Cell classification and counting in immunohistochemical cytoplasm staining images play a pivotal role in cancer diagnosis. Weakly supervised learning is a potential method to deal with labor-intensive labeling. However, the inconstant cell morphology and subtle differences between classes also bring challenges. To this end, we present a novel cell recognition framework based on multi-task learning, which utilizes two additional auxiliary tasks to guide robust representation learning of the main task. To deal with misclassification, the tissue prior learning branch is introduced to capture the spatial representation of tumor cells without additional tissue annotation. Moreover, dynamic masks and consistency learning are adopted to learn the invariance of cell scale and shape. We have evaluated our framework on immunohistochemical cytoplasm staining images, and the results demonstrate that our method outperforms recent cell recognition approaches. Besides, we have also done some ablation studies to show significant improvements after adding the auxiliary branches.
Despite the potential of weakly supervised learning to automatically annotate massive amounts of data, little is known about its limitations for use in computer-aided diagnosis (CAD). For CT specifically, interpreting the performance of CAD algorithms can be challenging given the large number of co-occurring diseases. This paper examines the effect of co-occurring diseases when training classification models by weakly supervised learning, specifically by comparing multi-label and multiple binary classifiers using the same training data. Our results demonstrated that the binary model outperformed the multi-label classification in every disease category in terms of AUC. However, this performance was heavily influenced by co-occurring diseases in the binary model, suggesting it did not always learn the correct appearance of the specific disease. For example, binary classification of lung nodules resulted in an AUC of < 0.65 when there were no other co-occurring diseases, but when lung nodules co-occurred with emphysema, the performance reached AUC > 0.80. We hope this paper revealed the complexity of interpreting disease classification performance in weakly supervised models and will encourage researchers to examine the effect of co-occurring diseases on classification performance in the future.
Multiple Instance Learning (MIL) is a weakly supervised learning problem where the aim is to assign labels to sets or bags of instances, as opposed to traditional supervised learning where each instance is assumed to be independent and identically distributed (IID) and is to be labeled individually. Recent work has shown promising results for neural network models in the MIL setting. Instead of focusing on each instance, these models are trained in an end-to-end fashion to learn effective bag-level representations by suitably combining permutation invariant pooling techniques with neural architectures. In this paper, we consider modelling the interactions between bags using a graph and employ Graph Neural Networks (GNNs) to facilitate end-to-end learning. Since a meaningful graph representing dependencies between bags is rarely available, we propose to use a Bayesian GNN framework that can generate a likely graph structure for scenarios where there is uncertainty in the graph or when no graph is available. Empirical results demonstrate the efficacy of the proposed technique for several MIL benchmark tasks and a distribution regression task.
Determining early-stage prognostic markers and stratifying patients for effective treatment are two key challenges for improving outcomes for melanoma patients. Previous studies have used tumour transcriptome data to stratify patients into immune subgroups, which were associated with differential melanoma specific survival and potential treatment strategies. However, acquiring transcriptome data is a time-consuming and costly process. Moreover, it is not routinely used in the current clinical workflow. Here we attempt to overcome this by developing deep learning models to classify gigapixel H&E stained pathology slides, which are well established in clinical workflows, into these immune subgroups. Previous subtyping approaches have employed supervised learning which requires fully annotated data, or have only examined single genetic mutations in melanoma patients. We leverage a multiple-instance learning approach, which only requires slide-level labels and uses an attention mechanism to highlight regions of high importance to the classification. Moreover, we show that pathology-specific self-supervised models generate better representations compared to pathology-agnostic models for improving our model performance, achieving a mean AUC of 0.76 for classifying histopathology images as high or low immune subgroups. We anticipate that this method may allow us to find new biomarkers of high importance and could act as a tool for clinicians to infer the immune landscape of tumours and stratify patients, without needing to carry out additional expensive genetic tests.
