Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userEvery Annotation Counts: Multi-label Deep Supervision for Medical Image Segmentation
112
0
0.0
(
0
)
Added by
Simon Rei{\\ss}
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Pixel-wise segmentation is one of the most data and annotation hungry tasks in our field. Providing representative and accurate annotations is often mission-critical especially for challenging medical applications. In this paper, we propose a semi-weakly supervised segmentation algorithm to overcome this barrier. Our approach is based on a new formulation of deep supervision and student-teacher model and allows for easy integration of different supervision signals. In contrast to previous work, we show that care has to be taken how deep supervision is integrated in lower layers and we present multi-label deep supervision as the most important secret ingredient for success. With our novel training regime for segmentation that flexibly makes use of images that are either fully labeled, marked with bounding boxes, just global labels, or not at all, we are able to cut the requirement for expensive labels by 94.22% - narrowing the gap to the best fully supervised baseline to only 5% mean IoU. Our approach is validated by extensive experiments on retinal fluid segmentation and we provide an in-depth analysis of the anticipated effect each annotation type can have in boosting segmentation performance.
rate research
Read More
Few-shot semantic segmentation (FSS) has great potential for medical imaging applications. Most of the existing FSS techniques require abundant annotated semantic classes for training. However, these methods may not be applicable for medical images due to the lack of annotations. To address this problem we make several contributions: (1) A novel self-supervised FSS framework for medical images in order to eliminate the requirement for annotations during training. Additionally, superpixel-based pseudo-labels are generated to provide supervision; (2) An adaptive local prototype pooling module plugged into prototypical networks, to solve the common challenging foreground-background imbalance problem in medical image segmentation; (3) We demonstrate the general applicability of the proposed approach for medical images using three different tasks: abdominal organ segmentation for CT and MRI, as well as cardiac segmentation for MRI. Our results show that, for medical image segmentation, the proposed method outperforms conventional FSS methods which require manual annotations for training.
Accurate image segmentation is crucial for medical imaging applications. The prevailing deep learning approaches typically rely on very large training datasets with high-quality manual annotations, which are often not available in medical imaging. We introduce Annotation-effIcient Deep lEarning (AIDE) to handle imperfect datasets with an elaborately designed cross-model self-correcting mechanism. AIDE improves the segmentation Dice scores of conventional deep learning models on open datasets possessing scarce or noisy annotations by up to 30%. For three clinical datasets containing 11,852 breast images of 872 patients from three medical centers, AIDE consistently produces segmentation maps comparable to those generated by the fully supervised counterparts as well as the manual annotations of independent radiologists by utilizing only 10% training annotations. Such a 10-fold improvement of efficiency in utilizing experts labels has the potential to promote a wide range of biomedical applications.
The success of deep learning methods in medical image segmentation tasks heavily depends on a large amount of labeled data to supervise the training. On the other hand, the annotation of biomedical images requires domain knowledge and can be laborious. Recently, contrastive learning has demonstrated great potential in learning latent representation of images even without any label. Existing works have explored its application to biomedical image segmentation where only a small portion of data is labeled, through a pre-training phase based on self-supervised contrastive learning without using any labels followed by a supervised fine-tuning phase on the labeled portion of data only. In this paper, we establish that by including the limited label in formation in the pre-training phase, it is possible to boost the performance of contrastive learning. We propose a supervised local contrastive loss that leverages limited pixel-wise annotation to force pixels with the same label to gather around in the embedding space. Such loss needs pixel-wise computation which can be expensive for large images, and we further propose two strategies, downsampling and block division, to address the issue. We evaluate our methods on two public biomedical image datasets of different modalities. With different amounts of labeled data, our methods consistently outperform the state-of-the-art contrast-based methods and other semi-supervised learning techniques.
Annotated images are required for both supervised model training and evaluation in image classification. Manually annotating images is arduous and expensive, especially for multi-labeled images. A recent trend for conducting such laboursome annotation tasks is through crowdsourcing, where images are annotated by volunteers or paid workers online (e.g., workers of Amazon Mechanical Turk) from scratch. However, the quality of crowdsourcing image annotations cannot be guaranteed, and incompleteness and incorrectness are two major concerns for crowdsourcing annotations. To address such concerns, we have a rethinking of crowdsourcing annotations: Our simple hypothesis is that if the annotators only partially annotate multi-label images with salient labels they are confident in, there will be fewer annotation errors and annotators will spend less time on uncertain labels. As a pleasant surprise, with the same annotation budget, we show a multi-label image classifier supervised by images with salient annotations can outperform models supervised by fully annotated images. Our method contributions are 2-fold: An active learning way is proposed to acquire salient labels for multi-label images; and a novel Adaptive Temperature Associated Model (ATAM) specifically using partial annotations is proposed for multi-label image classification. We conduct experiments on practical crowdsourcing data, the Open Street Map (OSM) dataset and benchmark dataset COCO 2014. When compared with state-of-the-art classification methods trained on fully annotated images, the proposed ATAM can achieve higher accuracy. The proposed idea is promising for crowdsourcing data annotation. Our code will be publicly available.
Despite the success of deep learning methods in medical image segmentation tasks, the human-level performance relies on massive training data with high-quality annotations, which are expensive and time-consuming to collect. The fact is that there exist low-quality annotations with label noise, which leads to suboptimal performance of learned models. Two prominent directions for segmentation learning with noisy labels include pixel-wise noise robust training and image-level noise robust training. In this work, we propose a novel framework to address segmenting with noisy labels by distilling effective supervision information from both pixel and image levels. In particular, we explicitly estimate the uncertainty of every pixel as pixel-wise noise estimation, and propose pixel-wise robust learning by using both the original labels and pseudo labels. Furthermore, we present an image-level robust learning method to accommodate more information as the complements to pixel-level learning. We conduct extensive experiments on both simulated and real-world noisy datasets. The results demonstrate the advantageous performance of our method compared to state-of-the-art baselines for medical image segmentation with noisy labels.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
