Accurate identification and quantification of unruptured intracranial aneurysms (UIAs) is crucial for the risk assessment and treatment of this cerebrovascular disorder. Current 2D manual assessment on 3D magnetic resonance angiography (MRA) is suboptimal and time-consuming. In addition, one major issue in medical image segmentation is the need for large well-annotated data, which can be expensive to obtain. Techniques that mitigate this requirement, such as weakly supervised learning with coarse labels are highly desirable. In the paper, we propose FocalSegNet, a novel 3D focal modulation UNet, to detect an aneurysm and offer an initial, coarse segmentation of it from time-of-flight MRA image patches, which is further refined with a dense conditional random field (CRF) post-processing layer to produce a final segmentation map. We trained and evaluated our model on a public dataset, and in terms of UIA detection, our model showed a low false-positive rate of 0.21 and a high sensitivity of 0.80. For voxel-wise aneurysm segmentation, we achieved a Dice score of 0.68 and a 95% Hausdorff distance of ~0.95 mm, demonstrating its strong performance. We evaluated our algorithms against the state-of-the-art 3D Residual-UNet and Swin-UNETR, and illustrated the superior performance of our proposed FocalSegNet, highlighting the advantages of employing focal modulation for this task.
Human tissue and its constituent cells form a microenvironment that is fundamentally three-dimensional (3D). However, the standard-of-care in pathologic diagnosis involves selecting a few two-dimensional (2D) sections for microscopic evaluation, risking sampling bias and misdiagnosis. Diverse methods for capturing 3D tissue morphologies have been developed, but they have yet had little translation to clinical practice; manual and computational evaluations of such large 3D data have so far been impractical and/or unable to provide patient-level clinical insights. Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting patient outcomes. Archived prostate cancer specimens were imaged with open-top light-sheet microscopy or microcomputed tomography and the resulting 3D datasets were used to train risk-stratification networks based on 5-year biochemical recurrence outcomes via MAMBA. With the 3D block-based approach, MAMBA achieves an area under the receiver operating characteristic curve (AUC) of 0.86 and 0.74, superior to 2D traditional single-slice-based prognostication (AUC of 0.79 and 0.57), suggesting superior prognostication with 3D morphological features. Further analyses reveal that the incorporation of greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, suggesting the value of capturing larger extents of heterogeneous 3D morphology. With the rapid growth and adoption of 3D spatial biology and pathology techniques by researchers and clinicians, MAMBA provides a general and efficient framework for 3D weakly supervised learning for clinical decision support and can help to reveal novel 3D morphological biomarkers for prognosis and therapeutic response.
Weakly-supervised change detection (WSCD) aims to detect pixel-level changes with only image-level annotations. Owing to its label efficiency, WSCD is drawing increasing attention recently. However, current WSCD methods often encounter the challenge of change missing and fabricating, i.e., the inconsistency between image-level annotations and pixel-level predictions. Specifically, change missing refer to the situation that the WSCD model fails to predict any changed pixels, even though the image-level label indicates changed, and vice versa for change fabricating. To address this challenge, in this work, we leverage global-scale and local-scale priors in WSCD and propose two components: a Dilated Prior (DP) decoder and a Label Gated (LG) constraint. The DP decoder decodes samples with the changed image-level label, skips samples with the unchanged label, and replaces them with an all-unchanged pixel-level label. The LG constraint is derived from the correspondence between changed representations and image-level labels, penalizing the model when it mispredicts the change status. Additionally, we develop TransWCD, a simple yet powerful transformer-based model, showcasing the potential of weakly-supervised learning in change detection. By integrating the DP decoder and LG constraint into TransWCD, we form TransWCD-DL. Our proposed TransWCD and TransWCD-DL achieve significant +6.33% and +9.55% F1 score improvements over the state-of-the-art methods on the WHU-CD dataset, respectively. Some performance metrics even exceed several fully-supervised change detection (FSCD) competitors. Code will be available at https://github.com/zhenghuizhao/TransWCD.