Nuclei segmentation is a crucial task for whole slide image analysis in digital pathology. Generally, the segmentation performance of fully-supervised learning heavily depends on the amount and quality of the annotated data. However, it is time-consuming and expensive for professional pathologists to provide accurate pixel-level ground truth, while it is much easier to get coarse labels such as point annotations. In this paper, we propose a weakly-supervised learning method for nuclei segmentation that only requires point annotations for training. First, coarse pixel-level labels are derived from the point annotations based on the Voronoi diagram and the k-means clustering method to avoid overfitting. Second, a co-training strategy with an exponential moving average method is designed to refine the incomplete supervision of the coarse labels. Third, a self-supervised visual representation learning method is tailored for nuclei segmentation of pathology images that transforms the hematoxylin component images into the H&E stained images to gain better understanding of the relationship between the nuclei and cytoplasm. We comprehensively evaluate the proposed method using two public datasets. Both visual and quantitative results demonstrate the superiority of our method to the state-of-the-art methods, and its competitive performance compared to the fully-supervised methods. Code: https://github.com/hust-linyi/SC-Net
Multi-modality imaging improves disease diagnosis and reveals distinct deviations in tissues with anatomical properties. The existence of completely aligned and paired multi-modality neuroimaging data has proved its effectiveness in brain research. However, collecting fully aligned and paired data is expensive or even impractical, since it faces many difficulties, including high cost, long acquisition time, image corruption, and privacy issues. An alternative solution is to explore unsupervised or weakly supervised learning methods to synthesize the absent neuroimaging data. In this paper, we provide a comprehensive review of cross-modality synthesis for neuroimages, from the perspectives of weakly supervised and unsupervised settings, loss functions, evaluation metrics, imaging modalities, datasets, and downstream applications based on synthesis. We begin by highlighting several opening challenges for cross-modality neuroimage synthesis. Then, we discuss representative architectures of cross-modality synthesis methods under different supervisions. This is followed by a stepwise in-depth analysis to evaluate how cross-modality neuroimage synthesis improves the performance of its downstream tasks. Finally, we summarize the existing research findings and point out future research directions. All resources are available at https://github.com/M-3LAB/awesome-multimodal-brain-image-systhesis
Domain Adaptation methodologies have shown to effectively generalize from a labeled source domain to a label scarce target domain. Previous research has either focused on unlabeled domain adaptation without any target supervision or semi-supervised domain adaptation with few labeled target examples per class. On the other hand Positive-Unlabeled (PU-) Learning has attracted increasing interest in the weakly supervised learning literature since in quite some real world applications positive labels are much easier to obtain than negative ones. In this work we are the first to introduce the challenge of Positive-Unlabeled Domain Adaptation where we aim to generalise from a fully labeled source domain to a target domain where only positive and unlabeled data is available. We present a novel two-step learning approach to this problem by firstly identifying reliable positive and negative pseudo-labels in the target domain guided by source domain labels and a positive-unlabeled risk estimator. This enables us to use a standard classifier on the target domain in a second step. We validate our approach by running experiments on benchmark datasets for visual object recognition. Furthermore we propose real world examples for our setting and validate our superior performance on parking occupancy data.
In many applications, training machine learning models involves using large amounts of human-annotated data. Obtaining precise labels for the data is expensive. Instead, training with weak supervision provides a low-cost alternative. We propose a novel weak supervision algorithm that processes noisy labels, i.e., weak signals, while also considering features of the training data to produce accurate labels for training. Our method searches over classifiers of the data representation to find plausible labelings. We call this paradigm data consistent weak supervision. A key facet of our framework is that we are able to estimate labels for data examples low or no coverage from the weak supervision. In addition, we make no assumptions about the joint distribution of the weak signals and true labels of the data. Instead, we use weak signals and the data features to solve a constrained optimization that enforces data consistency among the labels we generate. Empirical evaluation of our method on different datasets shows that it significantly outperforms state-of-the-art weak supervision methods on both text and image classification tasks.
