arXiv subjects

Zhiqiang Hu

Publications and source records attributed to Zhiqiang Hu.

At least 55 records · Page 3Linked to original sources

arXiv2023

Adaptive Supervised PatchNCE Loss for Learning H&E-to-IHC Stain Translation with Inconsistent Groundtruth Image Pairs

Immunohistochemical (IHC) staining highlights the molecular information critical to diagnostics in tissue samples. However, compared to H&E staining, IHC staining can be much more expensive in terms of both labor and the laboratory equipment required. This motivates recent research that demonstrates that the correlations between the morphological information present in the H&E-stained slides and the molecular information in the IHC-stained slides can be used for H&E-to-IHC stain translation. However, due to a lack of pixel-perfect H&E-IHC groundtruth pairs, most existing methods have resorted to relying on expert annotations. To remedy this situation, we present a new loss function, Adaptive Supervised PatchNCE (ASP), to directly deal with the input to target inconsistencies in a proposed H&E-to-IHC image-to-image translation framework. The ASP loss is built upon a patch-based contrastive learning criterion, named Supervised PatchNCE (SP), and augments it further with weight scheduling to mitigate the negative impact of noisy supervision. Lastly, we introduce the Multi-IHC Stain Translation (MIST) dataset, which contains aligned H&E-IHC patches for 4 different IHC stains critical to breast cancer diagnosis. In our experiment, we demonstrate that our proposed method outperforms existing image-to-image translation methods for stain translation to multiple IHC stains. All of our code and datasets are available at https://github.com/lifangda01/AdaptiveSupervisedPatchNCE.

cs.CV↗

arXiv2023

Text Style Transfer: A Review and Experimental Evaluation

The stylistic properties of text have intrigued computational linguistics researchers in recent years. Specifically, researchers have investigated the Text Style Transfer (TST) task, which aims to change the stylistic properties of the text while retaining its style independent content. Over the last few years, many novel TST algorithms have been developed, while the industry has leveraged these algorithms to enable exciting TST applications. The field of TST research has burgeoned because of this symbiosis. This article aims to provide a comprehensive review of recent research efforts on text style transfer. More concretely, we create a taxonomy to organize the TST models and provide a comprehensive summary of the state of the art. We review the existing evaluation methodologies for TST tasks and conduct a large-scale reproducibility study where we experimentally benchmark 19 state-of-the-art TST algorithms on two publicly available datasets. Finally, we expand on current trends and provide new perspectives on the new and exciting developments in the TST field.

cs.CL↗

arXiv2022

Are Current Task-oriented Dialogue Systems Able to Satisfy Impolite Users?

Task-oriented dialogue (TOD) systems have assisted users on many tasks, including ticket booking and service inquiries. While existing TOD systems have shown promising performance in serving customer needs, these systems mostly assume that users would interact with the dialogue agent politely. This assumption is unrealistic as impatient or frustrated customers may also interact with TOD systems impolitely. This paper aims to address this research gap by investigating impolite users' effects on TOD systems. Specifically, we constructed an impolite dialogue corpus and conducted extensive experiments to evaluate the state-of-the-art TOD systems on our impolite dialogue corpus. Our experimental results show that existing TOD systems are unable to handle impolite user utterances. We also present a data augmentation method to improve TOD performance in impolite dialogues. Nevertheless, handling impolite dialogues remains a very challenging research task. We hope by releasing the impolite dialogue corpus and establishing the benchmark evaluations, more researchers are encouraged to investigate this new challenging research task.

cs.CL↗

arXiv2022

Patient-specific mean teacher UNet for enhancing PET image and low-dose PET reconstruction on RefleXion X1 biology-guided radiotherapy system

