Medical images used in clinical practice are heterogeneous and not the same quality as scans studied in academic research. Preprocessing breaks down in extreme cases when anatomy, artifacts, or imaging parameters are unusual or protocols are different. Methods robust to these variations are most needed. A novel deep learning method is proposed for fast and accurate segmentation of the human brain into 132 regions. The proposed model uses an efficient U-Net-like network and benefits from the intersection points of different views and hierarchical relations for the fusion of the orthogonal 2D planes and brain labels during the end-to-end training. Weakly supervised learning is deployed to take the advantage of partially labeled data for the whole brain segmentation and estimation of the intracranial volume (ICV). Moreover, data augmentation is used to expand the magnetic resonance imaging (MRI) data by generating realistic brain scans with high variability for robust training of the model while preserving data privacy. The proposed method can be applied to brain MRI data including skull or any other artifacts without preprocessing the images or a drop in performance. Several experiments using different atlases are conducted to evaluate the segmentation performance of the trained model compared to the state-of-the-art, and the results show higher segmentation accuracy and robustness of the proposed model compared to the existing methods across different intra- and inter-domain datasets.
Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point annotations with an integer linear program (ILP) for optimal cell lineage extraction. Our work specifically addresses the following challenging properties of C. elegans embryo recordings: (1) Many cell divisions as compared to benchmark recordings of other organisms, and (2) the presence of polar bodies that are easily mistaken as cell nuclei. To cope with (1), we devise and incorporate a learnt cell division detector. To cope with (2), we employ a learnt polar body detector. We further propose automated ILP weights tuning via a structured SVM, alleviating the need for tedious manual set-up of a respective grid search. Our method outperforms the previous leader of the cell tracking challenge on the Fluo-N3DH-CE embryo dataset. We report a further extensive quantitative evaluation on two more C. elegans datasets. We will make these datasets public to serve as an extended benchmark for future method development. Our results suggest considerable improvements yielded by our method, especially in terms of the correctness of division event detection and the number and length of fully correct track segments. Code: https://github.com/funkelab/linajea
The success of Convolutional Neural Networks (CNNs) in 3D medical image segmentation relies on massive fully annotated 3D volumes for training that are time-consuming and labor-intensive to acquire. In this paper, we propose to annotate a segmentation target with only seven points in 3D medical images, and design a two-stage weakly supervised learning framework PA-Seg. In the first stage, we employ geodesic distance transform to expand the seed points to provide more supervision signal. To further deal with unannotated image regions during training, we propose two contextual regularization strategies, i.e., multi-view Conditional Random Field (mCRF) loss and Variance Minimization (VM) loss, where the first one encourages pixels with similar features to have consistent labels, and the second one minimizes the intensity variance for the segmented foreground and background, respectively. In the second stage, we use predictions obtained by the model pre-trained in the first stage as pseudo labels. To overcome noises in the pseudo labels, we introduce a Self and Cross Monitoring (SCM) strategy, which combines self-training with Cross Knowledge Distillation (CKD) between a primary model and an auxiliary model that learn from soft labels generated by each other. Experiments on public datasets for Vestibular Schwannoma (VS) segmentation and Brain Tumor Segmentation (BraTS) demonstrated that our model trained in the first stage outperformed existing state-of-the-art weakly supervised approaches by a large margin, and after using SCM for additional training, the model's performance was close to its fully supervised counterpart on the BraTS dataset.
Understanding human emotions is a crucial ability for intelligent robots to provide better human-robot interactions. The existing works are limited to trimmed video-level emotion classification, failing to locate the temporal window corresponding to the emotion. In this paper, we introduce a new task, named Temporal Emotion Localization in videos~(TEL), which aims to detect human emotions and localize their corresponding temporal boundaries in untrimmed videos with aligned subtitles. TEL presents three unique challenges compared to temporal action localization: 1) The emotions have extremely varied temporal dynamics; 2) The emotion cues are embedded in both appearances and complex plots; 3) The fine-grained temporal annotations are complicated and labor-intensive. To address the first two challenges, we propose a novel dilated context integrated network with a coarse-fine two-stream architecture. The coarse stream captures varied temporal dynamics by modeling multi-granularity temporal contexts. The fine stream achieves complex plots understanding by reasoning the dependency between the multi-granularity temporal contexts from the coarse stream and adaptively integrates them into fine-grained video segment features. To address the third challenge, we introduce a cross-modal consensus learning paradigm, which leverages the inherent semantic consensus between the aligned video and subtitle to achieve weakly-supervised learning. We contribute a new testing set with 3,000 manually-annotated temporal boundaries so that future research on the TEL problem can be quantitatively evaluated. Extensive experiments show the effectiveness of our approach on temporal emotion localization. The repository of this work is at https://github.com/YYJMJC/Temporal-Emotion-Localization-in-Videos.