Coronary artery segmentation on coronary-computed tomography angiography (CCTA) images is crucial for clinical use. Due to the expertise-required and labor-intensive annotation process, there is a growing demand for the relevant label-efficient learning algorithms. To this end, we propose partial vessels annotation (PVA) based on the challenges of coronary artery segmentation and clinical diagnostic characteristics. Further, we propose a progressive weakly supervised learning framework to achieve accurate segmentation under PVA. First, our proposed framework learns the local features of vessels to propagate the knowledge to unlabeled regions. Subsequently, it learns the global structure by utilizing the propagated knowledge, and corrects the errors introduced in the propagation process. Finally, it leverages the similarity between feature embeddings and the feature prototype to enhance testing outputs. Experiments on clinical data reveals that our proposed framework outperforms the competing methods under PVA (24.29% vessels), and achieves comparable performance in trunk continuity with the baseline model using full annotation (100% vessels).
The automated segmentation of Intracranial Arteries (IA) in Digital Subtraction Angiography (DSA) plays a crucial role in the quantification of vascular morphology, significantly contributing to computer-assisted stroke research and clinical practice. Current research primarily focuses on the segmentation of single-frame DSA using proprietary datasets. However, these methods face challenges due to the inherent limitation of single-frame DSA, which only partially displays vascular contrast, thereby hindering accurate vascular structure representation. In this work, we introduce DIAS, a dataset specifically developed for IA segmentation in DSA sequences. We establish a comprehensive benchmark for evaluating DIAS, covering full, weak, and semi-supervised segmentation methods. Specifically, we propose the vessel sequence segmentation network, in which the sequence feature extraction module effectively captures spatiotemporal representations of intravascular contrast, achieving intracranial artery segmentation in 2D+Time DSA sequences. For weakly-supervised IA segmentation, we propose a novel scribble learning-based image segmentation framework, which, under the guidance of scribble labels, employs cross pseudo-supervision and consistency regularization to improve the performance of the segmentation network. Furthermore, we introduce the random patch-based self-training framework, aimed at alleviating the performance constraints encountered in IA segmentation due to the limited availability of annotated DSA data. Our extensive experiments on the DIAS dataset demonstrate the effectiveness of these methods as potential baselines for future research and clinical applications. The dataset and code are publicly available at https://doi.org/10.5281/zenodo.11396520 and https://github.com/lseventeen/DIAS.
Nuclei instance segmentation on histopathology images is of great clinical value for disease analysis. Generally, fully-supervised algorithms for this task require pixel-wise manual annotations, which is especially time-consuming and laborious for the high nuclei density. To alleviate the annotation burden, we seek to solve the problem through image-level weakly supervised learning, which is underexplored for nuclei instance segmentation. Compared with most existing methods using other weak annotations (scribble, point, etc.) for nuclei instance segmentation, our method is more labor-saving. The obstacle to using image-level annotations in nuclei instance segmentation is the lack of adequate location information, leading to severe nuclei omission or overlaps. In this paper, we propose a novel image-level weakly supervised method, called cyclic learning, to solve this problem. Cyclic learning comprises a front-end classification task and a back-end semi-supervised instance segmentation task to benefit from multi-task learning (MTL). We utilize a deep learning classifier with interpretability as the front-end to convert image-level labels to sets of high-confidence pseudo masks and establish a semi-supervised architecture as the back-end to conduct nuclei instance segmentation under the supervision of these pseudo masks. Most importantly, cyclic learning is designed to circularly share knowledge between the front-end classifier and the back-end semi-supervised part, which allows the whole system to fully extract the underlying information from image-level labels and converge to a better optimum. Experiments on three datasets demonstrate the good generality of our method, which outperforms other image-level weakly supervised methods for nuclei instance segmentation, and achieves comparable performance to fully-supervised methods.
While the predictions produced by conformal prediction are set-valued, the data used for training and calibration is supposed to be precise. In the setting of superset learning or learning from partial labels, a variant of weakly supervised learning, it is exactly the other way around: training data is possibly imprecise (set-valued), but the model induced from this data yields precise predictions. In this paper, we combine the two settings by making conformal prediction amenable to set-valued training data. We propose a generalization of the conformal prediction procedure that can be applied to set-valued training and calibration data. We prove the validity of the proposed method and present experimental studies in which it compares favorably to natural baselines.
