Precision medicine in the quantitative management of chronic diseases and oncology would be greatly improved if the Computed Tomography (CT) scan of any patient could be segmented, parsed and analyzed in a precise and detailed way. However, there is no such fully annotated CT dataset with all anatomies delineated for training because of the exceptionally high manual cost, the need for specialized clinical expertise, and the time required to finish the task. To this end, we proposed a novel continual learning-driven CT model that can segment complete anatomies presented using dozens of previously partially labeled datasets, dynamically expanding its capacity to segment new ones without compromising previously learned organ knowledge. Existing multi-dataset approaches are not able to dynamically segment new anatomies without catastrophic forgetting and would encounter optimization difficulty or infeasibility when segmenting hundreds of anatomies across the whole range of body regions. Our single unified CT segmentation model, CL-Net, can highly accurately segment a clinically comprehensive set of 235 fine-grained whole-body anatomies. Composed of a universal encoder, multiple optimized and pruned decoders, CL-Net is developed using 13,952 CT scans from 20 public and 16 private high-quality partially labeled CT datasets of various vendors, different contrast phases, and pathologies. Extensive evaluation demonstrates that CL-Net consistently outperforms the upper limit of an ensemble of 36 specialist nnUNets trained per dataset with the complexity of 5% model size and significantly surpasses the segmentation accuracy of recent leading Segment Anything-style medical image foundation models by large margins. Our continual learning-driven CL-Net model would lay a solid foundation to facilitate many downstream tasks of oncology and chronic diseases using the most widely adopted CT imaging.
Machine Learning models thrive on vast datasets, continuously adapting to provide accurate predictions and recommendations. However, in an era dominated by privacy concerns, Machine Unlearning emerges as a transformative approach, enabling the selective removal of data from trained models. This paper examines methods such as Naive Retraining and Exact Unlearning via the SISA framework, evaluating their Computational Costs, Consistency, and feasibility using the $\texttt{HSpam14}$ dataset. We explore the potential of integrating unlearning principles into Positive Unlabeled (PU) Learning to address challenges posed by partially labeled datasets. Our findings highlight the promise of unlearning frameworks like $\textit{DaRE}$ for ensuring privacy compliance while maintaining model performance, albeit with significant computational trade-offs. This study underscores the importance of Machine Unlearning in achieving ethical AI and fostering trust in data-driven systems.
In medical imaging, developing generalized segmentation models that can handle multiple organs and lesions is crucial. However, the scarcity of fully annotated datasets and strict privacy regulations present significant barriers to data sharing. Federated Learning (FL) allows decentralized model training, but existing FL methods often struggle with partial labeling, leading to model divergence and catastrophic forgetting. We propose ConDistFL, a novel FL framework incorporating conditional distillation to address these challenges. ConDistFL enables effective learning from partially labeled datasets, significantly improving segmentation accuracy across distributed and non-uniform datasets. In addition to its superior segmentation performance, ConDistFL maintains computational and communication efficiency, ensuring its scalability for real-world applications. Furthermore, ConDistFL demonstrates remarkable generalizability, significantly outperforming existing FL methods in out-of-federation tests, even adapting to unseen contrast phases (e.g., non-contrast CT images) in our experiments. Extensive evaluations on 3D CT and 2D chest X-ray datasets show that ConDistFL is an efficient, adaptable solution for collaborative medical image segmentation in privacy-constrained settings.
This research addresses the need for high-definition (HD) maps for autonomous vehicles (AVs), focusing on road lane information derived from aerial imagery. While Earth observation data offers valuable resources for map creation, specialized models for road lane extraction are still underdeveloped in remote sensing. In this study, we perform an extensive comparison of twelve foundational deep learning-based semantic segmentation models for road lane marking extraction from high-definition remote sensing images, assessing their performance under transfer learning with partially labeled datasets. These models were fine-tuned on the partially labeled Waterloo Urban Scene dataset, and pre-trained on the SkyScapes dataset, simulating a likely scenario of real-life model deployment under partial labeling. We observed and assessed the fine-tuning performance and overall performance. Models showed significant performance improvements after fine-tuning, with mean IoU scores ranging from 33.56% to 76.11%, and recall ranging from 66.0% to 98.96%. Transformer-based models outperformed convolutional neural networks, emphasizing the importance of model pre-training and fine-tuning in enhancing HD map development for AV navigation.
