arXiv subjects

Dufan Wu

Publications and source records attributed to Dufan Wu.

31 records · Page 2Linked to original sources

arXiv2023

MA-SAM: Modality-agnostic SAM Adaptation for 3D Medical Image Segmentation

The Segment Anything Model (SAM), a foundation model for general image segmentation, has demonstrated impressive zero-shot performance across numerous natural image segmentation tasks. However, SAM's performance significantly declines when applied to medical images, primarily due to the substantial disparity between natural and medical image domains. To effectively adapt SAM to medical images, it is important to incorporate critical third-dimensional information, i.e., volumetric or temporal knowledge, during fine-tuning. Simultaneously, we aim to harness SAM's pre-trained weights within its original 2D backbone to the fullest extent. In this paper, we introduce a modality-agnostic SAM adaptation framework, named as MA-SAM, that is applicable to various volumetric and video medical data. Our method roots in the parameter-efficient fine-tuning strategy to update only a small portion of weight increments while preserving the majority of SAM's pre-trained weights. By injecting a series of 3D adapters into the transformer blocks of the image encoder, our method enables the pre-trained 2D backbone to extract third-dimensional information from input data. The effectiveness of our method has been comprehensively evaluated on four medical image segmentation tasks, by using 10 public datasets across CT, MRI, and surgical video data. Remarkably, without using any prompt, our method consistently outperforms various state-of-the-art 3D approaches, surpassing nnU-Net by 0.9%, 2.6%, and 9.9% in Dice for CT multi-organ segmentation, MRI prostate segmentation, and surgical scene segmentation respectively. Our model also demonstrates strong generalization, and excels in challenging tumor segmentation when prompts are used. Our code is available at: https://github.com/cchen-cc/MA-SAM.

cs.CV↗

arXiv2023

CohortGPT: An Enhanced GPT for Participant Recruitment in Clinical Study

Participant recruitment based on unstructured medical texts such as clinical notes and radiology reports has been a challenging yet important task for the cohort establishment in clinical research. Recently, Large Language Models (LLMs) such as ChatGPT have achieved tremendous success in various downstream tasks thanks to their promising performance in language understanding, inference, and generation. It is then natural to test their feasibility in solving the cohort recruitment task, which involves the classification of a given paragraph of medical text into disease label(s). However, when applied to knowledge-intensive problem settings such as medical text classification, where the LLMs are expected to understand the decision made by human experts and accurately identify the implied disease labels, the LLMs show a mediocre performance. A possible explanation is that, by only using the medical text, the LLMs neglect to use the rich context of additional information that languages afford. To this end, we propose to use a knowledge graph as auxiliary information to guide the LLMs in making predictions. Moreover, to further boost the LLMs adapt to the problem setting, we apply a chain-of-thought (CoT) sample selection strategy enhanced by reinforcement learning, which selects a set of CoT samples given each individual medical report. Experimental results and various ablation studies show that our few-shot learning method achieves satisfactory performance compared with fine-tuning strategies and gains superb advantages when the available data is limited. The code and sample dataset of the proposed CohortGPT model is available at: https://anonymous.4open.science/r/CohortGPT-4872/

cs.CL↗

arXiv2022

Trained Model in Supervised Deep Learning is a Conditional Risk Minimizer

We proved that a trained model in supervised deep learning minimizes the conditional risk for each input (Theorem 2.1). This property provided insights into the behavior of trained models and established a connection between supervised and unsupervised learning in some cases. In addition, when the labels are intractable but can be written as a conditional risk minimizer, we proved an equivalent form of the original supervised learning problem with accessible labels (Theorem 2.2). We demonstrated that many existing works, such as Noise2Score, Noise2Noise and score function estimation can be explained by our theorem. Moreover, we derived a property of classification problem with noisy labels using Theorem 2.1 and validated it using MNIST dataset. Furthermore, We proposed a method to estimate uncertainty in image super-resolution based on Theorem 2.2 and validated it using ImageNet dataset. Our code is available on github.

cs.LG↗

arXiv2021

Deep Learning Based Detection and Localization of Intracranial Aneurysms in Computed Tomography Angiography

