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Add to EdgeDeep learning automates Cobb angle measurement compared with multi-expert observers
Mar 18, 2024
Scoliosis, a prevalent condition characterized by abnormal spinal curvature leading to deformity, requires precise assessment methods for effective diagnosis and management. The Cobb angle is a widely used scoliosis quantification method that measures the degree of curvature between the tilted vertebrae. Yet, manual measuring of Cobb angles is time-consuming and labor-intensive, fraught with significant interobserver and intraobserver variability. To address these challenges and the lack of interpretability found in certain existing automated methods, we have created fully automated software that not only precisely measures the Cobb angle but also provides clear visualizations of these measurements. This software integrates deep neural network-based spine region detection and segmentation, spine centerline identification, pinpointing the most significantly tilted vertebrae, and direct visualization of Cobb angles on the original images. Upon comparison with the assessments of 7 expert readers, our algorithm exhibited a mean deviation in Cobb angle measurements of 4.17 degrees, notably surpassing the manual approach's average intra-reader discrepancy of 5.16 degrees. The algorithm also achieved intra-class correlation coefficients (ICC) exceeding 0.96 and Pearson correlation coefficients above 0.944, reflecting robust agreement with expert assessments and superior measurement reliability. Through the comprehensive reader study and statistical analysis, we believe this algorithm not only ensures a higher consensus with expert readers but also enhances interpretability and reproducibility during assessments. It holds significant promise for clinical application, potentially aiding physicians in more accurate scoliosis assessment and diagnosis, thereby improving patient care.
Causal Mediation Analysis with Multi-dimensional and Indirectly Observed Mediators
Jun 13, 2023
Causal mediation analysis (CMA) is a powerful method to dissect the total effect of a treatment into direct and mediated effects within the potential outcome framework. This is important in many scientific applications to identify the underlying mechanisms of a treatment effect. However, in many scientific applications the mediator is unobserved, but there may exist related measurements. For example, we may want to identify how changes in brain activity or structure mediate an antidepressant's effect on behavior, but we may only have access to electrophysiological or imaging brain measurements. To date, most CMA methods assume that the mediator is one-dimensional and observable, which oversimplifies such real-world scenarios. To overcome this limitation, we introduce a CMA framework that can handle complex and indirectly observed mediators based on the identifiable variational autoencoder (iVAE) architecture. We prove that the true joint distribution over observed and latent variables is identifiable with the proposed method. Additionally, our framework captures a disentangled representation of the indirectly observed mediator and yields accurate estimation of the direct and mediated effects in synthetic and semi-synthetic experiments, providing evidence of its potential utility in real-world applications.
Style Transfer Enabled Sim2Real Framework for Efficient Learning of Robotic Ultrasound Image Analysis Using Simulated Data
May 16, 2023
Robotic ultrasound (US) systems have shown great potential to make US examinations easier and more accurate. Recently, various machine learning techniques have been proposed to realize automatic US image interpretation for robotic US acquisition tasks. However, obtaining large amounts of real US imaging data for training is usually expensive or even unfeasible in some clinical applications. An alternative is to build a simulator to generate synthetic US data for training, but the differences between simulated and real US images may result in poor model performance. This work presents a Sim2Real framework to efficiently learn robotic US image analysis tasks based only on simulated data for real-world deployment. A style transfer module is proposed based on unsupervised contrastive learning and used as a preprocessing step to convert the real US images into the simulation style. Thereafter, a task-relevant model is designed to combine CNNs with vision transformers to generate the task-dependent prediction with improved generalization ability. We demonstrate the effectiveness of our method in an image regression task to predict the probe position based on US images in robotic transesophageal echocardiography (TEE). Our results show that using only simulated US data and a small amount of unlabelled real data for training, our method can achieve comparable performance to semi-supervised and fully supervised learning methods. Moreover, the effectiveness of our previously proposed CT-based US image simulation method is also indirectly confirmed.
