Ti Bai

Biling Wang, Michael Dohopolski, Ti Bai et al.

We evaluated the temporal performance of a deep learning (DL) based artificial intelligence (AI) model for auto segmentation in prostate radiotherapy, seeking to correlate its efficacy with changes in clinical landscapes. Our study involved 1328 prostate cancer patients who underwent definitive radiotherapy from January 2006 to August 2022 at the University of Texas Southwestern Medical Center. We trained a UNet based segmentation model on data from 2006 to 2011 and tested it on data from 2012 to 2022 to simulate real world clinical deployment. We measured the model performance using the Dice similarity coefficient (DSC), visualized the trends in contour quality using exponentially weighted moving average (EMA) curves. Additionally, we performed Wilcoxon Rank Sum Test to analyze the differences in DSC distributions across distinct periods, and multiple linear regression to investigate the impact of various clinical factors. The model exhibited peak performance in the initial phase (from 2012 to 2014) for segmenting the prostate, rectum, and bladder. However, we observed a notable decline in performance for the prostate and rectum after 2015, while bladder contour quality remained stable. Key factors that impacted the prostate contour quality included physician contouring styles, the use of various hydrogel spacer, CT scan slice thickness, MRI-guided contouring, and using intravenous (IV) contrast. Rectum contour quality was influenced by factors such as slice thickness, physician contouring styles, and the use of various hydrogel spacers. The bladder contour quality was primarily affected by using IV contrast. This study highlights the challenges in maintaining AI model performance consistency in a dynamic clinical setting. It underscores the need for continuous monitoring and updating of AI models to ensure their ongoing effectiveness and relevance in patient care.

Xiao Liang, Howard Morgan, Ti Bai et al.

Cone-beam CT (CBCT)-based online adaptive radiotherapy calls for accurate auto-segmentation to reduce the time cost for physicians to edit contours. However, deep learning (DL)-based direct segmentation of CBCT images is a challenging task, mainly due to the poor image quality and lack of well-labelled large training datasets. Deformable image registration (DIR) is often used to propagate the manual contours on the planning CT (pCT) of the same patient to CBCT. In this work, we undertake solving the problems mentioned above with the assistance of DIR. Our method consists of three main components. First, we use deformed pCT contours derived from multiple DIR methods between pCT and CBCT as pseudo labels for initial training of the DL-based direct segmentation model. Second, we use deformed pCT contours from another DIR algorithm as influencer volumes to define the region of interest for DL-based direct segmentation. Third, the initially trained DL model is further fine-tuned using a smaller set of true labels. We found that DL-based direct segmentation on CBCT trained with pseudo labels and without influencer volumes shows poor performance compared to DIR-based segmentation. However, adding deformed pCT contours as influencer volumes in the direct segmentation network dramatically improves segmentation performance, reaching the accuracy level of DIR-based segmentation. The DL model with influencer volumes can be further improved through fine-tuning using a smaller set of true labels. Experiments showed that 7 out of 19 structures have an at least 0.2 Dice similarity coefficient increase compared to DIR-based segmentation. A DL-based direct CBCT segmentation model can be improved to outperform DIR-based segmentation models by using deformed pCT contours as pseudo labels and influencer volumes for initial training, and by using a smaller set of true labels for model fine tuning.

Michael Dohopolski, Kai Wang, Biling Wang et al.

Prediction uncertainty estimation has clinical significance as it can potentially quantify prediction reliability. Clinicians may trust 'blackbox' models more if robust reliability information is available, which may lead to more models being adopted into clinical practice. There are several deep learning-inspired uncertainty estimation techniques, but few are implemented on medical datasets -- fewer on single institutional datasets/models. We sought to compare dropout variational inference (DO), test-time augmentation (TTA), conformal predictions, and single deterministic methods for estimating uncertainty using our model trained to predict feeding tube placement for 271 head and neck cancer patients treated with radiation. We compared the area under the curve (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) trends for each method at various cutoffs that sought to stratify patients into 'certain' and 'uncertain' cohorts. These cutoffs were obtained by calculating the percentile "uncertainty" within the validation cohort and applied to the testing cohort. Broadly, the AUC, sensitivity, and NPV increased as the predictions were more 'certain' -- i.e., lower uncertainty estimates. However, when a majority vote (implementing 2/3 criteria: DO, TTA, conformal predictions) or a stricter approach (3/3 criteria) were used, AUC, sensitivity, and NPV improved without a notable loss in specificity or PPV. Especially for smaller, single institutional datasets, it may be important to evaluate multiple estimations techniques before incorporating a model into clinical practice.

