OpenRaiser/Intern-Atlas huggingface dataset:
Personalizing Federated Medical Image Segmentation via Local Calibration
Venue: Conference ECCV 2022
Year: 2022

Medical image segmentation under federated learning (FL) is a promising direction by allowing multiple clinical sites to collaboratively learn a global model without centralizing datasets. However, using a single model to adapt to various data distributions from different sites is extremely challenging. Personalized FL tackles this issue by only utilizing partial model parameters shared from global server, while keeping the rest to adapt to its own data distribution in the local training of each site. However, most existing methods concentrate on the partial parameter splitting, while do not consider the \textit{inter-site in-consistencies} during the local training, which in fact can facilitate the knowledge communication over sites to benefit the model learning for improving the local accuracy. In this paper, we propose a personalized federated framework with \textbf{L}ocal \textbf{C}alibration (LC-Fed), to leverage the inter-site in-consistencies in both \textit{feature- and prediction- levels} to boost the segmentation. Concretely, as each local site has its alternative attention on the various features, we first design the contrastive site embedding coupled with channel selection operation to calibrate the encoded features. Moreover, we propose to exploit the knowledge of prediction-level in-consistency to guide the personalized modeling on the ambiguous regions, e.g., anatomical boundaries. It is achieved by computing a disagreement-aware map to calibrate the prediction. Effectiveness of our method has been verified on three medical image segmentation tasks with different modalities, where our method consistently shows superior performance to the state-of-the-art personalized FL methods. Code is available at https://github.com/jcwang123/FedLC.
One-Shot Medical Landmark Localization by Edge-Guided Transform and Noisy Landmark Refinement
Venue: Conference ECCV 2022
Year: 2022

As an important upstream task for many medical applications, supervised landmark localization still requires non-negligible annotation costs to achieve desirable performance. Besides, due to cumbersome collection procedures, the limited size of medical landmark datasets impacts the effectiveness of large-scale self-supervised pre-training methods. To address these challenges, we propose a two-stage framework for one-shot medical landmark localization, which first infers landmarks by unsupervised registration from the labeled exemplar to unlabeled targets, and then utilizes these noisy pseudo labels to train robust detectors. To handle the significant structure variations, we learn an end-to-end cascade of global alignment and local deformations, under the guidance of novel loss functions which incorporate edge information. In stage II, we explore self-consistency for selecting reliable pseudo labels and cross-consistency for semi-supervised learning. Our method achieves state-of-the-art performances on public datasets of different body parts, which demonstrates its general applicability.
Ultra-High-Resolution Unpaired Stain Transformation via Kernelized Instance Normalization
Venue: Conference ECCV 2022
Year: 2022

While hematoxylin and eosin (H&E) is a standard staining procedure, immunohistochemistry (IHC) staining further serves as a diagnostic and prognostic method. However, acquiring special staining results requires substantial costs. Hence, we proposed a strategy for ultra-high-resolution unpaired image-to-image translation: Kernelized Instance Normalization (KIN), which preserves local information and successfully achieves seamless stain transformation with constant GPU memory usage. Given a patch, corresponding position, and a kernel, KIN computes local statistics using convolution operation. In addition, KIN can be easily plugged into most currently developed frameworks without re-training. We demonstrate that KIN achieves state-of-the-art stain transformation by replacing instance normalization (IN) layers with KIN layers in three popular frameworks and testing on two histopathological datasets. Furthermore, we manifest the generalizability of KIN with high-resolution natural images. Finally, human evaluation and several objective metrics are used to compare the performance of different approaches. Overall, this is the first successful study for the ultra-high-resolution unpaired image-to-image translation with constant space complexity. Code is available at: https://github.com/Kaminyou/URUST
ConCL: Concept Contrastive Learning for Dense Prediction Pre-training in Pathology Images
Venue: Conference ECCV 2022
Year: 2022

Detectingandsegmentingobjectswithinwholeslideimagesis essential in computational pathology workflow. Self-supervised learning (SSL) is appealing to such annotation-heavy tasks. Despite the extensive benchmarks in natural images for dense tasks, such studies are, unfortunately, absent in current works for pathology. Our paper intends to narrow this gap. We first benchmark representative SSL methods for dense prediction tasks in pathology images. Then, we propose concept contrastive learning (ConCL), an SSL framework for dense pre-training. We explore how ConCL performs with concepts provided by different sources and end up with proposing a simple dependency-free concept generating method that does not rely on external segmentation algorithms or saliency detection models. Extensive experiments demonstrate the superiority of ConCL over previous state-of-the-art SSL methods across different settings. Along our exploration, we distll several important and intriguing components contributing to the success of dense pre-training for pathology images. We hope this work could provide useful data points and encourage the community to conduct ConCL pre-training for problems of interest. Code is available.
CryoAI: Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Real Cryo-EM Images
Venue: Conference ECCV 2022
Year: 2022

Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses and the 3D electron scattering potential of a biomolecule from millions of extremely noisy 2D images. Existing reconstruction algorithms, however, cannot easily keep pace with the rapidly growing size of cryo-EM datasets due to their high computational and memory cost. We introduce cryoAI, an ab initio reconstruction algorithm for homogeneous conformations that uses direct gradient-based optimization of particle poses and the electron scattering potential from single-particle cryo-EM data. CryoAI combines a learned encoder that predicts the poses of each particle image with a physics-based decoder to aggregate each particle image into an implicit representation of the scattering potential volume. This volume is stored in the Fourier domain for computational efficiency and leverages a modern coordinate network architecture for memory efficiency. Combined with a symmetrized loss function, this framework achieves results of a quality on par with state-of-the-art cryo-EM solvers for both simulated and experimental data, one order of magnitude faster for large datasets and with significantly lower memory requirements than existing methods.
UniMiSS: Universal Medical Self-Supervised Learning via Breaking Dimensionality Barrier
Venue: Conference ECCV 2022
Year: 2022

Self-supervised learning (SSL) opens up huge opportunities for medical image analysis that is well known for its lack of annotations. However, aggregating massive (unlabeled) 3D medical images like computerized tomography (CT) remains challenging due to its high imaging cost and privacy restrictions. In this paper, we advocate bringing a wealth of 2D images like chest X-rays as compensation for the lack of 3D data, aiming to build a universal medical self-supervised representation learning framework, called UniMiSS. The following problem is how to break the dimensionality barrier, \ie, making it possible to perform SSL with both 2D and 3D images? To achieve this, we design a pyramid U-like medical Transformer (MiT). It is composed of the switchable patch embedding (SPE) module and Transformers. The SPE module adaptively switches to either 2D or 3D patch embedding, depending on the input dimension. The embedded patches are converted into a sequence regardless of their original dimensions. The Transformers model the long-term dependencies in a sequence-to-sequence manner, thus enabling UniMiSS to learn representations from both 2D and 3D images. With the MiT as the backbone, we perform the UniMiSS in a self-distillation manner. We conduct expensive experiments on six 3D/2D medical image analysis tasks, including segmentation and classification. The results show that the proposed UniMiSS achieves promising performance on various downstream tasks, outperforming the ImageNet pre-training and other advanced SSL counterparts substantially. Code is available at \def\UrlFont{\rm\small\ttfamily} \url{https://github.com/YtongXie/UniMiSS-code}.
DLME: Deep Local-Flatness Manifold Embedding
Venue: Conference ECCV 2022
Year: 2022

Manifold learning (ML) aims to seek low-dimensional embedding from high-dimensional data. The problem is challenging on real-world datasets, especially with under-sampling data, and we find that previous methods perform poorly in this case. Generally, ML methods first transform input data into a low-dimensional embedding space to maintain the data's geometric structure and subsequently perform downstream tasks therein. The poor local connectivity of under-sampling data in the former step and inappropriate optimization objectives in the latter step leads to two problems: structural distortion and underconstrained embedding. This paper proposes a novel ML framework named Deep Local-flatness Manifold Embedding (DLME) to solve these problems. The proposed DLME constructs semantic manifolds by data augmentation and overcomes the structural distortion problem using a smoothness constrained based on a local flatness assumption about the manifold. To overcome the underconstrained embedding problem, we design a loss and theoretically demonstrate that it leads to a more suitable embedding based on the local flatness. Experiments on three types of datasets (toy, biological, and image) for various downstream tasks (classification, clustering, and visualization) show that our proposed DLME outperforms state-of-the-art ML and contrastive learning methods.
Semi-Supervised Keypoint Detector and Descriptor for Retinal Image Matching
Venue: Conference ECCV 2022
Year: 2022

For retinal image matching (RIM), we propose SuperRetina, the first end-to-end method with jointly trainable keypoint detector and descriptor. SuperRetina is trained in a novel semi-supervised manner. A small set of (nearly 100) images are incompletely labeled and used to supervise the network to detect keypoints on the vascular tree. To attack the incompleteness of manual labeling, we propose Progressive Keypoint Expansion to enrich the keypoint labels at each training epoch. By utilizing a keypoint-based improved triplet loss as its description loss, SuperRetina produces highly discriminative descriptors at full input image size. Extensive experiments on multiple real-world datasets justify the viability of SuperRetina. Even with manual labeling replaced by auto labeling and thus making the training process fully manual-annotation free, SuperRetina compares favorably against a number of strong baselines for two RIM tasks, i.e. image registration and identity verification. SuperRetina will be open source.
Graph Neural Network for Cell Tracking in Microscopy Videos
Venue: Conference ECCV 2022
Year: 2022