Handwritten Chinese text recognition (HCTR) has been an active research topic for decades. However, most previous studies solely focus on the recognition of cropped text line images, ignoring the error caused by text line detection in real-world applications. Although some approaches aimed at page-level text recognition have been proposed in recent years, they either are limited to simple layouts or require very detailed annotations including expensive line-level and even character-level bounding boxes. To this end, we propose PageNet for end-to-end weakly supervised page-level HCTR. PageNet detects and recognizes characters and predicts the reading order between them, which is more robust and flexible when dealing with complex layouts including multi-directional and curved text lines. Utilizing the proposed weakly supervised learning framework, PageNet requires only transcripts to be annotated for real data; however, it can still output detection and recognition results at both the character and line levels, avoiding the labor and cost of labeling bounding boxes of characters and text lines. Extensive experiments conducted on five datasets demonstrate the superiority of PageNet over existing weakly supervised and fully supervised page-level methods. These experimental results may spark further research beyond the realms of existing methods based on connectionist temporal classification or attention. The source code is available at https://github.com/shannanyinxiang/PageNet.
While there have been increased researches using deep learning techniques for the extraction of vascular structure from the 2D en face OCTA, for such approach, it is known that the data annotation process on the curvilinear structure like the retinal vasculature is very costly and time consuming, albeit few tried to address the annotation problem. In this work, we propose the application of the scribble-base weakly-supervised learning method to automate the pixel-level annotation. The proposed method, called OCTAve, combines the weakly-supervised learning using scribble-annotated ground truth augmented with an adversarial and a novel self-supervised deep supervision. Our novel mechanism is designed to utilize the discriminative outputs from the discrimination layer of a UNet-like architecture where the Kullback-Liebler Divergence between the aggregate discriminative outputs and the segmentation map predicate is minimized during the training. This combined method leads to the better localization of the vascular structure as shown in our experiments. We validate our proposed method on the large public datasets i.e., ROSE, OCTA-500. The segmentation performance is compared against both state-of-the-art fully-supervised and scribble-based weakly-supervised approaches. The implementation of our work used in the experiments is located at [LINK].
Although deep learning algorithms have been intensively developed for computer-aided tuberculosis diagnosis (CTD), they mainly depend on carefully annotated datasets, leading to much time and resource consumption. Weakly supervised learning (WSL), which leverages coarse-grained labels to accomplish fine-grained tasks, has the potential to solve this problem. In this paper, we first propose a new large-scale tuberculosis (TB) chest X-ray dataset, namely the tuberculosis chest X-ray attribute dataset (TBX-Att), and then establish an attribute-assisted weakly-supervised framework to classify and localize TB by leveraging the attribute information to overcome the insufficiency of supervision in WSL scenarios. Specifically, first, the TBX-Att dataset contains 2000 X-ray images with seven kinds of attributes for TB relational reasoning, which are annotated by experienced radiologists. It also includes the public TBX11K dataset with 11200 X-ray images to facilitate weakly supervised detection. Second, we exploit a multi-scale feature interaction model for TB area classification and detection with attribute relational reasoning. The proposed model is evaluated on the TBX-Att dataset and will serve as a solid baseline for future research. The code and data will be available at https://github.com/GangmingZhao/tb-attribute-weak-localization.