Anjali Balagopal, Dan Nguyen, Ti Bai et al.

When a pre-trained general auto-segmentation model is deployed at a new institution, a support framework in the proposed Prior-guided DDL network will learn the systematic difference between the model predictions and the final contours revised and approved by clinicians for an initial group of patients. The learned style feature differences are concatenated with the new patients (query) features and then decoded to get the style-adapted segmentations. The model is independent of practice styles and anatomical structures. It meta-learns with simulated style differences and does not need to be exposed to any real clinical stylized structures during training. Once trained on the simulated data, it can be deployed for clinical use to adapt to new practice styles and new anatomical structures without further training. To show the proof of concept, we tested the Prior-guided DDL network on six different practice style variations for three different anatomical structures. Pre-trained segmentation models were adapted from post-operative clinical target volume (CTV) segmentation to segment CTVstyle1, CTVstyle2, and CTVstyle3, from parotid gland segmentation to segment Parotidsuperficial, and from rectum segmentation to segment Rectumsuperior and Rectumposterior. The mode performance was quantified with Dice Similarity Coefficient (DSC). With adaptation based on only the first three patients, the average DSCs were improved from 78.6, 71.9, 63.0, 52.2, 46.3 and 69.6 to 84.4, 77.8, 73.0, 77.8, 70.5, 68.1, for CTVstyle1, CTVstyle2, and CTVstyle3, Parotidsuperficial, Rectumsuperior, and Rectumposterior, respectively, showing the great potential of the Priorguided DDL network for a fast and effortless adaptation to new practice styles

Anjali Balagopal, Michael Dohopolski, Young Suk Kwon et al.

Background and purpose: Radiation-induced erectile dysfunction (RiED) is commonly seen in prostate cancer patients. Clinical trials have been developed in multiple institutions to investigate whether dose-sparing to the internal-pudendal-arteries (IPA) will improve retention of sexual potency. The IPA is usually not considered a conventional organ-at-risk (OAR) due to segmentation difficulty. In this work, we propose a deep learning (DL)-based auto-segmentation model for the IPA that utilizes CT and MRI or CT alone as the input image modality to accommodate variation in clinical practice. Materials and methods: 86 patients with CT and MRI images and noisy IPA labels were recruited in this study. We split the data into 42/14/30 for model training, testing, and a clinical observer study, respectively. There were three major innovations in this model: 1) we designed an architecture with squeeze-and-excite blocks and modality attention for effective feature extraction and production of accurate segmentation, 2) a novel loss function was used for training the model effectively with noisy labels, and 3) modality dropout strategy was used for making the model capable of segmentation in the absence of MRI. Results: The DSC, ASD, and HD95 values for the test dataset were 62.2%, 2.54mm, and 7mm, respectively. AI segmented contours were dosimetrically equivalent to the expert physician's contours. The observer study showed that expert physicians' scored AI contours (mean=3.7) higher than inexperienced physicians' contours (mean=3.1). When inexperienced physicians started with AI contours, the score improved to 3.7. Conclusion: The proposed model achieved good quality IPA contours to improve uniformity of segmentation and to facilitate introduction of standardized IPA segmentation into clinical trials and practice.

Ti Bai, Muhan Lin, Xiao Liang et al.

Medical image registration is a fundamental and vital task which will affect the efficacy of many downstream clinical tasks. Deep learning (DL)-based deformable image registration (DIR) methods have been investigated, showing state-of-the-art performance. A test time optimization (TTO) technique was proposed to further improve the DL models' performance. Despite the substantial accuracy improvement with this TTO technique, there still remained some regions that exhibited large registration errors even after many TTO iterations. To mitigate this challenge, we firstly identified the reason why the TTO technique was slow, or even failed, to improve those regions' registration results. We then proposed a two-levels TTO technique, i.e., image-specific optimization (ISO) and region-specific optimization (RSO), where the region can be interactively indicated by the clinician during the registration result reviewing process. For both efficiency and accuracy, we further envisioned a three-step DL-based image registration workflow. Experimental results showed that our proposed method outperformed the conventional method qualitatively and quantitatively.