We present a novel graph neural network (GNN) approach for cell tracking in high-throughput microscopy videos. By modeling the entire time-lapse sequence as a direct graph where cell instances are represented by its nodes and their associations by its edges, we extract the entire set of cell trajectories by looking for the maximal paths in the graph. This is accomplished by several key contributions incorporated into an end-to-end deep learning framework. We exploit a deep metric learning algorithm to extract cell feature vectors that distinguish between instances of different biological cells and assemble same cell instances. We introduce a new GNN block type which enables a mutual update of node and edge feature vectors, thus facilitating the underlying message passing process. The message passing concept, whose extent is determined by the number of GNN blocks, is of fundamental importance as it enables the `flow' of information between nodes and edges much behind their neighbors in consecutive frames. Finally, we solve an edge classification problem and use the identified active edges to construct the cells' tracks and lineage trees. We demonstrate the strengths of the proposed cell tracking approach by applying it to 2D and 3D datasets of different cell types, imaging setups, and experimental conditions. We show that our framework outperforms current state-of-the-art methods on most of the evaluated datasets. The code is available at our repository: https://github.com/talbenha/cell-tracker-gnn.
RadioTransformer: A Cascaded Global-Focal Transformer for Visual Attention-Guided Disease Classification
Venue: Conference ECCV 2022
Year: 2022

In this work, we present RadioTransformer, a novel visual attention-driven transformer framework, that leverages radiologists' gaze patterns and models their visuo-cognitive behavior for disease diagnosis on chest radiographs. Domain experts, such as radiologists, rely on visual information for medical image interpretation. On the other hand, deep neural networks have demonstrated significant promise in similar tasks even where visual interpretation is challenging. Eye-gaze tracking has been used to capture the viewing behavior of domain experts, lending insights into the complexity of visual search. However, deep learning frameworks, even those that rely on attention mechanisms, do not leverage this rich domain information. RadioTransformer fills this critical gap by learning from radiologists' visual search patterns, encoded as 'human visual attention regions' in a cascaded global-focal transformer framework. The overall 'global' image characteristics and the more detailed 'local' features are captured by the proposed global and focal modules, respectively. We experimentally validate the efficacy of our student-teacher approach for 8 datasets involving different disease classification tasks where eye-gaze data is not available during the inference phase. Code: https://github.com/bmi-imaginelab/radiotransformer.
Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images
Venue: Conference ECCV 2022
Year: 2022

Multiple Instance Learning (MIL) methods have become increasingly popular for classifying giga-pixel sized Whole-Slide Images (WSIs) in digital pathology. Most MIL methods operate at a single WSI magnification, by processing all the tissue patches. Such a formulation induces high computational requirements, and constrains the contextualization of the WSI-level representation to a single scale. A few MIL methods extend to multiple scales, but are computationally more demanding. In this paper, inspired by the pathological diagnostic process, we propose ZoomMIL, a method that learns to perform multi-level zooming in an end-to-end manner. ZoomMIL builds WSI representations by aggregating tissue-context information from multiple magnifications. The proposed method outperforms the state-of-the-art MIL methods in WSI classification on two large datasets, while significantly reducing the computational demands with regard to Floating-Point Operations (FLOPs) and processing time by up to 40x.
Towards Grand Unification of Object Tracking
Venue: Conference ECCV 2022
Year: 2022

We present a unified method, termed Unicorn, that can simultaneously solve four tracking problems (SOT, MOT, VOS, MOTS) with a single network using the same model parameters. Due to the fragmented definitions of the object tracking problem itself, most existing trackers are developed to address a single or part of tasks and overspecialize on the characteristics of specific tasks. By contrast, Unicorn provides a unified solution, adopting the same input, backbone, embedding, and head across all tracking tasks. For the first time, we accomplish the great unification of the tracking network architecture and learning paradigm. Unicorn performs on-par or better than its task-specific counterparts in 8 tracking datasets, including LaSOT, TrackingNet, MOT17, BDD100K, DAVIS16-17, MOTS20, and BDD100K MOTS. We believe that Unicorn will serve as a solid step towards the general vision model. Code is available at https://github.com/MasterBin-IIAU/Unicorn.
ByteTrack: Multi-Object Tracking by Associating Every Detection Box
Venue: Conference ECCV 2022
Year: 2022