Model pre-training is a cornerstone of modern visual recognition systems. Although fully supervised pre-training on datasets like ImageNet is still the de-facto standard, recent studies suggest that large-scale weakly supervised pre-training can outperform fully supervised approaches. This paper revisits weakly-supervised pre-training of models using hashtag supervision with modern versions of residual networks and the largest-ever dataset of images and corresponding hashtags. We study the performance of the resulting models in various transfer-learning settings including zero-shot transfer. We also compare our models with those obtained via large-scale self-supervised learning. We find our weakly-supervised models to be very competitive across all settings, and find they substantially outperform their self-supervised counterparts. We also include an investigation into whether our models learned potentially troubling associations or stereotypes. Overall, our results provide a compelling argument for the use of weakly supervised learning in the development of visual recognition systems. Our models, Supervised Weakly through hashtAGs (SWAG), are available publicly.
Understanding a plant's root system architecture (RSA) is crucial for a variety of plant science problem domains including sustainability and climate adaptation. Minirhizotron (MR) technology is a widely-used approach for phenotyping RSA non-destructively by capturing root imagery over time. Precisely segmenting roots from the soil in MR imagery is a critical step in studying RSA features. In this paper, we introduce a large-scale dataset of plant root images captured by MR technology. In total, there are over 72K RGB root images across six different species including cotton, papaya, peanut, sesame, sunflower, and switchgrass in the dataset. The images span a variety of conditions including varied root age, root structures, soil types, and depths under the soil surface. All of the images have been annotated with weak image-level labels indicating whether each image contains roots or not. The image-level labels can be used to support weakly supervised learning in plant root segmentation tasks. In addition, 63K images have been manually annotated to generate pixel-level binary masks indicating whether each pixel corresponds to root or not. These pixel-level binary masks can be used as ground truth for supervised learning in semantic segmentation tasks. By introducing this dataset, we aim to facilitate the automatic segmentation of roots and the research of RSA with deep learning and other image analysis algorithms.
This dissertation addresses visual scene understanding and enhances segmentation performance and generalization, training efficiency of networks, and holistic understanding. First, we investigate semantic segmentation in the context of street scenes and train semantic segmentation networks on combinations of various datasets. In Chapter 2 we design a framework of hierarchical classifiers over a single convolutional backbone, and train it end-to-end on a combination of pixel-labeled datasets, improving generalizability and the number of recognizable semantic concepts. Chapter 3 focuses on enriching semantic segmentation with weak supervision and proposes a weakly-supervised algorithm for training with bounding box-level and image-level supervision instead of only with per-pixel supervision. The memory and computational load challenges that arise from simultaneous training on multiple datasets are addressed in Chapter 4. We propose two methodologies for selecting informative and diverse samples from datasets with weak supervision to reduce our networks' ecological footprint without sacrificing performance. Motivated by memory and computation efficiency requirements, in Chapter 5, we rethink simultaneous training on heterogeneous datasets and propose a universal semantic segmentation framework. This framework achieves consistent increases in performance metrics and semantic knowledgeability by exploiting various scene understanding datasets. Chapter 6 introduces the novel task of part-aware panoptic segmentation, which extends our reasoning towards holistic scene understanding. This task combines scene and parts-level semantics with instance-level object detection. In conclusion, our contributions span over convolutional network architectures, weakly-supervised learning, part and panoptic segmentation, paving the way towards a holistic, rich, and sustainable visual scene understanding.
Weakly supervised learning can help local feature methods to overcome the obstacle of acquiring a large-scale dataset with densely labeled correspondences. However, since weak supervision cannot distinguish the losses caused by the detection and description steps, directly conducting weakly supervised learning within a joint describe-then-detect pipeline suffers limited performance. In this paper, we propose a decoupled describe-then-detect pipeline tailored for weakly supervised local feature learning. Within our pipeline, the detection step is decoupled from the description step and postponed until discriminative and robust descriptors are learned. In addition, we introduce a line-to-window search strategy to explicitly use the camera pose information for better descriptor learning. Extensive experiments show that our method, namely PoSFeat (Camera Pose Supervised Feature), outperforms previous fully and weakly supervised methods and achieves state-of-the-art performance on a wide range of downstream tasks.