Partially-supervised multi-organ medical image segmentation aims to develop a unified semantic segmentation model by utilizing multiple partially-labeled datasets, with each dataset providing labels for a single class of organs. However, the limited availability of labeled foreground organs and the absence of supervision to distinguish unlabeled foreground organs from the background pose a significant challenge, which leads to a distribution mismatch between labeled and unlabeled pixels. Although existing pseudo-labeling methods can be employed to learn from both labeled and unlabeled pixels, they are prone to performance degradation in this task, as they rely on the assumption that labeled and unlabeled pixels have the same distribution. In this paper, to address the problem of distribution mismatch, we propose a labeled-to-unlabeled distribution alignment (LTUDA) framework that aligns feature distributions and enhances discriminative capability. Specifically, we introduce a cross-set data augmentation strategy, which performs region-level mixing between labeled and unlabeled organs to reduce distribution discrepancy and enrich the training set. Besides, we propose a prototype-based distribution alignment method that implicitly reduces intra-class variation and increases the separation between the unlabeled foreground and background. This can be achieved by encouraging consistency between the outputs of two prototype classifiers and a linear classifier. Extensive experimental results on the AbdomenCT-1K dataset and a union of four benchmark datasets (including LiTS, MSD-Spleen, KiTS, and NIH82) demonstrate that our method outperforms the state-of-the-art partially-supervised methods by a considerable margin, and even surpasses the fully-supervised methods. The source code is publicly available at https://github.com/xjiangmed/LTUDA.
Partial-Label Learning (PLL) is a typical problem of weakly supervised learning, where each training instance is annotated with a set of candidate labels. Self-training PLL models achieve state-of-the-art performance but suffer from error accumulation problem caused by mistakenly disambiguated instances. Although co-training can alleviate this issue by training two networks simultaneously and allowing them to interact with each other, most existing co-training methods train two structurally identical networks with the same task, i.e., are symmetric, rendering it insufficient for them to correct each other due to their similar limitations. Therefore, in this paper, we propose an asymmetric dual-task co-training PLL model called AsyCo, which forces its two networks, i.e., a disambiguation network and an auxiliary network, to learn from different views explicitly by optimizing distinct tasks. Specifically, the disambiguation network is trained with self-training PLL task to learn label confidence, while the auxiliary network is trained in a supervised learning paradigm to learn from the noisy pairwise similarity labels that are constructed according to the learned label confidence. Finally, the error accumulation problem is mitigated via information distillation and confidence refinement. Extensive experiments on both uniform and instance-dependent partially labeled datasets demonstrate the effectiveness of AsyCo. The code is available at https://github.com/libeibeics/AsyCo.
The task of labeling multiple organs for segmentation is a complex and time-consuming process, resulting in a scarcity of comprehensively labeled multi-organ datasets while the emergence of numerous partially labeled datasets. Current methods are inadequate in effectively utilizing the supervised information available from these datasets, thereby impeding the progress in improving the segmentation accuracy. This paper proposes a two-stage multi-organ segmentation method based on mutual learning, aiming to improve multi-organ segmentation performance by complementing information among partially labeled datasets. In the first stage, each partial-organ segmentation model utilizes the non-overlapping organ labels from different datasets and the distinct organ features extracted by different models, introducing additional mutual difference learning to generate higher quality pseudo labels for unlabeled organs. In the second stage, each full-organ segmentation model is supervised by fully labeled datasets with pseudo labels and leverages true labels from other datasets, while dynamically sharing accurate features across different models, introducing additional mutual similarity learning to enhance multi-organ segmentation performance. Extensive experiments were conducted on nine datasets that included the head and neck, chest, abdomen, and pelvis. The results indicate that our method has achieved SOTA performance in segmentation tasks that rely on partial labels, and the ablation studies have thoroughly confirmed the efficacy of the mutual learning mechanism.
Federated learning is a renowned technique for utilizing decentralized data while preserving privacy. However, real-world applications often face challenges like partially labeled datasets, where only a few locations have certain expert annotations, leaving large portions of unlabeled data unused. Leveraging these could enhance transformer architectures ability in regimes with small and diversely annotated sets. We conduct the largest federated cardiac CT analysis to date (n=8,104) in a real-world setting across eight hospitals. Our two-step semi-supervised strategy distills knowledge from task-specific CNNs into a transformer. First, CNNs predict on unlabeled data per label type and then the transformer learns from these predictions with label-specific heads. This improves predictive accuracy and enables simultaneous learning of all partial labels across the federation, and outperforms UNet-based models in generalizability on downstream tasks. Code and model weights are made openly available for leveraging future cardiac CT analysis.