Purpose: To develop CADIA, a supervised deep learning model based on a region proposal network coupled with a false-positive reduction module for the detection and localization of intracranial aneurysms (IA) from computed tomography angiography (CTA), and to assess our model's performance to a similar detection network. Methods: In this retrospective study, we evaluated 1,216 patients from two separate institutions who underwent CT for the presence of saccular IA>=2.5 mm. A two-step model was implemented: a 3D region proposal network for initial aneurysm detection and 3D DenseNetsfor false-positive reduction and further determination of suspicious IA. Free-response receiver operative characteristics (FROC) curve and lesion-/patient-level performance at established false positive per volume (FPPV) were also performed. Fisher's exact test was used to compare with a similar available model. Results: CADIA's sensitivities at 0.25 and 1 FPPV were 63.9% and 77.5%, respectively. Our model's performance varied with size and location, and the best performance was achieved in IA between 5-10 mm and in those at anterior communicating artery, with sensitivities at 1 FPPV of 95.8% and 94%, respectively. Our model showed statistically higher patient-level accuracy, sensitivity, and specificity when compared to the available model at 0.25 FPPV and the best F-1 score (P<=0.001). At 1 FPPV threshold, our model showed better accuracy and specificity (P<=0.001) and equivalent sensitivity. Conclusions: CADIA outperformed a comparable network in the detection task of IA. The addition of a false-positive reduction module is a feasible step to improve the IA detection models.

eess.IV↗

arXiv2021

Learning to Scan: A Deep Reinforcement Learning Approach for Personalized Scanning in CT Imaging

Computed Tomography (CT) takes X-ray measurements on the subjects to reconstruct tomographic images. As X-ray is radioactive, it is desirable to control the total amount of dose of X-ray for safety concerns. Therefore, we can only select a limited number of measurement angles and assign each of them limited amount of dose. Traditional methods such as compressed sensing usually randomly select the angles and equally distribute the allowed dose on them. In most CT reconstruction models, the emphasize is on designing effective image representations, while much less emphasize is on improving the scanning strategy. The simple scanning strategy of random angle selection and equal dose distribution performs well in general, but they may not be ideal for each individual subject. It is more desirable to design a personalized scanning strategy for each subject to obtain better reconstruction result. In this paper, we propose to use Reinforcement Learning (RL) to learn a personalized scanning policy to select the angles and the dose at each chosen angle for each individual subject. We first formulate the CT scanning process as an MDP, and then use modern deep RL methods to solve it. The learned personalized scanning strategy not only leads to better reconstruction results, but also shows strong generalization to be combined with different reconstruction algorithms.

physics.med-ph↗

arXiv2021

Development and Validation of a Deep Learning Model for Prediction of Severe Outcomes in Suspected COVID-19 Infection

COVID-19 patient triaging with predictive outcome of the patients upon first present to emergency department (ED) is crucial for improving patient prognosis, as well as better hospital resources management and cross-infection control. We trained a deep feature fusion model to predict patient outcomes, where the model inputs were EHR data including demographic information, co-morbidities, vital signs and laboratory measurements, plus patient's CXR images. The model output was patient outcomes defined as the most insensitive oxygen therapy required. For patients without CXR images, we employed Random Forest method for the prediction. Predictive risk scores for COVID-19 severe outcomes ("CO-RISK" score) were derived from model output and evaluated on the testing dataset, as well as compared to human performance. The study's dataset (the "MGB COVID Cohort") was constructed from all patients presenting to the Mass General Brigham (MGB) healthcare system from March 1st to June 1st, 2020. ED visits with incomplete or erroneous data were excluded. Patients with no test order for COVID or confirmed negative test results were excluded. Patients under the age of 15 were also excluded. Finally, electronic health record (EHR) data from a total of 11060 COVID-19 confirmed or suspected patients were used in this study. Chest X-ray (CXR) images were also collected from each patient if available. Results show that CO-RISK score achieved area under the Curve (AUC) of predicting MV/death (i.e. severe outcomes) in 24 hours of 0.95, and 0.92 in 72 hours on the testing dataset. The model shows superior performance to the commonly used risk scores in ED (CURB-65 and MEWS). Comparing with physician's decisions, CO-RISK score has demonstrated superior performance to human in making ICU/floor decisions.

