Deep learning empowers the mainstream medical image segmentation methods. Nevertheless current deep segmentation approaches are not capable of efficiently and effectively adapting and updating the trained models when new incremental segmentation classes (along with new training datasets or not) are required to be added. In real clinical environment, it can be preferred that segmentation models could be dynamically extended to segment new organs/tumors without the (re-)access to previous training datasets due to obstacles of patient privacy and data storage. This process can be viewed as a continual semantic segmentation (CSS) problem, being understudied for multi-organ segmentation. In this work, we propose a new architectural CSS learning framework to learn a single deep segmentation model for segmenting a total of 143 whole-body organs. Using the encoder/decoder network structure, we demonstrate that a continually-trained then frozen encoder coupled with incrementally-added decoders can extract and preserve sufficiently representative image features for new classes to be subsequently and validly segmented. To maintain a single network model complexity, we trim each decoder progressively using neural architecture search and teacher-student based knowledge distillation. To incorporate with both healthy and pathological organs appearing in different datasets, a novel anomaly-aware and confidence learning module is proposed to merge the overlapped organ predictions, originated from different decoders. Trained and validated on 3D CT scans of 2500+ patients from four datasets, our single network can segment total 143 whole-body organs with very high accuracy, closely reaching the upper bound performance level by training four separate segmentation models (i.e., one model per dataset/task).
As few-shot object detectors are often trained with abundant base samples and fine-tuned on few-shot novel examples,the learned models are usually biased to base classes and sensitive to the variance of novel examples. To address this issue, we propose a meta-learning framework with two novel feature aggregation schemes. More precisely, we first present a Class-Agnostic Aggregation (CAA) method, where the query and support features can be aggregated regardless of their categories. The interactions between different classes encourage class-agnostic representations and reduce confusion between base and novel classes. Based on the CAA, we then propose a Variational Feature Aggregation (VFA) method, which encodes support examples into class-level support features for robust feature aggregation. We use a variational autoencoder to estimate class distributions and sample variational features from distributions that are more robust to the variance of support examples. Besides, we decouple classification and regression tasks so that VFA is performed on the classification branch without affecting object localization. Extensive experiments on PASCAL VOC and COCO demonstrate that our method significantly outperforms a strong baseline (up to 16\%) and previous state-of-the-art methods (4\% in average). Code will be available at: \url{https://github.com/csuhan/VFA}
Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.
Automatic parsing of human anatomies at instance-level from 3D computed tomography (CT) scans is a prerequisite step for many clinical applications. The presence of pathologies, broken structures or limited field-of-view (FOV) all can make anatomy parsing algorithms vulnerable. In this work, we explore how to exploit and conduct the prosperous detection-then-segmentation paradigm in 3D medical data, and propose a steerable, robust, and efficient computing framework for detection, identification, and segmentation of anatomies in CT scans. Considering complicated shapes, sizes and orientations of anatomies, without lose of generality, we present the nine degrees-of-freedom (9-DoF) pose estimation solution in full 3D space using a novel single-stage, non-hierarchical forward representation. Our whole framework is executed in a steerable manner where any anatomy of interest can be directly retrieved to further boost the inference efficiency. We have validated the proposed method on three medical imaging parsing tasks of ribs, spine, and abdominal organs. For rib parsing, CT scans have been annotated at the rib instance-level for quantitative evaluation, similarly for spine vertebrae and abdominal organs. Extensive experiments on 9-DoF box detection and rib instance segmentation demonstrate the effectiveness of our framework (with the identification rate of 97.0% and the segmentation Dice score of 90.9%) in high efficiency, compared favorably against several strong baselines (e.g., CenterNet, FCOS, and nnU-Net). For spine identification and segmentation, our method achieves a new state-of-the-art result on the public CTSpine1K dataset. Last, we report highly competitive results in multi-organ segmentation at FLARE22 competition. Our annotations, code and models will be made publicly available at: https://github.com/alibaba-damo-academy/Med_Query.
Accurate and robust abdominal multi-organ segmentation from CT imaging of different modalities is a challenging task due to complex inter- and intra-organ shape and appearance variations among abdominal organs. In this paper, we propose a probabilistic multi-organ segmentation network with hierarchical spatial-wise feature modulation to capture flexible organ semantic variants and inject the learnt variants into different scales of feature maps for guiding segmentation. More specifically, we design an input decomposition module via a conditional variational auto-encoder to learn organ-specific distributions on the low dimensional latent space and model richer organ semantic variations that is conditioned on input images.Then by integrating these learned variations into the V-Net decoder hierarchically via spatial feature transformation, which has the ability to convert the variations into conditional Affine transformation parameters for spatial-wise feature maps modulating and guiding the fine-scale segmentation. The proposed method is trained on the publicly available AbdomenCT-1K dataset and evaluated on two other open datasets, i.e., 100 challenging/pathological testing patient cases from AbdomenCT-1K fully-supervised abdominal organ segmentation benchmark and 90 cases from TCIA+&BTCV dataset. Highly competitive or superior quantitative segmentation results have been achieved using these datasets for four abdominal organs of liver, kidney, spleen and pancreas with reported Dice scores improved by 7.3% for kidneys and 9.7% for pancreas, while being ~7 times faster than two strong baseline segmentation methods(nnUNet and CoTr).
