arXiv subjects

Xiaofeng Yang

Publications and source records attributed to Xiaofeng Yang.

At least 145 records · Page 8Linked to original sources

arXiv2023

Hippocampus Substructure Segmentation Using Morphological Vision Transformer Learning

Background: The hippocampus plays a crucial role in memory and cognition. Because of the associated toxicity from whole brain radiotherapy, more advanced treatment planning techniques prioritize hippocampal avoidance, which depends on an accurate segmentation of the small and complexly shaped hippocampus. Purpose: To achieve accurate segmentation of the anterior and posterior regions of the hippocampus from T1 weighted (T1w) MRI images, we developed a novel model, Hippo-Net, which uses a mutually enhanced strategy. Methods: The proposed model consists of two major parts: 1) a localization model is used to detect the volume-of-interest (VOI) of hippocampus. 2) An end-to-end morphological vision transformer network is used to perform substructures segmentation within the hippocampus VOI. A total of 260 T1w MRI datasets were used in this study. We conducted a five-fold cross-validation on the first 200 T1w MR images and then performed a hold-out test on the remaining 60 T1w MR images with the model trained on the first 200 images. Results: In five-fold cross-validation, the DSCs were 0.900+-0.029 and 0.886+-0.031for the hippocampus proper and parts of the subiculum, respectively. The MSD were 0.426+-0.115mm and 0.401+-0.100 mm for the hippocampus proper and parts of the subiculum, respectively. Conclusions: The proposed method showed great promise in automatically delineating hippocampus substructures on T1w MRI images. It may facilitate the current clinical workflow and reduce the physician effort.

physics.med-ph↗

arXiv2023

Synthetic CT Generation from MRI using 3D Transformer-based Denoising Diffusion Model

Magnetic resonance imaging (MRI)-based synthetic computed tomography (sCT) simplifies radiation therapy treatment planning by eliminating the need for CT simulation and error-prone image registration, ultimately reducing patient radiation dose and setup uncertainty. We propose an MRI-to-CT transformer-based denoising diffusion probabilistic model (MC-DDPM) to transform MRI into high-quality sCT to facilitate radiation treatment planning. MC-DDPM implements diffusion processes with a shifted-window transformer network to generate sCT from MRI. The proposed model consists of two processes: a forward process which adds Gaussian noise to real CT scans, and a reverse process in which a shifted-window transformer V-net (Swin-Vnet) denoises the noisy CT scans conditioned on the MRI from the same patient to produce noise-free CT scans. With an optimally trained Swin-Vnet, the reverse diffusion process was used to generate sCT scans matching MRI anatomy. We evaluated the proposed method by generating sCT from MRI on a brain dataset and a prostate dataset. Qualitative evaluation was performed using the mean absolute error (MAE) of Hounsfield unit (HU), peak signal to noise ratio (PSNR), multi-scale Structure Similarity index (MS-SSIM) and normalized cross correlation (NCC) indexes between ground truth CTs and sCTs. MC-DDPM generated brain sCTs with state-of-the-art quantitative results with MAE 43.317 HU, PSNR 27.046 dB, SSIM 0.965, and NCC 0.983. For the prostate dataset, MC-DDPM achieved MAE 59.953 HU, PSNR 26.920 dB, SSIM 0.849, and NCC 0.948. In conclusion, we have developed and validated a novel approach for generating CT images from routine MRIs using a transformer-based DDPM. This model effectively captures the complex relationship between CT and MRI images, allowing for robust and high-quality synthetic CT (sCT) images to be generated in minutes.

eess.IV↗

arXiv2023

BreastSAM: A Study of Segment Anything Model for Breast Tumor Detection in Ultrasound Images