cs.LG↗

arXiv2020

Deep Metric Learning-based Image Retrieval System for Chest Radiograph and its Clinical Applications in COVID-19

In recent years, deep learning-based image analysis methods have been widely applied in computer-aided detection, diagnosis and prognosis, and has shown its value during the public health crisis of the novel coronavirus disease 2019 (COVID-19) pandemic. Chest radiograph (CXR) has been playing a crucial role in COVID-19 patient triaging, diagnosing and monitoring, particularly in the United States. Considering the mixed and unspecific signals in CXR, an image retrieval model of CXR that provides both similar images and associated clinical information can be more clinically meaningful than a direct image diagnostic model. In this work we develop a novel CXR image retrieval model based on deep metric learning. Unlike traditional diagnostic models which aims at learning the direct mapping from images to labels, the proposed model aims at learning the optimized embedding space of images, where images with the same labels and similar contents are pulled together. It utilizes multi-similarity loss with hard-mining sampling strategy and attention mechanism to learn the optimized embedding space, and provides similar images to the query image. The model is trained and validated on an international multi-site COVID-19 dataset collected from 3 different sources. Experimental results of COVID-19 image retrieval and diagnosis tasks show that the proposed model can serve as a robust solution for CXR analysis and patient management for COVID-19. The model is also tested on its transferability on a different clinical decision support task, where the pre-trained model is applied to extract image features from a new dataset without any further training. These results demonstrate our deep metric learning based image retrieval model is highly efficient in the CXR retrieval, diagnosis and prognosis, and thus has great clinical value for the treatment and management of COVID-19 patients.

eess.IV↗

arXiv2020

Deep Learning-based Four-region Lung Segmentation in Chest Radiography for COVID-19 Diagnosis

Purpose. Imaging plays an important role in assessing severity of COVID 19 pneumonia. However, semantic interpretation of chest radiography (CXR) findings does not include quantitative description of radiographic opacities. Most current AI assisted CXR image analysis framework do not quantify for regional variations of disease. To address these, we proposed a four region lung segmentation method to assist accurate quantification of COVID 19 pneumonia. Methods. A segmentation model to separate left and right lung is firstly applied, and then a carina and left hilum detection network is used, which are the clinical landmarks to separate the upper and lower lungs. To improve the segmentation performance of COVID 19 images, ensemble strategy incorporating five models is exploited. Using each region, we evaluated the clinical relevance of the proposed method with the Radiographic Assessment of the Quality of Lung Edema (RALE). Results. The proposed ensemble strategy showed dice score of 0.900, which is significantly higher than conventional methods (0.854 0.889). Mean intensities of segmented four regions indicate positive correlation to the extent and density scores of pulmonary opacities under the RALE framework. Conclusion. A deep learning based model in CXR can accurately segment and quantify regional distribution of pulmonary opacities in patients with COVID 19 pneumonia.

eess.IV↗

arXiv2020

Self-supervised Dynamic CT Perfusion Image Denoising with Deep Neural Networks

Dynamic computed tomography perfusion (CTP) imaging is a promising approach for acute ischemic stroke diagnosis and evaluation. Hemodynamic parametric maps of cerebral parenchyma are calculated from repeated CT scans of the first pass of iodinated contrast through the brain. It is necessary to reduce the dose of CTP for routine applications due to the high radiation exposure from the repeated scans, where image denoising is necessary to achieve a reliable diagnosis. In this paper, we proposed a self-supervised deep learning method for CTP denoising, which did not require any high-dose reference images for training. The network was trained by mapping each frame of CTP to an estimation from its adjacent frames. Because the noise in the source and target was independent, this approach could effectively remove the noise. Being free from high-dose training images granted the proposed method easier adaptation to different scanning protocols. The method was validated on both simulation and a public real dataset. The proposed method achieved improved image quality compared to conventional denoising methods. On the real data, the proposed method also had improved spatial resolution and contrast-to-noise ratio compared to supervised learning which was trained on the simulation data

physics.med-ph↗

arXiv2019

Consensus Neural Network for Medical Imaging Denoising with Only Noisy Training Samples

