Real-to-Sim Deformable Object Manipulation: Optimizing Physics Models with Residual Mappings for Robotic Surgery

Accurate deformable object manipulation (DOM) is essential for achieving autonomy in robotic surgery, where soft tissues are being displaced, stretched, and dissected. Many DOM methods can be powered by simulation, which ensures realistic deformation by adhering to the governing physical constraints and allowing for model prediction and control. However, real soft objects in robotic surgery, such as membranes and soft tissues, have complex, anisotropic physical parameters that a simulation with simple initialization from cameras may not fully capture. To use the simulation techniques in real surgical tasks, the "real-to-sim" gap needs to be properly compensated. In this work, we propose an online, adaptive parameter tuning approach for simulation optimization that (1) bridges the real-to-sim gap between a physics simulation and observations obtained 3D perceptions through estimating a residual mapping and (2) optimizes its stiffness parameters online. Our method ensures a small residual gap between the simulation and observation and improves the simulation's predictive capabilities. The effectiveness of the proposed mechanism is evaluated in the manipulation of both a thin-shell and volumetric tissue, representative of most tissue scenarios. This work contributes to the advancement of simulation-based deformable tissue manipulation and holds potential for improving surgical autonomy.

AnyOKP: One-Shot and Instance-Aware Object Keypoint Extraction with Pretrained ViT

Towards flexible object-centric visual perception, we propose a one-shot instance-aware object keypoint (OKP) extraction approach, AnyOKP, which leverages the powerful representation ability of pretrained vision transformer (ViT), and can obtain keypoints on multiple object instances of arbitrary category after learning from a support image. An off-the-shelf petrained ViT is directly deployed for generalizable and transferable feature extraction, which is followed by training-free feature enhancement. The best-prototype pairs (BPPs) are searched for in support and query images based on appearance similarity, to yield instance-unaware candidate keypoints.Then, the entire graph with all candidate keypoints as vertices are divided to sub-graphs according to the feature distributions on the graph edges. Finally, each sub-graph represents an object instance. AnyOKP is evaluated on real object images collected with the cameras of a robot arm, a mobile robot, and a surgical robot, which not only demonstrates the cross-category flexibility and instance awareness, but also show remarkable robustness to domain shift and viewpoint change.

BAA-NGP: Bundle-Adjusting Accelerated Neural Graphics Primitives

Implicit neural representation has emerged as a powerful method for reconstructing 3D scenes from 2D images. Given a set of camera poses and associated images, the models can be trained to synthesize novel, unseen views. In order to expand the use cases for implicit neural representations, we need to incorporate camera pose estimation capabilities as part of the representation learning, as this is necessary for reconstructing scenes from real-world video sequences where cameras are generally not being tracked. Existing approaches like COLMAP and, most recently, bundle-adjusting neural radiance field methods often suffer from lengthy processing times. These delays ranging from hours to days, arise from laborious feature matching, hardware limitations, dense point sampling, and long training times required by a multi-layer perceptron structure with a large number of parameters. To address these challenges, we propose a framework called bundle-adjusting accelerated neural graphics primitives (BAA-NGP). Our approach leverages accelerated sampling and hash encoding to expedite both pose refinement/estimation and 3D scene reconstruction. Experimental results demonstrate that our method achieves a more than 10 to 20 $\times$ speed improvement in novel view synthesis compared to other bundle-adjusting neural radiance field methods without sacrificing the quality of pose estimation.

ORRN: An ODE-based Recursive Registration Network for Deformable Respiratory Motion Estimation with Lung 4DCT Images

Deformable Image Registration (DIR) plays a significant role in quantifying deformation in medical data. Recent Deep Learning methods have shown promising accuracy and speedup for registering a pair of medical images. However, in 4D (3D + time) medical data, organ motion, such as respiratory motion and heart beating, can not be effectively modeled by pair-wise methods as they were optimized for image pairs but did not consider the organ motion patterns necessary when considering 4D data. This paper presents ORRN, an Ordinary Differential Equations (ODE)-based recursive image registration network. Our network learns to estimate time-varying voxel velocities for an ODE that models deformation in 4D image data. It adopts a recursive registration strategy to progressively estimate a deformation field through ODE integration of voxel velocities. We evaluate the proposed method on two publicly available lung 4DCT datasets, DIRLab and CREATIS, for two tasks: 1) registering all images to the extreme inhale image for 3D+t deformation tracking and 2) registering extreme exhale to inhale phase images. Our method outperforms other learning-based methods in both tasks, producing the smallest Target Registration Error of 1.24mm and 1.26mm, respectively. Additionally, it produces less than 0.001\% unrealistic image folding, and the computation speed is less than 1 second for each CT volume. ORRN demonstrates promising registration accuracy, deformation plausibility, and computation efficiency on group-wise and pair-wise registration tasks. It has significant implications in enabling fast and accurate respiratory motion estimation for treatment planning in radiation therapy or robot motion planning in thoracic needle insertion.