Fluorescence labeling is the standard approach to reveal cellular structures and other subcellular constituents for microscopy images. However, this invasive procedure may perturb or even kill the cells and the procedure itself is highly time-consuming and complex. Recently, in silico labeling has emerged as a promising alternative, aiming to use machine learning models to directly predict the fluorescently labeled images from label-free microscopy. In this paper, we propose a deep learning-based in silico labeling method for the Light My Cells challenge. Built upon pix2pix, our proposed method can be trained using the partially labeled datasets with an adaptive loss. Moreover, we explore the effectiveness of several training strategies to handle different input modalities, such as training them together or separately. The results show that our method achieves promising performance for in silico labeling. Our code is available at https://github.com/MedICL-VU/LightMyCells.
Multi-label image classification datasets are often partially labeled where many labels are missing, posing a significant challenge to training accurate deep classifiers. However, the powerful Mixup sample-mixing data augmentation cannot be well utilized to address this challenge, as it cannot perform linear interpolation on the unknown labels to construct augmented samples. In this paper, we propose LogicMix, a Mixup variant designed for such partially labeled datasets. LogicMix mixes the sample labels by logical OR so that the unknown labels can be correctly mixed by utilizing OR's logical equivalences, including the domination and identity laws. Unlike Mixup, which mixes exactly two samples, LogicMix can mix multiple ($\geq2$) partially labeled samples, constructing visually more confused augmented samples to regularize training. LogicMix is more general and effective than other compared Mixup variants in the experiments on various partially labeled dataset scenarios. Moreover, it is plug-and-play and only requires minimal computation, hence it can be easily inserted into existing frameworks to collaborate with other methods to improve model performance with a negligible impact on training time, as demonstrated through extensive experiments. In particular, through the collaboration of LogicMix, RandAugment, Curriculum Labeling, and Category-wise Fine-Tuning, we attain state-of-the-art performance on MS-COCO, VG-200, and Pascal VOC 2007 benchmarking datasets. The remarkable generality, effectiveness, collaboration, and simplicity suggest that LogicMix promises to be a popular and vital data augmentation method.
Generalized Continual Category Discovery (GCCD) tackles learning from sequentially arriving, partially labeled datasets while uncovering new categories. Traditional methods depend on feature distillation to prevent forgetting the old knowledge. However, this strategy restricts the model's ability to adapt and effectively distinguish new categories. To address this, we introduce a novel technique integrating a learnable projector with feature distillation, thus enhancing model adaptability without sacrificing past knowledge. The resulting distribution shift of the previously learned categories is mitigated with the auxiliary category adaptation network. We demonstrate that while each component offers modest benefits individually, their combination - dubbed CAMP (Category Adaptation Meets Projected distillation) - significantly improves the balance between learning new information and retaining old. CAMP exhibits superior performance across several GCCD and Class Incremental Learning scenarios. The code is available at https://github.com/grypesc/CAMP.
In modern large-scale observational studies, data collection constraints often result in partially labeled datasets, posing challenges for reliable causal inference, especially due to potential labeling bias and relatively small size of the labeled data. This paper introduces a decaying missing-at-random (decaying MAR) framework and associated approaches for doubly robust causal inference on treatment effects in such semi-supervised (SS) settings. This simultaneously addresses selection bias in the labeling mechanism and the extreme imbalance between labeled and unlabeled groups, bridging the gap between the standard SS and missing data literatures, while throughout allowing for confounded treatment assignment and high-dimensional confounders under appropriate sparsity conditions. To ensure robust causal conclusions, we propose a bias-reduced SS (BRSS) estimator for the average treatment effect, a type of 'model doubly robust' estimator appropriate for such settings, establishing asymptotic normality at the appropriate rate under decaying labeling propensity scores, provided that at least one nuisance model is correctly specified. Our approach also relaxes sparsity conditions beyond those required in existing methods, including standard supervised approaches. Recognizing the asymmetry between labeling and treatment mechanisms, we further introduce a de-coupled BRSS (DC-BRSS) estimator, which integrates inverse probability weighting (IPW) with bias-reducing techniques in nuisance estimation. This refinement further weakens model specification and sparsity requirements. Numerical experiments confirm the effectiveness and adaptability of our estimators in addressing labeling bias and model misspecification.