Breast cancer is one of the most common cancers among women worldwide, with early detection significantly increasing survival rates. Ultrasound imaging is a critical diagnostic tool that aids in early detection by providing real-time imaging of the breast tissue. We conducted a thorough investigation of the Segment Anything Model (SAM) for the task of interactive segmentation of breast tumors in ultrasound images. We explored three pre-trained model variants: ViT_h, ViT_l, and ViT_b, among which ViT_l demonstrated superior performance in terms of mean pixel accuracy, Dice score, and IoU score. The significance of prompt interaction in improving the model's segmentation performance was also highlighted, with substantial improvements in performance metrics when prompts were incorporated. The study further evaluated the model's differential performance in segmenting malignant and benign breast tumors, with the model showing exceptional proficiency in both categories, albeit with slightly better performance for benign tumors. Furthermore, we analyzed the impacts of various breast tumor characteristics - size, contrast, aspect ratio, and complexity - on segmentation performance. Our findings reveal that tumor contrast and size positively impact the segmentation result, while complex boundaries pose challenges. The study provides valuable insights for using SAM as a robust and effective algorithm for breast tumor segmentation in ultrasound images.

eess.IV↗

arXiv2023

Data-Driven Volumetric Image Generation from Surface Structures using a Patient-Specific Deep Leaning Model

The advent of computed tomography significantly improves patient health regarding diagnosis, prognosis, and treatment planning and verification. However, tomographic imaging escalates concomitant radiation doses to patients, inducing potential secondary cancer. We demonstrate the feasibility of a data-driven approach to synthesize volumetric images using patient surface images, which can be obtained from a zero-dose surface imaging system. This study includes 500 computed tomography (CT) image sets from 50 patients. Compared to the ground truth CT, the synthetic images result in the evaluation metric values of 26.9 Hounsfield units, 39.1dB, and 0.965 regarding the mean absolute error, peak signal-to-noise ratio, and structural similarity index measure. This approach provides a data integration solution that can potentially enable real-time imaging, which is free of radiation-induced risk and could be applied to image-guided medical procedures.

physics.med-ph↗

arXiv2023

Polyp-SAM: Transfer SAM for Polyp Segmentation

Colon polyps are considered important precursors for colorectal cancer. Automatic segmentation of colon polyps can significantly reduce the misdiagnosis of colon cancer and improve physician annotation efficiency. While many methods have been proposed for polyp segmentation, training large-scale segmentation networks with limited colonoscopy data remains a challenge. Recently, the Segment Anything Model (SAM) has recently gained much attention in both natural and medical image segmentation. SAM demonstrates superior performance in several image benchmarks and therefore shows great potential for medical image segmentation. In this study, we propose Poly-SAM, a finetuned SAM model for polyp segmentation, and compare its performance to several state-of-the-art polyp segmentation models. We also compare two transfer learning strategies of SAM with and without finetuning its encoders. Evaluated on five public datasets, our Polyp-SAM achieves state-of-the-art performance on two datasets and impressive performance on three datasets, with dice scores all above 88%. This study demonstrates the great potential of adapting SAM to medical image segmentation tasks. We plan to release the code and model weights for this paper at: https://github.com/ricklisz/Polyp-SAM.

eess.IV↗

arXiv2023

Cycle-guided Denoising Diffusion Probability Model for 3D Cross-modality MRI Synthesis

This study aims to develop a novel Cycle-guided Denoising Diffusion Probability Model (CG-DDPM) for cross-modality MRI synthesis. The CG-DDPM deploys two DDPMs that condition each other to generate synthetic images from two different MRI pulse sequences. The two DDPMs exchange random latent noise in the reverse processes, which helps to regularize both DDPMs and generate matching images in two modalities. This improves image-to-image translation ac-curacy. We evaluated the CG-DDPM quantitatively using mean absolute error (MAE), multi-scale structural similarity index measure (MSSIM), and peak sig-nal-to-noise ratio (PSNR), as well as the network synthesis consistency, on the BraTS2020 dataset. Our proposed method showed high accuracy and reliable consistency for MRI synthesis. In addition, we compared the CG-DDPM with several other state-of-the-art networks and demonstrated statistically significant improvements in the image quality of synthetic MRIs. The proposed method enhances the capability of current multimodal MRI synthesis approaches, which could contribute to more accurate diagnosis and better treatment planning for patients by synthesizing additional MRI modalities.

