Incremental Learning for Multi-organ Segmentation with Partially Labeled Datasets
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）
Pengbo Liu, Li Xiao, S. Kevin Zhou
发表信息：
Medical Image Computing and Computer Assisted Intervention--MICCAI 2022: 25th International Conference, Singapore, September 18--22, 2022, Proceedings, Part IV
There exists a large number of datasets for organ segmentation, which are partially annotated, and sequentially constructed. A typical dataset is constructed at a certain time by curating medical images and annotating the organs of interest. In other words, new datasets with annotations of new organ categories are built over time. To unleash the potential behind these partially labeled, sequentially-constructed datasets, we propose to learn a multi-organ segmentation model through incremental learning (IL). In each IL stage, we lose access to the previous annotations, whose knowledge is assumingly captured by the current model, and gain the access to a new dataset with annotations of new organ categories, from which we learn to update the organ segmentation model to include the new organs. We give the first attempt to conjecture that the different distribution is the key reason for 'catastrophic forgetting' that commonly exists in IL methods, and verify that IL has the natural adaptability to medical image scenarios. Extensive experiments on five open-sourced datasets are conducted to prove the effectiveness of our method and the conjecture mentioned above.
Cooperative Medianet Innovation Center, Shanghai Jiao Tong University（上海交通大学媒体网络协同创新中心）
Annotating multiple organs in 3D medical images is time-consuming and costly. Meanwhile, there exist many single-organ datasets with one specific organ annotated. This paper investigates how to learn a multi-organ segmentation model leveraging a set of binary-labeled datasets. A novel Multi-teacher Single-student Knowledge Distillation (MS-KD) framework is proposed, where the teacher models are pre-trained single-organ segmentation networks, and the student model is a multi-organ segmentation network. Considering that each teacher focuses on different organs, a region-based supervision method,…
National University of Defense Technology（国防科技大学）；University of Oulu（奥卢大学）；Nanyang Technological University（南洋理工大学）；Stanford University（斯坦福大学）
Few-Shot Class-Incremental Learning (FSCIL) aims at incrementally learning novel classes from a few labeled samples by avoiding the overfitting and catastrophic forgetting simultaneously. The current protocol of FSCIL is built by mimicking the general class-incremental learning setting, while it is not totally appropriate due to the different data configuration, i.e., novel classes are all in the limited data regime. In this paper, we rethink the configuration of FSCIL with the open-set hypothesis by reserving the possibility in the first session for incoming categories. To assign better perfo…
Deep Mutual Learning among Partially Labeled Datasets for Multi-Organ Segmentation
Digital Medical Research Center, School of Basic Medical Science, Fudan University（复旦大学基础医学院数字医学研究中心）；Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention（上海市医学影像计算与计算机辅助介入重点实验室）
National University of Defense Technology（国防科技大学）；University of Oulu（奥卢大学）
Given a model well-trained with a large-scale base dataset, Few-Shot Class-Incremental Learning (FSCIL) aims at incrementally learning novel classes from a few labeled samples by avoiding overfitting, without catastrophically forgetting all encountered classes previously. Currently, semi-supervised learning technique that harnesses freely-available unlabeled data to compensate for limited labeled data can boost the performance in numerous vision tasks, which heuristically can be applied to tackle issues in FSCIL, i.e., the Semi-supervised FSCIL (Semi-FSCIL). So far, very limited work focuses o…
The First Affiliated Hospital of Anhui Medical University（安徽医科大学第一附属医院）；Huawei Cloud Computing Technology Co. Ltd（华为云计算技术有限公司）；University of Science and Technology of China（中国科学技术大学）
There exists a large number of datasets for organ segmentation, which are partially annotated and sequentially constructed. A typical dataset is constructed at a certain time by curating medical images and annotating the organs of interest. In other words, new datasets with annotations of new organ categories are built over time. To unleash the potential behind these partially labeled, sequentially-constructed datasets, we propose to incrementally learn a multi-organ segmentation model. In each incremental learning (IL) stage, we lose the access to previous data and annotations, whose knowledg…
Computer Aided Medical Procedures, Technische Universität München（慕尼黑工业大学计算机辅助医疗程序）；Canon Medical Research Europe ltd.（佳能医疗研究欧洲有限公司）；Computer Aided Medical Procedures, Johns Hopkins University, Baltimore, USA（约翰斯·霍普金斯大学计算机辅助医疗程序）
