Jiancheng Yang

Liang Jin, Shixuan Gu, Donglai Wei et al. · harvard

Automatic rib labeling and anatomical centerline extraction are common prerequisites for various clinical applications. Prior studies either use in-house datasets that are inaccessible to communities, or focus on rib segmentation that neglects the clinical significance of rib labeling. To address these issues, we extend our prior dataset (RibSeg) on the binary rib segmentation task to a comprehensive benchmark, named RibSeg v2, with 660 CT scans (15,466 individual ribs in total) and annotations manually inspected by experts for rib labeling and anatomical centerline extraction. Based on the RibSeg v2, we develop a pipeline including deep learning-based methods for rib labeling, and a skeletonization-based method for centerline extraction. To improve computational efficiency, we propose a sparse point cloud representation of CT scans and compare it with standard dense voxel grids. Moreover, we design and analyze evaluation metrics to address the key challenges of each task. Our dataset, code, and model are available online to facilitate open research at https://github.com/M3DV/RibSeg

Chinmay Prabhakar, Hongwei Bran Li, Jiancheng Yang et al.

Self-supervised learning has attracted increasing attention as it learns data-driven representation from data without annotations. Vision transformer-based autoencoder (ViT-AE) by He et al. (2021) is a recent self-supervised learning technique that employs a patch-masking strategy to learn a meaningful latent space. In this paper, we focus on improving ViT-AE (nicknamed ViT-AE++) for a more effective representation of 2D and 3D medical images. We propose two new loss functions to enhance the representation during training. The first loss term aims to improve self-reconstruction by considering the structured dependencies and indirectly improving the representation. The second loss term leverages contrastive loss to optimize the representation from two randomly masked views directly. We extended ViT-AE++ to a 3D fashion for volumetric medical images as an independent contribution. We extensively evaluate ViT-AE++ on both natural images and medical images, demonstrating consistent improvement over vanilla ViT-AE and its superiority over other contrastive learning approaches. Codes are here: https://github.com/chinmay5/vit_ae_plus_plus.git.

Xiaoyang Huang, Jiancheng Yang, Yanjun Wang et al.

3D shape analysis has been widely explored in the era of deep learning. Numerous models have been developed for various 3D data representation formats, e.g., MeshCNN for meshes, PointNet for point clouds and VoxNet for voxels. In this study, we present Representation-Agnostic Shape Fields (RASF), a generalizable and computation-efficient shape embedding module for 3D deep learning. RASF is implemented with a learnable 3D grid with multiple channels to store local geometry. Based on RASF, shape embeddings for various 3D shape representations (point clouds, meshes and voxels) are retrieved by coordinate indexing. While there are multiple ways to optimize the learnable parameters of RASF, we provide two effective schemes among all in this paper for RASF pre-training: shape reconstruction and normal estimation. Once trained, RASF becomes a plug-and-play performance booster with negligible cost. Extensive experiments on diverse 3D representation formats, networks and applications, validate the universal effectiveness of the proposed RASF. Code and pre-trained models are publicly available https://github.com/seanywang0408/RASF

Jiancheng Yang, Rui Shi, Udaranga Wickramasinghe et al.

The human annotations are imperfect, especially when produced by junior practitioners. Multi-expert consensus is usually regarded as golden standard, while this annotation protocol is too expensive to implement in many real-world projects. In this study, we propose a method to refine human annotation, named Neural Annotation Refinement (NeAR). It is based on a learnable implicit function, which decodes a latent vector into represented shape. By integrating the appearance as an input of implicit functions, the appearance-aware NeAR fixes the annotation artefacts. Our method is demonstrated on the application of adrenal gland analysis. We first show that the NeAR can repair distorted golden standards on a public adrenal gland segmentation dataset. Besides, we develop a new Adrenal gLand ANalysis (ALAN) dataset with the proposed NeAR, where each case consists of a 3D shape of adrenal gland and its diagnosis label (normal vs. abnormal) assigned by experts. We show that models trained on the shapes repaired by the NeAR can diagnose adrenal glands better than the original ones. The ALAN dataset will be open-source, with 1,584 shapes for adrenal gland diagnosis, which serves as a new benchmark for medical shape analysis. Code and dataset are available at https://github.com/M3DV/NeAR.

Ziqiao Weng, Jiancheng Yang, Dongnan Liu et al.

Accurate segmentation of pulmonary airways and vessels is crucial for the diagnosis and treatment of pulmonary diseases. However, current deep learning approaches suffer from disconnectivity issues that hinder their clinical usefulness. To address this challenge, we propose a post-processing approach that leverages a data-driven method to repair the topology of disconnected pulmonary tubular structures. Our approach formulates the problem as a keypoint detection task, where a neural network is trained to predict keypoints that can bridge disconnected components. We use a training data synthesis pipeline that generates disconnected data from complete pulmonary structures. Moreover, the new Pulmonary Tree Repairing (PTR) dataset is publicly available, which comprises 800 complete 3D models of pulmonary airways, arteries, and veins, as well as the synthetic disconnected data. Our code and data are available at https://github.com/M3DV/pulmonary-tree-repairing.