eess.IV↗

arXiv2023

SkinSAM: Empowering Skin Cancer Segmentation with Segment Anything Model

Skin cancer is a prevalent and potentially fatal disease that requires accurate and efficient diagnosis and treatment. Although manual tracing is the current standard in clinics, automated tools are desired to reduce human labor and improve accuracy. However, developing such tools is challenging due to the highly variable appearance of skin cancers and complex objects in the background. In this paper, we present SkinSAM, a fine-tuned model based on the Segment Anything Model that showed outstanding segmentation performance. The models are validated on HAM10000 dataset which includes 10015 dermatoscopic images. While larger models (ViT_L, ViT_H) performed better than the smaller one (ViT_b), the finetuned model (ViT_b_finetuned) exhibited the greatest improvement, with a Mean pixel accuracy of 0.945, Mean dice score of 0.8879, and Mean IoU score of 0.7843. Among the lesion types, vascular lesions showed the best segmentation results. Our research demonstrates the great potential of adapting SAM to medical image segmentation tasks.

cs.CV↗

arXiv2023

Advancing Medical Imaging with Language Models: A Journey from N-grams to ChatGPT

In this paper, we aimed to provide a review and tutorial for researchers in the field of medical imaging using language models to improve their tasks at hand. We began by providing an overview of the history and concepts of language models, with a special focus on large language models. We then reviewed the current literature on how language models are being used to improve medical imaging, emphasizing different applications such as image captioning, report generation, report classification, finding extraction, visual question answering, interpretable diagnosis, and more for various modalities and organs. The ChatGPT was specially highlighted for researchers to explore more potential applications. We covered the potential benefits of accurate and efficient language models for medical imaging analysis, including improving clinical workflow efficiency, reducing diagnostic errors, and assisting healthcare professionals in providing timely and accurate diagnoses. Overall, our goal was to bridge the gap between language models and medical imaging and inspire new ideas and innovations in this exciting area of research. We hope that this review paper will serve as a useful resource for researchers in this field and encourage further exploration of the possibilities of language models in medical imaging.

cs.CV↗

arXiv2023

Deep Learning in MRI-guided Radiation Therapy: A Systematic Review

MRI-guided radiation therapy (MRgRT) offers a precise and adaptive approach to treatment planning. Deep learning applications which augment the capabilities of MRgRT are systematically reviewed. MRI-guided radiation therapy offers a precise, adaptive approach to treatment planning. Deep learning applications which augment the capabilities of MRgRT are systematically reviewed with emphasis placed on underlying methods. Studies are further categorized into the areas of segmentation, synthesis, radiomics, and real time MRI. Finally, clinical implications, current challenges, and future directions are discussed.

physics.med-ph↗

arXiv2023

Denoising Magnetic Resonance Spectroscopy (MRS) Data Using Stacked Autoencoder for Improving Signal-to-Noise Ratio and Speed of MRS

Background: Magnetic resonance spectroscopy (MRS) enables non-invasive detection and measurement of biochemicals and metabolites. However, MRS has low signal-to-noise ratio (SNR) when concentrations of metabolites are in the range of the million molars. Standard approach of using a high number of signal averaging (NSA) to achieve sufficient NSR comes at the cost of a long acquisition time. Purpose: We propose to use deep-learning approaches to denoise MRS data without increasing the NSA. Methods: The study was conducted using data collected from the brain spectroscopy phantom and human subjects. We utilized a stack auto-encoder (SAE) network to train deep learning models for denoising low NSA data (NSA = 1, 2, 4, 8, and 16) randomly truncated from high SNR data collected with high NSA (NSA=192) which were also used to obtain the ground truth. We applied both self-supervised and fully-supervised training approaches and compared their performance of denoising low NSA data based on improved SNRs. Results: With the SAE model, the SNR of low NSA data (NSA = 1) obtained from the phantom increased by 22.8% and the MSE decreased by 47.3%. For low NSA images of the human parietal and temporal lobes, the SNR increased by 43.8% and the MSE decreased by 68.8%. In all cases, the chemical shift of NAA in the denoised spectra closely matched with the high SNR spectra, suggesting no distortion to the spectra from denoising. Furthermore, the denoising performance of the SAE model was more effective in denoising spectra with higher noise levels. Conclusions: The reported SAE denoising method is a model-free approach to enhance the SNR of low NSA MRS data. With the denoising capability, it is possible to acquire MRS data with a few NSA, resulting in shorter scan times while maintaining adequate spectroscopic information for detecting and quantifying the metabolites of interest.