The RefleXion X1 is the first biology-guided radiotherapy (BgRT) system. Its dual 90-degree PET detector collects fewer pair production events compared to a full-ring diagnostic PET system. In the proposed BgRT workflow, a short scan is acquired before treatment delivery to ensure image quality and consistency. The shorter scan time, a quarter of the simulation scan time, also leads to fewer coincidence events and hence reduced image quality. In this study, we proposed a patient-specific mean teacher UNet (MT-UNet) to enhance PET image quality and low-dose PET reconstruction on RefleXion X1. PET/CT scans of nine cancer patients were acquired using RefleXion X1. Every patient had one simulation scan. Five patients had additional scans acquired during the first and the final treatment fractions. Treatment scans were acquired using the same imaging protocol as the simulation scan. For each scan, we reconstructed a full-dose image and evenly split coincidence events into four sessions to reconstruct four quarter-dose PET images. For each patient, our proposed MT-UNet was trained using quarter-dose and full-dose images of the simulation scan. For the image quality enhancement task, we applied nine trained MT-UNets to full-dose simulation PET images of the nine patients to generate enhanced images, respectively. The enhanced images were compared with the original full-dose images using CNR and SNR. For the low-dose image reconstruction task, we applied five trained MT-UNets to ten quarter-dose treatment images of five patients to predict full-dose images, respectively. The predicted and ground truth full-dose images were compared using SSIM and PSNR. We also trained and evaluated patient-specific UNets for model comparison. Our proposed patient-specific MT-UNet achieved better performance in improving the quality of RefleXion low-dose and full-dose images compared to the patient-specific UNet.

physics.med-ph↗

arXiv2022

SenseCare: A Research Platform for Medical Image Informatics and Interactive 3D Visualization

Clinical research on smart health has an increasing demand for intelligent and clinic-oriented medical image computing algorithms and platforms that support various applications. To this end, we have developed SenseCare research platform, which is designed to facilitate translational research on intelligent diagnosis and treatment planning in various clinical scenarios. To enable clinical research with Artificial Intelligence (AI), SenseCare provides a range of AI toolkits for different tasks, including image segmentation, registration, lesion and landmark detection from various image modalities ranging from radiology to pathology. In addition, SenseCare is clinic-oriented and supports a wide range of clinical applications such as diagnosis and surgical planning for lung cancer, pelvic tumor, coronary artery disease, etc. SenseCare provides several appealing functions and features such as advanced 3D visualization, concurrent and efficient web-based access, fast data synchronization and high data security, multi-center deployment, support for collaborative research, etc. In this report, we present an overview of SenseCare as an efficient platform providing comprehensive toolkits and high extensibility for intelligent image analysis and clinical research in different application scenarios. We also summarize the research outcome through the collaboration with multiple hospitals.

cs.HC↗

arXiv2022

Contrastive and Selective Hidden Embeddings for Medical Image Segmentation

Medical image segmentation has been widely recognized as a pivot procedure for clinical diagnosis, analysis, and treatment planning. However, the laborious and expensive annotation process lags down the speed of further advances. Contrastive learning-based weight pre-training provides an alternative by leveraging unlabeled data to learn a good representation. In this paper, we investigate how contrastive learning benefits the general supervised medical segmentation tasks. To this end, patch-dragsaw contrastive regularization (PDCR) is proposed to perform patch-level tugging and repulsing with the extent controlled by a continuous affinity score. And a new structure dubbed uncertainty-aware feature selection block (UAFS) is designed to perform the feature selection process, which can handle the learning target shift caused by minority features with high uncertainty. By plugging the proposed 2 modules into the existing segmentation architecture, we achieve state-of-the-art results across 8 public datasets from 6 domains. Newly designed modules further decrease the amount of training data to a quarter while achieving comparable, if not better, performances. From this perspective, we take the opposite direction of the original self/un-supervised contrastive learning by further excavating information contained within the label.

