Self-Supervised Neuron Segmentation with Multi-Agent Reinforcement Learning

The performance of existing supervised neuron segmentation methods is highly dependent on the number of accurate annotations, especially when applied to large scale electron microscopy (EM) data. By extracting semantic information from unlabeled data, self-supervised methods can improve the performance of downstream tasks, among which the mask image model (MIM) has been widely used due to its simplicity and effectiveness in recovering original information from masked images. However, due to the high degree of structural locality in EM images, as well as the existence of considerable noise, many voxels contain little discriminative information, making MIM pretraining inefficient on the neuron segmentation task. To overcome this challenge, we propose a decision-based MIM that utilizes reinforcement learning (RL) to automatically search for optimal image masking ratio and masking strategy. Due to the vast exploration space, using single-agent RL for voxel prediction is impractical. Therefore, we treat each input patch as an agent with a shared behavior policy, allowing for multi-agent collaboration. Furthermore, this multi-agent model can capture dependencies between voxels, which is beneficial for the downstream segmentation task. Experiments conducted on representative EM datasets demonstrate that our approach has a significant advantage over alternative self-supervised methods on the task of neuron segmentation. Code is available at \url{https://github.com/ydchen0806/dbMiM}.Comment: IJCAI 23 main track pape

Deep active learning for suggestive segmentation of biomedical image stacks via optimisation of Dice scores and traced boundary length

Manual segmentation of stacks of 2D biomedical images (e.g., histology) is a time-consuming task which can be sped up with semi-automated techniques. In this article, we present a suggestive deep active learning framework that seeks to minimise the annotation effort required to achieve a certain level of accuracy when labelling such a stack. The framework suggests, at every iteration, a specific region of interest (ROI) in one of the images for manual delineation. Using a deep segmentation neural network and a mixed cross-entropy loss function, we propose a principled strategy to estimate class probabilities for the whole stack, conditioned on heterogeneous partial segmentations of the 2D images, as well as on weak supervision in the form of image indices that bound each ROI. Using the estimated probabilities, we propose a novel active learning criterion based on predictions for the estimated segmentation performance and delineation effort, measured with average Dice scores and total delineated boundary length, respectively, rather than common surrogates such as entropy. The query strategy suggests the ROI that is expected to maximise the ratio between performance and effort, while considering the adjacency of structures that may have already been labelled – which decrease the length of the boundary to trace. We provide quantitative results on synthetically deformed MRI scans and real histological data, showing that our framework can reduce labelling effort by up to 60–70% without compromising accuracy

Transforming the Interactive Segmentation for Medical Imaging

The goal of this paper is to interactively refine the automatic segmentation on challenging structures that fall behind human performance, either due to the scarcity of available annotations or the difficulty nature of the problem itself, for example, on segmenting cancer or small organs. Specifically, we propose a novel Transformer-based architecture for Interactive Segmentation (TIS), that treats the refinement task as a procedure for grouping pixels with similar features to those clicks given by the end users. Our proposed architecture is composed of Transformer Decoder variants, which naturally fulfills feature comparison with the attention mechanisms. In contrast to existing approaches, our proposed TIS is not limited to binary segmentations, and allows the user to edit masks for arbitrary number of categories. To validate the proposed approach, we conduct extensive experiments on three challenging datasets and demonstrate superior performance over the existing state-of-the-art methods. The project page is: https://wtliu7.github.io/tis/.Comment: Accepted to MICCAI 202

Tools of Trade of the Next Blue-Collar Job? Antecedents, Design Features, and Outcomes of Interactive Labeling Systems

Supervised machine learning is becoming increasingly popular - and so is the need for annotated training data. Such data often needs to be manually labeled by human workers, not unlikely to negatively impact the involved workforce. To alleviate this issue, a new information systems class has emerged - interactive labeling systems. However, this young, but rapidly growing field lacks guidance and structure regarding the design of such systems. Against this backdrop, this paper describes antecedents, design features, and outcomes of interactive labeling systems. We perform a systematic literature review, identifying 188 relevant articles. Our results are presented as a morphological box with 14 dimensions, which we evaluate using card sorting. By additionally offering this box as a web-based artifact, we provide actionable guidance for interactive labeling system development for scholars and practitioners. Lastly, we discuss imbalances in the article distribution of our morphological box and suggest future work directions

Delineation of Road Networks from Remote Sensor Data with Deep Learning

In this thesis we address the problem of semantic segmentation in geospatial data. We investigate different deep neural network architectures and present a complete pipeline for extracting road network vector data from satellite RGB orthophotos of urban areas. Firstly, we present a network based on the SegNeXt architecture for the semantic segmentation of the roads. A novel loss function is introduced for training the network. The results show that the proposed network produces on average better results than other state-of-the-art semantic segmentation techniques. Secondly, we propose a fast post-processing technique for vectorizing the rasterized segmentation result, removing erroneous lines, and refining the road network. The result is a set of vectors representing the road network. We have extensively tested the proposed pipeline and provide quantitative comparisons with other state-of-the-art based on a number of known metrics. This work has been published and presented at the 14 th International Symposium on Visual Computing, 2019. Finally, we present an altogether different approach to road extraction. We reformulate the task of extracting vectorized road networks as a deep reinforcement learning problem with partially observable state-space and present our preliminary results and future work

Deep Reinforcement Learning Framework for Thoracic Diseases Classification via Prior Knowledge Guidance

The chest X-ray is often utilized for diagnosing common thoracic diseases. In recent years, many approaches have been proposed to handle the problem of automatic diagnosis based on chest X-rays. However, the scarcity of labeled data for related diseases still poses a huge challenge to an accurate diagnosis. In this paper, we focus on the thorax disease diagnostic problem and propose a novel deep reinforcement learning framework, which introduces prior knowledge to direct the learning of diagnostic agents and the model parameters can also be continuously updated as the data increases, like a person's learning process. Especially, 1) prior knowledge can be learned from the pre-trained model based on old data or other domains' similar data, which can effectively reduce the dependence on target domain data, and 2) the framework of reinforcement learning can make the diagnostic agent as exploratory as a human being and improve the accuracy of diagnosis through continuous exploration. The method can also effectively solve the model learning problem in the case of few-shot data and improve the generalization ability of the model. Finally, our approach's performance was demonstrated using the well-known NIH ChestX-ray 14 and CheXpert datasets, and we achieved competitive results. The source code can be found here: \url{https://github.com/NeaseZ/MARL}