arXiv subjects

Chi Liu

Publications and source records attributed to Chi Liu.

At least 91 records · Page 5Linked to original sources

arXiv2023

Cross-domain Iterative Network for Simultaneous Denoising, Limited-angle Reconstruction, and Attenuation Correction of Low-dose Cardiac SPECT

Single-Photon Emission Computed Tomography (SPECT) is widely applied for the diagnosis of ischemic heart diseases. Low-dose (LD) SPECT aims to minimize radiation exposure but leads to increased image noise. Limited-angle (LA) SPECT enables faster scanning and reduced hardware costs but results in lower reconstruction accuracy. Additionally, computed tomography (CT)-derived attenuation maps ($μ$-maps) are commonly used for SPECT attenuation correction (AC), but it will cause extra radiation exposure and SPECT-CT misalignments. In addition, the majority of SPECT scanners in the market are not hybrid SPECT/CT scanners. Although various deep learning methods have been introduced to separately address these limitations, the solution for simultaneously addressing these challenges still remains highly under-explored and challenging. To this end, we propose a Cross-domain Iterative Network (CDI-Net) for simultaneous denoising, LA reconstruction, and CT-free AC in cardiac SPECT. In CDI-Net, paired projection- and image-domain networks are end-to-end connected to fuse the emission and anatomical information across domains and iterations. Adaptive Weight Recalibrators (AWR) adjust the multi-channel input features to enhance prediction accuracy. Our experiments using clinical data showed that CDI-Net produced more accurate $μ$-maps, projections, and reconstructions compared to existing approaches that addressed each task separately. Ablation studies demonstrated the significance of cross-domain and cross-iteration connections, as well as AWR, in improving the reconstruction performance.

cs.CV↗

arXiv2023

Joint Denoising and Few-angle Reconstruction for Low-dose Cardiac SPECT Using a Dual-domain Iterative Network with Adaptive Data Consistency

Myocardial perfusion imaging (MPI) by single-photon emission computed tomography (SPECT) is widely applied for the diagnosis of cardiovascular diseases. Reducing the dose of the injected tracer is essential for lowering the patient's radiation exposure, but it will lead to increased image noise. Additionally, the latest dedicated cardiac SPECT scanners typically acquire projections in fewer angles using fewer detectors to reduce hardware expenses, potentially resulting in lower reconstruction accuracy. To overcome these challenges, we propose a dual-domain iterative network for end-to-end joint denoising and reconstruction from low-dose and few-angle projections of cardiac SPECT. The image-domain network provides a prior estimate for the projection-domain networks. The projection-domain primary and auxiliary modules are interconnected for progressive denoising and few-angle reconstruction. Adaptive Data Consistency (ADC) modules improve prediction accuracy by efficiently fusing the outputs of the primary and auxiliary modules. Experiments using clinical MPI data show that our proposed method outperforms existing image-, projection-, and dual-domain techniques, producing more accurate projections and reconstructions. Ablation studies confirm the significance of the image-domain prior estimate and ADC modules in enhancing network performance.

cs.CV↗

arXiv2023

Global Prompt Cell: A Portable Control Module for Effective Prompt Tuning

As a novel approach to tuning pre-trained models, prompt tuning involves freezing the parameters in downstream tasks while inserting trainable embeddings into inputs in the first layer. However, previous methods have mainly focused on the initialization of prompt embeddings. The strategy of training and utilizing prompt embeddings in a reasonable way has become a limiting factor in the effectiveness of prompt tuning. To address this issue, we introduce the Global Prompt Cell (GPC), a portable control module for prompt tuning that selectively preserves prompt information across all encoder layers. Our experimental results demonstrate a 5.8% improvement on SuperGLUE datasets compared to vanilla prompt tuning.