Shaohua Zhi, Yinghui Wang, Haonan Xiao et al.

Four-dimensional magnetic resonance imaging (4D-MRI) is an emerging technique for tumor motion management in image-guided radiation therapy (IGRT). However, current 4D-MRI suffers from low spatial resolution and strong motion artifacts owing to the long acquisition time and patients' respiratory variations; these limitations, if not managed properly, can adversely affect treatment planning and delivery in IGRT. Herein, we developed a novel deep learning framework called the coarse-super-resolution-fine network (CoSF-Net) to achieve simultaneous motion estimation and super-resolution in a unified model. We designed CoSF-Net by fully excavating the inherent properties of 4D-MRI, with consideration of limited and imperfectly matched training datasets. We conducted extensive experiments on multiple real patient datasets to verify the feasibility and robustness of the developed network. Compared with existing networks and three state-of-the-art conventional algorithms, CoSF-Net not only accurately estimated the deformable vector fields between the respiratory phases of 4D-MRI but also simultaneously improved the spatial resolution of 4D-MRI with enhanced anatomic features, yielding 4D-MR images with high spatiotemporal resolution.

Biling Wang, Austen Maniscalco, Ti Bai et al.

Purpose: This study presents a Deep Learning (DL)-based quality assessment (QA) approach for evaluating auto-generated contours (auto-contours) in radiotherapy, with emphasis on Online Adaptive Radiotherapy (OART). Leveraging Bayesian Ordinal Classification (BOC) and calibrated uncertainty thresholds, the method enables confident QA predictions without relying on ground truth contours or extensive manual labeling. Methods: We developed a BOC model to classify auto-contour quality and quantify prediction uncertainty. A calibration step was used to optimize uncertainty thresholds that meet clinical accuracy needs. The method was validated under three data scenarios: no manual labels, limited labels, and extensive labels. For rectum contours in prostate cancer, we applied geometric surrogate labels when manual labels were absent, transfer learning when limited, and direct supervision when ample labels were available. Results: The BOC model delivered robust performance across all scenarios. Fine-tuning with just 30 manual labels and calibrating with 34 subjects yielded over 90% accuracy on test data. Using the calibrated threshold, over 93% of the auto-contours' qualities were accurately predicted in over 98% of cases, reducing unnecessary manual reviews and highlighting cases needing correction. Conclusion: The proposed QA model enhances contouring efficiency in OART by reducing manual workload and enabling fast, informed clinical decisions. Through uncertainty quantification, it ensures safer, more reliable radiotherapy workflows.

Xiao Liang, Jaehee Chun, Howard Morgan et al.

Online adaptive radiotherapy (ART) requires accurate and efficient auto-segmentation of target volumes and organs-at-risk (OARs) in mostly cone-beam computed tomography (CBCT) images. Propagating expert-drawn contours from the pre-treatment planning CT (pCT) through traditional or deep learning (DL) based deformable image registration (DIR) can achieve improved results in many situations. Typical DL-based DIR models are population based, that is, trained with a dataset for a population of patients, so they may be affected by the generalizability problem. In this paper, we propose a method called test-time optimization (TTO) to refine a pre-trained DL-based DIR population model, first for each individual test patient, and then progressively for each fraction of online ART treatment. Our proposed method is less susceptible to the generalizability problem, and thus can improve overall performance of different DL-based DIR models by improving model accuracy, especially for outliers. Our experiments used data from 239 patients with head and neck squamous cell carcinoma to test the proposed method. Firstly, we trained a population model with 200 patients, and then applied TTO to the remaining 39 test patients by refining the trained population model to obtain 39 individualized models. We compared each of the individualized models with the population model in terms of segmentation accuracy. The number of patients with at least 0.05 DSC improvement or 2 mm HD95 improvement by TTO averaged over the 17 selected structures for the state-of-the-art architecture Voxelmorph is 10 out of 39 test patients. The average time for deriving the individualized model using TTO from the pre-trained population model is approximately four minutes. When adapting the individualized model to a later fraction of the same patient, the average time is reduced to about one minute and the accuracy is slightly improved.