Deep learning models have demonstrated remarkable success in multi-organ segmentation but typically require large-scale datasets with all organs of interest annotated. However, medical image datasets are often low in sample size and only partially labeled, i.e., only a subset of organs are annotated. Therefore, it is crucial to investigate how to learn a unified model on the available partially labeled datasets to leverage their synergistic potential. In this paper, we systematically investigate the partial-label segmentation problem with theoretical and empirical analyses on the prior techniques. We revisit the problem from a perspective of partial label supervision signals and identify two signals derived from ground truth and one from pseudo labels. We propose a novel two-stage framework termed COSST, which effectively and efficiently integrates comprehensive supervision signals with self-training. Concretely, we first train an initial unified model using two ground truth-based signals and then iteratively incorporate the pseudo label signal to the initial model using self-training. To mitigate performance degradation caused by unreliable pseudo labels, we assess the reliability of pseudo labels via outlier detection in latent space and exclude the most unreliable pseudo labels from each self-training iteration. Extensive experiments are conducted on one public and three private partial-label segmentation tasks over 12 CT datasets. Experimental results show that our proposed COSST achieves significant improvement over the baseline method, i.e., individual networks trained on each partially labeled dataset. Compared to the state-of-the-art partial-label segmentation methods, COSST demonstrates consistent superior performance on various segmentation tasks and with different training data sizes.
Precise delineation of multiple organs or abnormal regions in the human body from medical images plays an essential role in computer-aided diagnosis, surgical simulation, image-guided interventions, and especially in radiotherapy treatment planning. Thus, it is of great significance to explore automatic segmentation approaches, among which deep learning-based approaches have evolved rapidly and witnessed remarkable progress in multi-organ segmentation. However, obtaining an appropriately sized and fine-grained annotated dataset of multiple organs is extremely hard and expensive. Such scarce annotation limits the development of high-performance multi-organ segmentation models but promotes many annotation-efficient learning paradigms. Among these, studies on transfer learning leveraging external datasets, semi-supervised learning using unannotated datasets and partially-supervised learning integrating partially-labeled datasets have led the dominant way to break such dilemma in multi-organ segmentation. We first review the traditional fully supervised method, then present a comprehensive and systematic elaboration of the 3 abovementioned learning paradigms in the context of multi-organ segmentation from both technical and methodological perspectives, and finally summarize their challenges and future trends.
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. Specifically, TransDoDNet has a hybrid backbone that is composed of the convolutional neural network and Transformer. A dynamic head enables the network to accomplish multiple segmentation tasks flexibly. Unlike existing approaches that fix kernels after training, the kernels in the dynamic head are generated adaptively by the Transformer, which employs the self-attention mechanism to model long-range organ-wise dependencies and decodes the organ embedding that can represent each organ. We create a large-scale partially labeled Multi-Organ and Tumor Segmentation benchmark, termed MOTS, and demonstrate the superior performance of our TransDoDNet over other competitors on seven organ and tumor segmentation tasks. This study also provides a general 3D medical image segmentation model, which has been pre-trained on the large-scale MOTS benchmark and has demonstrated advanced performance over BYOL, the current predominant self-supervised learning method. Code will be available at \url{https://git.io/DoDNet}.
Multi-task learning promises better model generalization on a target task by jointly optimizing it with an auxiliary task. However, the current practice requires additional labeling efforts for the auxiliary task, while not guaranteeing better model performance. In this paper, we find that jointly training a dense prediction (target) task with a self-supervised (auxiliary) task can consistently improve the performance of the target task, while eliminating the need for labeling auxiliary tasks. We refer to this joint training as Composite Learning (CompL). Experiments of CompL on monocular depth estimation, semantic segmentation, and boundary detection show consistent performance improvements in fully and partially labeled datasets. Further analysis on depth estimation reveals that joint training with self-supervision outperforms most labeled auxiliary tasks. We also find that CompL can improve model robustness when the models are evaluated in new domains. These results demonstrate the benefits of self-supervision as an auxiliary task, and establish the design of novel task-specific self-supervised methods as a new axis of investigation for future multi-task learning research.