Kaiming Kuang, Li Zhang, Jingyu Li et al.

3D reconstruction of pulmonary segments plays an important role in surgical treatment planning of lung cancer, which facilitates preservation of pulmonary function and helps ensure low recurrence rates. However, automatic reconstruction of pulmonary segments remains unexplored in the era of deep learning. In this paper, we investigate what makes for automatic reconstruction of pulmonary segments. First and foremost, we formulate, clinically and geometrically, the anatomical definitions of pulmonary segments, and propose evaluation metrics adhering to these definitions. Second, we propose ImPulSe (Implicit Pulmonary Segment), a deep implicit surface model designed for pulmonary segment reconstruction. The automatic reconstruction of pulmonary segments by ImPulSe is accurate in metrics and visually appealing. Compared with canonical segmentation methods, ImPulSe outputs continuous predictions of arbitrary resolutions with higher training efficiency and fewer parameters. Lastly, we experiment with different network inputs to analyze what matters in the task of pulmonary segment reconstruction. Our code is available at https://github.com/M3DV/ImPulSe.

Zhihao Li, Jiancheng Yang, Yongchao Xu et al.

Pulmonary nodules and masses are crucial imaging features in lung cancer screening that require careful management in clinical diagnosis. Despite the success of deep learning-based medical image segmentation, the robust performance on various sizes of lesions of nodule and mass is still challenging. In this paper, we propose a multi-scale neural network with scale-aware test-time adaptation to address this challenge. Specifically, we introduce an adaptive Scale-aware Test-time Click Adaptation method based on effortlessly obtainable lesion clicks as test-time cues to enhance segmentation performance, particularly for large lesions. The proposed method can be seamlessly integrated into existing networks. Extensive experiments on both open-source and in-house datasets consistently demonstrate the effectiveness of the proposed method over some CNN and Transformer-based segmentation methods. Our code is available at https://github.com/SplinterLi/SaTTCA

Minghui Zhang, Yangqian Wu, Hanxiao Zhang et al. · harvard

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.

Rui Xu, Yong Luo, Bo Du et al.

Convolutional neural networks (CNNs) have been demonstrated to be highly effective in the field of pulmonary nodule detection. However, existing CNN based pulmonary nodule detection methods lack the ability to capture long-range dependencies, which is vital for global information extraction. In computer vision tasks, non-local operations have been widely utilized, but the computational cost could be very high for 3D computed tomography (CT) images. To address this issue, we propose a long short slice-aware network (LSSANet) for the detection of pulmonary nodules. In particular, we develop a new non-local mechanism termed long short slice grouping (LSSG), which splits the compact non-local embeddings into a short-distance slice grouped one and a long-distance slice grouped counterpart. This not only reduces the computational burden, but also keeps long-range dependencies among any elements across slices and in the whole feature map. The proposed LSSG is easy-to-use and can be plugged into many pulmonary nodule detection networks. To verify the performance of LSSANet, we compare with several recently proposed and competitive detection approaches based on 2D/3D CNN. Promising evaluation results on the large-scale PN9 dataset demonstrate the effectiveness of our method. Code is at https://github.com/Ruixxxx/LSSANet.

Rui Xu, Zhi Liu, Yong Luo et al.

Lung cancer is the leading cause of cancer death worldwide. The best solution for lung cancer is to diagnose the pulmonary nodules in the early stage, which is usually accomplished with the aid of thoracic computed tomography (CT). As deep learning thrives, convolutional neural networks (CNNs) have been introduced into pulmonary nodule detection to help doctors in this labor-intensive task and demonstrated to be very effective. However, the current pulmonary nodule detection methods are usually domain-specific, and cannot satisfy the requirement of working in diverse real-world scenarios. To address this issue, we propose a slice grouped domain attention (SGDA) module to enhance the generalization capability of the pulmonary nodule detection networks. This attention module works in the axial, coronal, and sagittal directions. In each direction, we divide the input feature into groups, and for each group, we utilize a universal adapter bank to capture the feature subspaces of the domains spanned by all pulmonary nodule datasets. Then the bank outputs are combined from the perspective of domain to modulate the input group. Extensive experiments demonstrate that SGDA enables substantially better multi-domain pulmonary nodule detection performance compared with the state-of-the-art multi-domain learning methods.