cs.CV↗

arXiv2021

Hybrid Supervision Learning for Pathology Whole Slide Image Classification

Weak supervision learning on classification labels has demonstrated high performance in various tasks, while a few pixel-level fine annotations are also affordable. Naturally a question comes to us that whether the combination of pixel-level (e.g., segmentation) and image level (e.g., classification) annotation can introduce further improvement. However in computational pathology this is a difficult task for this reason: High resolution of whole slide images makes it difficult to do end-to-end classification model training, which is challenging to research of weak or hybrid supervision learning in the past. To handle this problem, we propose a hybrid supervision learning framework for this kind of high resolution images with sufficient image-level coarse annotations and a few pixel-level fine labels. This framework, when applied in training patch model, can carefully make use of coarse image-level labels to refine generated pixel-level pseudo labels. Complete strategy is proposed to suppress pixel-level false positives and false negatives. A large hybrid annotated dataset is used to evaluate the effectiveness of hybrid supervision learning. By extracting pixel-level pseudo labels in initially image-level labeled samples, we achieve 5.2% higher specificity than purely training on existing labels while retaining 100% sensitivity, in the task of image-level classification to be positive or negative.

cs.CV↗

arXiv2021

Evolution of electronic structure in pristine and hole-doped kagome metal RbV$_3$Sb$_5$

We report on in situ low-temperature (4 K) scanning tunneling microscope measurements of atomic and electronic structures of the cleaved surfaces of an alkali-based kagome metal RbV$_3$Sb$_5$ single crystals. We find that the dominant pristine surface exhibits Rb-1x1 structure, in which a unique unidirectional $\sqrt{3}a_0$ charge order is discovered. As the sample temperature slightly rises, Rb-$\sqrt{3}$x1 and Rb-$\sqrt{3}$x$\sqrt{3}$ reconstructions form due to desorption of surface Rb atoms. Our conductance mapping results demonstrate that Rb desorption not only gives rise to hole doping, but also renormalizes the electronic band structures. Surprisingly, we find a ubiquitous gap opening near the Fermi level in tunneling spectra on all the surfaces despite their large differences of hole-carrier concentration, indicating an orbital-selective band reconstruction in RbV$_3$Sb$_5$.

cond-mat.supr-con↗

arXiv2021

Improving Text Auto-Completion with Next Phrase Prediction

Language models such as GPT-2 have performed well on constructing syntactically sound sentences for text auto-completion task. However, such models often require considerable training effort to adapt to specific writing domains (e.g., medical). In this paper, we propose an intermediate training strategy to enhance pre-trained language models' performance in the text auto-completion task and fastly adapt them to specific domains. Our strategy includes a novel self-supervised training objective called Next Phrase Prediction (NPP), which encourages a language model to complete the partial query with enriched phrases and eventually improve the model's text auto-completion performance. Preliminary experiments have shown that our approach is able to outperform the baselines in auto-completion for email and academic writing domains.

cs.CL↗

arXiv2021

Syntax Matters! Syntax-Controlled in Text Style Transfer

Existing text style transfer (TST) methods rely on style classifiers to disentangle the text's content and style attributes for text style transfer. While the style classifier plays a critical role in existing TST methods, there is no known investigation on its effect on the TST methods. In this paper, we conduct an empirical study on the limitations of the style classifiers used in existing TST methods. We demonstrate that the existing style classifiers cannot learn sentence syntax effectively and ultimately worsen existing TST models' performance. To address this issue, we propose a novel Syntax-Aware Controllable Generation (SACG) model, which includes a syntax-aware style classifier that ensures learned style latent representations effectively capture the syntax information for TST. Through extensive experiments on two popular TST tasks, we show that our proposed method significantly outperforms the state-of-the-art methods. Our case studies have also demonstrated SACG's ability to generate fluent target-style sentences that preserved the original content.

cs.CL↗

arXiv2021

Multi-frame Collaboration for Effective Endoscopic Video Polyp Detection via Spatial-Temporal Feature Transformation