cs.CL↗

arXiv2023

Unified Noise-aware Network for Low-count PET Denoising

As PET imaging is accompanied by substantial radiation exposure and cancer risk, reducing radiation dose in PET scans is an important topic. However, low-count PET scans often suffer from high image noise, which can negatively impact image quality and diagnostic performance. Recent advances in deep learning have shown great potential for recovering underlying signal from noisy counterparts. However, neural networks trained on a specific noise level cannot be easily generalized to other noise levels due to different noise amplitude and variances. To obtain optimal denoised results, we may need to train multiple networks using data with different noise levels. But this approach may be infeasible in reality due to limited data availability. Denoising dynamic PET images presents additional challenge due to tracer decay and continuously changing noise levels across dynamic frames. To address these issues, we propose a Unified Noise-aware Network (UNN) that combines multiple sub-networks with varying denoising power to generate optimal denoised results regardless of the input noise levels. Evaluated using large-scale data from two medical centers with different vendors, presented results showed that the UNN can consistently produce promising denoised results regardless of input noise levels, and demonstrate superior performance over networks trained on single noise level data, especially for extremely low-count data.

eess.IV↗

arXiv2023

HuaTuo: Tuning LLaMA Model with Chinese Medical Knowledge

Large Language Models (LLMs), such as the LLaMA model, have demonstrated their effectiveness in various general-domain natural language processing (NLP) tasks. Nevertheless, LLMs have not yet performed optimally in biomedical domain tasks due to the need for medical expertise in the responses. In response to this challenge, we propose HuaTuo, a LLaMA-based model that has been supervised-fine-tuned with generated QA (Question-Answer) instances. The experimental results demonstrate that HuaTuo generates responses that possess more reliable medical knowledge. Our proposed HuaTuo model is accessible at https://github.com/SCIR-HI/Huatuo-Llama-Med-Chinese.

cs.CL↗

arXiv2023

Meta-information-aware Dual-path Transformer for Differential Diagnosis of Multi-type Pancreatic Lesions in Multi-phase CT

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.

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arXiv2023

Dual-Domain Self-Supervised Learning for Accelerated Non-Cartesian MRI Reconstruction

While enabling accelerated acquisition and improved reconstruction accuracy, current deep MRI reconstruction networks are typically supervised, require fully sampled data, and are limited to Cartesian sampling patterns. These factors limit their practical adoption as fully-sampled MRI is prohibitively time-consuming to acquire clinically. Further, non-Cartesian sampling patterns are particularly desirable as they are more amenable to acceleration and show improved motion robustness. To this end, we present a fully self-supervised approach for accelerated non-Cartesian MRI reconstruction which leverages self-supervision in both k-space and image domains. In training, the undersampled data are split into disjoint k-space domain partitions. For the k-space self-supervision, we train a network to reconstruct the input undersampled data from both the disjoint partitions and from itself. For the image-level self-supervision, we enforce appearance consistency obtained from the original undersampled data and the two partitions. Experimental results on our simulated multi-coil non-Cartesian MRI dataset demonstrate that DDSS can generate high-quality reconstruction that approaches the accuracy of the fully supervised reconstruction, outperforming previous baseline methods. Finally, DDSS is shown to scale to highly challenging real-world clinical MRI reconstruction acquired on a portable low-field (0.064 T) MRI scanner with no data available for supervised training while demonstrating improved image quality as compared to traditional reconstruction, as determined by a radiologist study.

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arXiv2023

High-frequency Matters: An Overwriting Attack and defense for Image-processing Neural Network Watermarking

In recent years, there has been significant advancement in the field of model watermarking techniques. However, the protection of image-processing neural networks remains a challenge, with only a limited number of methods being developed. The objective of these techniques is to embed a watermark in the output images of the target generative network, so that the watermark signal can be detected in the output of a surrogate model obtained through model extraction attacks. This promising technique, however, has certain limits. Analysis of the frequency domain reveals that the watermark signal is mainly concealed in the high-frequency components of the output. Thus, we propose an overwriting attack that involves forging another watermark in the output of the generative network. The experimental results demonstrate the efficacy of this attack in sabotaging existing watermarking schemes for image-processing networks, with an almost 100% success rate. To counter this attack, we devise an adversarial framework for the watermarking network. The framework incorporates a specially designed adversarial training step, where the watermarking network is trained to defend against the overwriting network, thereby enhancing its robustness. Additionally, we observe an overfitting phenomenon in the existing watermarking method, which can render it ineffective. To address this issue, we modify the training process to eliminate the overfitting problem.