Jiancheng Yang, Hongwei Bran Li, Donglai Wei

This study investigates the transformative potential of Large Language Models (LLMs), such as OpenAI ChatGPT, in medical imaging. With the aid of public data, these models, which possess remarkable language understanding and generation capabilities, are augmenting the interpretive skills of radiologists, enhancing patient-physician communication, and streamlining clinical workflows. The paper introduces an analytic framework for presenting the complex interactions between LLMs and the broader ecosystem of medical imaging stakeholders, including businesses, insurance entities, governments, research institutions, and hospitals (nicknamed BIGR-H). Through detailed analyses, illustrative use cases, and discussions on the broader implications and future directions, this perspective seeks to raise discussion in strategic planning and decision-making in the era of AI-enabled healthcare.

Kangxian Xie, Jiancheng Yang, Donglai Wei et al.

Pulmonary diseases rank prominently among the principal causes of death worldwide. Curing them will require, among other things, a better understanding of the complex 3D tree-shaped structures within the pulmonary system, such as airways, arteries, and veins. Traditional approaches using high-resolution image stacks and standard CNNs on dense voxel grids face challenges in computational efficiency, limited resolution, local context, and inadequate preservation of shape topology. Our method addresses these issues by shifting from dense voxel to sparse point representation, offering better memory efficiency and global context utilization. However, the inherent sparsity in point representation can lead to a loss of crucial connectivity in tree-shaped structures. To mitigate this, we introduce graph learning on skeletonized structures, incorporating differentiable feature fusion for improved topology and long-distance context capture. Furthermore, we employ an implicit function for efficient conversion of sparse representations into dense reconstructions end-to-end. The proposed method not only delivers state-of-the-art performance in labeling accuracy, both overall and at key locations, but also enables efficient inference and the generation of closed surface shapes. Addressing data scarcity in this field, we have also curated a comprehensive dataset to validate our approach. Data and code are available at \url{https://github.com/M3DV/pulmonary-tree-labeling}.

Dingyi Rong, Jiancheng Yang, Bingbing Ni et al.

Projection map (PM) from optical coherence tomography (OCT) B-scan is an important tool to diagnose retinal diseases, which typically requires retinal layer segmentation. In this study, we present a novel end-to-end framework to predict PMs from B-scans. Instead of segmenting retinal layers explicitly, we represent them implicitly as predicted coordinates. By pixel interpolation on uniformly sampled coordinates between retinal layers, the corresponding PMs could be easily obtained with pooling. Notably, all the operators are differentiable; therefore, this Differentiable Projection Module (DPM) enables end-to-end training with the ground truth of PMs rather than retinal layer segmentation. Our framework produces high-quality PMs, significantly outperforming baselines, including a vanilla CNN without DPM and an optimization-based DPM without a deep prior. Furthermore, the proposed DPM, as a novel neural representation of areas/volumes between curves/surfaces, could be of independent interest for geometric deep learning.

Hieu Le, Jingyi Xu, Nicolas Talabot et al.

Accurate 3D models of the human heart require not only correct outer surfaces but also realistic inner structures, such as the ventricles, atria, and myocardial layers. Approaches relying on implicit surfaces, such as signed distance functions (SDFs), are primarily designed for single watertight surfaces, making them ill-suited for multi-layered anatomical structures. They often produce gaps or overlaps in shared boundaries. Unsigned distance functions (UDFs) can model non-watertight geometries but are harder to optimize, while voxel-based methods are limited in resolution and struggle to produce smooth, anatomically realistic surfaces. We introduce a pairwise-constrained SDF approach that models the heart as a set of interdependent SDFs, each representing a distinct anatomical component. By enforcing proper contact between adjacent SDFs, we ensure that they form anatomically correct shared walls, preserving the internal structure of the heart and preventing overlaps, or unwanted gaps. Our method significantly improves inner structure accuracy over single-SDF, UDF-based, voxel-based, and segmentation-based reconstructions. We further demonstrate its generalizability by applying it to a vertebrae dataset, preventing unwanted contact between structures.

Hantao Zhang, Yuhe Liu, Jiancheng Yang et al.

Patient data from real-world clinical practice often suffers from data scarcity and long-tail imbalances, leading to biased outcomes or algorithmic unfairness. This study addresses these challenges by generating lesion-containing image-segmentation pairs from lesion-free images. Previous efforts in medical imaging synthesis have struggled with separating lesion information from background, resulting in low-quality backgrounds and limited control over the synthetic output. Inspired by diffusion-based image inpainting, we propose LeFusion, a lesion-focused diffusion model. By redesigning the diffusion learning objectives to focus on lesion areas, we simplify the learning process and improve control over the output while preserving high-fidelity backgrounds by integrating forward-diffused background contexts into the reverse diffusion process. Additionally, we tackle two major challenges in lesion texture synthesis: 1) multi-peak and 2) multi-class lesions. We introduce two effective strategies: histogram-based texture control and multi-channel decomposition, enabling the controlled generation of high-quality lesions in difficult scenarios. Furthermore, we incorporate lesion mask diffusion, allowing control over lesion size, location, and boundary, thus increasing lesion diversity. Validated on 3D cardiac lesion MRI and lung nodule CT datasets, LeFusion-generated data significantly improves the performance of state-of-the-art segmentation models, including nnUNet and SwinUNETR. Code and model are available at https://github.com/M3DV/LeFusion.

