new

Get trending papers in your email inbox!

Subscribe

byAK and the research community

Mar 14

Neural Deformable Models for 3D Bi-Ventricular Heart Shape Reconstruction and Modeling from 2D Sparse Cardiac Magnetic Resonance Imaging

We propose a novel neural deformable model (NDM) targeting at the reconstruction and modeling of 3D bi-ventricular shape of the heart from 2D sparse cardiac magnetic resonance (CMR) imaging data. We model the bi-ventricular shape using blended deformable superquadrics, which are parameterized by a set of geometric parameter functions and are capable of deforming globally and locally. While global geometric parameter functions and deformations capture gross shape features from visual data, local deformations, parameterized as neural diffeomorphic point flows, can be learned to recover the detailed heart shape.Different from iterative optimization methods used in conventional deformable model formulations, NDMs can be trained to learn such geometric parameter functions, global and local deformations from a shape distribution manifold. Our NDM can learn to densify a sparse cardiac point cloud with arbitrary scales and generate high-quality triangular meshes automatically. It also enables the implicit learning of dense correspondences among different heart shape instances for accurate cardiac shape registration. Furthermore, the parameters of NDM are intuitive, and can be used by a physician without sophisticated post-processing. Experimental results on a large CMR dataset demonstrate the improved performance of NDM over conventional methods.

YOCO: You Only Calibrate Once for Accurate Extrinsic Parameter in LiDAR-Camera Systems

In a multi-sensor fusion system composed of cameras and LiDAR, precise extrinsic calibration contributes to the system's long-term stability and accurate perception of the environment. However, methods based on extracting and registering corresponding points still face challenges in terms of automation and precision. This paper proposes a novel fully automatic extrinsic calibration method for LiDAR-camera systems that circumvents the need for corresponding point registration. In our approach, a novel algorithm to extract required LiDAR correspondence point is proposed. This method can effectively filter out irrelevant points by computing the orientation of plane point clouds and extracting points by applying distance- and density-based thresholds. We avoid the need for corresponding point registration by introducing extrinsic parameters between the LiDAR and camera into the projection of extracted points and constructing co-planar constraints. These parameters are then optimized to solve for the extrinsic. We validated our method across multiple sets of LiDAR-camera systems. In synthetic experiments, our method demonstrates superior performance compared to current calibration techniques. Real-world data experiments further confirm the precision and robustness of the proposed algorithm, with average rotation and translation calibration errors between LiDAR and camera of less than 0.05 degree and 0.015m, respectively. This method enables automatic and accurate extrinsic calibration in a single one step, emphasizing the potential of calibration algorithms beyond using corresponding point registration to enhance the automation and precision of LiDAR-camera system calibration.

FreeReg: Image-to-Point Cloud Registration Leveraging Pretrained Diffusion Models and Monocular Depth Estimators

Matching cross-modality features between images and point clouds is a fundamental problem for image-to-point cloud registration. However, due to the modality difference between images and points, it is difficult to learn robust and discriminative cross-modality features by existing metric learning methods for feature matching. Instead of applying metric learning on cross-modality data, we propose to unify the modality between images and point clouds by pretrained large-scale models first, and then establish robust correspondence within the same modality. We show that the intermediate features, called diffusion features, extracted by depth-to-image diffusion models are semantically consistent between images and point clouds, which enables the building of coarse but robust cross-modality correspondences. We further extract geometric features on depth maps produced by the monocular depth estimator. By matching such geometric features, we significantly improve the accuracy of the coarse correspondences produced by diffusion features. Extensive experiments demonstrate that without any task-specific training, direct utilization of both features produces accurate image-to-point cloud registration. On three public indoor and outdoor benchmarks, the proposed method averagely achieves a 20.6 percent improvement in Inlier Ratio, a three-fold higher Inlier Number, and a 48.6 percent improvement in Registration Recall than existing state-of-the-arts.

SE(3) Diffusion Model-based Point Cloud Registration for Robust 6D Object Pose Estimation

In this paper, we introduce an SE(3) diffusion model-based point cloud registration framework for 6D object pose estimation in real-world scenarios. Our approach formulates the 3D registration task as a denoising diffusion process, which progressively refines the pose of the source point cloud to obtain a precise alignment with the model point cloud. Training our framework involves two operations: An SE(3) diffusion process and an SE(3) reverse process. The SE(3) diffusion process gradually perturbs the optimal rigid transformation of a pair of point clouds by continuously injecting noise (perturbation transformation). By contrast, the SE(3) reverse process focuses on learning a denoising network that refines the noisy transformation step-by-step, bringing it closer to the optimal transformation for accurate pose estimation. Unlike standard diffusion models used in linear Euclidean spaces, our diffusion model operates on the SE(3) manifold. This requires exploiting the linear Lie algebra se(3) associated with SE(3) to constrain the transformation transitions during the diffusion and reverse processes. Additionally, to effectively train our denoising network, we derive a registration-specific variational lower bound as the optimization objective for model learning. Furthermore, we show that our denoising network can be constructed with a surrogate registration model, making our approach applicable to different deep registration networks. Extensive experiments demonstrate that our diffusion registration framework presents outstanding pose estimation performance on the real-world TUD-L, LINEMOD, and Occluded-LINEMOD datasets.