Multi-object tracking (MOT) aims at estimating bounding boxes and identities of objects in videos. Most methods obtain identities by associating detection boxes whose scores are higher than a threshold. The objects with low detection scores, e.g. occluded objects, are simply thrown away, which brings non-negligible true object missing and fragmented trajectories. To solve this problem, we present a simple, effective and generic association method, tracking by associating almost every detection box instead of only the high score ones. For the low score detection boxes, we utilize their similarities with tracklets to recover true objects and filter out the background detections. When applied to 9 different state-of-the-art trackers, our method achieves consistent improvement on IDF1 score ranging from 1 to 10 points. To put forwards the state-of-the-art performance of MOT, we design a simple and strong tracker, named ByteTrack. For the first time, we achieve 80.3 MOTA, 77.3 IDF1 and 63.1 HOTA on the test set of MOT17 with 30 FPS running speed on a single V100 GPU. ByteTrack also achieves state-of-the-art performance on MOT20, HiEve and BDD100K tracking benchmarks. The source code, pre-trained models with deploy versions and tutorials of applying to other trackers are released at https://github.com/ifzhang/ByteTrack.
Robust Multi-Object Tracking by Marginal Inference
Venue: Conference ECCV 2022
Year: 2022

Multi-object tracking in videos requires to solve a fundamental problem of one-to-one assignment between objects in adjacent frames. Most methods address the problem by first discarding impossible pairs whose feature distances are larger than a threshold, followed by linking objects using Hungarian algorithm to minimize the overall distance. However, we find that the distribution of the distances computed from Re-ID features may vary significantly for different videos. So there isn't a single optimal threshold which allows us to safely discard impossible pairs. To address the problem, we present an efficient approach to compute a marginal probability for each pair of objects in real time. The marginal probability can be regarded as a normalized distance which is significantly more stable than the original feature distance. As a result, we can use a single threshold for all videos. The approach is general and can be applied to the existing trackers to obtain about one point improvement in terms of IDF1 metric. It achieves competitive results on MOT17 and MOT20 benchmarks. In addition, the computed probability is more interpretable which facilitates subsequent post-processing operations.
PolarMOT: How Far Can Geometric Relations Take Us in 3D Multi-Object Tracking?
Venue: Conference ECCV 2022
Year: 2022

Most (3D) multi-object tracking methods rely on appearance-based cues for data association. By contrast, we investigate how far we can get by only encoding geometric relationships between objects in 3D space as cues for data-driven data association. We encode 3D detections as nodes in a graph, where spatial and temporal pairwise relations among objects are encoded via localized polar coordinates on graph edges. This representation makes our geometric relations invariant to global transformations and smooth trajectory changes, especially under non-holonomic motion. This allows our graph neural network to learn to effectively encode temporal and spatial interactions and fully leverage contextual and motion cues to obtain final scene interpretation by posing data association as edge classification. We establish a new state-of-the-art on nuScenes dataset and, more importantly, show that our method, PolarMOT, generalizes remarkably well across different locations (Boston, Singapore, Karlsruhe) and datasets (nuScenes and KITTI).
Particle Video Revisited: Tracking through Occlusions Using Point Trajectories
Venue: Conference ECCV 2022
Year: 2022

Tracking pixels in videos is typically studied as an optical flow estimation problem, where every pixel is described with a displacement vector that locates it in the next frame. Even though wider temporal context is freely available, prior efforts to take this into account have yielded only small gains over 2-frame methods. In this paper, we revisit Sand and Teller's "particle video" approach, and study pixel tracking as a long-range motion estimation problem, where every pixel is described with a trajectory that locates it in multiple future frames. We re-build this classic approach using components that drive the current state-of-the-art in flow and object tracking, such as dense cost maps, iterative optimization, and learned appearance updates. We train our models using long-range amodal point trajectories mined from existing optical flow data that we synthetically augment with multi-frame occlusions. We test our approach in trajectory estimation benchmarks and in keypoint label propagation tasks, and compare favorably against state-of-the-art optical flow and feature tracking methods.
Tracking Objects As Pixel-Wise Distributions
Venue: Conference ECCV 2022
Year: 2022

Multi-object tracking (MOT) requires detecting and associating objects through frames. Unlike tracking via detected bounding boxes or tracking objects as points, we propose tracking objects as pixel-wise distributions. We instantiate this idea on a transformer-based architecture, P3AFormer, with pixel-wise propagation, prediction, and association. P3AFormer propagates pixel-wise features guided by flow information to pass messages between frames. Furthermore, P3AFormer adopts a meta-architecture to produce multi-scale object feature maps. During inference, a pixel-wise association procedure is proposed to recover object connections through frames based on the pixel-wise prediction. P3AFormer yields 81.2\% in terms of MOTA on the MOT17 benchmark -- the first among all transformer networks to reach 80\% MOTA in literature. P3AFormer also outperforms state-of-the-arts on the MOT20 and KITTI benchmarks.