Kangxian Xie, Yufei Zhu, Kaiming Kuang et al.

High-quality 3D reconstruction of pulmonary segments plays a crucial role in segmentectomy and surgical treatment planning for lung cancer. Due to the resolution requirement of the target reconstruction, conventional deep learning-based methods often suffer from computational resource constraints or limited granularity. Conversely, implicit modeling is favored due to its computational efficiency and continuous representation at any resolution. We propose a neural implicit function-based method to learn a 3D surface to achieve anatomy-aware, precise pulmonary segment reconstruction, represented as a shape by deforming a learnable template. Additionally, we introduce two clinically relevant evaluation metrics to assess the reconstruction comprehensively. Further, due to the absence of publicly available shape datasets to benchmark reconstruction algorithms, we developed a shape dataset named Lung3D, including the 3D models of 800 labeled pulmonary segments and the corresponding airways, arteries, veins, and intersegmental veins. We demonstrate that the proposed approach outperforms existing methods, providing a new perspective for pulmonary segment reconstruction. Code and data will be available at https://github.com/M3DV/ImPulSe.

Sihan Shang, Jiancheng Yang, Zhenglong Sun et al.

In the realm of healthcare, the challenges of copyright protection and unauthorized third-party misuse are increasingly significant. Traditional methods for data copyright protection are applied prior to data distribution, implying that models trained on these data become uncontrollable. This paper introduces a novel approach, named DataCook, designed to safeguard the copyright of healthcare data during the deployment phase. DataCook operates by "cooking" the raw data before distribution, enabling the development of models that perform normally on this processed data. However, during the deployment phase, the original test data must be also "cooked" through DataCook to ensure normal model performance. This process grants copyright holders control over authorization during the deployment phase. The mechanism behind DataCook is by crafting anti-adversarial examples (AntiAdv), which are designed to enhance model confidence, as opposed to standard adversarial examples (Adv) that aim to confuse models. Similar to Adv, AntiAdv introduces imperceptible perturbations, ensuring that the data processed by DataCook remains easily understandable. We conducted extensive experiments on MedMNIST datasets, encompassing both 2D/3D data and the high-resolution variants. The outcomes indicate that DataCook effectively meets its objectives, preventing models trained on AntiAdv from analyzing unauthorized data effectively, without compromising the validity and accuracy of the data in legitimate scenarios. Code and data are available at https://github.com/MedMNIST/DataCook.

Jiancheng Yang, Rui Shi, Donglai Wei et al.

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/.

Jiancheng Yang, Yi He, Kaiming Kuang et al.

Modeling 3D context is essential for high-performance 3D medical image analysis. Although 2D networks benefit from large-scale 2D supervised pretraining, it is weak in capturing 3D context. 3D networks are strong in 3D context yet lack supervised pretraining. As an emerging technique, \emph{3D context fusion operator}, which enables conversion from 2D pretrained networks, leverages the advantages of both and has achieved great success. Existing 3D context fusion operators are designed to be spatially symmetric, i.e., performing identical operations on each 2D slice like convolutions. However, these operators are not truly equivariant to translation, especially when only a few 3D slices are used as inputs. In this paper, we propose a novel asymmetric 3D context fusion operator (A3D), which uses different weights to fuse 3D context from different 2D slices. Notably, A3D is NOT translation-equivariant while it significantly outperforms existing symmetric context fusion operators without introducing large computational overhead. We validate the effectiveness of the proposed method by extensive experiments on DeepLesion benchmark, a large-scale public dataset for universal lesion detection from computed tomography (CT). The proposed A3D consistently outperforms symmetric context fusion operators by considerable margins, and establishes a new \emph{state of the art} on DeepLesion. To facilitate open research, our code and model in PyTorch are available at https://github.com/M3DV/AlignShift.

Jiancheng Yang, Shixuan Gu, Donglai Wei et al.