Chaoyang Zhang, Shaojie Chang, Ti Bai et al.

Photon counting spectral CT (PCCT) can produce reconstructed attenuation maps in different energy channels, reflecting energy properties of the scanned object. Due to the limited photon numbers and the non-ideal detector response of each energy channel, the reconstructed images usually contain much noise. With the development of Deep Learning (DL) technique, different kinds of DL-based models have been proposed for noise reduction. However, most of the models require clean data set as the training labels, which are not always available in medical imaging field. Inspiring by the similarities of each channel's reconstructed image, we proposed a self-supervised learning based PCCT image enhancement framework via multi-spectral channels (S2MS). In S2MS framework, both the input and output labels are noisy images. Specifically, one single channel image was used as output while images of other single channels and channel-sum image were used as input to train the network, which can fully use the spectral data information without extra cost. The simulation results based on the AAPM Low-dose CT Challenge database showed that the proposed S2MS model can suppress the noise and preserve details more effectively in comparison with the traditional DL models, which has potential to improve the image quality of PCCT in clinical applications.

Ti Bai, Anjali Balagopal, Michael Dohopolski et al.

Automatic segmentation of anatomical structures is critical for many medical applications. However, the results are not always clinically acceptable and require tedious manual revision. Here, we present a novel concept called artificial intelligence assisted contour revision (AIACR) and demonstrate its feasibility. The proposed clinical workflow of AIACR is as follows given an initial contour that requires a clinicians revision, the clinician indicates where a large revision is needed, and a trained deep learning (DL) model takes this input to update the contour. This process repeats until a clinically acceptable contour is achieved. The DL model is designed to minimize the clinicians input at each iteration and to minimize the number of iterations needed to reach acceptance. In this proof-of-concept study, we demonstrated the concept on 2D axial images of three head-and-neck cancer datasets, with the clinicians input at each iteration being one mouse click on the desired location of the contour segment. The performance of the model is quantified with Dice Similarity Coefficient (DSC) and 95th percentile of Hausdorff Distance (HD95). The average DSC/HD95 (mm) of the auto-generated initial contours were 0.82/4.3, 0.73/5.6 and 0.67/11.4 for three datasets, which were improved to 0.91/2.1, 0.86/2.4 and 0.86/4.7 with three mouse clicks, respectively. Each DL-based contour update requires around 20 ms. We proposed a novel AIACR concept that uses DL models to assist clinicians in revising contours in an efficient and effective way, and we demonstrated its feasibility by using 2D axial CT images from three head-and-neck cancer datasets.

Ti Bai, Dan Nguyen, Biling Wang et al.

Low Dose Computed Tomography (LDCT) is clinically desirable due to the reduced radiation to patients. However, the quality of LDCT images is often sub-optimal because of the inevitable strong quantum noise. Inspired by their unprecedent success in computer vision, deep learning (DL)-based techniques have been used for LDCT denoising. Despite the promising noise removal ability of DL models, people have observed that the resolution of the DL-denoised images is compromised, decreasing their clinical value. Aiming at relieving this problem, in this work, we developed a more effective denoiser by introducing a high-resolution network (HRNet). Since HRNet consists of multiple branches of subnetworks to extract multiscale features which are later fused together, the quality of the generated features can be substantially enhanced, leading to improved denoising performance. Experimental results demonstrated that the introduced HRNet-based denoiser outperforms the benchmarked UNet-based denoiser in terms of superior image resolution preservation ability while comparable, if not better, noise suppression ability. Quantitative metrics in terms of root-mean-squared-errors (RMSE)/structure similarity index (SSIM) showed that the HRNet-based denoiser can improve the values from 113.80/0.550 (LDCT) to 55.24/0.745 (HRNet), in comparison to 59.87/0.712 for the UNet-based denoiser.

Ti Bai, Biling Wang, Dan Nguyen et al.

