Yuanhong Chen

Yuyuan Liu, Yu Tian, Chong Wang et al.

3D medical image segmentation methods have been successful, but their dependence on large amounts of voxel-level annotated data is a disadvantage that needs to be addressed given the high cost to obtain such annotation. Semi-supervised learning (SSL) solve this issue by training models with a large unlabelled and a small labelled dataset. The most successful SSL approaches are based on consistency learning that minimises the distance between model responses obtained from perturbed views of the unlabelled data. These perturbations usually keep the spatial input context between views fairly consistent, which may cause the model to learn segmentation patterns from the spatial input contexts instead of the segmented objects. In this paper, we introduce the Translation Consistent Co-training (TraCoCo) which is a consistency learning SSL method that perturbs the input data views by varying their spatial input context, allowing the model to learn segmentation patterns from visual objects. Furthermore, we propose the replacement of the commonly used mean squared error (MSE) semi-supervised loss by a new Cross-model confident Binary Cross entropy (CBC) loss, which improves training convergence and keeps the robustness to co-training pseudo-labelling mistakes. We also extend CutMix augmentation to 3D SSL to further improve generalisation. Our TraCoCo shows state-of-the-art results for the Left Atrium (LA) and Brain Tumor Segmentation (BRaTS19) datasets with different backbones. Our code is available at https://github.com/yyliu01/TraCoCo.

Chong Wang, Yuyuan Liu, Yuanhong Chen et al.

Prototypical part network (ProtoPNet) methods have been designed to achieve interpretable classification by associating predictions with a set of training prototypes, which we refer to as trivial prototypes because they are trained to lie far from the classification boundary in the feature space. Note that it is possible to make an analogy between ProtoPNet and support vector machine (SVM) given that the classification from both methods relies on computing similarity with a set of training points (i.e., trivial prototypes in ProtoPNet, and support vectors in SVM). However, while trivial prototypes are located far from the classification boundary, support vectors are located close to this boundary, and we argue that this discrepancy with the well-established SVM theory can result in ProtoPNet models with inferior classification accuracy. In this paper, we aim to improve the classification of ProtoPNet with a new method to learn support prototypes that lie near the classification boundary in the feature space, as suggested by the SVM theory. In addition, we target the improvement of classification results with a new model, named ST-ProtoPNet, which exploits our support prototypes and the trivial prototypes to provide more effective classification. Experimental results on CUB-200-2011, Stanford Cars, and Stanford Dogs datasets demonstrate that ST-ProtoPNet achieves state-of-the-art classification accuracy and interpretability results. We also show that the proposed support prototypes tend to be better localised in the object of interest rather than in the background region.

Yuanhong Chen, Hu Wang, Chong Wang et al.

When analysing screening mammograms, radiologists can naturally process information across two ipsilateral views of each breast, namely the cranio-caudal (CC) and mediolateral-oblique (MLO) views. These multiple related images provide complementary diagnostic information and can improve the radiologist's classification accuracy. Unfortunately, most existing deep learning systems, trained with globally-labelled images, lack the ability to jointly analyse and integrate global and local information from these multiple views. By ignoring the potentially valuable information present in multiple images of a screening episode, one limits the potential accuracy of these systems. Here, we propose a new multi-view global-local analysis method that mimics the radiologist's reading procedure, based on a global consistency learning and local co-occurrence learning of ipsilateral views in mammograms. Extensive experiments show that our model outperforms competing methods, in terms of classification accuracy and generalisation, on a large-scale private dataset and two publicly available datasets, where models are exclusively trained and tested with global labels.

Chong Wang, Yuanhong Chen, Yuyuan Liu et al.

