Semantic segmentation of various tissue and nuclei types in histology images is fundamental to many downstream tasks in the area of computational pathology (CPath). In recent years, Deep Learning (DL) methods have been shown to perform well on segmentation tasks but DL methods generally require a large amount of pixel-wise annotated data. Pixel-wise annotation sometimes requires expert's knowledge and time which is laborious and costly to obtain. In this paper, we present a consistency based semi-supervised learning (SSL) approach that can help mitigate this challenge by exploiting a large amount of unlabelled data for model training thus alleviating the need for a large annotated dataset. However, SSL models might also be susceptible to changing context and features perturbations exhibiting poor generalisation due to the limited training data. We propose an SSL method that learns robust features from both labelled and unlabelled images by enforcing consistency against varying contexts and feature perturbations. The proposed method incorporates context-aware consistency by contrasting pairs of overlapping images in a pixel-wise manner from changing contexts resulting in robust and context invariant features. We show that cross-consistency training makes the encoder features invariant to different perturbations and improves the prediction confidence. Finally, entropy minimisation is employed to further boost the confidence of the final prediction maps from unlabelled data. We conduct an extensive set of experiments on two publicly available large datasets (BCSS and MoNuSeg) and show superior performance compared to the state-of-the-art methods.
Institute of Building Materials Science, Leibniz University Hannover（莱布尼茨汉诺威大学建筑材料科学研究所）；Institute of Photogrammetry and GeoInformation, Leibniz University Hannover（莱布尼茨汉诺威大学摄影测量与地理信息研究所）
In order to leverage and profit from unlabelled data, semi-supervised frameworks for semantic segmentation based on consistency training have been proven to be powerful tools to significantly improve the performance of purely supervised segmentation learning. However, the consensus principle behind consistency training has at least one drawback, which we identify in this paper: imbalanced label distributions within the data. To overcome the limitations of standard consistency training, we propose a novel semi-supervised framework for semantic segmentation, introducing additional losses based o…
The Hong Kong University of Science and Technology（香港科技大学）
Nuclei Segmentation from histology images is a fundamental task in digital pathology analysis. However, deep-learning-based nuclei segmentation methods often suffer from limited annotations. This paper proposes a realistic data augmentation method for nuclei segmentation, named InsMix, that follows a Copy-Paste-Smooth principle and performs morphology-constrained generative instance augmentation. Specifically, we propose morphology constraints that enable the augmented images to acquire luxuriant information about nuclei while maintaining their morphology characteristics (e.g., geometry and lo…
AI Clearing, Inc.（AI清算公司）；Semantic Technology Institute, Department of Computer Science, University of Innsbruck（因斯布鲁克大学语义技术研究所）；Institute of Informatics, University of Warsaw（华沙大学信息学研究所）
We present n-CPS - a generalisation of the recent state-of-the-art cross pseudo supervision (CPS) approach for the task of semi-supervised semantic segmentation. In n-CPS, there are n simultaneously trained subnetworks that learn from each other through one-hot encoding perturbation and consistency regularisation. We also show that ensembling techniques applied to subnetworks outputs can significantly improve the performance. To the best of our knowledge, n-CPS paired with CutMix outperforms CPS and sets the new state-of-the-art for Pascal VOC 2012 with (1/16, 1/8, 1/4, and 1/2 supervised regi…
Queen Mary University of London（伦敦玛丽女王大学）；Vision Semantics Limited（视觉语义有限公司）
Existing facial image super-resolution (SR) methods focus mostly on improving artificially down-sampled low-resolution (LR) imagery. Such SR models, although strong at handling artificial LR images, often suffer from significant performance drop on genuine LR test data. Previous unsupervised domain adaptation (UDA) methods address this issue by training a model using unpaired genuine LR and HR data as well as cycle consistency loss formulation. However, this renders the model overstretched with two tasks: consistifying the visual characteristics and enhancing the image resolution. Importantly,…