An Ensemble Learning Approach for Exercise Detection in Type 1 Diabetes Patients

Type 1 diabetes is a serious disease in which individuals are unable to regulate their blood glucose levels, leading to various medical complications. Artificial pancreas (AP) systems have been developed as a solution for type 1 diabetic patients to mimic the behavior of the pancreas and regulate blood glucose levels. However, current AP systems lack detection capabilities for exercise-induced glucose intake, which can last up to 4 to 8 hours. This incapability can lead to hypoglycemia, which if left untreated, could have serious consequences, including death. Existing exercise detection methods are either limited to single sensor data or use inaccurate models for exercise detection, making them less effective in practice. In this work, we propose an ensemble learning framework that combines a data-driven physiological model and a Siamese network to leverage multiple physiological signal streams for exercise detection with high accuracy. To evaluate the effectiveness of our proposed approach, we utilized a public dataset with 12 diabetic patients collected from an 8-week clinical trial. Our approach achieves a true positive rate for exercise detection of 86.4% and a true negative rate of 99.1%, outperforming state-of-the-art solutions.

SemHint-MD: Learning from Noisy Semantic Labels for Self-Supervised Monocular Depth Estimation

Without ground truth supervision, self-supervised depth estimation can be trapped in a local minimum due to the gradient-locality issue of the photometric loss. In this paper, we present a framework to enhance depth by leveraging semantic segmentation to guide the network to jump out of the local minimum. Prior works have proposed to share encoders between these two tasks or explicitly align them based on priors like the consistency between edges in the depth and segmentation maps. Yet, these methods usually require ground truth or high-quality pseudo labels, which may not be easily accessible in real-world applications. In contrast, we investigate self-supervised depth estimation along with a segmentation branch that is supervised with noisy labels provided by models pre-trained with limited data. We extend parameter sharing from the encoder to the decoder and study the influence of different numbers of shared decoder parameters on model performance. Also, we propose to use cross-task information to refine current depth and segmentation predictions to generate pseudo-depth and semantic labels for training. The advantages of the proposed method are demonstrated through extensive experiments on the KITTI benchmark and a downstream task for endoscopic tissue deformation tracking.

CarFi: Rider Localization Using Wi-Fi CSI

With the rise of hailing services, people are increasingly relying on shared mobility (e.g., Uber, Lyft) drivers to pick up for transportation. However, such drivers and riders have difficulties finding each other in urban areas as GPS signals get blocked by skyscrapers, in crowded environments (e.g., in stadiums, airports, and bars), at night, and in bad weather. It wastes their time, creates a bad user experience, and causes more CO2 emissions due to idle driving. In this work, we explore the potential of Wi-Fi to help drivers to determine the street side of the riders. Our proposed system is called CarFi that uses Wi-Fi CSI from two antennas placed inside a moving vehicle and a data-driven technique to determine the street side of the rider. By collecting real-world data in realistic and challenging settings by blocking the signal with other people and other parked cars, we see that CarFi is 95.44% accurate in rider-side determination in both line of sight (LoS) and non-line of sight (nLoS) conditions, and can be run on an embedded GPU in real-time.

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Semantic-SuPer: A Semantic-aware Surgical Perception Framework for Endoscopic Tissue Classification, Reconstruction, and Tracking

Accurate and robust tracking and reconstruction of the surgical scene is a critical enabling technology toward autonomous robotic surgery. Existing algorithms for 3D perception in surgery mainly rely on geometric information, while we propose to also leverage semantic information inferred from the endoscopic video using image segmentation algorithms. In this paper, we present a novel, comprehensive surgical perception framework, Semantic-SuPer, that integrates geometric and semantic information to facilitate data association, 3D reconstruction, and tracking of endoscopic scenes, benefiting downstream tasks like surgical navigation. The proposed framework is demonstrated on challenging endoscopic data with deforming tissue, showing its advantages over our baseline and several other state-of the-art approaches. Our code and dataset will be available at https://github.com/ucsdarclab/Python-SuPer.