physics.med-ph↗

arXiv2023

CBCT-Based Synthetic CT Image Generation Using Conditional Denoising Diffusion Probabilistic Model

Background: Daily or weekly cone-beam computed tomography (CBCT) scans are commonly used for accurate patient positioning during the image-guided radiotherapy (IGRT) process, making it an ideal option for adaptive radiotherapy (ART) replanning. However, the presence of severe artifacts and inaccurate Hounsfield unit (HU) values prevent its use for quantitative applications such as organ segmentation and dose calculation. To enable the clinical practice of online ART, it is crucial to obtain CBCT scans with a quality comparable to that of a CT scan. Purpose: This work aims to develop a conditional diffusion model to perform image translation from the CBCT to the CT domain for the image quality improvement of CBCT. Methods: The proposed method is a conditional denoising diffusion probabilistic model (DDPM) that utilizes a time-embedded U-net architecture with residual and attention blocks to gradually transform standard Gaussian noise to the target CT distribution conditioned on the CBCT. The model was trained on deformed planning CT (dpCT) and CBCT image pairs, and its feasibility was verified in brain patient study and head-and-neck (H&N) patient study. The performance of the proposed algorithm was evaluated using mean absolute error (MAE), peak signal-to-noise ratio (PSNR) and normalized cross-correlation (NCC) metrics on generated synthetic CT (sCT) samples. The proposed method was also compared to four other diffusion model-based sCT generation methods. Conclusions: The proposed conditional DDPM method can generate sCT from CBCT with accurate HU numbers and reduced artifacts, enabling accurate CBCT-based organ segmentation and dose calculation for online ART.

physics.med-ph↗

arXiv2023

Deep Learning-based Multi-Organ CT Segmentation with Adversarial Data Augmentation

In this work, we propose an adversarial attack-based data augmentation method to improve the deep-learning-based segmentation algorithm for the delineation of Organs-At-Risk (OAR) in abdominal Computed Tomography (CT) to facilitate radiation therapy. We introduce Adversarial Feature Attack for Medical Image (AFA-MI) augmentation, which forces the segmentation network to learn out-of-distribution statistics and improve generalization and robustness to noises. AFA-MI augmentation consists of three steps: 1) generate adversarial noises by Fast Gradient Sign Method (FGSM) on the intermediate features of the segmentation network's encoder; 2) inject the generated adversarial noises into the network, intentionally compromising performance; 3) optimize the network with both clean and adversarial features. Experiments are conducted segmenting the heart, left and right kidney, liver, left and right lung, spinal cord, and stomach. We first evaluate the AFA-MI augmentation using nnUnet and TT-Vnet on the test data from a public abdominal dataset and an institutional dataset. In addition, we validate how AFA-MI affects the networks' robustness to the noisy data by evaluating the networks with added Gaussian noises of varying magnitudes to the institutional dataset. Network performance is quantitatively evaluated using Dice Similarity Coefficient (DSC) for volume-based accuracy. Also, Hausdorff Distance (HD) is applied for surface-based accuracy. On the public dataset, nnUnet with AFA-MI achieves DSC = 0.85 and HD = 6.16 millimeters (mm); and TT-Vnet achieves DSC = 0.86 and HD = 5.62 mm. AFA-MI augmentation further improves all contour accuracies up to 0.217 DSC score when tested on images with Gaussian noises. AFA-MI augmentation is therefore demonstrated to improve segmentation performance and robustness in CT multi-organ segmentation.