Whole slide image (WSI) classification is a fundamental task for the diagnosis and treatment of diseases; but, curation of accurate labels is time-consuming and limits the application of fully-supervised methods. To address this, multiple instance learning (MIL) is a popular method that poses classification as a weakly supervised learning task with slide-level labels only. While current MIL methods apply variants of the attention mechanism to re-weight instance features with stronger models, scant attention is paid to the properties of the data distribution. In this work, we propose to re-calibrate the distribution of a WSI bag (instances) by using the statistics of the max-instance (critical) feature. We assume that in binary MIL, positive bags have larger feature magnitudes than negatives, thus we can enforce the model to maximize the discrepancy between bags with a metric feature loss that models positive bags as out-of-distribution. To achieve this, unlike existing MIL methods that use single-batch training modes, we propose balanced-batch sampling to effectively use the feature loss i.e., (+/-) bags simultaneously. Further, we employ a position encoding module (PEM) to model spatial/morphological information, and perform pooling by multi-head self-attention (PSMA) with a Transformer encoder. Experimental results on existing benchmark datasets show our approach is effective and improves over state-of-the-art MIL methods.
As a widely used weakly supervised learning scheme, modern multiple instance learning (MIL) models achieve competitive performance at the bag level. However, instance-level prediction, which is essential for many important applications, remains largely unsatisfactory. We propose to conduct novel active deep multiple instance learning that samples a small subset of informative instances for annotation, aiming to significantly boost the instance-level prediction. A variance regularized loss function is designed to properly balance the bias and variance of instance-level predictions, aiming to effectively accommodate the highly imbalanced instance distribution in MIL and other fundamental challenges. Instead of directly minimizing the variance regularized loss that is non-convex, we optimize a distributionally robust bag level likelihood as its convex surrogate. The robust bag likelihood provides a good approximation of the variance based MIL loss with a strong theoretical guarantee. It also automatically balances bias and variance, making it effective to identify the potentially positive instances to support active sampling. The robust bag likelihood can be naturally integrated with a deep architecture to support deep model training using mini-batches of positive-negative bag pairs. Finally, a novel P-F sampling function is developed that combines a probability vector and predicted instance scores, obtained by optimizing the robust bag likelihood. By leveraging the key MIL assumption, the sampling function can explore the most challenging bags and effectively detect their positive instances for annotation, which significantly improves the instance-level prediction. Experiments conducted over multiple real-world datasets clearly demonstrate the state-of-the-art instance-level prediction achieved by the proposed model.
Recent advances in contrastive learning have enlightened diverse applications across various semi-supervised fields. Jointly training supervised learning and unsupervised learning with a shared feature encoder becomes a common scheme. Though it benefits from taking advantage of both feature-dependent information from self-supervised learning and label-dependent information from supervised learning, this scheme remains suffering from bias of the classifier. In this work, we systematically explore the relationship between self-supervised learning and supervised learning, and study how self-supervised learning helps robust data-efficient deep learning. We propose hyperspherical consistency regularization (HCR), a simple yet effective plug-and-play method, to regularize the classifier using feature-dependent information and thus avoid bias from labels. Specifically, HCR first projects logits from the classifier and feature projections from the projection head on the respective hypersphere, then it enforces data points on hyperspheres to have similar structures by minimizing binary cross entropy of pairwise distances' similarity metrics. Extensive experiments on semi-supervised and weakly-supervised learning demonstrate the effectiveness of our method, by showing superior performance with HCR.
Data of general object images have two most common structures: (1) each object of a given shape can be rendered in multiple different views, and (2) shapes of objects can be categorized in such a way that the diversity of shapes is much larger across categories than within a category. Existing deep generative models can typically capture either structure, but not both. In this work, we introduce a novel deep generative model, called CIGMO, that can learn to represent category, shape, and view factors from image data. The model is comprised of multiple modules of shape representations that are each specialized to a particular category and disentangled from view representation, and can be learned using a group-based weakly supervised learning method. By empirical investigation, we show that our model can effectively discover categories of object shapes despite large view variation and quantitatively supersede various previous methods including the state-of-the-art invariant clustering algorithm. Further, we show that our approach using category-specialization can enhance the learned shape representation to better perform down-stream tasks such as one-shot object identification as well as shape-view disentanglement.