We present a semi-supervised method for panoptic segmentation based on ConsInstancy regularisation, a novel strategy for semi-supervised learning. It leverages completely unlabelled data by enforcing consistency between predicted instance representations and semantic segmentations during training in order to improve the segmentation performance. To this end, we also propose new types of instance representations that can be predicted by one simple forward path through a fully convolutional network (FCN), delivering a convenient and simple-to-train framework for panoptic segmentation. More speci…
Score-based Diffusion Model for Unpaired Virtual Histology Staining
Department of Health Technology and Informatics, Hong Kong Polytechnic University, China（香港理工大学健康科技与信息学系）；Department of Clinical Neurosciences, University of Cambridge, UK（剑桥大学临床神经科学系）；School of Science and Engineering, University of Dundee, UK（邓迪大学科学与工程学院）；Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK（剑桥大学应用数学与理论物理系）
IMT School for Advanced Studies Lucca（卢卡IMT高等研究院）；University of Edinburgh（爱丁堡大学）
Collecting large-scale medical datasets with fine-grained annotations is time-consuming and requires experts. For this reason, weakly supervised learning aims at optimising machine learning models using weaker forms of annotations, such as scribbles, which are easier and faster to collect. Unfortunately, training with weak labels is challenging and needs regularisation. Herein, we introduce a novel self-supervised multi-scale consistency loss, which, coupled with an attention mechanism, encourages the segmentor to learn multi-scale relationships between objects and improves performance. We sho…
Virtual staining for 3D X-ray histology of bone implants
Institute of Materials Physics（材料物理研究所）；Helmholtz-Zentrum Hereon（海德堡研究中心）；Institute of Metallic Biomaterials（金属生物材料研究所）；Bruker Daltonics SPR（布鲁克尔达特利克斯SPR）；Data-Driven Analysis and Design of Materials（数据驱动的材料分析与设计）；University of Rostock（罗斯托克大学）
Learning Structurally Consistent Representations for Multi-View Radar Semantic Segmentation
School of Computing, Engineering and Mathematical Sciences, La Trobe University（拉筹伯大学计算、工程与数学科学学院）；La Trobe Institute for Sustainable Agriculture & Food (LISAF)（拉筹伯大学可持续农业与食品研究所）；School of Engineering and Applied Sciences, GIFT University（GIFT大学工程与应用科学学院）；Commonwealth Scientific and Industrial Research Organisation (CSIRO)（澳大利亚联邦科学与工业研究组织）
Sunnybrook Research Institute（桑尼布鲁克研究所）；University of Toronto（多伦多大学）
Training a neural network with a large labeled dataset is still a dominant paradigm in computational histopathology. However, obtaining such exhaustive manual annotations is often expensive, laborious, and prone to inter and Intra-observer variability. While recent self-supervised and semi-supervised methods can alleviate this need by learn-ing unsupervised feature representations, they still struggle to generalize well to downstream tasks when the number of labeled instances is small. In this work, we overcome this challenge by leveraging both task-agnostic and task-specific unlabeled data ba…
Jiangnan University（江南大学）；University of Surrey（萨里大学）
With efficient appearance learning models, Discriminative Correlation Filter (DCF) has been proven to be very successful in recent video object tracking benchmarks and competitions. However, the existing DCF paradigm suffers from two major issues, i.e., spatial boundary effect and temporal filter degradation. To mitigate these challenges, we propose a new DCF-based tracking method. The key innovations of the proposed method include adaptive spatial feature selection and temporal consistent constraints, with which the new tracker enables joint spatial-temporal filter learning in a lower dimensi…
Hyperspectral imaging has the potential to improve intraoperative decision making if tissue characterisation is performed in real-time and with high-resolution. Hyperspectral snapshot mosaic sensors offer a promising approach due to their fast acquisition speed and compact size. However, a demosaicking algorithm is required to fully recover the spatial and spectral information of the snapshot images. Most state-of-the-art demosaicking algorithms require ground-truth training data with paired snapshot and high-resolution hyperspectral images, but such imagery pairs with the exact same scene are…
South Australian Health and Medical Research Institute（南澳大利亚健康与医学研究所）；Research & Development Institute of Northwestern Polytechnical University in Shenzhen（西北工业大学深圳研究院）；National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology（空天地海一体化大数据应用技术国家工程实验室）；Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）