Precise localization of polyp is crucial for early cancer screening in gastrointestinal endoscopy. Videos given by endoscopy bring both richer contextual information as well as more challenges than still images. The camera-moving situation, instead of the common camera-fixed-object-moving one, leads to significant background variation between frames. Severe internal artifacts (e.g. water flow in the human body, specular reflection by tissues) can make the quality of adjacent frames vary considerately. These factors hinder a video-based model to effectively aggregate features from neighborhood frames and give better predictions. In this paper, we present Spatial-Temporal Feature Transformation (STFT), a multi-frame collaborative framework to address these issues. Spatially, STFT mitigates inter-frame variations in the camera-moving situation with feature alignment by proposal-guided deformable convolutions. Temporally, STFT proposes a channel-aware attention module to simultaneously estimate the quality and correlation of adjacent frames for adaptive feature aggregation. Empirical studies and superior results demonstrate the effectiveness and stability of our method. For example, STFT improves the still image baseline FCOS by 10.6% and 20.6% on the comprehensive F1-score of the polyp localization task in CVC-Clinic and ASUMayo datasets, respectively, and outperforms the state-of-the-art video-based method by 3.6% and 8.0%, respectively. Code is available at \url{https://github.com/lingyunwu14/STFT}.

cs.CV↗

arXiv2021

Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction

The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation when tested in unseen dataset. In this paper, we investigate the problem and find that it is mainly attributed to the poor performance for inter-novel-protein interaction prediction. However, current evaluations overlook the inter-novel-protein interactions, and thus fail to give an instructive assessment. As a result, we propose to address the problem from both the evaluation and the methodology. Firstly, we design a new evaluation framework that fully respects the inter-novel-protein interactions and gives consistent assessment across datasets. Secondly, we argue that correlations between proteins must provide useful information for analysis of novel proteins, and based on this, we propose a graph neural network based method (GNN-PPI) for better inter-novel-protein interaction prediction. Experimental results on real-world datasets of different scales demonstrate that GNN-PPI significantly outperforms state-of-the-art PPI prediction methods, especially for the inter-novel-protein interaction prediction.

cs.LG↗

arXiv2021

DeepStyle: User Style Embedding for Authorship Attribution of Short Texts

Authorship attribution (AA), which is the task of finding the owner of a given text, is an important and widely studied research topic with many applications. Recent works have shown that deep learning methods could achieve significant accuracy improvement for the AA task. Nevertheless, most of these proposed methods represent user posts using a single type of feature (e.g., word bi-grams) and adopt a text classification approach to address the task. Furthermore, these methods offer very limited explainability of the AA results. In this paper, we address these limitations by proposing DeepStyle, a novel embedding-based framework that learns the representations of users' salient writing styles. We conduct extensive experiments on two real-world datasets from Twitter and Weibo. Our experiment results show that DeepStyle outperforms the state-of-the-art baselines on the AA task.

cs.CL↗

arXiv2020

Large-scale Gastric Cancer Screening and Localization Using Multi-task Deep Neural Network

Gastric cancer is one of the most common cancers, which ranks third among the leading causes of cancer death. Biopsy of gastric mucosa is a standard procedure in gastric cancer screening test. However, manual pathological inspection is labor-intensive and time-consuming. Besides, it is challenging for an automated algorithm to locate the small lesion regions in the gigapixel whole-slide image and make the decision correctly.To tackle these issues, we collected large-scale whole-slide image dataset with detailed lesion region annotation and designed a whole-slide image analyzing framework consisting of 3 networks which could not only determine the screening result but also present the suspicious areas to the pathologist for reference. Experiments demonstrated that our proposed framework achieves sensitivity of 97.05% and specificity of 92.72% in screening task and Dice coefficient of 0.8331 in segmentation task. Furthermore, we tested our best model in real-world scenario on 10,315 whole-slide images collected from 4 medical centers.

eess.IV↗

arXiv2020

Multi-organ Segmentation via Co-training Weight-averaged Models from Few-organ Datasets