Manual rib inspections in computed tomography (CT) scans are clinically critical but labor-intensive, as 24 ribs are typically elongated and oblique in 3D volumes. Automatic rib segmentation methods can speed up the process through rib measurement and visualization. However, prior arts mostly use in-house labeled datasets that are publicly unavailable and work on dense 3D volumes that are computationally inefficient. To address these issues, we develop a labeled rib segmentation benchmark, named \emph{RibSeg}, including 490 CT scans (11,719 individual ribs) from a public dataset. For ground truth generation, we used existing morphology-based algorithms and manually refined its results. Then, considering the sparsity of ribs in 3D volumes, we thresholded and sampled sparse voxels from the input and designed a point cloud-based baseline method for rib segmentation. The proposed method achieves state-of-the-art segmentation performance (Dice~$\approx95\%$) with significant efficiency ($10\sim40\times$ faster than prior arts). The RibSeg dataset, code, and model in PyTorch are available at https://github.com/M3DV/RibSeg.

Linguo Li, Minsi Wang, Bingbing Ni et al.

In this work, we propose a Cross-view Contrastive Learning framework for unsupervised 3D skeleton-based action Representation (CrosSCLR), by leveraging multi-view complementary supervision signal. CrosSCLR consists of both single-view contrastive learning (SkeletonCLR) and cross-view consistent knowledge mining (CVC-KM) modules, integrated in a collaborative learning manner. It is noted that CVC-KM works in such a way that high-confidence positive/negative samples and their distributions are exchanged among views according to their embedding similarity, ensuring cross-view consistency in terms of contrastive context, i.e., similar distributions. Extensive experiments show that CrosSCLR achieves remarkable action recognition results on NTU-60 and NTU-120 datasets under unsupervised settings, with observed higher-quality action representations. Our code is available at https://github.com/LinguoLi/CrosSCLR.

Jiancheng Yang, Rui Shi, Bingbing Ni

We present MedMNIST, a collection of 10 pre-processed medical open datasets. MedMNIST is standardized to perform classification tasks on lightweight 28x28 images, which requires no background knowledge. Covering the primary data modalities in medical image analysis, it is diverse on data scale (from 100 to 100,000) and tasks (binary/multi-class, ordinal regression and multi-label). MedMNIST could be used for educational purpose, rapid prototyping, multi-modal machine learning or AutoML in medical image analysis. Moreover, MedMNIST Classification Decathlon is designed to benchmark AutoML algorithms on all 10 datasets; We have compared several baseline methods, including open-source or commercial AutoML tools. The datasets, evaluation code and baseline methods for MedMNIST are publicly available at https://medmnist.github.io/.

Jiancheng Yang, Yangzhou Jiang, Xiaoyang Huang et al.

This paper addresses the challenging black-box adversarial attack problem, where only classification confidence of a victim model is available. Inspired by consistency of visual saliency between different vision models, a surrogate model is expected to improve the attack performance via transferability. By combining transferability-based and query-based black-box attack, we propose a surprisingly simple baseline approach (named SimBA++) using the surrogate model, which significantly outperforms several state-of-the-art methods. Moreover, to efficiently utilize the query feedback, we update the surrogate model in a novel learning scheme, named High-Order Gradient Approximation (HOGA). By constructing a high-order gradient computation graph, we update the surrogate model to approximate the victim model in both forward and backward pass. The SimBA++ and HOGA result in Learnable Black-Box Attack (LeBA), which surpasses previous state of the art by considerable margins: the proposed LeBA significantly reduces queries, while keeping higher attack success rates close to 100% in extensive ImageNet experiments, including attacking vision benchmarks and defensive models. Code is open source at https://github.com/TrustworthyDL/LeBA.

Jiancheng Yang, Rui Shi, Liang Jin et al. · harvard

Rib fractures are a common and potentially severe injury that can be challenging and labor-intensive to detect in CT scans. While there have been efforts to address this field, the lack of large-scale annotated datasets and evaluation benchmarks has hindered the development and validation of deep learning algorithms. To address this issue, the RibFrac Challenge was introduced, providing a benchmark dataset of over 5,000 rib fractures from 660 CT scans, with voxel-level instance mask annotations and diagnosis labels for four clinical categories (buckle, nondisplaced, displaced, or segmental). The challenge includes two tracks: a detection (instance segmentation) track evaluated by an FROC-style metric and a classification track evaluated by an F1-style metric. During the MICCAI 2020 challenge period, 243 results were evaluated, and seven teams were invited to participate in the challenge summary. The analysis revealed that several top rib fracture detection solutions achieved performance comparable or even better than human experts. Nevertheless, the current rib fracture classification solutions are hardly clinically applicable, which can be an interesting area in the future. As an active benchmark and research resource, the data and online evaluation of the RibFrac Challenge are available at the challenge website. As an independent contribution, we have also extended our previous internal baseline by incorporating recent advancements in large-scale pretrained networks and point-based rib segmentation techniques. The resulting FracNet+ demonstrates competitive performance in rib fracture detection, which lays a foundation for further research and development in AI-assisted rib fracture detection and diagnosis.