Domain Adaptation via Rebalanced Sub-domain Alignment
Feb 03, 2023
Unsupervised domain adaptation (UDA) is a technique used to transfer knowledge from a labeled source domain to a different but related unlabeled target domain. While many UDA methods have shown success in the past, they often assume that the source and target domains must have identical class label distributions, which can limit their effectiveness in real-world scenarios. To address this limitation, we propose a novel generalization bound that reweights source classification error by aligning source and target sub-domains. We prove that our proposed generalization bound is at least as strong as existing bounds under realistic assumptions, and we empirically show that it is much stronger on real-world data. We then propose an algorithm to minimize this novel generalization bound. We demonstrate by numerical experiments that this approach improves performance in shifted class distribution scenarios compared to state-of-the-art methods.
Estimating Causal Effects using a Multi-task Deep Ensemble
Jan 26, 2023
Over the past few decades, a number of methods have been proposed for causal effect estimation, yet few have been demonstrated to be effective in handling data with complex structures, such as images. To fill this gap, we propose a Causal Multi-task Deep Ensemble (CMDE) framework to learn both shared and group-specific information from the study population and prove its equivalence to a multi-task Gaussian process (GP) with coregionalization kernel a priori. Compared to multi-task GP, CMDE efficiently handles high-dimensional and multi-modal covariates and provides pointwise uncertainty estimates of causal effects. We evaluate our method across various types of datasets and tasks and find that CMDE outperforms state-of-the-art methods on a majority of these tasks.
Closed-Loop Magnetic Manipulation for Robotic Transesophageal Echocardiography
Jan 16, 2023
This paper presents a closed-loop magnetic manipulation framework for robotic transesophageal echocardiography (TEE) acquisitions. Different from previous work on intracorporeal robotic ultrasound acquisitions that focus on continuum robot control, we first investigate the use of magnetic control methods for more direct, intuitive, and accurate manipulation of the distal tip of the probe. We modify a standard TEE probe by attaching a permanent magnet and an inertial measurement unit sensor to the probe tip and replacing the flexible gastroscope with a soft tether containing only wires for transmitting ultrasound signals, and show that 6-DOF localization and 5-DOF closed-loop control of the probe can be achieved with an external permanent magnet based on the fusion of internal inertial measurement and external magnetic field sensing data. The proposed method does not require complex structures or motions of the actuator and the probe compared with existing magnetic manipulation methods. We have conducted extensive experiments to validate the effectiveness of the framework in terms of localization accuracy, update rate, workspace size, and tracking accuracy. In addition, our results obtained on a realistic cardiac tissue-mimicking phantom show that the proposed framework is applicable in real conditions and can generally meet the requirements for tele-operated TEE acquisitions.
Enabling Augmented Segmentation and Registration in Ultrasound-Guided Spinal Surgery via Realistic Ultrasound Synthesis from Diagnostic CT Volume
Jan 05, 2023
This paper aims to tackle the issues on unavailable or insufficient clinical US data and meaningful annotation to enable bone segmentation and registration for US-guided spinal surgery. While the US is not a standard paradigm for spinal surgery, the scarcity of intra-operative clinical US data is an insurmountable bottleneck in training a neural network. Moreover, due to the characteristics of US imaging, it is difficult to clearly annotate bone surfaces which causes the trained neural network missing its attention to the details. Hence, we propose an In silico bone US simulation framework that synthesizes realistic US images from diagnostic CT volume. Afterward, using these simulated bone US we train a lightweight vision transformer model that can achieve accurate and on-the-fly bone segmentation for spinal sonography. In the validation experiments, the realistic US simulation was conducted by deriving from diagnostic spinal CT volume to facilitate a radiation-free US-guided pedicle screw placement procedure. When it is employed for training bone segmentation task, the Chamfer distance achieves 0.599mm; when it is applied for CT-US registration, the associated bone segmentation accuracy achieves 0.93 in Dice, and the registration accuracy based on the segmented point cloud is 0.13~3.37mm in a complication-free manner. While bone US images exhibit strong echoes at the medium interface, it may enable the model indistinguishable between thin interfaces and bone surfaces by simply relying on small neighborhood information. To overcome these shortcomings, we propose to utilize a Long-range Contrast Learning Module to fully explore the Long-range Contrast between the candidates and their surrounding pixels.