Multi-organ segmentation has extensive applications in many clinical applications. To segment multiple organs of interest, it is generally quite difficult to collect full annotations of all the organs on the same images, as some medical centers might only annotate a portion of the organs due to their own clinical practice. In most scenarios, one might obtain annotations of a single or a few organs from one training set, and obtain annotations of the the other organs from another set of training images. Existing approaches mostly train and deploy a single model for each subset of organs, which are memory intensive and also time inefficient. In this paper, we propose to co-train weight-averaged models for learning a unified multi-organ segmentation network from few-organ datasets. We collaboratively train two networks and let the coupled networks teach each other on un-annotated organs. To alleviate the noisy teaching supervisions between the networks, the weighted-averaged models are adopted to produce more reliable soft labels. In addition, a novel region mask is utilized to selectively apply the consistent constraint on the un-annotated organ regions that require collaborative teaching, which further boosts the performance. Extensive experiments on three public available single-organ datasets LiTS, KiTS, Pancreas and manually-constructed single-organ datasets from MOBA show that our method can better utilize the few-organ datasets and achieves superior performance with less inference computational cost.

cs.CV↗

arXiv2020

A Global Benchmark of Algorithms for Segmenting Late Gadolinium-Enhanced Cardiac Magnetic Resonance Imaging

Segmentation of cardiac images, particularly late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) widely used for visualizing diseased cardiac structures, is a crucial first step for clinical diagnosis and treatment. However, direct segmentation of LGE-MRIs is challenging due to its attenuated contrast. Since most clinical studies have relied on manual and labor-intensive approaches, automatic methods are of high interest, particularly optimized machine learning approaches. To address this, we organized the "2018 Left Atrium Segmentation Challenge" using 154 3D LGE-MRIs, currently the world's largest cardiac LGE-MRI dataset, and associated labels of the left atrium segmented by three medical experts, ultimately attracting the participation of 27 international teams. In this paper, extensive analysis of the submitted algorithms using technical and biological metrics was performed by undergoing subgroup analysis and conducting hyper-parameter analysis, offering an overall picture of the major design choices of convolutional neural networks (CNNs) and practical considerations for achieving state-of-the-art left atrium segmentation. Results show the top method achieved a dice score of 93.2% and a mean surface to a surface distance of 0.7 mm, significantly outperforming prior state-of-the-art. Particularly, our analysis demonstrated that double, sequentially used CNNs, in which a first CNN is used for automatic region-of-interest localization and a subsequent CNN is used for refined regional segmentation, achieved far superior results than traditional methods and pipelines containing single CNNs. This large-scale benchmarking study makes a significant step towards much-improved segmentation methods for cardiac LGE-MRIs, and will serve as an important benchmark for evaluating and comparing the future works in the field.

cs.CV↗

arXiv2019

Accurate Nuclear Segmentation with Center Vector Encoding

Nuclear segmentation is important and frequently demanded for pathology image analysis, yet is also challenging due to nuclear crowdedness and possible occlusion. In this paper, we present a novel bottom-up method for nuclear segmentation. The concepts of Center Mask and Center Vector are introduced to better depict the relationship between pixels and nuclear instances. The instance differentiation process are thus largely simplified and easier to understand. Experiments demonstrate the effectiveness of Center Vector Encoding, where our method outperforms state-of-the-arts by a clear margin.

cs.CV↗

arXiv2019

Signet Ring Cell Detection With a Semi-supervised Learning Framework

Signet ring cell carcinoma is a type of rare adenocarcinoma with poor prognosis. Early detection leads to huge improvement of patients' survival rate. However, pathologists can only visually detect signet ring cells under the microscope. This procedure is not only laborious but also prone to omission. An automatic and accurate signet ring cell detection solution is thus important but has not been investigated before. In this paper, we take the first step to present a semi-supervised learning framework for the signet ring cell detection problem. Self-training is proposed to deal with the challenge of incomplete annotations, and cooperative-training is adapted to explore the unlabeled regions. Combining the two techniques, our semi-supervised learning framework can make better use of both labeled and unlabeled data. Experiments on large real clinical data demonstrate the effectiveness of our design. Our framework achieves accurate signet ring cell detection and can be readily applied in the clinical trails. The dataset will be released soon to facilitate the development of the area.

cs.CV↗