Deep learning organ segmentation approaches require large amounts of annotated training data, which is limited in supply due to reasons of confidentiality and the time required for expert manual annotation. Therefore, being able to train models incrementally without having access to previously used data is desirable. A common form of sequential training is fine tuning (FT). In this setting, a model learns a new task effectively, but loses performance on previously learned tasks. The Learning without Forgetting (LwF) approach addresses this issue via replaying its own prediction for past tasks …
University of Melbourne（墨尔本大学）；Walter and Eliza Hall Institute for Medical Research（沃尔特与伊丽莎·霍尔医学研究所）
Non-parametric dimensionality reduction techniques, such as t-SNE and UMAP, are proficient in providing visualizations for datasets of fixed sizes. However, they cannot incrementally map and insert new data points into an already provided data visualization. We present Self-Organizing Nebulous Growths (SONG), a parametric nonlinear dimensionality reduction technique that supports incremental data visualization, i.e., incremental addition of new data while preserving the structure of the existing visualization. In addition, SONG is capable of handling new data increments, no matter whether they…
College of Computer Science, Nankai University（南开大学计算机学院）；MICC, University of Florence（佛罗伦萨大学MICC）；Huawei Kirin Solution（华为麒麟解决方案）
Most meta-learning approaches assume the existence of a very large set of labeled data available for episodic meta-learning of base knowledge. This contrasts with the more realistic continual learning paradigm in which data arrives incrementally in the form of tasks containing disjoint classes. In this paper we consider this problem of Incremental Meta-Learning (IML) in which classes are presented incrementally in discrete tasks. We propose an approach to IML, which we call Episodic Replay Distillation (ERD), that mixes classes from the current task with class exemplars from previous tasks whe…
Multi-Granularity Class Prototype Topology Distillation for Class-Incremental Source-Free Unsupervised Domain Adaptation
Hangzhou Dianzi University（杭州电子科技大学）；Macao Polytechnic University（澳门理工大学）；Beijing Institute of Technology（北京理工大学）；Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）
Peking University（北京大学）；South China University of Technology（华南理工大学）；National University of Singapore（新加坡国立大学）；MIT-IBM Watson AI Lab（麻省理工学院-IBM沃森人工智能实验室）
This paper studies a new, practical but challenging problem, called Class-Incremental Unsupervised Domain Adaptation (CI-UDA), where the labeled source domain contains all classes, but the classes in the unlabeled target domain increase sequentially. This problem is challenging due to two difficulties. First, source and target label sets are inconsistent at each time step, which makes it difficult to conduct accurate domain alignment. Second, previous target classes are unavailable in the current step, resulting in the forgetting of previous knowledge. To address this problem, we propose a nov…
We introduce a practical Domain Adaptation (DA) paradigm called Class-Incremental Domain Adaptation (CIDA). Existing DA methods tackle domain-shift but are unsuitable for learning novel target-domain classes. Meanwhile, class-incremental (CI) methods enable learning of new classes in absence of source training data but fail under a domain-shift without labeled supervision. In this work, we effectively identify the limitations of these approaches in the CIDA paradigm. Motivated by theoretical and empirical observations, we propose an effective method, inspired by prototypical networks, that ena…
Indian Institute of Technology Bombay（印度理工学院孟买分校）；Goethe University Frankfurt（法兰克福歌德大学）
We tackle the novel problem of incremental unsupervised domain adaptation (IDA) in this paper. We assume that a labeled source domain and different unlabeled target domains are incrementally observed with the constraint that data corresponding to the current domain is only available at a time. The goal is to preserve the accuracies for all the past domains while generalizing well for the current domain. The IDA setup suffers due to the abrupt differences among the domains and the unavailability of past data including the source domain. Inspired by the notion of generative feature replay, we pr…
École de technologie supérieure（高等技术学院）；Genetec Inc.（捷泰科公司）
Recent advances in unsupervised domain adaptation have significantly improved the recognition accuracy of CNNs by alleviating the domain shift between (labeled) source and (unlabeled) target data distributions. While the problem of single-target domain adaptation (STDA) for object detection has recently received much attention, multi-target domain adaptation (MTDA) remains largely unexplored, despite its practical relevance in several real-world applications, such as multi-camera video surveillance. Compared to the STDA problem that may involve large domain shifts between complex source and ta…
RPTU Kaiserslautern-Landau（莱茵兰-普法尔茨州凯泽斯劳滕-兰道应用技术大学）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；Heidelberg University（海德堡大学）；German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心（DFKI））