Cubify Anything: Scaling Indoor 3D Object Detection

We consider indoor 3D object detection with respect to a single RGB(-D) frame acquired from a commodity handheld device. We seek to significantly advance the status quo with respect to both data and modeling. First, we establish that existing datasets have significant limitations to scale, accuracy, and diversity of objects. As a result, we introduce the Cubify-Anything 1M (CA-1M) dataset, which exhaustively labels over 400K 3D objects on over 1K highly accurate laser-scanned scenes with near-perfect registration to over 3.5K handheld, egocentric captures. Next, we establish Cubify Transformer (CuTR), a fully Transformer 3D object detection baseline which rather than operating in 3D on point or voxel-based representations, predicts 3D boxes directly from 2D features derived from RGB(-D) inputs. While this approach lacks any 3D inductive biases, we show that paired with CA-1M, CuTR outperforms point-based methods - accurately recalling over 62% of objects in 3D, and is significantly more capable at handling noise and uncertainty present in commodity LiDAR-derived depth maps while also providing promising RGB only performance without architecture changes. Furthermore, by pre-training on CA-1M, CuTR can outperform point-based methods on a more diverse variant of SUN RGB-D - supporting the notion that while inductive biases in 3D are useful at the smaller sizes of existing datasets, they fail to scale to the data-rich regime of CA-1M. Overall, this dataset and baseline model provide strong evidence that we are moving towards models which can effectively Cubify Anything.

Deformable MRI Sequence Registration for AI-based Prostate Cancer Diagnosis

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

G3Reg: Pyramid Graph-based Global Registration using Gaussian Ellipsoid Model

This study introduces a novel framework, G3Reg, for fast and robust global registration of LiDAR point clouds. In contrast to conventional complex keypoints and descriptors, we extract fundamental geometric primitives, including planes, clusters, and lines (PCL) from the raw point cloud to obtain low-level semantic segments. Each segment is represented as a unified Gaussian Ellipsoid Model (GEM), using a probability ellipsoid to ensure the ground truth centers are encompassed with a certain degree of probability. Utilizing these GEMs, we present a distrust-and-verify scheme based on a Pyramid Compatibility Graph for Global Registration (PAGOR). Specifically, we establish an upper bound, which can be traversed based on the confidence level for compatibility testing to construct the pyramid graph. Then, we solve multiple maximum cliques (MAC) for each level of the pyramid graph, thus generating the corresponding transformation candidates. In the verification phase, we adopt a precise and efficient metric for point cloud alignment quality, founded on geometric primitives, to identify the optimal candidate. The algorithm's performance is validated on three publicly available datasets and a self-collected multi-session dataset. Parameter settings remained unchanged during the experiment evaluations. The results exhibit superior robustness and real-time performance of the G3Reg framework compared to state-of-the-art methods. Furthermore, we demonstrate the potential for integrating individual GEM and PAGOR components into other registration frameworks to enhance their efficacy. Code: https://github.com/HKUST-Aerial-Robotics/G3Reg

PRISM: Patient Records Interpretation for Semantic Clinical Trial Matching using Large Language Models

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

Transformation Decoupling Strategy based on Screw Theory for Deterministic Point Cloud Registration with Gravity Prior

Point cloud registration is challenging in the presence of heavy outlier correspondences. This paper focuses on addressing the robust correspondence-based registration problem with gravity prior that often arises in practice. The gravity directions are typically obtained by inertial measurement units (IMUs) and can reduce the degree of freedom (DOF) of rotation from 3 to 1. We propose a novel transformation decoupling strategy by leveraging screw theory. This strategy decomposes the original 4-DOF problem into three sub-problems with 1-DOF, 2-DOF, and 1-DOF, respectively, thereby enhancing the computation efficiency. Specifically, the first 1-DOF represents the translation along the rotation axis and we propose an interval stabbing-based method to solve it. The second 2-DOF represents the pole which is an auxiliary variable in screw theory and we utilize a branch-and-bound method to solve it. The last 1-DOF represents the rotation angle and we propose a global voting method for its estimation. The proposed method sequentially solves three consensus maximization sub-problems, leading to efficient and deterministic registration. In particular, it can even handle the correspondence-free registration problem due to its significant robustness. Extensive experiments on both synthetic and real-world datasets demonstrate that our method is more efficient and robust than state-of-the-art methods, even when dealing with outlier rates exceeding 99%.

