arXiv subjects

Qifan Xu

Publications and source records attributed to Qifan Xu.

7 recordsLinked to original sources

arXiv2026

4$\pi$ Planning for the Reduction of Predicted Hematologic Toxicity Risk in Cervical Cancer Radiotherapy

Purpose: In conventional coplanar radiotherapy for cervical cancer, nearby pelvic bones receive high radiation doses, increasing the risk of acute hematologic toxicity (HT). This study aims to estimate the HT risk reduction achievable with non-coplanar (4$\pi$) radiotherapy. Methods: We retrospectively analyzed 114 cervical cancer patients treated with coplanar volumetric modulated arc therapy (VMAT) between 2021 and 2023. Radiomic features from planning CTs were extracted and combined with clinical and dosimetric data to train predictive machine learning models. Patients were then replanned using integrated non-coplanar beam orientation and fluence map optimization (4$\pi$ planning). The top performing model was applied to these new plans to evaluate potential HT reduction. Results: Models combined radiomics, clinical, and dosimetric features achieved the highest predictive performance (AUC = 0.79). Feature importance analysis highlighted CT radiomic and dosimetric variables as the strongest predictors. Compared to VMAT, 4$\pi$ non-coplanar planning significantly reduced doses to the bone marrow (V10Gy, V20Gy, V30Gy, and V40Gy by 28%, 52%, 47%, and 33%, respectively) while significantly reducing dose to other pelvic organs at risk (OAR). When evaluated by the model, this improved dosimetry translated into a 23% reduction in predicted HT risk (risk ratio: 0.77; 95% CI: 0.75-0.79 and odds ratio: 0.68; 95% CI:0.65-0.71). Conclusions: Non-coplanar 4$\pi$ radiotherapy significantly lowers radiation doses to major pelvic bones during cervical cancer treatment without compromising target coverage or sparing of other OARs. Based on our predictive model, this superior dosimetry should translate to a marked reduction in acute hematologic toxicity.

physics.med-ph↗

arXiv2024

Exploring Automated Contouring Across Institutional Boundaries: A Deep Learning Approach with Mouse Micro-CT Datasets

Image-guided mouse irradiation is essential to understand interventions involving radiation prior to human studies. Our objective is to employ Swin UNEt Transformers (Swin UNETR) to segment native micro-CT and contrast-enhanced micro-CT scans and benchmark the results against 3D no-new-Net (nnU-Net). Swin UNETR reformulates mouse organ segmentation as a sequence-to-sequence prediction task, using a hierarchical Swin Transformer encoder to extract features at 5 resolution levels, and connects to a Fully Convolutional Neural Network (FCNN)-based decoder via skip connections. The models were trained and evaluated on open datasets, with data separation based on individual mice. Further evaluation on an external mouse dataset acquired on a different micro-CT with lower kVp and higher imaging noise was also employed to assess model robustness and generalizability. Results indicate that Swin UNETR consistently outperforms nnU-Net and AIMOS in terms of average dice similarity coefficient (DSC) and Hausdorff distance (HD95p), except in two mice of intestine contouring. This superior performance is especially evident in the external dataset, confirming the model's robustness to variations in imaging conditions, including noise and quality, thereby positioning Swin UNETR as a highly generalizable and efficient tool for automated contouring in pre-clinical workflows.

physics.med-ph↗

arXiv2023

An Efficient and Robust Method for Chest X-Ray Rib Suppression that Improves Pulmonary Abnormality Diagnosis

Suppression of thoracic bone shadows on chest X-rays (CXRs) has been indicated to improve the diagnosis of pulmonary disease. Previous approaches can be categorized as unsupervised physical and supervised deep learning models. Nevertheless, with physical models able to preserve morphological details but at the cost of extremely long processing time, existing DL methods face challenges of gathering sufficient/qualitative ground truth (GT) for robust training, thus leading to failure in maintaining clinically acceptable false positive rates. We hereby propose a generalizable yet efficient workflow of two stages: (1) training pairs generation with GT bone shadows eliminated in by a physical model in spatially transformed gradient fields. (2) fully supervised image denoising network training on stage-one datasets for fast rib removal on incoming CXRs. For step two, we designed a densely connected network called SADXNet, combined with peak signal to noise ratio and multi-scale structure similarity index measure objective minimization to suppress bony structures. The SADXNet organizes spatial filters in U shape (e.g., X=7; filters = 16, 64, 256, 512, 256, 64, 16) and preserves the feature map dimension throughout the network flow. Visually, SADXNet can suppress the rib edge and that near the lung wall/vertebra without jeopardizing the vessel/abnormality conspicuity. Quantitively, it achieves RMSE of ~0 during testing with one prediction taking <1s. Downstream tasks including lung nodule detection as well as common lung disease classification and localization are used to evaluate our proposed rib suppression mechanism. We observed 3.23% and 6.62% area under the curve (AUC) increase as well as 203 and 385 absolute false positive decrease for lung nodule detection and common lung disease localization, separately.

