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Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that facilitates the study of macromolecular structures at near-atomic resolution. Recent volumetric segmentation approaches on cryo-ET images have drawn widespread interest in the biological sector. However, existing methods heavily rely on manually labeled data, which requires highly professional skills, thereby hindering the adoption of fully-supervised approaches for cryo-ET images. Some unsupervised domain adaptation (UDA) approaches have been designed to enhance the segmentation network performance using unlabeled data. However, applying these methods directly to cryo-ET image segmentation tasks remains challenging due to two main issues: 1) the source dataset, usually obtained through simulation, contains a fixed level of noise, while the target dataset, directly collected from raw-data from the real-world scenario, have unpredictable noise levels. 2) the source data used for training typically consists of known macromoleculars. In contrast, the target domain data are often unknown, causing the model to be biased towards those known macromolecules, leading to a domain shift problem. To address such challenges, in this work, we introduce a voxel-wise unsupervised domain adaptation approach, termed Vox-UDA, specifically for cryo-ET subtomogram segmentation. Vox-UDA incorporates a noise generation module to simulate target-like noises in the source dataset for cross-noise level adaptation. Additionally, we propose a denoised pseudo-labeling strategy based on the improved Bilateral Filter to alleviate the domain shift problem. More importantly, we construct the first UDA cryo-ET subtomogram segmentation benchmark on three experimental datasets. Extensive experimental results on multiple benchmarks and newly curated real-world datasets demonstrate the superiority of our proposed approach compared to state-of-the-art UDA methods.
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Semi-supervised Multi-source Domain Adaptation in Wearable Activity Recognition
The scarcity of labeled data has traditionally been the primary hindrance in building scalable supervised deep learning models that can retain adequate performance in the presence of various heterogeneities in sample distributions. Domain adaptation tries to address this issue by adapting features learned from a smaller set of labeled samples to that of the incoming unlabeled samples. The traditional domain adaptation approaches normally consider only a single source of labeled samples, but in real world use cases, labeled samples can originate from multiple-sources – providing motivation for multi-source domain adaptation (MSDA). Several MSDA approaches have been investigated for wearable sensor-based human activity recognition (HAR) in recent times, but their performance improvement compared to single source counterpart remained marginal. To remedy this performance gap that, we explore multiple avenues to align the conditional distributions in addition to the usual alignment of marginal ones. In our investigation, we extend an existing multi-source domain adaptation approach under semi-supervised settings. We assume the availability of partially labeled target domain data and further explore the pseudo labeling usage with a goal to achieve a performance similar to the former. In our experiments on three publicly available datasets, we find that a limited labeled target domain data and pseudo label data boost the performance over the unsupervised approach by 10-35% and 2-6%, respectively, in various domain adaptation scenarios.
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- Award ID(s):
- 1750936
- PAR ID:
- 10406631
- Date Published:
- Journal Name:
- 2022 18th International Conference on Distributed Computing in Sensor Systems (DCOSS)
- Page Range / eLocation ID:
- 35 to 44
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that facilitates the study of macromolecular structures at near-atomic resolution. Recent volumetric segmentation approaches on cryo-ET images have drawn widespread interest in the biological sector. However, existing methods heavily rely on manually labeled data, which requires highly professional skills, thereby hindering the adoption of fully-supervised approaches for cryo-ET images. Some unsupervised domain adaptation (UDA) approaches have been designed to enhance the segmentation network performance using unlabeled data. However, applying these methods directly to cryo-ET image segmentation tasks remains challenging due to two main issues: 1) the source dataset, usually obtained through simulation, contains a fixed level of noise, while the target dataset, directly collected from raw-data from the real-world scenario, have unpredictable noise levels. 2) the source data used for training typically consists of known macromoleculars. In contrast, the target domain data are often unknown, causing the model to be biased towards those known macromolecules, leading to a domain shift problem. To address such challenges, in this work, we introduce a voxel-wise unsupervised domain adaptation approach, termed Vox-UDA, specifically for cryo-ET subtomogram segmentation. Vox-UDA incorporates a noise generation module to simulate target-like noises in the source dataset for cross-noise level adaptation. Additionally, we propose a denoised pseudo-labeling strategy based on the improved Bilateral Filter to alleviate the domain shift problem. More importantly, we construct the first UDA cryo-ET subtomogram segmentation benchmark on three experimental datasets. Extensive experimental results on multiple benchmarks and newly curated real-world datasets demonstrate the superiority of our proposed approach compared to state-of-the-art UDA methods.more » « less
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- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Conference Paper:
- https://doi.org/10.1109/DCOSS54816.2022.00017