State-of-the-art (SOTA) deep learning mammogram classifiers, trained with weakly-labelled images, often rely on global models that produce predictions with limited interpretability, which is a key barrier to their successful translation into clinical practice. On the other hand, prototype-based models improve interpretability by associating predictions with training image prototypes, but they are less accurate than global models and their prototypes tend to have poor diversity. We address these two issues with the proposal of BRAIxProtoPNet++, which adds interpretability to a global model by ensembling it with a prototype-based model. BRAIxProtoPNet++ distills the knowledge of the global model when training the prototype-based model with the goal of increasing the classification accuracy of the ensemble. Moreover, we propose an approach to increase prototype diversity by guaranteeing that all prototypes are associated with different training images. Experiments on weakly-labelled private and public datasets show that BRAIxProtoPNet++ has higher classification accuracy than SOTA global and prototype-based models. Using lesion localisation to assess model interpretability, we show BRAIxProtoPNet++ is more effective than other prototype-based models and post-hoc explanation of global models. Finally, we show that the diversity of the prototypes learned by BRAIxProtoPNet++ is superior to SOTA prototype-based approaches.

Hu Wang, Jianpeng Zhang, Yuanhong Chen et al.

Multi-modal learning focuses on training models by equally combining multiple input data modalities during the prediction process. However, this equal combination can be detrimental to the prediction accuracy because different modalities are usually accompanied by varying levels of uncertainty. Using such uncertainty to combine modalities has been studied by a couple of approaches, but with limited success because these approaches are either designed to deal with specific classification or segmentation problems and cannot be easily translated into other tasks, or suffer from numerical instabilities. In this paper, we propose a new Uncertainty-aware Multi-modal Learner that estimates uncertainty by measuring feature density via Cross-modal Random Network Prediction (CRNP). CRNP is designed to require little adaptation to translate between different prediction tasks, while having a stable training process. From a technical point of view, CRNP is the first approach to explore random network prediction to estimate uncertainty and to combine multi-modal data. Experiments on two 3D multi-modal medical image segmentation tasks and three 2D multi-modal computer vision classification tasks show the effectiveness, adaptability and robustness of CRNP. Also, we provide an extensive discussion on different fusion functions and visualization to validate the proposed model.

Yuyuan Liu, Yuanhong Chen, Hu Wang et al.

The costly and time-consuming annotation process to produce large training sets for modelling semantic LiDAR segmentation methods has motivated the development of semi-supervised learning (SSL) methods. However, such SSL approaches often concentrate on employing consistency learning only for individual LiDAR representations. This narrow focus results in limited perturbations that generally fail to enable effective consistency learning. Additionally, these SSL approaches employ contrastive learning based on the sampling from a limited set of positive and negative embedding samples. This paper introduces a novel semi-supervised LiDAR semantic segmentation framework called ItTakesTwo (IT2). IT2 is designed to ensure consistent predictions from peer LiDAR representations, thereby improving the perturbation effectiveness in consistency learning. Furthermore, our contrastive learning employs informative samples drawn from a distribution of positive and negative embeddings learned from the entire training set. Results on public benchmarks show that our approach achieves remarkable improvements over the previous state-of-the-art (SOTA) methods in the field. The code is available at: https://github.com/yyliu01/IT2.

Chong Wang, Yuanhong Chen, Fengbei Liu et al.

Prototypical-part methods, e.g., ProtoPNet, enhance interpretability in image recognition by linking predictions to training prototypes, thereby offering intuitive insights into their decision-making. Existing methods, which rely on a point-based learning of prototypes, typically face two critical issues: 1) the learned prototypes have limited representation power and are not suitable to detect Out-of-Distribution (OoD) inputs, reducing their decision trustworthiness; and 2) the necessary projection of the learned prototypes back into the space of training images causes a drastic degradation in the predictive performance. Furthermore, current prototype learning adopts an aggressive approach that considers only the most active object parts during training, while overlooking sub-salient object regions which still hold crucial classification information. In this paper, we present a new generative paradigm to learn prototype distributions, termed as Mixture of Gaussian-distributed Prototypes (MGProto). The distribution of prototypes from MGProto enables both interpretable image classification and trustworthy recognition of OoD inputs. The optimisation of MGProto naturally projects the learned prototype distributions back into the training image space, thereby addressing the performance degradation caused by prototype projection. Additionally, we develop a novel and effective prototype mining strategy that considers not only the most active but also sub-salient object parts. To promote model compactness, we further propose to prune MGProto by removing prototypes with low importance priors. Experiments on CUB-200-2011, Stanford Cars, Stanford Dogs, and Oxford-IIIT Pets datasets show that MGProto achieves state-of-the-art image recognition and OoD detection performances, while providing encouraging interpretability results.