In the past decade, deep neural networks have achieved significant progress in point cloud learning. However, collecting large-scale precisely-annotated training data is extremely laborious and expensive, which hinders the scalability of existing point cloud datasets and poses a bottleneck for efficient exploration of point cloud data in various tasks and applications. Label-efficient learning offers a promising solution by enabling effective deep network training with much-reduced annotation efforts. This paper presents the first comprehensive survey of label-efficient learning of point clouds. We address three critical questions in this emerging research field: i) the importance and urgency of label-efficient learning in point cloud processing, ii) the subfields it encompasses, and iii) the progress achieved in this area. To achieve this, we propose a taxonomy that organizes label-efficient learning methods based on the data prerequisites provided by different types of labels. We categorize four typical label-efficient learning approaches that significantly reduce point cloud annotation efforts: data augmentation, domain transfer learning, weakly-supervised learning, and pretrained foundation models. For each approach, we outline the problem setup and provide an extensive literature review that showcases relevant progress and challenges. Finally, we share insights into current research challenges and potential future directions. A project associated with this survey has been built at https://github.com/xiaoaoran/3D_label_efficient_learning.
Weakly supervised learning is a popular approach for training machine learning models in low-resource settings. Instead of requesting high-quality yet costly human annotations, it allows training models with noisy annotations obtained from various weak sources. Recently, many sophisticated approaches have been proposed for robust training under label noise, reporting impressive results. In this paper, we revisit the setup of these approaches and find that the benefits brought by these approaches are significantly overestimated. Specifically, we find that the success of existing weakly supervised learning approaches heavily relies on the availability of clean validation samples which, as we show, can be leveraged much more efficiently by simply training on them. After using these clean labels in training, the advantages of using these sophisticated approaches are mostly wiped out. This remains true even when reducing the size of the available clean data to just five samples per class, making these approaches impractical. To understand the true value of weakly supervised learning, we thoroughly analyze diverse NLP datasets and tasks to ascertain when and why weakly supervised approaches work. Based on our findings, we provide recommendations for future research.
This paper introduces the novel concept of few-shot weakly supervised learning for pathology Whole Slide Image (WSI) classification, denoted as FSWC. A solution is proposed based on prompt learning and the utilization of a large language model, GPT-4. Since a WSI is too large and needs to be divided into patches for processing, WSI classification is commonly approached as a Multiple Instance Learning (MIL) problem. In this context, each WSI is considered a bag, and the obtained patches are treated as instances. The objective of FSWC is to classify both bags and instances with only a limited number of labeled bags. Unlike conventional few-shot learning problems, FSWC poses additional challenges due to its weak bag labels within the MIL framework. Drawing inspiration from the recent achievements of vision-language models (V-L models) in downstream few-shot classification tasks, we propose a two-level prompt learning MIL framework tailored for pathology, incorporating language prior knowledge. Specifically, we leverage CLIP to extract instance features for each patch, and introduce a prompt-guided pooling strategy to aggregate these instance features into a bag feature. Subsequently, we employ a small number of labeled bags to facilitate few-shot prompt learning based on the bag features. Our approach incorporates the utilization of GPT-4 in a question-and-answer mode to obtain language prior knowledge at both the instance and bag levels, which are then integrated into the instance and bag level language prompts. Additionally, a learnable component of the language prompts is trained using the available few-shot labeled data. We conduct extensive experiments on three real WSI datasets encompassing breast cancer, lung cancer, and cervical cancer, demonstrating the notable performance of the proposed method in bag and instance classification. All codes will be available.
The past decade has witnessed many great successes of machine learning (ML) and deep learning (DL) applications in agricultural systems, including weed control, plant disease diagnosis, agricultural robotics, and precision livestock management. Despite tremendous progresses, one downside of such ML/DL models is that they generally rely on large-scale labeled datasets for training, and the performance of such models is strongly influenced by the size and quality of available labeled data samples. In addition, collecting, processing, and labeling such large-scale datasets is extremely costly and time-consuming, partially due to the rising cost in human labor. Therefore, developing label-efficient ML/DL methods for agricultural applications has received significant interests among researchers and practitioners. In fact, there are more than 50 papers on developing and applying deep-learning-based label-efficient techniques to address various agricultural problems since 2016, which motivates the authors to provide a timely and comprehensive review of recent label-efficient ML/DL methods in agricultural applications. To this end, we first develop a principled taxonomy to organize these methods according to the degree of supervision, including weak supervision (i.e., active learning and semi-/weakly- supervised learning), and no supervision (i.e., un-/self- supervised learning), supplemented by representative state-of-the-art label-efficient ML/DL methods. In addition, a systematic review of various agricultural applications exploiting these label-efficient algorithms, such as precision agriculture, plant phenotyping, and postharvest quality assessment, is presented. Finally, we discuss the current problems and challenges, as well as future research directions. A well-classified paper list can be accessed at https://github.com/DongChen06/Label-efficient-in-Agriculture.