cs.CR↗

arXiv2023

Fast-MC-PET: A Novel Deep Learning-aided Motion Correction and Reconstruction Framework for Accelerated PET

Patient motion during PET is inevitable. Its long acquisition time not only increases the motion and the associated artifacts but also the patient's discomfort, thus PET acceleration is desirable. However, accelerating PET acquisition will result in reconstructed images with low SNR, and the image quality will still be degraded by motion-induced artifacts. Most of the previous PET motion correction methods are motion type specific that require motion modeling, thus may fail when multiple types of motion present together. Also, those methods are customized for standard long acquisition and could not be directly applied to accelerated PET. To this end, modeling-free universal motion correction reconstruction for accelerated PET is still highly under-explored. In this work, we propose a novel deep learning-aided motion correction and reconstruction framework for accelerated PET, called Fast-MC-PET. Our framework consists of a universal motion correction (UMC) and a short-to-long acquisition reconstruction (SL-Reon) module. The UMC enables modeling-free motion correction by estimating quasi-continuous motion from ultra-short frame reconstructions and using this information for motion-compensated reconstruction. Then, the SL-Recon converts the accelerated UMC image with low counts to a high-quality image with high counts for our final reconstruction output. Our experimental results on human studies show that our Fast-MC-PET can enable 7-fold acceleration and use only 2 minutes acquisition to generate high-quality reconstruction images that outperform/match previous motion correction reconstruction methods using standard 15 minutes long acquisition data.

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arXiv2022

Segmentation-free PVC for Cardiac SPECT using a Densely-connected Multi-dimensional Dynamic Network

In nuclear imaging, limited resolution causes partial volume effects (PVEs) that affect image sharpness and quantitative accuracy. Partial volume correction (PVC) methods incorporating high-resolution anatomical information from CT or MRI have been demonstrated to be effective. However, such anatomical-guided methods typically require tedious image registration and segmentation steps. Accurately segmented organ templates are also hard to obtain, particularly in cardiac SPECT imaging, due to the lack of hybrid SPECT/CT scanners with high-end CT and associated motion artifacts. Slight mis-registration/mis-segmentation would result in severe degradation in image quality after PVC. In this work, we develop a deep-learning-based method for fast cardiac SPECT PVC without anatomical information and associated organ segmentation. The proposed network involves a densely-connected multi-dimensional dynamic mechanism, allowing the convolutional kernels to be adapted based on the input images, even after the network is fully trained. Intramyocardial blood volume (IMBV) is introduced as an additional clinical-relevant loss function for network optimization. The proposed network demonstrated promising performance on 28 canine studies acquired on a GE Discovery NM/CT 570c dedicated cardiac SPECT scanner with a 64-slice CT using Technetium-99m-labeled red blood cells. This work showed that the proposed network with densely-connected dynamic mechanism produced superior results compared with the same network without such mechanism. Results also showed that the proposed network without anatomical information could produce images with statistically comparable IMBV measurements to the images generated by anatomical-guided PVC methods, which could be helpful in clinical translation.

eess.IV↗

arXiv2022

Issues and Challenges in Applications of Artificial Intelligence to Nuclear Medicine -- The Bethesda Report (AI Summit 2022)

The SNMMI Artificial Intelligence (SNMMI-AI) Summit, organized by the SNMMI AI Task Force, took place in Bethesda, MD on March 21-22, 2022. It brought together various community members and stakeholders from academia, healthcare, industry, patient representatives, and government (NIH, FDA), and considered various key themes to envision and facilitate a bright future for routine, trustworthy use of AI in nuclear medicine. In what follows, essential issues, challenges, controversies and findings emphasized in the meeting are summarized.

physics.med-ph↗

arXiv2022

Prompt Combines Paraphrase: Teaching Pre-trained Models to Understand Rare Biomedical Words