Morphological atlases are an important tool in organismal studies, and modern high-throughput Computed Tomography (CT) facilities can produce hundreds of full-body high-resolution volumetric images of organisms. However, creating an atlas from these volumes requires accurate organ segmentation. In the last decade, machine learning approaches have achieved incredible results in image segmentation tasks, but they require large amounts of annotated data for training. In this paper, we propose a self-training framework for multi-organ segmentation in tomographic images of Medaka fish. We utilize t…
Short internet video clips like vines present a significantly wild distribution compared to traditional video datasets. In this paper, we focus on the problem of unsupervised action classification in wild vines using traditional labeled datasets. To this end, we use a data augmentation based simple domain adaptation strategy. We utilise semantic word2vec space as a common subspace to embed video features from both, labeled source domain and unlablled target domain. Our method incrementally augments the labeled source with target samples and iteratively modifies the embedding function to bring …
Few-shot class incremental learning -- the problem of updating a trained classifier to discriminate among an expanded set of classes with limited labeled data -- is a key challenge for machine learning systems deployed in non-stationary environments. Existing approaches to the problem rely on complex model architectures and training procedures that are difficult to tune and re-use. In this paper, we present an extremely simple approach that enables the use of ordinary logistic regression classifiers for few-shot incremental learning. The key to this approach is a new family of subspace regular…
Continual Segment: Towards a Single, Unified and Accessible Continual Segmentation Model of 143 Whole-body Organs in CT Scans
DAMO Academy, Alibaba Group（阿里巴巴集团达摩院）；Hupan Lab（湖畔实验室）；University at Buffalo（布法罗大学）；Sichuan Cancer Hospital（四川省肿瘤医院）；The First Affiliated Hospital of Zhejiang University（浙江大学医学院附属第一医院）
University of Oulu（奥卢大学）；Nanyang Technological University（南洋理工大学）；ByteDance（字节跳动）；National University of Defense Technology（国防科技大学）
The goal of Few-Shot Continual Learning (FSCL) is to incrementally learn novel tasks with limited labeled samples and preserve previous capabilities simultaneously, while current FSCL methods are all for the class-incremental purpose. Moreover, the evaluation of FSCL solutions is only the cumulative performance of all encountered tasks, but there is no work on exploring the domain generalization ability. Domain generalization is a challenging yet practical task that aims to generalize beyond training domains. In this paper, we set up a Generalized FSCL (GFSCL) protocol involving both class- an…
The Chinese University of Hong Kong（香港中文大学）；University of Leicester（莱斯特大学）
Domain adaptation is crucial for transferring the knowledge from the source labeled CT dataset to the target unlabeled MR dataset in abdominal multi-organ segmentation. Meanwhile, it is highly desirable to avoid the high annotation cost related to the target dataset and protect the source dataset privacy. Therefore, we propose an effective source-free unsupervised domain adaptation method for cross-modality abdominal multi-organ segmentation without source dataset access. The proposed framework comprises two stages. In the first stage, the feature map statistics-guided model adaptation combine…
University of Balamand（巴拉曼大学）；Institut Mines Telecom（法国矿业电信学院）；Telecom ParisTech（巴黎高等电信学院）；Université Paris-Saclay（巴黎萨克雷大学）
Historical documents present many challenges for offline handwriting recognition systems, among them, the segmentation and labeling steps. Carefully annotated textlines are needed to train an HTR system. In some scenarios, transcripts are only available at the paragraph level with no text-line information. In this work, we demonstrate how to train an HTR system with few labeled data. Specifically, we train a deep convolutional recurrent neural network (CRNN) system on only 10% of manually labeled text-line data from a dataset and propose an incremental training procedure that covers the rest o…
Most existing approaches to train a unified multi-organ segmentation model from several single-organ datasets require simultaneously access multiple datasets during training. In the real scenarios, due to privacy and ethics concerns, the training data of the organs of interest may not be publicly available. To this end, we investigate a data-free incremental organ segmentation scenario and propose a novel incremental training framework to solve it. We use the pretrained model instead of its own training data for privacy protection. Specifically, given a pretrained $K$ organ segmentation model …
Armed Forces Yangju Hospital（杨州武装部队医院）；Seoul National University（首尔国立大学）
For more clinical applications of deep learning models for medical image segmentation, high demands on labeled data and computational resources must be addressed. This study proposes a coarse-to-fine framework with two teacher models and a student model that combines knowledge distillation and cross teaching, a consistency regularization based on pseudo-labels, for efficient semi-supervised learning. The proposed method is demonstrated on the abdominal multi-organ segmentation task in CT images under the MICCAI FLARE 2022 challenge, with mean Dice scores of 0.8429 and 0.8520 in the validation …
