Code is available at \url{https://github.com/LX-doctorAI1/DeltaNet}.

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arXiv2022

Knowing the Past to Predict the Future: Reinforcement Virtual Learning

Reinforcement Learning (RL)-based control system has received considerable attention in recent decades. However, in many real-world problems, such as Batch Process Control, the environment is uncertain, which requires expensive interaction to acquire the state and reward values. In this paper, we present a cost-efficient framework, such that the RL model can evolve for itself in a Virtual Space using the predictive models with only historical data. The proposed framework enables a step-by-step RL model to predict the future state and select optimal actions for long-sight decisions. The main focuses are summarized as: 1) how to balance the long-sight and short-sight rewards with an optimal strategy; 2) how to make the virtual model interacting with real environment to converge to a final learning policy. Under the experimental settings of Fed-Batch Process, our method consistently outperforms the existing state-of-the-art methods.

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arXiv2022

Decoupled Mixup for Generalized Visual Recognition

Convolutional neural networks (CNN) have demonstrated remarkable performance when the training and testing data are from the same distribution. However, such trained CNN models often largely degrade on testing data which is unseen and Out-Of-the-Distribution (OOD). To address this issue, we propose a novel "Decoupled-Mixup" method to train CNN models for OOD visual recognition. Different from previous work combining pairs of images homogeneously, our method decouples each image into discriminative and noise-prone regions, and then heterogeneously combines these regions of image pairs to train CNN models. Since the observation is that noise-prone regions such as textural and clutter backgrounds are adverse to the generalization ability of CNN models during training, we enhance features from discriminative regions and suppress noise-prone ones when combining an image pair. To further improve the generalization ability of trained models, we propose to disentangle discriminative and noise-prone regions in frequency-based and context-based fashions. Experiment results show the high generalization performance of our method on testing data that are composed of unseen contexts, where our method achieves 85.76\% top-1 accuracy in Track-1 and 79.92\% in Track-2 in the NICO Challenge. The source code is available at https://github.com/HaozheLiu-ST/NICOChallenge-OOD-Classification.

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arXiv2022

MCSCSet: A Specialist-annotated Dataset for Medical-domain Chinese Spelling Correction

Chinese Spelling Correction (CSC) is gaining increasing attention due to its promise of automatically detecting and correcting spelling errors in Chinese texts. Despite its extensive use in many applications, like search engines and optical character recognition systems, little has been explored in medical scenarios in which complex and uncommon medical entities are easily misspelled. Correcting the misspellings of medical entities is arguably more difficult than those in the open domain due to its requirements of specificdomain knowledge. In this work, we define the task of Medical-domain Chinese Spelling Correction and propose MCSCSet, a large scale specialist-annotated dataset that contains about 200k samples. In contrast to the existing open-domain CSC datasets, MCSCSet involves: i) extensive real-world medical queries collected from Tencent Yidian, ii) corresponding misspelled sentences manually annotated by medical specialists. To ensure automated dataset curation, MCSCSet further offers a medical confusion set consisting of the commonly misspelled characters of given Chinese medical terms. This enables one to create the medical misspelling dataset automatically. Extensive empirical studies have shown significant performance gaps between the open-domain and medical-domain spelling correction, highlighting the need to develop high-quality datasets that allow for Chinese spelling correction in specific domains. Moreover, our work benchmarks several representative Chinese spelling correction models, establishing baselines for future work.

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