Deep neural networks have been proved efficient for medical image denoising. Current training methods require both noisy and clean images. However, clean images cannot be acquired for many practical medical applications due to naturally noisy signal, such as dynamic imaging, spectral computed tomography, arterial spin labeling magnetic resonance imaging, etc. In this paper we proposed a training method which learned denoising neural networks from noisy training samples only. Training data in the acquisition domain was split to two subsets and the network was trained to map one noisy set to the other. A consensus loss function was further proposed to efficiently combine the outputs from both subsets. A mathematical proof was provided that the proposed training scheme was equivalent to training with noisy and clean samples when the noise in the two subsets was uncorrelated and zero-mean. The method was validated on Low-dose CT Challenge dataset and NYU MRI dataset and achieved improved performance compared to existing unsupervised methods.

eess.IV↗

arXiv2019

Computationally Efficient Deep Neural Network for Computed Tomography Image Reconstruction

Deep-neural-network-based image reconstruction has demonstrated promising performance in medical imaging for under-sampled and low-dose scenarios. However, it requires large amount of memory and extensive time for the training. It is especially challenging to train the reconstruction networks for three-dimensional computed tomography (CT) because of the high resolution of CT images. The purpose of this work is to reduce the memory and time consumption of the training of the reconstruction networks for CT to make it practical for current hardware, while maintaining the quality of the reconstructed images. We unrolled the proximal gradient descent algorithm for iterative image reconstruction to finite iterations and replaced the terms related to the penalty function with trainable convolutional neural networks (CNN). The network was trained greedily iteration by iteration in the image-domain on patches, which requires reasonable amount of memory and time on mainstream graphics processing unit (GPU). To overcome the local-minimum problem caused by greedy learning, we used deep UNet as the CNN and incorporated separable quadratic surrogate with ordered subsets for data fidelity, so that the solution could escape from easy local minimums and achieve better image quality. The proposed method achieved comparable image quality with state-of-the-art neural network for CT image reconstruction on 2D sparse-view and limited-angle problems on the low-dose CT challenge dataset.

cs.CV↗

arXiv2018

End-to-end Lung Nodule Detection in Computed Tomography

Computer aided diagnostic (CAD) system is crucial for modern med-ical imaging. But almost all CAD systems operate on reconstructed images, which were optimized for radiologists. Computer vision can capture features that is subtle to human observers, so it is desirable to design a CAD system op-erating on the raw data. In this paper, we proposed a deep-neural-network-based detection system for lung nodule detection in computed tomography (CT). A primal-dual-type deep reconstruction network was applied first to convert the raw data to the image space, followed by a 3-dimensional convolutional neural network (3D-CNN) for the nodule detection. For efficient network training, the deep reconstruction network and the CNN detector was trained sequentially first, then followed by one epoch of end-to-end fine tuning. The method was evaluated on the Lung Image Database Consortium image collection (LIDC-IDRI) with simulated forward projections. With 144 multi-slice fanbeam pro-jections, the proposed end-to-end detector could achieve comparable sensitivity with the reference detector, which was trained and applied on the fully-sampled image data. It also demonstrated superior detection performance compared to detectors trained on the reconstructed images. The proposed method is general and could be expanded to most detection tasks in medical imaging.

cs.CV↗

arXiv2017

A Cascaded Convolutional Neural Network for X-ray Low-dose CT Image Denoising

Image denoising techniques are essential to reducing noise levels and enhancing diagnosis reliability in low-dose computed tomography (CT). Machine learning based denoising methods have shown great potential in removing the complex and spatial-variant noises in CT images. However, some residue artifacts would appear in the denoised image due to complexity of noises. A cascaded training network was proposed in this work, where the trained CNN was applied on the training dataset to initiate new trainings and remove artifacts induced by denoising. A cascades of convolutional neural networks (CNN) were built iteratively to achieve better performance with simple CNN structures. Experiments were carried out on 2016 Low-dose CT Grand Challenge datasets to evaluate the method's performance.

cs.CV↗