Hispathological image segmentation algorithms play a critical role in computer aided diagnosis technology. The development of weakly supervised segmentation algorithm alleviates the problem of medical image annotation that it is time-consuming and labor-intensive. As a subset of weakly supervised learning, Multiple Instance Learning (MIL) has been proven to be effective in segmentation. However, there is a lack of related information between instances in MIL, which limits the further improvement of segmentation performance. In this paper, we propose a novel weakly supervised method for pixel-level segmentation in histopathology images, which introduces Transformer into the MIL framework to capture global or long-range dependencies. The multi-head self-attention in the Transformer establishes the relationship between instances, which solves the shortcoming that instances are independent of each other in MIL. In addition, deep supervision is introduced to overcome the limitation of annotations in weakly supervised methods and make the better utilization of hierarchical information. The state-of-the-art results on the colon cancer dataset demonstrate the superiority of the proposed method compared with other weakly supervised methods. It is worth believing that there is a potential of our approach for various applications in medical images.
A cost-effective alternative to manual data labeling is weak supervision (WS), where data samples are automatically annotated using a predefined set of labeling functions (LFs), rule-based mechanisms that generate artificial labels for the associated classes. In this work, we investigate noise reduction techniques for WS based on the principle of k-fold cross-validation. We introduce a new algorithm ULF for Unsupervised Labeling Function correction, which denoises WS data by leveraging models trained on all but some LFs to identify and correct biases specific to the held-out LFs. Specifically, ULF refines the allocation of LFs to classes by re-estimating this assignment on highly reliable cross-validated samples. Evaluation on multiple datasets confirms ULF's effectiveness in enhancing WS learning without the need for manual labeling.
Partial label learning (PLL) is a typical weakly supervised learning problem, where each training example is associated with a set of candidate labels among which only one is true. Most existing PLL approaches assume that the incorrect labels in each training example are randomly picked as the candidate labels and model the generation process of the candidate labels in a simple way. However, these approaches usually do not perform as well as expected due to the fact that the generation process of the candidate labels is always instance-dependent. Therefore, it deserves to be modeled in a refined way. In this paper, we consider instance-dependent PLL and assume that the generation process of the candidate labels could decompose into two sequential parts, where the correct label emerges first in the mind of the annotator but then the incorrect labels related to the feature are also selected with the correct label as candidate labels due to uncertainty of labeling. Motivated by this consideration, we propose a novel PLL method that performs Maximum A Posterior (MAP) based on an explicitly modeled generation process of candidate labels via decomposed probability distribution models. Extensive experiments on manually corrupted benchmark datasets and real-world datasets validate the effectiveness of the proposed method. Source code is available at https://github.com/palm-ml/idgp.
While weakly supervised multi-view face reconstruction (MVR) is garnering increased attention, one critical issue still remains open: how to effectively interact and fuse multiple image information to reconstruct high-precision 3D models. In this regard, we propose a novel pipeline called Deep Fusion MVR (DF-MVR) to explore the feature correspondences between multi-view images and reconstruct high-precision 3D faces. Specifically, we present a novel multi-view feature fusion backbone that utilizes face masks to align features from multiple encoders and integrates one multi-layer attention mechanism to enhance feature interaction and fusion, resulting in one unified facial representation. Additionally, we develop one concise face mask mechanism that facilitates multi-view feature fusion and facial reconstruction by identifying common areas and guiding the network's focus on critical facial features (e.g., eyes, brows, nose, and mouth). Experiments on Pixel-Face and Bosphorus datasets indicate the superiority of our model. Without 3D annotation, DF-MVR achieves 5.2% and 3.0% RMSE improvement over the existing weakly supervised MVRs respectively on Pixel-Face and Bosphorus dataset. Code will be available publicly at https://github.com/weiguangzhao/DF_MVR.