Accurate and automated gland segmentation on histology tissue images is an essential but challenging task in the computer-aided diagnosis of adenocarcinoma. Despite their prevalence, deep learning models always require a myriad number of densely annotated training images, which are difficult to obtain due to extensive labor and associated expert costs related to histology image annotations. In this paper, we propose the pairwise relation-based semi-supervised (PRS^2) model for gland segmentation on histology images. This model consists of a segmentation network (S-Net) and a pairwise relation …
HIBMatch: Hypergraph Information Bottleneck for Semi-supervised Alzheimer's Progression
Department of Applied Mathematics and Theoretical Physics, University of Cambridge（应用数学与理论物理系，剑桥大学）；Department of Biomedical Engineering, The Hong Kong Polytechnic University（生物医学工程系，香港理工大学）；Research Institute for Artificial Intelligence of Things, The Hong Kong Polytechnic University（物联网人工智能研究所，香港理工大学）；Yau Mathematical Sciences Centre, Tsinghua University（叶德平数学科学中心，清华大学）
Unsupervised Domain Adaptation (UDA) aims to adapt models trained on a source domain to a new target domain where no labelled data is available. In this work, we investigate the problem of UDA from a synthetic computer-generated domain to a similar but real-world domain for learning semantic segmentation. We propose a semantically consistent image-to-image translation method in combination with a consistency regularisation method for UDA. We overcome previous limitations on transferring synthetic images to real looking images. We leverage pseudo-labels in order to learn a generative image-to-i…
RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency
Stony Brook University（石英溪大学）；Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School（阿提诺拉A.马丁努斯生物医学影像中心，麻省总医院和哈佛医学院）；Department of Biomedical Data Science, Stanford University（生物医学数据科学系，斯坦福大学）；Department of Pathology and Cell Biology, Columbia University（病理学与细胞生物学系，哥伦比亚大学）
Recent advances in end-to-end unsupervised learning has significantly improved the performance of monocular depth prediction and alleviated the requirement of ground truth depth. Although a plethora of work has been done in enforcing various structural constraints by incorporating multiple losses utilising smoothness, left-right consistency, regularisation and matching surface normals, a few of them take into consideration multi-scale structures present in real world images. Most works utilise a VGG16 or ResNet50 model pre-trained on ImageNet weights for predicting depth. We propose a deep fea…
Self-supervised learning of depth has been a highly studied topic of research as it alleviates the requirement of having ground truth annotations for predicting depth. Depth is learnt as an intermediate solution to the task of view synthesis, utilising warped photometric consistency. Although it gives good results when trained using stereo data, the predicted depth is still sensitive to noise, illumination changes and specular reflections. Also, occlusion can be tackled better by learning depth from a single camera. We propose ADAA, utilising depth augmentation as depth supervision for learnin…
Centre For Medical Image Computing, UCL（伦敦大学学院医学图像计算中心）；UCL（伦敦大学学院）；Department of Medical Physics and Biomedical Engineering, UCL（伦敦大学学院医学物理与生物医学工程系）；Department of Computer Science, UCL（伦敦大学学院计算机科学系）；GlaxoSmithKline Research & Development（葛兰素史克研发部）；UCL Respiratory, University College London Hospital, UCL（伦敦大学学院医院伦敦大学学院呼吸科）
We propose MisMatch, a novel consistency-driven semi-supervised segmentation framework which produces predictions that are invariant to learnt feature perturbations. MisMatch consists of an encoder and a two-head decoders. One decoder learns positive attention to the foreground regions of interest (RoI) on unlabelled images thereby generating dilated features. The other decoder learns negative attention to the foreground on the same unlabelled images thereby generating eroded features. We then apply a consistency regularisation on the paired predictions. MisMatch outperforms state-of-the-art s…
A neurosymbolic Approach with Epistemic Deep Learning for Hierarchical Image Classification
Institute for AI, Data Analysis and Systems (AIDAS) School of Engineering, Computing and Mathematics, Oxford Brookes University, UK（人工智能、数据分析和系统研究所（AIDAS）工程、计算与数学学院，英国奥克斯福德布鲁克斯大学）
University College London（伦敦大学学院）；GSK R & D（葛兰素史克研发部）
This paper concerns pseudo labelling in segmentation. Our contribution is fourfold. Firstly, we present a new formulation of pseudo-labelling as an Expectation-Maximization (EM) algorithm for clear statistical interpretation. Secondly, we propose a semi-supervised medical image segmentation method purely based on the original pseudo labelling, namely SegPL. We demonstrate SegPL is a competitive approach against state-of-the-art consistency regularisation based methods on semi-supervised segmentation on a 2D multi-class MRI brain tumour segmentation task and a 3D binary CT lung vessel segmentat…