Using only global image-class labels, weakly-supervised learning methods, such as class activation mapping, allow training CNNs to jointly classify an image, and locate regions of interest associated with the predicted class. However, without any guidance at the pixel level, such methods may yield inaccurate regions. This problem is known to be more challenging with histology images than with natural ones, since objects are less salient, structures have more variations, and foreground and background regions have stronger similarities. Therefore, computer vision methods for visual interpretation of CNNs may not directly apply. In this paper, a simple yet efficient method based on a composite loss is proposed to learn information from the fully negative samples (i.e., samples without positive regions), and thereby reduce false positives/negatives. Our new loss function contains two complementary terms: the first exploits positive evidence collected from the CNN classifier, while the second leverages the fully negative samples from training data. In particular, a pre-trained CNN is equipped with a decoder that allows refining the regions of interest. The CNN is exploited to collect both positive and negative evidence at the pixel level to train the decoder. Our method called NEGEV benefits from the fully negative samples that naturally occur in the data, without any additional supervision signals beyond image-class labels. Extensive experiments show that our proposed method can substantial outperform related state-of-art methods on GlaS (public benchmark for colon cancer), and Camelyon16 (patch-based benchmark for breast cancer using three different backbones). Our results highlight the benefits of using both positive and negative evidence, the first obtained from a classifier, and the other naturally available in datasets.
Over the past several years, legal applications of deep learning have been on the rise. However, as with other high-stakes decision making areas, the requirement for interpretability is of crucial importance. Current models utilized by legal practitioners are more of the conventional machine learning type, wherein they are inherently interpretable, yet unable to harness the performance capabilities of data-driven deep learning models. In this work, we utilize deep learning models in the area of trademark law to shed light on the issue of likelihood of confusion between trademarks. Specifically, we introduce a model-agnostic interpretable intermediate layer, a technique which proves to be effective for legal documents. Furthermore, we utilize weakly supervised learning by means of a curriculum learning strategy, effectively demonstrating the improved performance of a deep learning model. This is in contrast to the conventional models which are only able to utilize the limited number of expensive manually-annotated samples by legal experts. Although the methods presented in this work tackles the task of risk of confusion for trademarks, it is straightforward to extend them to other fields of law, or more generally, to other similar high-stakes application scenarios.
In response to pathogens, the adaptive immune system generates specific antibodies that bind and neutralize foreign antigens. Understanding the composition of an individual's immune repertoire can provide insights into this process and reveal potential therapeutic antibodies. In this work, we explore the application of antibody-specific language models to aid understanding of immune repertoires. We introduce AntiBERTy, a language model trained on 558M natural antibody sequences. We find that within repertoires, our model clusters antibodies into trajectories resembling affinity maturation. Importantly, we show that models trained to predict highly redundant sequences under a multiple instance learning framework identify key binding residues in the process. With further development, the methods presented here will provide new insights into antigen binding from repertoire sequences alone.
Large scale datasets created from crowdsourced labels or openly available data have become crucial to provide training data for large scale learning algorithms. While these datasets are easier to acquire, the data are frequently noisy and unreliable, which is motivating research on weakly supervised learning techniques. In this paper we propose original ideas that help us to leverage such datasets in the context of change detection. First, we propose the guided anisotropic diffusion (GAD) algorithm, which improves semantic segmentation results using the input images as guides to perform edge preserving filtering. We then show its potential in two weakly-supervised learning strategies tailored for change detection. The first strategy is an iterative learning method that combines model optimisation and data cleansing using GAD to extract the useful information from a large scale change detection dataset generated from open vector data. The second one incorporates GAD within a novel spatial attention layer that increases the accuracy of weakly supervised networks trained to perform pixel-level predictions from image-level labels. Improvements with respect to state-of-the-art are demonstrated on 4 different public datasets.