Yuyuan Liu, Yu Tian, Yuanhong Chen et al.

Consistency learning using input image, feature, or network perturbations has shown remarkable results in semi-supervised semantic segmentation, but this approach can be seriously affected by inaccurate predictions of unlabelled training images. There are two consequences of these inaccurate predictions: 1) the training based on the "strict" cross-entropy (CE) loss can easily overfit prediction mistakes, leading to confirmation bias; and 2) the perturbations applied to these inaccurate predictions will use potentially erroneous predictions as training signals, degrading consistency learning. In this paper, we address the prediction accuracy problem of consistency learning methods with novel extensions of the mean-teacher (MT) model, which include a new auxiliary teacher, and the replacement of MT's mean square error (MSE) by a stricter confidence-weighted cross-entropy (Conf-CE) loss. The accurate prediction by this model allows us to use a challenging combination of network, input data and feature perturbations to improve the consistency learning generalisation, where the feature perturbations consist of a new adversarial perturbation. Results on public benchmarks show that our approach achieves remarkable improvements over the previous SOTA methods in the field. Our code is available at https://github.com/yyliu01/PS-MT.

Yuanhong Chen, Yuyuan Liu, Chong Wang et al.

Methods to detect malignant lesions from screening mammograms are usually trained with fully annotated datasets, where images are labelled with the localisation and classification of cancerous lesions. However, real-world screening mammogram datasets commonly have a subset that is fully annotated and another subset that is weakly annotated with just the global classification (i.e., without lesion localisation). Given the large size of such datasets, researchers usually face a dilemma with the weakly annotated subset: to not use it or to fully annotate it. The first option will reduce detection accuracy because it does not use the whole dataset, and the second option is too expensive given that the annotation needs to be done by expert radiologists. In this paper, we propose a middle-ground solution for the dilemma, which is to formulate the training as a weakly- and semi-supervised learning problem that we refer to as malignant breast lesion detection with incomplete annotations. To address this problem, our new method comprises two stages, namely: 1) pre-training a multi-view mammogram classifier with weak supervision from the whole dataset, and 2) extending the trained classifier to become a multi-view detector that is trained with semi-supervised student-teacher learning, where the training set contains fully and weakly-annotated mammograms. We provide extensive detection results on two real-world screening mammogram datasets containing incomplete annotations, and show that our proposed approach achieves state-of-the-art results in the detection of malignant breast lesions with incomplete annotations.

Fengbei Liu, Yu Tian, Yuanhong Chen et al.

Effective semi-supervised learning (SSL) in medical image analysis (MIA) must address two challenges: 1) work effectively on both multi-class (e.g., lesion classification) and multi-label (e.g., multiple-disease diagnosis) problems, and 2) handle imbalanced learning (because of the high variance in disease prevalence). One strategy to explore in SSL MIA is based on the pseudo labelling strategy, but it has a few shortcomings. Pseudo-labelling has in general lower accuracy than consistency learning, it is not specifically designed for both multi-class and multi-label problems, and it can be challenged by imbalanced learning. In this paper, unlike traditional methods that select confident pseudo label by threshold, we propose a new SSL algorithm, called anti-curriculum pseudo-labelling (ACPL), which introduces novel techniques to select informative unlabelled samples, improving training balance and allowing the model to work for both multi-label and multi-class problems, and to estimate pseudo labels by an accurate ensemble of classifiers (improving pseudo label accuracy). We run extensive experiments to evaluate ACPL on two public medical image classification benchmarks: Chest X-Ray14 for thorax disease multi-label classification and ISIC2018 for skin lesion multi-class classification. Our method outperforms previous SOTA SSL methods on both datasets