Rethinking Polyp Segmentation from an Out-of-Distribution Perspective

Unlike existing fully-supervised approaches, we rethink colorectal polyp segmentation from an out-of-distribution perspective with a simple but effective self-supervised learning approach. We leverage the ability of masked autoencoders -- self-supervised vision transformers trained on a reconstruction task -- to learn in-distribution representations; here, the distribution of healthy colon images. We then perform out-of-distribution reconstruction and inference, with feature space standardisation to align the latent distribution of the diverse abnormal samples with the statistics of the healthy samples. We generate per-pixel anomaly scores for each image by calculating the difference between the input and reconstructed images and use this signal for out-of-distribution (ie, polyp) segmentation. Experimental results on six benchmarks show that our model has excellent segmentation performance and generalises across datasets. Our code is publicly available at https://github.com/GewelsJI/Polyp-OOD.Comment: Technical repor

Deep learning for unsupervised domain adaptation in medical imaging: Recent advancements and future perspectives

Deep learning has demonstrated remarkable performance across various tasks in medical imaging. However, these approaches primarily focus on supervised learning, assuming that the training and testing data are drawn from the same distribution. Unfortunately, this assumption may not always hold true in practice. To address these issues, unsupervised domain adaptation (UDA) techniques have been developed to transfer knowledge from a labeled domain to a related but unlabeled domain. In recent years, significant advancements have been made in UDA, resulting in a wide range of methodologies, including feature alignment, image translation, self-supervision, and disentangled representation methods, among others. In this paper, we provide a comprehensive literature review of recent deep UDA approaches in medical imaging from a technical perspective. Specifically, we categorize current UDA research in medical imaging into six groups and further divide them into finer subcategories based on the different tasks they perform. We also discuss the respective datasets used in the studies to assess the divergence between the different domains. Finally, we discuss emerging areas and provide insights and discussions on future research directions to conclude this survey.Comment: Under Revie

Confident-Anchor-Induced Multi-Source-Free Domain Adaptation

Unsupervised domain adaptation has attracted appealing academic attentions by transferring knowledge from labeled source domain to unlabeled target domain. However, most existing methods assume the source data are drawn from a single domain, which cannot be successfully applied to explore complementarily transferable knowledge from multiple source domains with large distribution discrepancies. Moreover, they require access to source data during training, which are inefficient and unpractical due to privacy preservation and memory storage. To address these challenges, we develop a novel Confident-Anchor-induced multi-source-free Domain Adaptation (CAiDA) model, which is a pioneer exploration of knowledge adaptation from multiple source domains to the unlabeled target domain without any source data, but with only pre-trained source models. Specifically, a source-specific transferable perception module is proposed to automatically quantify the contributions of the complementary knowledge transferred from multi-source domains to the target domain. To generate pseudo labels for the target domain without access to the source data, we develop a confident-anchor-induced pseudo label generator by constructing a confident anchor group and assigning each unconfident target sample with a semantic-nearest confident anchor. Furthermore, a class-relationship-aware consistency loss is proposed to preserve consistent inter-class relationships by aligning soft confusion matrices across domains. Theoretical analysis answers why multi-source domains are better than a single source domain, and establishes a novel learning bound to show the effectiveness of exploiting multi-source domains. Experiments on several representative datasets illustrate the superiority of our proposed CAiDA model. The code is available at https://github.com/Learning-group123/CAiDA

Weakly-Supervised Dense Action Anticipation

Dense anticipation aims to forecast future actions and their durations for long horizons. Existing approaches rely on fully-labelled data, i.e. sequences labelled with all future actions and their durations. We present a (semi-) weakly supervised method using only a small number of fully-labelled sequences and predominantly sequences in which only the (one) upcoming action is labelled. To this end, we propose a framework that generates pseudo-labels for future actions and their durations and adaptively refines them through a refinement module. Given only the upcoming action label as input, these pseudo-labels guide action/duration prediction for the future. We further design an attention mechanism to predict context-aware durations. Experiments on the Breakfast and 50Salads benchmarks verify our method's effectiveness; we are competitive even when compared to fully supervised state-of-the-art models. We will make our code available at: https://github.com/zhanghaotong1/WSLVideoDenseAnticipation.Comment: BMVC 202

Confocal Laser Endomicroscopy Image Analysis with Deep Convolutional Neural Networks

abstract: Rapid intraoperative diagnosis of brain tumors is of great importance for planning treatment and guiding the surgeon about the extent of resection. Currently, the standard for the preliminary intraoperative tissue analysis is frozen section biopsy that has major limitations such as tissue freezing and cutting artifacts, sampling errors, lack of immediate interaction between the pathologist and the surgeon, and time consuming. Handheld, portable confocal laser endomicroscopy (CLE) is being explored in neurosurgery for its ability to image histopathological features of tissue at cellular resolution in real time during brain tumor surgery. Over the course of examination of the surgical tumor resection, hundreds to thousands of images may be collected. The high number of images requires significant time and storage load for subsequent reviewing, which motivated several research groups to employ deep convolutional neural networks (DCNNs) to improve its utility during surgery. DCNNs have proven to be useful in natural and medical image analysis tasks such as classification, object detection, and image segmentation. This thesis proposes using DCNNs for analyzing CLE images of brain tumors. Particularly, it explores the practicality of DCNNs in three main tasks. First, off-the shelf DCNNs were used to classify images into diagnostic and non-diagnostic. Further experiments showed that both ensemble modeling and transfer learning improved the classifier’s accuracy in evaluating the diagnostic quality of new images at test stage. Second, a weakly-supervised learning pipeline was developed for localizing key features of diagnostic CLE images from gliomas. Third, image style transfer was used to improve the diagnostic quality of CLE images from glioma tumors by transforming the histology patterns in CLE images of fluorescein sodium-stained tissue into the ones in conventional hematoxylin and eosin-stained tissue slides. These studies suggest that DCNNs are opted for analysis of CLE images. They may assist surgeons in sorting out the non-diagnostic images, highlighting the key regions and enhancing their appearance through pattern transformation in real time. With recent advances in deep learning such as generative adversarial networks and semi-supervised learning, new research directions need to be followed to discover more promises of DCNNs in CLE image analysis.Dissertation/ThesisDoctoral Dissertation Neuroscience 201