More efficient manual review of automatically transcribed tabular data

Machine learning methods have proven useful in transcribing historical data. However, results from even highly accurate methods require manual verification and correction. Such manual review can be time-consuming and expensive, therefore the objective of this paper was to make it more efficient. Previously, we used machine learning to transcribe 2.3 million handwritten occupation codes from the Norwegian 1950 census with high accuracy (97%). We manually reviewed the 90,000 (3%) codes with the lowest model confidence. We allocated those 90,000 codes to human reviewers, who used our annotation tool to review the codes. To assess reviewer agreement, some codes were assigned to multiple reviewers. We then analyzed the review results to understand the relationship between accuracy improvements and effort. Additionally, we interviewed the reviewers to improve the workflow. The reviewers corrected 62.8% of the labels and agreed with the model label in 31.9% of cases. About 0.2% of the images could not be assigned a label, while for 5.1% the reviewers were uncertain, or they assigned an invalid label. 9,000 images were independently reviewed by multiple reviewers, resulting in an agreement of 86.43% and disagreement of 8.96%. We learned that our automatic transcription is biased towards the most frequent codes, with a higher degree of misclassification for the lowest frequency codes. Our interview findings show that the reviewers did internal quality control and found our custom tool well-suited. So, only one reviewer is needed, but they should report uncertainty.

A Quantitative Evaluation of Dense 3D Reconstruction of Sinus Anatomy from Monocular Endoscopic Video

Generating accurate 3D reconstructions from endoscopic video is a promising avenue for longitudinal radiation-free analysis of sinus anatomy and surgical outcomes. Several methods for monocular reconstruction have been proposed, yielding visually pleasant 3D anatomical structures by retrieving relative camera poses with structure-from-motion-type algorithms and fusion of monocular depth estimates. However, due to the complex properties of the underlying algorithms and endoscopic scenes, the reconstruction pipeline may perform poorly or fail unexpectedly. Further, acquiring medical data conveys additional challenges, presenting difficulties in quantitatively benchmarking these models, understanding failure cases, and identifying critical components that contribute to their precision. In this work, we perform a quantitative analysis of a self-supervised approach for sinus reconstruction using endoscopic sequences paired with optical tracking and high-resolution computed tomography acquired from nine ex-vivo specimens. Our results show that the generated reconstructions are in high agreement with the anatomy, yielding an average point-to-mesh error of 0.91 mm between reconstructions and CT segmentations. However, in a point-to-point matching scenario, relevant for endoscope tracking and navigation, we found average target registration errors of 6.58 mm. We identified that pose and depth estimation inaccuracies contribute equally to this error and that locally consistent sequences with shorter trajectories generate more accurate reconstructions. These results suggest that achieving global consistency between relative camera poses and estimated depths with the anatomy is essential. In doing so, we can ensure proper synergy between all components of the pipeline for improved reconstructions that will facilitate clinical application of this innovative technology.

FIRST: Teach A Reliable Large Language Model Through Efficient Trustworthy Distillation

Large language models (LLMs) have become increasingly prevalent in our daily lives, leading to an expectation for LLMs to be trustworthy -- - both accurate and well-calibrated (the prediction confidence should align with its ground truth correctness likelihood). Nowadays, fine-tuning has become the most popular method for adapting a model to practical usage by significantly increasing accuracy on downstream tasks. Despite the great accuracy it achieves, we found fine-tuning is still far away from satisfactory trustworthiness due to "tuning-induced mis-calibration". In this paper, we delve deeply into why and how mis-calibration exists in fine-tuned models, and how distillation can alleviate the issue. Then we further propose a brand new method named Efficient Trustworthy Distillation (FIRST), which utilizes a small portion of teacher's knowledge to obtain a reliable language model in a cost-efficient way. Specifically, we identify the "concentrated knowledge" phenomenon during distillation, which can significantly reduce the computational burden. Then we apply a "trustworthy maximization" process to optimize the utilization of this small portion of concentrated knowledge before transferring it to the student. Experimental results demonstrate the effectiveness of our method, where better accuracy (+2.3%) and less mis-calibration (-10%) are achieved on average across both in-domain and out-of-domain scenarios, indicating better trustworthiness.

MICDIR: Multi-scale Inverse-consistent Deformable Image Registration using UNetMSS with Self-Constructing Graph Latent

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

SciClaimHunt: A Large Dataset for Evidence-based Scientific Claim Verification

Verifying scientific claims presents a significantly greater challenge than verifying political or news-related claims. Unlike the relatively broad audience for political claims, the users of scientific claim verification systems can vary widely, ranging from researchers testing specific hypotheses to everyday users seeking information on a medication. Additionally, the evidence for scientific claims is often highly complex, involving technical terminology and intricate domain-specific concepts that require specialized models for accurate verification. Despite considerable interest from the research community, there is a noticeable lack of large-scale scientific claim verification datasets to benchmark and train effective models. To bridge this gap, we introduce two large-scale datasets, SciClaimHunt and SciClaimHunt_Num, derived from scientific research papers. We propose several baseline models tailored for scientific claim verification to assess the effectiveness of these datasets. Additionally, we evaluate models trained on SciClaimHunt and SciClaimHunt_Num against existing scientific claim verification datasets to gauge their quality and reliability. Furthermore, we conduct human evaluations of the claims in proposed datasets and perform error analysis to assess the effectiveness of the proposed baseline models. Our findings indicate that SciClaimHunt and SciClaimHunt_Num serve as highly reliable resources for training models in scientific claim verification.