eess.IV↗

arXiv2023

Self-Training Vision Language BERTs with a Unified Conditional Model

Natural language BERTs are trained with language corpus in a self-supervised manner. Unlike natural language BERTs, vision language BERTs need paired data to train, which restricts the scale of VL-BERT pretraining. We propose a self-training approach that allows training VL-BERTs from unlabeled image data. The proposed method starts with our unified conditional model -- a vision language BERT model that can perform zero-shot conditional generation. Given different conditions, the unified conditional model can generate captions, dense captions, and even questions. We use the labeled image data to train a teacher model and use the trained model to generate pseudo captions on unlabeled image data. We then combine the labeled data and pseudo labeled data to train a student model. The process is iterated by putting the student model as a new teacher. By using the proposed self-training approach and only 300k unlabeled extra data, we are able to get competitive or even better performances compared to the models of similar model size trained with 3 million extra image data.

cs.CV↗

arXiv2023

Effective End-to-End Vision Language Pretraining with Semantic Visual Loss

Current vision language pretraining models are dominated by methods using region visual features extracted from object detectors. Given their good performance, the extract-then-process pipeline significantly restricts the inference speed and therefore limits their real-world use cases. However, training vision language models from raw image pixels is difficult, as the raw image pixels give much less prior knowledge than region features. In this paper, we systematically study how to leverage auxiliary visual pretraining tasks to help training end-to-end vision language models. We introduce three types of visual losses that enable much faster convergence and better finetuning accuracy. Compared with region feature models, our end-to-end models could achieve similar or better performance on downstream tasks and run more than 10 times faster during inference. Compared with other end-to-end models, our proposed method could achieve similar or better performance when pretrained for only 10% of the pretraining GPU hours.

cs.CV↗

arXiv2022

Error estimates for the scalar auxiliary variable (SAV) scheme to the Cahn-Hilliard equation

The optimal error estimate that depending only on the polynomial degree of $ \varepsilon^{-1}$ is established for the temporal semi-discrete scheme of the Cahn-Hilliard equation, which is based on the scalar auxiliary variable (SAV) formulation. The key to our analysis is to convert the structure of the SAV time-stepping scheme back to a form compatible with the original format of the Cahn-Hilliard equation, which makes it feasible to use spectral estimates to handle the nonlinear term. Based on the transformation of the SAV numerical scheme, the optimal error estimate for the temporal semi-discrete scheme which depends only on the low polynomial order of $\varepsilon^{-1}$ instead of the exponential order, is derived by using mathematical induction, spectral arguments, and the superconvergence properties of some nonlinear terms. Numerical examples are provided to illustrate the discrete energy decay property and validate our theoretical convergence analysis.

math.NA↗

arXiv2022

A Retrospective Study on the Investigation of Potential Clinical Benefits of Online Adaptive Proton Therapy for Head and Neck Cancer

Online adaptive proton therapy (APT) is an ideal solution theoretically, which however is challenging to proton clinics. Although multiple groups have been endeavoring to develop online APT technology, there is a concern in the radiotherapy community about the necessity of online APT because of its unknown impact on treatment outcomes. Hence, we have performed a retrospective study to investigate the potential clinical effects of online APT for HN cancer patients in relative to the current offline APT via simulations. To mimic an online APT treatment course, we have recalculated and evaluated the actual dose of the current treatment plan on patient actual treatment anatomy captured by cone beam CT for each fraction. The cumulative dose of simulated online APT courses was compared to actual offline APT courses and the initially designed treatment plan dose. For patients 1 and 2, the simulated online ART course maintained a relatively higher CTV dose coverages than the offline ART course, particularly for CTV-Low, which led to an improvement of 2.66% and 4.52% in TCP of CTV-Low. For patients 3 and 4, with clinically comparable CTV dose coverages, the simulated online ART course achieved better OAR sparing than the offline ART course. The mean doses of right parotid and oral cavity were decreased from 29.52 Gy relative biological effectiveness (RBE) and 41.89 Gy RBE to 22.16 Gy RBE and 34.61 Gy RBE for patient 3, leading to a reduce of 1.67% and 3.40% in NTCP for the two organs. Compared to the current clinical practice, the retrospective study indicated that online APT tended to spare more normal tissues by achieving the clinical goal with merely half of the positional uncertainty margin. Future studies are needed to help identify the patients with large potential benefits prior to treatment to conserve scarce clinical resources.