Semi- and weakly-supervised learning have recently attracted considerable attention in the object detection literature since they can alleviate the cost of annotation needed to successfully train deep learning models. State-of-art approaches for semi-supervised learning rely on student-teacher models trained using a multi-stage process, and considerable data augmentation. Custom networks have been developed for the weakly-supervised setting, making it difficult to adapt to different detectors. In this paper, a weakly semi-supervised training method is introduced that reduces these training challenges, yet achieves state-of-the-art performance by leveraging only a small fraction of fully-labeled images with information in weakly-labeled images. In particular, our generic sampling-based learning strategy produces pseudo-ground-truth (GT) bounding box annotations in an online fashion, eliminating the need for multi-stage training, and student-teacher network configurations. These pseudo GT boxes are sampled from weakly-labeled images based on the categorical score of object proposals accumulated via a score propagation process. Empirical results on the Pascal VOC dataset, indicate that the proposed approach improves performance by 5.0% when using VOC 2007 as fully-labeled, and VOC 2012 as weak-labeled data. Also, with 5-10% fully annotated images, we observed an improvement of more than 10% in mAP, showing that a modest investment in image-level annotation, can substantially improve detection performance.
Due to the difficulty of collecting exhaustive multi-label annotations, multi-label datasets often contain partial labels. We consider an extreme of this weakly supervised learning problem, called single positive multi-label learning (SPML), where each multi-label training image has only one positive label. Traditionally, all unannotated labels are assumed as negative labels in SPML, which introduces false negative labels and causes model training to be dominated by assumed negative labels. In this work, we choose to treat all unannotated labels from an alternative perspective, i.e. acknowledging they are unknown. Hence, we propose entropy-maximization (EM) loss to attain a special gradient regime for providing proper supervision signals. Moreover, we propose asymmetric pseudo-labeling (APL), which adopts asymmetric-tolerance strategies and a self-paced procedure, to cooperate with EM loss and then provide more precise supervision. Experiments show that our method significantly improves performance and achieves state-of-the-art results on all four benchmarks. Code is available at https://github.com/Correr-Zhou/SPML-AckTheUnknown.
Learning from Label Proportions (LLP) is a weakly supervised learning method that aims to perform instance classification from training data consisting of pairs of bags containing multiple instances and the class label proportions within the bags. Previous studies on multiclass LLP can be divided into two categories according to the learning task: per-instance label classification and per-bag label proportion estimation. However, these methods often results in high variance estimates of the risk when applied to complex models, or lack statistical learning theory arguments. To address this issue, we propose new learning methods based on statistical learning theory for both per-instance and per-bag policies. We demonstrate that the proposed methods are respectively risk-consistent and classifier-consistent in an instance-wise manner, and analyze the estimation error bounds. Additionally, we present a heuristic approximation method that utilizes an existing method for regressing label proportions to reduce the computational complexity of the proposed methods. Through benchmark experiments, we demonstrated the effectiveness of the proposed methods.
Weakly-supervised learning (WSL) has shown promising results in addressing label scarcity on many NLP tasks, but manually designing a comprehensive, high-quality labeling rule set is tedious and difficult. We study interactive weakly-supervised learning -- the problem of iteratively and automatically discovering novel labeling rules from data to improve the WSL model. Our proposed model, named PRBoost, achieves this goal via iterative prompt-based rule discovery and model boosting. It uses boosting to identify large-error instances and then discovers candidate rules from them by prompting pre-trained LMs with rule templates. The candidate rules are judged by human experts, and the accepted rules are used to generate complementary weak labels and strengthen the current model. Experiments on four tasks show PRBoost outperforms state-of-the-art WSL baselines up to 7.1% and bridges the gaps with fully supervised models. Our Implementation is available at \url{https://github.com/rz-zhang/PRBoost}.
We propose Probabilistic Warp Consistency, a weakly-supervised learning objective for semantic matching. Our approach directly supervises the dense matching scores predicted by the network, encoded as a conditional probability distribution. We first construct an image triplet by applying a known warp to one of the images in a pair depicting different instances of the same object class. Our probabilistic learning objectives are then derived using the constraints arising from the resulting image triplet. We further account for occlusion and background clutter present in real image pairs by extending our probabilistic output space with a learnable unmatched state. To supervise it, we design an objective between image pairs depicting different object classes. We validate our method by applying it to four recent semantic matching architectures. Our weakly-supervised approach sets a new state-of-the-art on four challenging semantic matching benchmarks. Lastly, we demonstrate that our objective also brings substantial improvements in the strongly-supervised regime, when combined with keypoint annotations.