Over the past decade, Deep Convolutional Neural Networks (DCNNs) have shown remarkable performance in most computer vision tasks. These tasks traditionally use a fixed dataset, and the model, once trained, is deployed as is. Adding new information to such a model presents a challenge due to complex training issues, such as "catastrophic forgetting", and sensitivity to hyper-parameter tuning. However, in this modern world, data is constantly evolving, and our deep learning models are required to adapt to these changes. In this paper, we propose an adaptive hierarchical network structure compose…
Few-shot Class-incremental Learning for Cross-domain Disease Classification
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；University of Chinese Academy of Sciences（中国科学院大学）；Pengcheng Laboratory（鹏城实验室）
Organizing Background to Explore Latent Classes for Incremental Few-shot Semantic Segmentation
University of Chinese Academy of Sciences（中国科学院大学）；Nanjing University of Posts and Telecommunications（南京邮电大学）；Beijing University of Posts and Telecommunications（北京邮电大学）
ThreshGuide: Class-Aware Labeled-Guided Thresholding for Semi-Supervised 3D Abdominal Multi-Organ Segmentation
School of Intelligent Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences（中国科学院大学杭州高等研究院智能科学与技术学院）
GuidedNet: Semi-Supervised Multi-Organ Segmentation via Labeled Data Guide Unlabeled Data
Beihang University（北京航空航天大学）；University of Chinese Academy of Sciences（中国科学院大学）；Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences（中国科学院大学杭州高等研究院）；University of Science and Technology Beijing（北京科技大学）
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）；Alibaba DAMO Academy（阿里巴巴达摩院）；Zhejiang University（浙江大学）
Medical image benchmarks for the segmentation of organs and tumors suffer from the partially labeling issue due to its intensive cost of labor and expertise. Current mainstream approaches follow the practice of one network solving one task. With this pipeline, not only the performance is limited by the typically small dataset of a single task, but also the computation cost linearly increases with the number of tasks. To address this, we propose a Transformer based dynamic on-demand network (TransDoDNet) that learns to segment organs and tumors on multiple partially labeled datasets. Specifical…
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）
Due to the intensive cost of labor and expertise in annotating 3D medical images at a voxel level, most benchmark datasets are equipped with the annotations of only one type of organs and/or tumors, resulting in the so-called partially labeling issue. To address this, we propose a dynamic on-demand network (DoDNet) that learns to segment multiple organs and tumors on partially labeled datasets. DoDNet consists of a shared encoder-decoder architecture, a task encoding module, a controller for generating dynamic convolution filters, and a single but dynamic segmentation head. The information of …
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；Southeast University（东南大学）
Annotating multiple organs in medical images is both costly and time-consuming; therefore, existing multi-organ datasets with labels are often low in sample size and mostly partially labeled, that is, a dataset has a few organs labeled but not all organs. In this paper, we investigate how to learn a single multi-organ segmentation network from a union of such datasets. To this end, we propose two types of novel loss function, particularly designed for this scenario: (i) marginal loss and (ii) exclusion loss. Because the background label for a partially labeled image is, in fact, a `merged' lab…
Shortage of fully annotated datasets has been a limiting factor in developing deep learning based image segmentation algorithms and the problem becomes more pronounced in multi-organ segmentation. In this paper, we propose a unified training strategy that enables a novel multi-scale deep neural network to be trained on multiple partially labeled datasets for multi-organ segmentation. In addition, a new network architecture for multi-scale feature abstraction is proposed to integrate pyramid input and feature analysis into a U-shape pyramid structure. To bridge the semantic gap caused by direct…
Johns Hopkins University（约翰斯·霍普金斯大学）；University of Oxford（牛津大学）；The Johns Hopkins Medical Institute（约翰斯·霍普金斯医学研究所）；Google AI（谷歌AI）；ByteDance Inc.（字节跳动公司）；Facebook（脸书）；PAII Inc.（PAII公司）
Accurate multi-organ abdominal CT segmentation is essential to many clinical applications such as computer-aided intervention. As data annotation requires massive human labor from experienced radiologists, it is common that training data are partially labeled, e.g., pancreas datasets only have the pancreas labeled while leaving the rest marked as background. However, these background labels can be misleading in multi-organ segmentation since the "background" usually contains some other organs of interest. To address the background ambiguity in these partially-labeled datasets, we propose Prior…