physics.med-ph↗

arXiv2022

Deep Learning-based Protoacoustic Signal Denoising for Proton Range Verification

Objective: Proton therapy offers an advantageous dose distribution compared to the photon therapy, since it deposits most of the energy at the end of range, namely the Bragg peak (BP). Protoacoustic technique was developed to in vivo determine the BP locations. However, it requires large dose delivery to the tissue to obtain an averaged acoustic signal with a sufficient signal to noise ratio (SNR), which is not suitable in clinics. We propose a deep learning-based technique to acquire denoised acoustic signals and reduce BP range uncertainty with much lower doses. Approach: Three accelerometers were placed on the distal surface of a cylindrical polyethylene (PE) phantom to collect protoacoustic signals. In total 512 raw signals were collected at each device. Device-specific stack autoencoder (SAE) denoising models were trained to denoise the input signals, which were generated by averaging 1, 2, 4, 8, 16, or 32 raw signals. Both supervised and unsupervised learning training strategies were tested for comparison. Mean squared error (MSE), signal-to-noise ratio (SNR) and the Bragg peak (BP) range uncertainty were used for model evaluation. Main results: After SAE denoising, the MSE was substantially reduced, and the SNR was enhanced. Overall, the supervised SAEs outperformed the unsupervised SAEs in BP range verification. For the high accuracy detector, it achieved a BP range uncertainty of 0.20 +/- 3.44 mm by averaging over 8 raw signals, while for the other two low accuracy detectors, they achieved the BP uncertainty of 1.44 +/- 6.45 mm and -0.23 +/- 4.88 mm by averaging 16 raw signals, respectively. Significance: We have proposed a deep learning based denoising method to enhance the SNR of protoacoustic measurements and improve the accuracy in BP range verification, which greatly reduces the dose and time for potential clinical applications.

physics.med-ph↗

arXiv2022

Radio observations of four active galactic nuclei hosting intermediate-mass black hole candidates: studying the outflow activity and evolution

Observational searches for intermediate-mass black holes (IMBHs; $10^2 - 10^6$ $M_\odot$) include relatively isolated dwarf galaxies. For those that host active galactic nuclei (AGNs), the IMBH nature may be discerned through the accretion - jet activity. We present radio observations of four AGN-hosting dwarf galaxies (which potentially harbor IMBHs). Very large array (VLA) observations indicate steep spectra (indices of $-$0.63 to $-$1.05) between 1.4 and 9 GHz. A comparison with the 9 GHz in-band spectral index however shows a steepening for GH047 and GH158 (implying older/relic emission) and flattening for GH106 and GH163 (implying recent activity). Overlapping emission regions in the VLA 1.4 GHz and our very long baseline array (VLBA) 1.5 GHz observations, and possibly symmetric pc-scale extensions are consistent with recent activity in the latter two. Using the compact VLBA radio luminosity, X-ray luminosity (probing the accretion activity) and the black hole masses, all AGNs are found to lie on the empirical fundamental plane relation. The four AGN are radio quiet with relatively higher Eddington ratios ($0.04 - 0.32$) and resemble the X-ray binaries during spectral state transitions that entail an outflow ejection. Furthermore, the radio to X-ray luminosity ratio $\log{R_\mathrm{X}}$ of $-3.9$ to $-5.6$ in these four sources support the scenarios including corona mass ejection from accretion disk and wind activity. The growth to kpc-scales likely proceeds along a trajectory similar to young AGNs and peaked spectrum sources. The above complex clues can thus aid in the detection and monitoring of IMBHs in the nearby Universe.

astro-ph.GA↗