Recent work in vision-and-language pretraining has investigated supervised signals from object detection data to learn better, fine-grained multimodal representations. In this work, we take a step further and explore how we can tap into supervision from small-scale visual relation data. In particular, we propose two pretraining approaches to contextualise visual entities in a multimodal setup. With verbalised scene graphs, we transform visual relation triplets into structured captions, and treat them as additional image descriptions. With masked relation prediction, we further encourage relating entities from image regions with visually masked contexts. When applied to strong baselines pretrained on large amounts of Web data, zero-shot evaluations on both coarse-grained and fine-grained tasks show the efficacy of our methods in learning multimodal representations from weakly-supervised relations data.
Weakly supervised learning based on scribble annotations in target extraction of remote sensing images has drawn much interest due to scribbles' flexibility in denoting winding objects and low cost of manually labeling. However, scribbles are too sparse to identify object structure and detailed information, bringing great challenges in target localization and boundary description. To alleviate these problems, in this paper, we construct two inner structure-constraints, a deformation consistency loss and a trainable active contour loss, together with a scribble-constraint to supervise the optimization of the encoder-decoder network without introducing any auxiliary module or extra operation based on prior cues. Comprehensive experiments demonstrate our method's superiority over five state-of-the-art algorithms in this field. Source code is available at https://github.com/yitongli123/ISC-TE.
Complementary-label learning (CLL) is a weakly-supervised learning paradigm that aims to train a multi-class classifier using only complementary labels, which indicate classes to which an instance does not belong. Despite numerous algorithmic proposals for CLL, their practical applicability remains unverified for two reasons. Firstly, these algorithms often rely on assumptions about the generation of complementary labels, and it is not clear how far the assumptions are from reality. Secondly, their evaluation has been limited to synthetic datasets. To gain insights into the real-world performance of CLL algorithms, we developed a protocol to collect complementary labels from human annotators. Our efforts resulted in the creation of four datasets: CLCIFAR10, CLCIFAR20, CLMicroImageNet10, and CLMicroImageNet20, derived from well-known classification datasets CIFAR10, CIFAR100, and TinyImageNet200. These datasets represent the very first real-world CLL datasets. Through extensive benchmark experiments, we discovered a notable decrease in performance when transitioning from synthetic datasets to real-world datasets. We investigated the key factors contributing to the decrease with a thorough dataset-level ablation study. Our analyses highlight annotation noise as the most influential factor in the real-world datasets. In addition, we discover that the biased-nature of human-annotated complementary labels and the difficulty to validate with only complementary labels are two outstanding barriers to practical CLL. These findings suggest that the community focus more research efforts on developing CLL algorithms and validation schemes that are robust to noisy and biased complementary-label distributions.
ROI extraction is an active but challenging task in remote sensing because of the complicated landform, the complex boundaries and the requirement of annotations. Weakly supervised learning (WSL) aims at learning a mapping from input image to pixel-wise prediction under image-wise labels, which can dramatically decrease the labor cost. However, due to the imprecision of labels, the accuracy and time consumption of WSL methods are relatively unsatisfactory. In this paper, we propose a two-step ROI extraction based on contractive learning. Firstly, we present to integrate multiscale Grad-CAM to obtain pseudo pixelwise annotations with well boundaries. Then, to reduce the compact of misjudgments in pseudo annotations, we construct a contrastive learning strategy to encourage the features inside ROI as close as possible and separate background features from foreground features. Comprehensive experiments demonstrate the superiority of our proposal. Code is available at https://github.com/HE-Lingfeng/ROI-Extraction
Image segmentation is a fundamental task in the field of imaging and vision. Supervised deep learning for segmentation has achieved unparalleled success when sufficient training data with annotated labels are available. However, annotation is known to be expensive to obtain, especially for histopathology images where the target regions are usually with high morphology variations and irregular shapes. Thus, weakly supervised learning with sparse annotations of points is promising to reduce the annotation workload. In this work, we propose a contrast-based variational model to generate segmentation results, which serve as reliable complementary supervision to train a deep segmentation model for histopathology images. The proposed method considers the common characteristics of target regions in histopathology images and can be trained in an end-to-end manner. It can generate more regionally consistent and smoother boundary segmentation, and is more robust to unlabeled `novel' regions. Experiments on two different histology datasets demonstrate its effectiveness and efficiency in comparison to previous models.