Partial-label learning is a kind of weakly-supervised learning with inexact labels, where for each training example, we are given a set of candidate labels instead of only one true label. Recently, various approaches on partial-label learning have been proposed under different generation models of candidate label sets. However, these methods require relatively strong distributional assumptions on the generation models. When the assumptions do not hold, the performance of the methods is not guaranteed theoretically. In this paper, we propose the notion of properness on partial labels. We show that this proper partial-label learning framework requires a weaker distributional assumption and includes many previous partial-label learning settings as special cases. We then derive a unified unbiased estimator of the classification risk. We prove that our estimator is risk-consistent, and we also establish an estimation error bound. Finally, we validate the effectiveness of our algorithm through experiments.
The Query Focused Text Summarization (QFTS) task aims at building systems that generate the summary of the text document(s) based on the given query. A key challenge in addressing this task is the lack of large labeled data for training the summarization model. In this paper, we address this challenge by exploring a series of domain adaptation techniques. Given the recent success of pre-trained transformer models in a wide range of natural language processing tasks, we utilize such models to generate abstractive summaries for the QFTS task for both single-document and multi-document scenarios. For domain adaptation, we apply a variety of techniques using pre-trained transformer-based summarization models including transfer learning, weakly supervised learning, and distant supervision. Extensive experiments on six datasets show that our proposed approach is very effective in generating abstractive summaries for the QFTS task while setting a new state-of-the-art result in several datasets across a set of automatic and human evaluation metrics.
Compared with contact detection techniques, pavement crack identification with visual images via deep learning algorithms has the advantages of not being limited by the material of object to be detected, fast speed and low cost. The fundamental frameworks and typical model architectures of transfer learning (TL), encoder-decoder (ED), generative adversarial networks (GAN), and their common modules were first reviewed, and then the evolution of convolutional neural network (CNN) backbone models and GAN models were summarized. The crack classification, segmentation performance, and effect were tested on the SDNET2018 and CFD public data sets. In the aspect of patch sample classification, the fine-tuned TL models can be equivalent to or even slightly better than the ED models in accuracy, and the predicting time is faster; In the aspect of accurate crack location, both ED and GAN algorithms can achieve pixel-level segmentation and is expected to be detected in real time on low computing power platform. Furthermore, a weakly supervised learning framework of combined TL-SSGAN and its performance enhancement measures are proposed, which can maintain comparable crack identification performance with that of the supervised learning, while greatly reducing the number of labeled samples required.
Population imaging studies rely upon good quality medical imagery before downstream image quantification. This study provides an automated approach to assess image quality from cardiovascular magnetic resonance (CMR) imaging at scale. We identify four common CMR imaging artefacts, including respiratory motion, cardiac motion, Gibbs ringing, and aliasing. The model can deal with images acquired in different views, including two, three, and four-chamber long-axis and short-axis cine CMR images. Two deep learning-based models in spatial and frequency domains are proposed. Besides recognising these artefacts, the proposed models are suitable to the common challenges of not having access to data labels. An unsupervised domain adaptation method and a Fourier-based convolutional neural network are proposed to overcome these challenges. We show that the proposed models reliably allow for CMR image quality assessment. The accuracies obtained for the spatial model in supervised and weakly supervised learning are 99.41+0.24 and 96.37+0.66 for the UK Biobank dataset, respectively. Using unsupervised domain adaptation can somewhat overcome the challenge of not having access to the data labels. The maximum achieved domain gap coverage in unsupervised domain adaptation is 16.86%. Domain adaptation can significantly improve a 5-class classification task and deal with considerable domain shift without data labels. Increasing the speed of training and testing can be achieved with the proposed model in the frequency domain. The frequency-domain model can achieve the same accuracy yet 1.548 times faster than the spatial model. This model can also be used directly on k-space data, and there is no need for image reconstruction.