Yue Wu, Yibo Guo, Yulong Yan et al.

We envision the "virtual eye" as a next-generation, AI-powered platform that uses interconnected foundation models to simulate the eye's intricate structure and biological function across all scales. Advances in AI, imaging, and multiomics provide a fertile ground for constructing a universal, high-fidelity digital replica of the human eye. This perspective traces the evolution from early mechanistic and rule-based models to contemporary AI-driven approaches, integrating in a unified model with multimodal, multiscale, dynamic predictive capabilities and embedded feedback mechanisms. We propose a development roadmap emphasizing the roles of large-scale multimodal datasets, generative AI, foundation models, agent-based architectures, and interactive interfaces. Despite challenges in interpretability, ethics, data processing and evaluation, the virtual eye holds the potential to revolutionize personalized ophthalmic care and accelerate research into ocular health and disease.

Leslie Gu, Jason Ken Adhinarta, Mikhail Bessmeltsev et al. · harvard

Accurately segmenting 3D curvilinear structures in medical imaging remains challenging due to their complex geometry and the scarcity of diverse, large-scale datasets for algorithm development and evaluation. In this paper, we use dendritic spine segmentation as a case study and address these challenges by introducing a novel Frenet--Serret Frame-based Decomposition, which decomposes 3D curvilinear structures into a globally \( C^2 \) continuous curve that captures the overall shape, and a cylindrical primitive that encodes local geometric properties. This approach leverages Frenet--Serret Frames and arc length parameterization to preserve essential geometric features while reducing representational complexity, facilitating data-efficient learning, improved segmentation accuracy, and generalization on 3D curvilinear structures. To rigorously evaluate our method, we introduce two datasets: CurviSeg, a synthetic dataset for 3D curvilinear structure segmentation that validates our method's key properties, and DenSpineEM, a benchmark for dendritic spine segmentation, which comprises 4,476 manually annotated spines from 70 dendrites across three public electron microscopy datasets, covering multiple brain regions and species. Our experiments on DenSpineEM demonstrate exceptional cross-region and cross-species generalization: models trained on the mouse somatosensory cortex subset achieve 91.9\% Dice, maintaining strong performance in zero-shot segmentation on both mouse visual cortex (94.1\% Dice) and human frontal lobe (81.8\% Dice) subsets. Moreover, we test the generalizability of our method on the IntrA dataset, where it achieves 77.08\% Dice (5.29\% higher than prior arts) on intracranial aneurysm segmentation. These findings demonstrate the potential of our approach for accurately analyzing complex curvilinear structures across diverse medical imaging fields.

Udaranga Wickramasinghe, Patrick M. Jensen, Mian Shah et al.

There are many approaches to weakly-supervised training of networks to segment 2D images. By contrast, existing approaches to segmenting volumetric images rely on full-supervision of a subset of 2D slices of the 3D volume. We propose an approach to volume segmentation that is truly weakly-supervised in the sense that we only need to provide a sparse set of 3D points on the surface of target objects instead of detailed 2D masks. We use the 3D points to deform a 3D template so that it roughly matches the target object outlines and we introduce an architecture that exploits the supervision it provides to train a network to find accurate boundaries. We evaluate our approach on Computed Tomography (CT), Magnetic Resonance Imagery (MRI) and Electron Microscopy (EM) image datasets and show that it substantially reduces the required amount of effort.

Jiancheng Yang, Jiajun Chen, Kaiming Kuang et al.

Predicting clinical outcome is remarkably important but challenging. Research efforts have been paid on seeking significant biomarkers associated with the therapy response or/and patient survival. However, these biomarkers are generally costly and invasive, and possibly dissatifactory for novel therapy. On the other hand, multi-modal, heterogeneous, unaligned temporal data is continuously generated in clinical practice. This paper aims at a unified deep learning approach to predict patient prognosis and therapy response, with easily accessible data, e.g., radiographics, laboratory and clinical information. Prior arts focus on modeling single data modality, or ignore the temporal changes. Importantly, the clinical time series is asynchronous in practice, i.e., recorded with irregular intervals. In this study, we formalize the prognosis modeling as a multi-modal asynchronous time series classification task, and propose a MIA-Prognosis framework with Measurement, Intervention and Assessment (MIA) information to predict therapy response, where a Simple Temporal Attention (SimTA) module is developed to process the asynchronous time series. Experiments on synthetic dataset validate the superiory of SimTA over standard RNN-based approaches. Furthermore, we experiment the proposed method on an in-house, retrospective dataset of real-world non-small cell lung cancer patients under anti-PD-1 immunotherapy. The proposed method achieves promising performance on predicting the immunotherapy response. Notably, our predictive model could further stratify low-risk and high-risk patients in terms of long-term survival.