Prompt-based fine-tuning for pre-trained models has proven effective for many natural language processing tasks under few-shot settings in general domain. However, tuning with prompt in biomedical domain has not been investigated thoroughly. Biomedical words are often rare in general domain, but quite ubiquitous in biomedical contexts, which dramatically deteriorates the performance of pre-trained models on downstream biomedical applications even after fine-tuning, especially in low-resource scenarios. We propose a simple yet effective approach to helping models learn rare biomedical words during tuning with prompt. Experimental results show that our method can achieve up to 6% improvement in biomedical natural language inference task without any extra parameters or training steps using few-shot vanilla prompt settings.

cs.CL↗

arXiv2022

DSFormer: A Dual-domain Self-supervised Transformer for Accelerated Multi-contrast MRI Reconstruction

Multi-contrast MRI (MC-MRI) captures multiple complementary imaging modalities to aid in radiological decision-making. Given the need for lowering the time cost of multiple acquisitions, current deep accelerated MRI reconstruction networks focus on exploiting the redundancy between multiple contrasts. However, existing works are largely supervised with paired data and/or prohibitively expensive fully-sampled MRI sequences. Further, reconstruction networks typically rely on convolutional architectures which are limited in their capacity to model long-range interactions and may lead to suboptimal recovery of fine anatomical detail. To these ends, we present a dual-domain self-supervised transformer (DSFormer) for accelerated MC-MRI reconstruction. DSFormer develops a deep conditional cascade transformer (DCCT) consisting of several cascaded Swin transformer reconstruction networks (SwinRN) trained under two deep conditioning strategies to enable MC-MRI information sharing. We further present a dual-domain (image and k-space) self-supervised learning strategy for DCCT to alleviate the costs of acquiring fully sampled training data. DSFormer generates high-fidelity reconstructions which experimentally outperform current fully-supervised baselines. Moreover, we find that DSFormer achieves nearly the same performance when trained either with full supervision or with our proposed dual-domain self-supervision.

eess.IV↗

arXiv2022

Unsupervised inter-frame motion correction for whole-body dynamic PET using convolutional long short-term memory in a convolutional neural network

Subject motion in whole-body dynamic PET introduces inter-frame mismatch and seriously impacts parametric imaging. Traditional non-rigid registration methods are generally computationally intense and time-consuming. Deep learning approaches are promising in achieving high accuracy with fast speed, but have yet been investigated with consideration for tracer distribution changes or in the whole-body scope. In this work, we developed an unsupervised automatic deep learning-based framework to correct inter-frame body motion. The motion estimation network is a convolutional neural network with a combined convolutional long short-term memory layer, fully utilizing dynamic temporal features and spatial information. Our dataset contains 27 subjects each under a 90-min FDG whole-body dynamic PET scan. With 9-fold cross-validation, compared with both traditional and deep learning baselines, we demonstrated that the proposed network obtained superior performance in enhanced qualitative and quantitative spatial alignment between parametric $K_{i}$ and $V_{b}$ images and in significantly reduced parametric fitting error. We also showed the potential of the proposed motion correction method for impacting downstream analysis of the estimated parametric images, improving the ability to distinguish malignant from benign hypermetabolic regions of interest. Once trained, the motion estimation inference time of our proposed network was around 460 times faster than the conventional registration baseline, showing its potential to be easily applied in clinical settings.

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arXiv2022

Making DeepFakes more spurious: evading deep face forgery detection via trace removal attack