Semi-supervised Anomaly Detection (AD) is a kind of data mining task which aims at learning features from partially-labeled datasets to help detect outliers. In this paper, we classify existing semi-supervised AD methods into two categories: unsupervised-based and supervised-based, and point out that most of them suffer from insufficient exploitation of labeled data and under-exploration of unlabeled data. To tackle these problems, we propose Deep Anomaly Detection and Search (DADS), which applies Reinforcement Learning (RL) to balance exploitation and exploration. During the training process, the agent searches for possible anomalies with hierarchically-structured datasets and uses the searched anomalies to enhance performance, which in essence draws lessons from the idea of ensemble learning. Experimentally, we compare DADS with several state-of-the-art methods in the settings of leveraging labeled known anomalies to detect both other known anomalies and unknown anomalies. Results show that DADS can efficiently and precisely search anomalies from unlabeled data and learn from them, thus achieving good performance.
Federated learning is an emerging paradigm allowing large-scale decentralized learning without sharing data across different data owners, which helps address the concern of data privacy in medical image analysis. However, the requirement for label consistency across clients by the existing methods largely narrows its application scope. In practice, each clinical site may only annotate certain organs of interest with partial or no overlap with other sites. Incorporating such partially labeled data into a unified federation is an unexplored problem with clinical significance and urgency. This work tackles the challenge by using a novel federated multi-encoding U-Net (Fed-MENU) method for multi-organ segmentation. In our method, a multi-encoding U-Net (MENU-Net) is proposed to extract organ-specific features through different encoding sub-networks. Each sub-network can be seen as an expert of a specific organ and trained for that client. Moreover, to encourage the organ-specific features extracted by different sub-networks to be informative and distinctive, we regularize the training of the MENU-Net by designing an auxiliary generic decoder (AGD). Extensive experiments on six public abdominal CT datasets show that our Fed-MENU method can effectively obtain a federated learning model using the partially labeled datasets with superior performance to other models trained by either localized or centralized learning methods. Source code is publicly available at https://github.com/DIAL-RPI/Fed-MENU.
Due to the high human cost of annotation, it is non-trivial to curate a large-scale medical dataset that is fully labeled for all classes of interest. Instead, it would be convenient to collect multiple small partially labeled datasets from different matching sources, where the medical images may have only been annotated for a subset of classes of interest. This paper offers an empirical understanding of an under-explored problem, namely partially supervised multi-label classification (PSMLC), where a multi-label classifier is trained with only partially labeled medical images. In contrast to the fully supervised counterpart, the partial supervision caused by medical data scarcity has non-trivial negative impacts on the model performance. A potential remedy could be augmenting the partial labels. Though vicinal risk minimization (VRM) has been a promising solution to improve the generalization ability of the model, its application to PSMLC remains an open question. To bridge the methodological gap, we provide the first VRM-based solution to PSMLC. The empirical results also provide insights into future research directions on partially supervised learning under data scarcity.
In the paper, we present an approach for learning a single model that universally segments 33 anatomical structures, including vertebrae, pelvic bones, and abdominal organs. Our model building has to address the following challenges. Firstly, while it is ideal to learn such a model from a large-scale, fully-annotated dataset, it is practically hard to curate such a dataset. Thus, we resort to learn from a union of multiple datasets, with each dataset containing the images that are partially labeled. Secondly, along the line of partial labelling, we contribute an open-source, large-scale vertebra segmentation dataset for the benefit of spine analysis community, CTSpine1K, boasting over 1,000 3D volumes and over 11K annotated vertebrae. Thirdly, in a 3D medical image segmentation task, due to the limitation of GPU memory, we always train a model using cropped patches as inputs instead a whole 3D volume, which limits the amount of contextual information to be learned. To this, we propose a cross-patch transformer module to fuse more information in adjacent patches, which enlarges the aggregated receptive field for improved segmentation performance. This is especially important for segmenting, say, the elongated spine. Based on 7 partially labeled datasets that collectively contain about 2,800 3D volumes, we successfully learn such a universal model. Finally, we evaluate the universal model on multiple open-source datasets, proving that our model has a good generalization performance and can potentially serve as a solid foundation for downstream tasks.