Human pose estimation (HPE) usually requires large-scale training data to reach high performance. However, it is rather time-consuming to collect high-quality and fine-grained annotations for human body. To alleviate this issue, we revisit HPE and propose a location-free framework without supervision of keypoint locations. We reformulate the regression-based HPE from the perspective of classification. Inspired by the CAM-based weakly-supervised object localization, we observe that the coarse keypoint locations can be acquired through the part-aware CAMs but unsatisfactory due to the gap between the fine-grained HPE and the object-level localization. To this end, we propose a customized transformer framework to mine the fine-grained representation of human context, equipped with the structural relation to capture subtle differences among keypoints. Concretely, we design a Multi-scale Spatial-guided Context Encoder to fully capture the global human context while focusing on the part-aware regions and a Relation-encoded Pose Prototype Generation module to encode the structural relations. All these works together for strengthening the weak supervision from image-level category labels on locations. Our model achieves competitive performance on three datasets when only supervised at a category-level and importantly, it can achieve comparable results with fully-supervised methods with only 25\% location labels on MS-COCO and MPII.
Object detection under imperfect data receives great attention recently. Weakly supervised object detection (WSOD) suffers from severe localization issues due to the lack of instance-level annotation, while semi-supervised object detection (SSOD) remains challenging led by the inter-image discrepancy between labeled and unlabeled data. In this study, we propose the Single Instance annotated Object Detection (SIOD), requiring only one instance annotation for each existing category in an image. Degraded from inter-task (WSOD) or inter-image (SSOD) discrepancies to the intra-image discrepancy, SIOD provides more reliable and rich prior knowledge for mining the rest of unlabeled instances and trades off the annotation cost and performance. Under the SIOD setting, we propose a simple yet effective framework, termed Dual-Mining (DMiner), which consists of a Similarity-based Pseudo Label Generating module (SPLG) and a Pixel-level Group Contrastive Learning module (PGCL). SPLG firstly mines latent instances from feature representation space to alleviate the annotation missing problem. To avoid being misled by inaccurate pseudo labels, we propose PGCL to boost the tolerance to false pseudo labels. Extensive experiments on MS COCO verify the feasibility of the SIOD setting and the superiority of the proposed method, which obtains consistent and significant improvements compared to baseline methods and achieves comparable results with fully supervised object detection (FSOD) methods with only 40% instances annotated.
Modern object detectors have achieved impressive progress under the close-set setup. However, open-set object detection (OSOD) remains challenging since objects of unknown categories are often misclassified to existing known classes. In this work, we propose to identify unknown objects by separating high/low-density regions in the latent space, based on the consensus that unknown objects are usually distributed in low-density latent regions. As traditional threshold-based methods only maintain limited low-density regions, which cannot cover all unknown objects, we present a novel Open-set Detector (OpenDet) with expanded low-density regions. To this aim, we equip OpenDet with two learners, Contrastive Feature Learner (CFL) and Unknown Probability Learner (UPL). CFL performs instance-level contrastive learning to encourage compact features of known classes, leaving more low-density regions for unknown classes; UPL optimizes unknown probability based on the uncertainty of predictions, which further divides more low-density regions around the cluster of known classes. Thus, unknown objects in low-density regions can be easily identified with the learned unknown probability. Extensive experiments demonstrate that our method can significantly improve the OSOD performance, e.g., OpenDet reduces the Absolute Open-Set Errors by 25%-35% on six OSOD benchmarks. Code is available at: https://github.com/csuhan/opendet2.
Semi-supervised object detection (SSOD) has achieved substantial progress in recent years. However, it is observed that the performances of self-labeling SSOD methods remain limited. Based on our experimental analysis, we reveal that the reason behind such phenomenon lies in the mutual error amplification between the pseudo labels and the trained detector. In this study, we propose a Cross Teaching (CT) method, aiming to mitigate the mutual error amplification by introducing a rectification mechanism of pseudo labels. CT simultaneously trains multiple detectors with an identical structure but different parameter initialization. In contrast to existing mutual teaching methods that directly treat predictions from other detectors as pseudo labels, we propose the Label Rectification Module (LRM), where the bounding boxes predicted by one detector are rectified by using the corresponding boxes predicted by all other detectors with higher confidence scores. In this way, CT can enhance the pseudo label quality compared with self-labeling and existing mutual teaching methods, and reasonably mitigate the mutual error amplification. Over two popular detector structures, i.e., SSD300 and Faster-RCNN-FPN, the proposed CT method obtains consistent improvements and outperforms the state-of-the-art SSOD methods by 2.2% absolute mAP improvements on the Pascal VOC and MS-COCO benchmarks. The code is available at github.com/machengcheng2016/CrossTeaching-SSOD.