This paper explores the properties of the plain Vision Transformer (ViT) for Weakly-supervised Semantic Segmentation (WSSS). The class activation map (CAM) is of critical importance for understanding a classification network and launching WSSS. We observe that different attention heads of ViT focus on different image areas. Thus a novel weight-based method is proposed to end-to-end estimate the importance of attention heads, while the self-attention maps are adaptively fused for high-quality CAM results that tend to have more complete objects. Besides, we propose a ViT-based gradient clipping decoder for online retraining with the CAM results to complete the WSSS task. We name this plain Transformer-based Weakly-supervised learning framework WeakTr. It achieves the state-of-the-art WSSS performance on standard benchmarks, i.e., 78.4% mIoU on the val set of PASCAL VOC 2012 and 50.3% mIoU on the val set of COCO 2014. Code is available at https://github.com/hustvl/WeakTr.
Regular physics-informed neural networks (PINNs) predict the solution of partial differential equations using sparse labeled data but only over a single domain. On the other hand, fully supervised learning models are first trained usually over a few thousand domains with known solutions (i.e., labeled data) and then predict the solution over a few hundred unseen domains. Physics-informed PointNet (PIPN) is primarily designed to fill this gap between PINNs (as weakly supervised learning models) and fully supervised learning models. In this article, we demonstrate that PIPN predicts the solution of desired partial differential equations over a few hundred domains simultaneously, while it only uses sparse labeled data. This framework benefits fast geometric designs in the industry when only sparse labeled data are available. Particularly, we show that PIPN predicts the solution of a plane stress problem over more than 500 domains with different geometries, simultaneously. Moreover, we pioneer implementing the concept of remarkable batch size (i.e., the number of geometries fed into PIPN at each sub-epoch) into PIPN. Specifically, we try batch sizes of 7, 14, 19, 38, 76, and 133. Additionally, the effect of the PIPN size, symmetric function in the PIPN architecture, and static and dynamic weights for the component of the sparse labeled data in the loss function are investigated.
Head MRI pre-processing involves converting raw images to an intensity-normalized, skull-stripped brain in a standard coordinate space. In this paper, we propose an end-to-end weakly supervised learning approach, called Neural Pre-processing (NPP), for solving all three sub-tasks simultaneously via a neural network, trained on a large dataset without individual sub-task supervision. Because the overall objective is highly under-constrained, we explicitly disentangle geometric-preserving intensity mapping (skull-stripping and intensity normalization) and spatial transformation (spatial normalization). Quantitative results show that our model outperforms state-of-the-art methods which tackle only a single sub-task. Our ablation experiments demonstrate the importance of the architecture design we chose for NPP. Furthermore, NPP affords the user the flexibility to control each of these tasks at inference time. The code and model are freely-available at \url{https://github.com/Novestars/Neural-Pre-processing}.
Self-paced learning has been beneficial for tasks where some initial knowledge is available, such as weakly supervised learning and domain adaptation, to select and order the training sample sequence, from easy to complex. However its applicability remains unexplored in unsupervised learning, whereby the knowledge of the task matures during training. We propose a novel HYperbolic Self-Paced model (HYSP) for learning skeleton-based action representations. HYSP adopts self-supervision: it uses data augmentations to generate two views of the same sample, and it learns by matching one (named online) to the other (the target). We propose to use hyperbolic uncertainty to determine the algorithmic learning pace, under the assumption that less uncertain samples should be more strongly driving the training, with a larger weight and pace. Hyperbolic uncertainty is a by-product of the adopted hyperbolic neural networks, it matures during training and it comes with no extra cost, compared to the established Euclidean SSL framework counterparts. When tested on three established skeleton-based action recognition datasets, HYSP outperforms the state-of-the-art on PKU-MMD I, as well as on 2 out of 3 downstream tasks on NTU-60 and NTU-120. Additionally, HYSP only uses positive pairs and bypasses therefore the complex and computationally-demanding mining procedures required for the negatives in contrastive techniques. Code is available at https://github.com/paolomandica/HYSP.