eess.IV↗

arXiv2022

Tesseract: Parallelize the Tensor Parallelism Efficiently

Together with the improvements in state-of-the-art accuracies of various tasks, deep learning models are getting significantly larger. However, it is extremely difficult to implement these large models because limited GPU memory makes it impossible to fit large models into a single GPU or even a GPU server. Besides, it is highly necessary to reduce the training time for large models. Previous methods like Megatron-LM implemented a 1-Dimensional distributed method to use GPUs to speed up the training. However, these methods have a high communication overhead and a low scaling efficiency on large-scale clusters. To solve these problems, we propose Tesseract, a highly scalable tensor parallelism with a novel design. It increases efficiency by reducing communication overhead and lowers the memory required for each GPU. By introducing the novel dimension into tensor parallelism, Tesseract greatly increases the memory capacity of tensor parallelism. Concretely, this new dimension furthermore increases the degree of tensor parallelism. Compared to previous 1-D and 2-D methods, Tesseract manages to reduce the communication cost on each layer, resulting in speedups of 1.38x and 1.53x respectively with strong scaling. In weak scaling experiments, Tesseract achieves a maximum of 4.0/1.7 times inference speedup and 3.4/1.7 times throughput improvement compared to 1-D/2-D methods, respectively. By introducing Tesseract, we offer a more efficient and scalable way to implement large deep learning models with limited GPU resources.

cs.DC↗

arXiv2022

To what extent can Plug-and-Play methods outperform neural networks alone in low-dose CT reconstruction

The Plug-and-Play (PnP) framework was recently introduced for low-dose CT reconstruction to leverage the interpretability and the flexibility of model-based methods to incorporate various plugins, such as trained deep learning (DL) neural networks. However, the benefits of PnP vs. state-of-the-art DL methods have not been clearly demonstrated. In this work, we proposed an improved PnP framework to address the previous limitations and develop clinical-relevant segmentation metrics for quantitative result assessment. Compared with the DL alone methods, our proposed PnP framework was slightly inferior in MSE and PSNR. However, the power spectrum of the resulting images better matched that of full-dose images than that of DL denoised images. The resulting images supported higher accuracy in airway segmentation than DL denoised images for all the ten patients in the test set, more substantially on the airways with a cross-section smaller than 0.61cm$^2$, and outperformed the DL denoised images for 45 out of 50 lung lobes in lobar segmentation. Our PnP method proved to be significantly better at preserving the image texture, which translated to task-specific benefits in automated structure segmentation and detection.

eess.IV↗

arXiv2021

Maximizing Parallelism in Distributed Training for Huge Neural Networks

The recent Natural Language Processing techniques have been refreshing the state-of-the-art performance at an incredible speed. Training huge language models is therefore an imperative demand in both industry and academy. However, huge language models impose challenges to both hardware and software. Graphical processing units (GPUs) are iterated frequently to meet the exploding demand, and a variety of ASICs like TPUs are spawned. However, there is still a tension between the fast growth of the extremely huge models and the fact that Moore's law is approaching the end. To this end, many model parallelism techniques are proposed to distribute the model parameters to multiple devices, so as to alleviate the tension on both memory and computation. Our work is the first to introduce a 3-dimensional model parallelism for expediting huge language models. By reaching a perfect load balance, our approach presents smaller memory and communication cost than existing state-of-the-art 1-D and 2-D model parallelism. Our experiments on 64 TACC's V100 GPUs show that our 3-D parallelism outperforms the 1-D and 2-D parallelism with 2.32x and 1.57x speedup, respectively.

cs.DC↗

arXiv2021

An Efficient 2D Method for Training Super-Large Deep Learning Models

Huge neural network models have shown unprecedented performance in real-world applications. However, due to memory constraints, model parallelism must be utilized to host large models that would otherwise not fit into the memory of a single device. Previous methods like Megatron partition the parameters of the entire model among multiple devices, while each device has to accommodate the redundant activations in forward and backward pass. In this work, we propose Optimus, a highly efficient and scalable 2D-partition paradigm of model parallelism that would facilitate the training of infinitely large language models. In Optimus, activations are partitioned and distributed among devices, further reducing redundancy. In terms of isoefficiency, Optimus significantly outperforms Megatron. On 64 GPUs of TACC Frontera, Optimus achieves 1.48X speedup for training, 1.78X speedup for inference, and 8X increase in maximum batch size over Megatron. Optimus surpasses Megatron in scaling efficiency by a great margin. The code is available at https://github.com/xuqifan897/Optimus.

cs.LG↗