Jiancheng Yang, Mingze Gao, Kaiming Kuang et al.

Diagnosis of pulmonary lesions from computed tomography (CT) is important but challenging for clinical decision making in lung cancer related diseases. Deep learning has achieved great success in computer aided diagnosis (CADx) area for lung cancer, whereas it suffers from label ambiguity due to the difficulty in the radiological diagnosis. Considering that invasive pathological analysis serves as the clinical golden standard of lung cancer diagnosis, in this study, we solve the label ambiguity issue via a large-scale radio-pathomics dataset containing 5,134 radiological CT images with pathologically confirmed labels, including cancers (e.g., invasive/non-invasive adenocarcinoma, squamous carcinoma) and non-cancer diseases (e.g., tuberculosis, hamartoma). This retrospective dataset, named Pulmonary-RadPath, enables development and validation of accurate deep learning systems to predict invasive pathological labels with a non-invasive procedure, i.e., radiological CT scans. A three-level hierarchical classification system for pulmonary lesions is developed, which covers most diseases in cancer-related diagnosis. We explore several techniques for hierarchical classification on this dataset, and propose a Leaky Dense Hierarchy approach with proven effectiveness in experiments. Our study significantly outperforms prior arts in terms of data scales (6x larger), disease comprehensiveness and hierarchies. The promising results suggest the potentials to facilitate precision medicine.

Jiancheng Yang, Haoran Deng, Xiaoyang Huang et al.

Diagnosis and treatment of multiple pulmonary nodules are clinically important but challenging. Prior studies on nodule characterization use solitary-nodule approaches on multiple nodular patients, which ignores the relations between nodules. In this study, we propose a multiple instance learning (MIL) approach and empirically prove the benefit to learn the relations between multiple nodules. By treating the multiple nodules from a same patient as a whole, critical relational information between solitary-nodule voxels is extracted. To our knowledge, it is the first study to learn the relations between multiple pulmonary nodules. Inspired by recent advances in natural language processing (NLP) domain, we introduce a self-attention transformer equipped with 3D CNN, named {NoduleSAT}, to replace typical pooling-based aggregation in multiple instance learning. Extensive experiments on lung nodule false positive reduction on LUNA16 database, and malignancy classification on LIDC-IDRI database, validate the effectiveness of the proposed method.

Tiancheng Lin, Yuanfan Guo, Canqian Yang et al.

Early diagnosis of signet ring cell carcinoma dramatically improves the survival rate of patients. Due to lack of public dataset and expert-level annotations, automatic detection on signet ring cell (SRC) has not been thoroughly investigated. In MICCAI DigestPath2019 challenge, apart from foreground (SRC region)-background (normal tissue area) class imbalance, SRCs are partially annotated due to costly medical image annotation, which introduces extra label noise. To address the issues simultaneously, we propose Decoupled Gradient Harmonizing Mechanism (DGHM) and embed it into classification loss, denoted as DGHM-C loss. Specifically, besides positive (SRCs) and negative (normal tissues) examples, we further decouple noisy examples from clean examples and harmonize the corresponding gradient distributions in classification respectively. Without whistles and bells, we achieved the 2nd place in the challenge. Ablation studies and controlled label missing rate experiments demonstrate that DGHM-C loss can bring substantial improvement in partially annotated object detection.

Jiancheng Yang, Xiaoyang Huang, Yi He et al.

There have been considerable debates over 2D and 3D representation learning on 3D medical images. 2D approaches could benefit from large-scale 2D pretraining, whereas they are generally weak in capturing large 3D contexts. 3D approaches are natively strong in 3D contexts, however few publicly available 3D medical dataset is large and diverse enough for universal 3D pretraining. Even for hybrid (2D + 3D) approaches, the intrinsic disadvantages within the 2D / 3D parts still exist. In this study, we bridge the gap between 2D and 3D convolutions by reinventing the 2D convolutions. We propose ACS (axial-coronal-sagittal) convolutions to perform natively 3D representation learning, while utilizing the pretrained weights on 2D datasets. In ACS convolutions, 2D convolution kernels are split by channel into three parts, and convoluted separately on the three views (axial, coronal and sagittal) of 3D representations. Theoretically, ANY 2D CNN (ResNet, DenseNet, or DeepLab) is able to be converted into a 3D ACS CNN, with pretrained weight of a same parameter size. Extensive experiments on several medical benchmarks (including classification, segmentation and detection tasks) validate the consistent superiority of the pretrained ACS CNNs, over the 2D / 3D CNN counterparts with / without pretraining. Even without pretraining, the ACS convolution can be used as a plug-and-play replacement of standard 3D convolution, with smaller model size and less computation.