DeepFakes are raising significant social concerns. Although various DeepFake detectors have been developed as forensic countermeasures, these detectors are still vulnerable to attacks. Recently, a few attacks, principally adversarial attacks, have succeeded in cloaking DeepFake images to evade detection. However, these attacks have typical detector-specific designs, which require prior knowledge about the detector, leading to poor transferability. Moreover, these attacks only consider simple security scenarios. Less is known about how effective they are in high-level scenarios where either the detectors or the attacker's knowledge varies. In this paper, we solve the above challenges with presenting a novel detector-agnostic trace removal attack for DeepFake anti-forensics. Instead of investigating the detector side, our attack looks into the original DeepFake creation pipeline, attempting to remove all detectable natural DeepFake traces to render the fake images more "authentic". To implement this attack, first, we perform a DeepFake trace discovery, identifying three discernible traces. Then a trace removal network (TR-Net) is proposed based on an adversarial learning framework involving one generator and multiple discriminators. Each discriminator is responsible for one individual trace representation to avoid cross-trace interference. These discriminators are arranged in parallel, which prompts the generator to remove various traces simultaneously. To evaluate the attack efficacy, we crafted heterogeneous security scenarios where the detectors were embedded with different levels of defense and the attackers' background knowledge of data varies. The experimental results show that the proposed attack can significantly compromise the detection accuracy of six state-of-the-art DeepFake detectors while causing only a negligible loss in visual quality to the original DeepFake samples.

cs.CV↗

arXiv2022

Label uncertainty-guided multi-stream model for disease screening

The annotation of disease severity for medical image datasets often relies on collaborative decisions from multiple human graders. The intra-observer variability derived from individual differences always persists in this process, yet the influence is often underestimated. In this paper, we cast the intra-observer variability as an uncertainty problem and incorporate the label uncertainty information as guidance into the disease screening model to improve the final decision. The main idea is dividing the images into simple and hard cases by uncertainty information, and then developing a multi-stream network to deal with different cases separately. Particularly, for hard cases, we strengthen the network's capacity in capturing the correct disease features and resisting the interference of uncertainty. Experiments on a fundus image-based glaucoma screening case study show that the proposed model outperforms several baselines, especially in screening hard cases.

cs.CV↗

arXiv2021

Artificial Intelligence-Based Image Enhancement in PET Imaging: Noise Reduction and Resolution Enhancement

High noise and low spatial resolution are two key confounding factors that limit the qualitative and quantitative accuracy of PET images. AI models for image denoising and deblurring are becoming increasingly popular for post-reconstruction enhancement of PET images. We present here a detailed review of recent efforts for AI-based PET image enhancement with a focus on network architectures, data types, loss functions, and evaluation metrics. We also highlight emerging areas in this field that are quickly gaining popularity, identify barriers to large-scale adoption of AI models for PET image enhancement, and discuss future directions.

eess.IV↗

arXiv2021

A Deep Learning-based Quality Assessment and Segmentation System with a Large-scale Benchmark Dataset for Optical Coherence Tomographic Angiography Image

Optical Coherence Tomography Angiography (OCTA) is a non-invasive and non-contacting imaging technique providing visualization of microvasculature of retina and optic nerve head in human eyes in vivo. The adequate image quality of OCTA is the prerequisite for the subsequent quantification of retinal microvasculature. Traditionally, the image quality score based on signal strength is used for discriminating low quality. However, it is insufficient for identifying artefacts such as motion and off-centration, which rely specialized knowledge and need tedious and time-consuming manual identification. One of the most primary issues in OCTA analysis is to sort out the foveal avascular zone (FAZ) region in the retina, which highly correlates with any visual acuity disease. However, the variations in OCTA visual quality affect the performance of deep learning in any downstream marginally. Moreover, filtering the low-quality OCTA images out is both labor-intensive and time-consuming. To address these issues, we develop an automated computer-aided OCTA image processing system using deep neural networks as the classifier and segmentor to help ophthalmologists in clinical diagnosis and research. This system can be an assistive tool as it can process OCTA images of different formats to assess the quality and segment the FAZ area. The source code is freely available at https://github.com/shanzha09/COIPS.git. Another major contribution is the large-scale OCTA dataset, namely OCTA-25K-IQA-SEG we publicize for performance evaluation. It is comprised of four subsets, namely sOCTA-3$\times$3-10k, sOCTA-6$\times$6-14k, sOCTA-3$\times$3-1.1k-seg, and dOCTA-6$\times$6-1.1k-seg, which contains a total number of 25,665 images. The large-scale OCTA dataset is available at https://doi.org/10.5281/zenodo.5111975, https://doi.org/10.5281/zenodo.5111972.

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