Goal-oriented Autonomous Driving
Dec 20, 2022
Modern autonomous driving system is characterized as modular tasks in sequential order, i.e., perception, prediction and planning. As sensors and hardware get improved, there is trending popularity to devise a system that can perform a wide diversity of tasks to fulfill higher-level intelligence. Contemporary approaches resort to either deploying standalone models for individual tasks, or designing a multi-task paradigm with separate heads. These might suffer from accumulative error or negative transfer effect. Instead, we argue that a favorable algorithm framework should be devised and optimized in pursuit of the ultimate goal, i.e. planning of the self-driving-car. Oriented at this goal, we revisit the key components within perception and prediction. We analyze each module and prioritize the tasks hierarchically, such that all these tasks contribute to planning (the goal). To this end, we introduce Unified Autonomous Driving (UniAD), the first comprehensive framework up-to-date that incorporates full-stack driving tasks in one network. It is exquisitely devised to leverage advantages of each module, and provide complementary feature abstractions for agent interaction from a global perspective. Tasks are communicated with unified query design to facilitate each other toward planning. We instantiate UniAD on the challenging nuScenes benchmark. With extensive ablations, the effectiveness of using such a philosophy is proven to surpass previous state-of-the-arts by a large margin in all aspects. The full suite of codebase and models would be available to facilitate future research in the community.
Automated Grading of Radiographic Knee Osteoarthritis Severity Combined with Joint Space Narrowing
Mar 16, 2022
The assessment of knee osteoarthritis (KOA) severity on knee X-rays is a central criteria for the use of total knee arthroplasty. However, this assessment suffers from imprecise standards and a remarkably high inter-reader variability. An algorithmic, automated assessment of KOA severity could improve overall outcomes of knee replacement procedures by increasing the appropriateness of its use. We propose a novel deep learning-based five-step algorithm to automatically grade KOA from posterior-anterior (PA) views of radiographs: (1) image preprocessing (2) localization of knees joints in the image using the YOLO v3-Tiny model, (3) initial assessment of the severity of osteoarthritis using a convolutional neural network-based classifier, (4) segmentation of the joints and calculation of the joint space narrowing (JSN), and (5), a combination of the JSN and the initial assessment to determine a final Kellgren-Lawrence (KL) score. Furthermore, by displaying the segmentation masks used to make the assessment, our algorithm demonstrates a higher degree of transparency compared to typical "black box" deep learning classifiers. We perform a comprehensive evaluation using two public datasets and one dataset from our institution, and show that our algorithm reaches state-of-the art performance. Moreover, we also collected ratings from multiple radiologists at our institution and showed that our algorithm performs at the radiologist level. The software has been made publicly available at https://github.com/MaciejMazurowski/osteoarthritis-classification.
Image-Guided Navigation of a Robotic Ultrasound Probe for Autonomous Spinal Sonography Using a Shadow-aware Dual-Agent Framework
Nov 10, 2021
Ultrasound (US) imaging is commonly used to assist in the diagnosis and interventions of spine diseases, while the standardized US acquisitions performed by manually operating the probe require substantial experience and training of sonographers. In this work, we propose a novel dual-agent framework that integrates a reinforcement learning (RL) agent and a deep learning (DL) agent to jointly determine the movement of the US probe based on the real-time US images, in order to mimic the decision-making process of an expert sonographer to achieve autonomous standard view acquisitions in spinal sonography. Moreover, inspired by the nature of US propagation and the characteristics of the spinal anatomy, we introduce a view-specific acoustic shadow reward to utilize the shadow information to implicitly guide the navigation of the probe toward different standard views of the spine. Our method is validated in both quantitative and qualitative experiments in a simulation environment built with US data acquired from 17 volunteers. The average navigation accuracy toward different standard views achieves 5.18mm/5.25deg and 12.87mm/17.49deg in the intra- and inter-subject settings, respectively. The results demonstrate that our method can effectively interpret the US images and navigate the probe to acquire multiple standard views of the spine.