Foundation Model-guided Iteratively Prompting and Pseudo-Labeling for Partially Labeled Medical Image Segmentation
Department of Biomedical Engineering, Columbia University（哥伦比亚大学生物医学工程系）；Department of Radiation Oncology, Columbia University Irving Medical Center（哥伦比亚大学欧文医学中心放射肿瘤科）；Data Science Institute, Columbia University（哥伦比亚大学数据科学研究所）；Herbert Irving Comprehensive Cancer Center, Columbia University（哥伦比亚大学赫伯特·欧文综合癌症中心）；Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院放射肿瘤科）
Few-shot instance segmentation methods are promising when labeled training data for novel classes is scarce. However, current approaches do not facilitate flexible addition of novel classes. They also require that examples of each class are provided at train and test time, which is memory intensive. In this paper, we address these limitations by presenting the first incremental approach to few-shot instance segmentation: iMTFA. We learn discriminative embeddings for object instances that are merged into class representatives. Storing embedding vectors rather than images effectively solves the …
Low-Rank Continual Pyramid Vision Transformer: Incrementally Segment Whole-Body Organs in CT with Light-Weighted Adaptation
DAMO Academy, Alibaba Group（阿里巴巴达摩院）；State University of New York at Stony Brook（纽约州立大学石溪分校）；Johns Hopkins University（约翰斯·霍普金斯大学）；The First Affiliated Hospital Zhejiang University（浙江大学医学院附属第一医院）
Label-efficient multi-organ segmentation with a diffusion model
College of Big Data and Internet, Shenzhen Technology University（深圳技术大学大数据与互联网学院）；School of Artificial Intelligence, Beijing University of Posts and Telecommunications（北京邮电大学人工智能学院）；Department of Radiology, Beijing Tiantan Hospital, Capital Medical University（首都医科大学附属北京天坛医院放射科）
Semantic segmentation is an import task in the medical field to identify the exact extent and orientation of significant structures like organs and pathology. Deep neural networks can perform this task well by leveraging the information from a large well-labeled data-set. This paper aims to present a method that mitigates the necessity of an extensive well-labeled data-set. This method also addresses semi-supervision by enabling segmentation based on bounding box annotations, avoiding the need for full pixel-level annotations. The network presented consists of a single U-Net based unbranched a…
Linköping University（林雪平大学）；The Swedish Police Authority（瑞典警察局）
Class-Incremental Learning is a challenging problem in machine learning that aims to extend previously trained neural networks with new classes. This is especially useful if the system is able to classify new objects despite the original training data being unavailable. While the semantic segmentation problem has received less attention than classification, it poses distinct problems and challenges since previous and future target classes can be unlabeled in the images of a single increment. In this case, the background, past and future classes are correlated and there exist a background-shift…
Xiamen University（厦门大学）；Chinese PLA General Hospital（中国人民解放军总医院）；Deepwise AI Laboratory（深度智耀人工智能实验室）
Standard segmentation of medical images based on full-supervised convolutional networks demands accurate dense annotations. Such learning framework is built on laborious manual annotation with restrict demands for expertise, leading to insufficient high-quality labels. To overcome such limitation and exploit massive weakly labeled data, we relaxed the rigid labeling requirement and developed a semi-supervised learning framework based on a teacher-student fashion for organ and lesion segmentation with partial dense-labeled supervision and supplementary loose bounding-box supervision which are e…
University of Guelph（圭尔夫大学）；Vector Institute（向量研究所）
In Digital Pathology (DP), labeled data is generally very scarce due to the requirement that medical experts provide annotations. We address this issue by learning transferable features from weakly labeled data, which are collected from various parts of the body and are organized by non-medical experts. In this paper, we show that features learned from such weakly labeled datasets are indeed transferable and allow us to achieve highly competitive patch classification results on the colorectal cancer (CRC) dataset [1] and the PatchCamelyon (PCam) dataset [2] while using an order of magnitude le…
Not Just Object, But State: Compositional Incremental Learning without Forgetting
International School of Information Science & Engineering, Dalian University of Technology（大连理工大学信息科学与工程国际学院）；MAIS&CRIPAC, Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）
Training data are critical in face recognition systems. However, labeling a large scale face data for a particular domain is very tedious. In this paper, we propose a method to automatically and incrementally construct datasets from massive weakly labeled data of the target domain which are readily available on the Internet under the help of a pretrained face model. More specifically, given a large scale weakly labeled dataset in which each face image is associated with a label, i.e. the name of an identity, we create a graph for each identity with edges linking matched faces verified by the e…