Monte Carlo (MC) simulation is considered the gold standard method for radiotherapy dose calculation. However, achieving high precision requires a large number of simulation histories, which is time consuming. The use of computer graphics processing units (GPUs) has greatly accelerated MC simulation and allows dose calculation within a few minutes for a typical radiotherapy treatment plan. However, some clinical applications demand real time efficiency for MC dose calculation. To tackle this problem, we have developed a real time, deep learning based dose denoiser that can be plugged into a current GPU based MC dose engine to enable real time MC dose calculation. We used two different acceleration strategies to achieve this goal: 1) we applied voxel unshuffle and voxel shuffle operators to decrease the input and output sizes without any information loss, and 2) we decoupled the 3D volumetric convolution into a 2D axial convolution and a 1D slice convolution. In addition, we used a weakly supervised learning framework to train the network, which greatly reduces the size of the required training dataset and thus enables fast fine tuning based adaptation of the trained model to different radiation beams. Experimental results show that the proposed denoiser can run in as little as 39 ms, which is around 11.6 times faster than the baseline model. As a result, the whole MC dose calculation pipeline can be finished within 0.15 seconds, including both GPU MC dose calculation and deep learning based denoising, achieving the real time efficiency needed for some radiotherapy applications, such as online adaptive radiotherapy.

Ti Bai, Biling Wang, Dan Nguyen et al.

Low dose computed tomography (LDCT) is desirable for both diagnostic imaging and image guided interventions. Denoisers are openly used to improve the quality of LDCT. Deep learning (DL)-based denoisers have shown state-of-the-art performance and are becoming one of the mainstream methods. However, there exists two challenges regarding the DL-based denoisers: 1) a trained model typically does not generate different image candidates with different noise-resolution tradeoffs which sometimes are needed for different clinical tasks; 2) the model generalizability might be an issue when the noise level in the testing images is different from that in the training dataset. To address these two challenges, in this work, we introduce a lightweight optimization process at the testing phase on top of any existing DL-based denoisers to generate multiple image candidates with different noise-resolution tradeoffs suitable for different clinical tasks in real-time. Consequently, our method allows the users to interact with the denoiser to efficiently review various image candidates and quickly pick up the desired one, and thereby was termed as deep interactive denoiser (DID). Experimental results demonstrated that DID can deliver multiple image candidates with different noise-resolution tradeoffs, and shows great generalizability regarding various network architectures, as well as training and testing datasets with various noise levels.

Ti Bai, Dan Nguyen, Biling Wang et al.

Despite the indispensable role of X-ray computed tomography (CT) in diagnostic medicine field, the associated ionizing radiation is still a major concern considering that it may cause genetic and cancerous diseases. Decreasing the exposure can reduce the dose and hence the radiation-related risk, but will also induce higher quantum noise. Supervised deep learning can be used to train a neural network to denoise the low-dose CT (LDCT). However, its success requires massive pixel-wise paired LDCT and normal-dose CT (NDCT) images, which are rarely available in real practice. To alleviate this problem, in this paper, a shift-invariant property based neural network was devised to learn the inherent pixel correlations and also the noise distribution by only using the LDCT images, shaping into our probabilistic self-learning framework. Experimental results demonstrated that the proposed method outperformed the competitors, producing an enhanced LDCT image that has similar image style as the routine NDCT which is highly-preferable in clinic practice.

Yuan Gao, Xingyuan Bu, Yang Hu et al.

This report demonstrates our solution for the Open Images 2018 Challenge. Based on our detailed analysis on the Open Images Datasets (OID), it is found that there are four typical features: large-scale, hierarchical tag system, severe annotation incompleteness and data imbalance. Considering these characteristics, an amount of strategies are employed, including SNIPER, soft sampling, class-aware sampling (CAS), hierarchical non-maximum suppression (HNMS) and so on. In virtue of these effective strategies, and further using the powerful SENet154 armed with feature pyramid module and deformable ROIalign as the backbone, our best single model could achieve a mAP of 56.9%. After a further ensemble with 9 models, the final mAP is boosted to 62.2% in the public leaderboard (ranked the 2nd place) and 58.6% in the private leaderboard (ranked the 3rd place, slightly inferior to the 1st place by only 0.04 point).