Jiancheng Yang, Rongyao Fang, Bingbing Ni et al.

Radiomics analysis has achieved great success in recent years. However, conventional Radiomics analysis suffers from insufficiently expressive hand-crafted features. Recently, emerging deep learning techniques, e.g., convolutional neural networks (CNNs), dominate recent research in Computer-Aided Diagnosis (CADx). Unfortunately, as black-box predictors, we argue that CNNs are "diagnosing" voxels (or pixels), rather than lesions; in other words, visual saliency from a trained CNN is not necessarily concentrated on the lesions. On the other hand, classification in clinical applications suffers from inherent ambiguities: radiologists may produce diverse diagnosis on challenging cases. To this end, we propose a controllable and explainable {\em Probabilistic Radiomics} framework, by combining the Radiomics analysis and probabilistic deep learning. In our framework, 3D CNN feature is extracted upon lesion region only, then encoded into lesion representation, by a controllable Non-local Shape Analysis Module (NSAM) based on self-attention. Inspired from variational auto-encoders (VAEs), an Ambiguity PriorNet is used to approximate the ambiguity distribution over human experts. The final diagnosis is obtained by combining the ambiguity prior sample and lesion representation, and the whole network named $DenseSharp^{+}$ is end-to-end trainable. We apply the proposed method on lung nodule diagnosis on LIDC-IDRI database to validate its effectiveness.

Xiaoyang Huang, Jiancheng Yang, Linguo Li et al.

Emergence of artificial intelligence techniques in biomedical applications urges the researchers to pay more attention on the uncertainty quantification (UQ) in machine-assisted medical decision making. For classification tasks, prior studies on UQ are difficult to compare with each other, due to the lack of a unified quantitative evaluation metric. Considering that well-performing UQ models ought to know when the classification models act incorrectly, we design a new evaluation metric, area under Confidence-Classification Characteristic curves (AUCCC), to quantitatively evaluate the performance of the UQ models. AUCCC is threshold-free, robust to perturbation, and insensitive to the classification performance. We evaluate several UQ methods (e.g., max softmax output) with AUCCC to validate its effectiveness. Furthermore, a simple scheme, named Uncertainty Distillation (UDist), is developed to boost the UQ performance, where a confidence model is distilling the confidence estimated by deep ensembles. The proposed method is easy to implement; it consistently outperforms strong baselines on natural and medical image datasets in our experiments.

Jiancheng Yang, Qiang Zhang, Bingbing Ni et al.

Geometric deep learning is increasingly important thanks to the popularity of 3D sensors. Inspired by the recent advances in NLP domain, the self-attention transformer is introduced to consume the point clouds. We develop Point Attention Transformers (PATs), using a parameter-efficient Group Shuffle Attention (GSA) to replace the costly Multi-Head Attention. We demonstrate its ability to process size-varying inputs, and prove its permutation equivariance. Besides, prior work uses heuristics dependence on the input data (e.g., Furthest Point Sampling) to hierarchically select subsets of input points. Thereby, we for the first time propose an end-to-end learnable and task-agnostic sampling operation, named Gumbel Subset Sampling (GSS), to select a representative subset of input points. Equipped with Gumbel-Softmax, it produces a "soft" continuous subset in training phase, and a "hard" discrete subset in test phase. By selecting representative subsets in a hierarchical fashion, the networks learn a stronger representation of the input sets with lower computation cost. Experiments on classification and segmentation benchmarks show the effectiveness and efficiency of our methods. Furthermore, we propose a novel application, to process event camera stream as point clouds, and achieve a state-of-the-art performance on DVS128 Gesture Dataset.

Jiancheng Yang, Qiang Zhang, Rongyao Fang et al.

Emergence of the utility of 3D point cloud data in safety-critical vision tasks (e.g., ADAS) urges researchers to pay more attention to the robustness of 3D representations and deep networks. To this end, we develop an attack and defense scheme, dedicated to 3D point cloud data, for preventing 3D point clouds from manipulated as well as pursuing noise-tolerable 3D representation. A set of novel 3D point cloud attack operations are proposed via pointwise gradient perturbation and adversarial point attachment / detachment. We then develop a flexible perturbation-measurement scheme for 3D point cloud data to detect potential attack data or noisy sensing data. Notably, the proposed defense methods are even effective to detect the adversarial point clouds generated by a proof-of-concept attack directly targeting the defense. Transferability of adversarial attacks between several point cloud networks is addressed, and we propose an momentum-enhanced pointwise gradient to improve the attack transferability. We further analyze the transferability from adversarial point clouds to grid CNNs and the inverse. Extensive experimental results on common point cloud benchmarks demonstrate the validity of the proposed 3D attack and defense framework.