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1. Target and task specific source-free domain adaptive image segmentation

   VS, Vibashan; Valanarasu, Jeya; Patel, Vishal M (June 2024, Proceedings of Machine Learning Research)

   Solving the domain shift problem during inference is essential in medical imaging as most deep-learning based solutions suffer from it. In practice, domain shifts are tackled by performing Unsupervised Domain Adaptation (UDA), where a model is adapted to an unlabeled target domain by leveraging the labelled source domain. In medical scenarios, the data comes with huge privacy concerns making it difficult to apply standard UDA techniques. Hence, a closer clinical setting is Source-Free UDA (SFUDA), where we have access to source trained model but not the source data during adaptation. Methods trying to solve SFUDA typically address the domain shift using pseudo-label based self-training techniques. However due to domain shift, these pseudo-labels are usually of high entropy and denoising them still does not make them perfect labels to supervise the model. Therefore, adapting the source model with noisy pseudo labels reduces its segmentation capability while addressing the domain shift. To this end, we propose a two-stage approach for source-free domain adaptive image segmentation: 1) Target-specific adaptation followed by 2) Task-specific adaptation. In the Stage-I, we focus on learning target-specific representation and generating high-quality pseudo labels by leveraging a proposed ensemble entropy minimization loss and selective voting strategy. In Stage II, we focus on improving segmentation performance by utilizing teacher-student self-training and augmentation-guided consistency loss, leveraging the pseudo labels obtained from Stage I. We evaluate our proposed method on both 2D fundus datasets and 3D MRI volumes across 7 different domain shifts where we achieve better performance than recent UDA and SF-UDA methods for medical image segmentation. Code is available at https://github.com/Vibashan/tt-sfuda. 

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2. Dynamic low-count PET image reconstruction using spatio-temporal primal dual network

   Hu R.; Cui J.; Li C.; Yu C.; Chen Y.; Liu H. (October 2023, Physics in medicine and biology)

   Objective. Dynamic positron emission tomography (PET) imaging, which can provide information on dynamic changes in physiological metabolism, is now widely used in clinical diagnosis and cancer treatment. However, the reconstruction from dynamic data is extremely challenging due to the limited counts received in individual frame, especially in ultra short frames. Recently, the unrolled modelbased deep learning methods have shown inspiring results for low-count PET image reconstruction with good interpretability. Nevertheless, the existing model-based deep learning methods mainly focus on the spatial correlations while ignore the temporal domain. Approach. In this paper, inspired by the learned primal dual (LPD) algorithm, we propose the spatio-temporal primal dual network (STPDnet) for dynamic low-count PET image reconstruction. Both spatial and temporal correlations are encoded by 3D convolution operators. The physical projection of PET is embedded in the iterative learning process of the network, which provides the physical constraints and enhances interpretability. Main results. The experiments of both simulation data and real rat scan data have shown that the proposed method can achieve substantial noise reduction in both temporal and spatial domains and outperform the maximum likelihood expectation maximization, spatio-temporal kernel method, LPD and FBPnet. Significance. Experimental results show STPDnet better reconstruction performance in the low count situation, which makes the proposed method particularly suitable in whole-body dynamic imaging and parametric PET imaging that require extreme short frames and usually suffer from high level of noise. 

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3. An Iterative Semi-Supervised Approach with Pixel-wise Contrastive Loss for Road Extraction in Aerial Images

   https://doi.org/10.1145/3606374  

   Zhang, Huijie; Li, Pu; Liu, Xiaobai; Yang, Xianfeng; An, Li (July 2023, ACM Transactions on Multimedia Computing, Communications, and Applications)

   Extracting roads in aerial images has numerous applications in artificial intelligence and multimedia computing, including traffic pattern analysis and parking space planning. Learning deep neural networks, though very successful, demands vast amounts of high-quality annotations, of which acquisition is time-consuming and expensive. In this work, we propose a semi-supervised approach for image-based road extraction where only a small set of labeled images are available for training to address this challenge. We design a pixel-wise contrastive loss to self-supervise the network training to utilize the large corpus of unlabeled images. The key idea is to identify pairs of overlapping image regions (positive) or non-overlapping image regions (negative) and encourage the network to make similar outputs for positive pairs or dissimilar outputs for negative pairs. We also develop a negative sampling strategy to filter false negative samples during the process. An iterative procedure is introduced to apply the network over raw images to generate pseudo-labels, filter and select high-quality labels with the proposed contrastive loss, and re-train the network with the enlarged training dataset. We repeat these iterative steps until convergence. We validate the effectiveness of the proposed methods by performing extensive experiments on the public SpaceNet3 and DeepGlobe Road datasets. Results show that our proposed method achieves state-of-the-art results on public image segmentation benchmarks and significantly outperforms other semi-supervised methods. 

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4. Weakly Supervised Spatial Deep Learning for Earth Image Segmentation Based on Imperfect Polyline Labels

   https://doi.org/10.1145/3480970  

   Jiang, Zhe; He, Wenchong; Kirby, Marcus Stephen; Sainju, Arpan Man; Wang, Shaowen; Stanislawski, Lawrence V.; Shavers, Ethan J.; Usery, E. Lynn (April 2022, ACM Transactions on Intelligent Systems and Technology)

   In recent years, deep learning has achieved tremendous success in image segmentation for computer vision applications. The performance of these models heavily relies on the availability of large-scale high-quality training labels (e.g., PASCAL VOC 2012). Unfortunately, such large-scale high-quality training data are often unavailable in many real-world spatial or spatiotemporal problems in earth science and remote sensing (e.g., mapping the nationwide river streams for water resource management). Although extensive efforts have been made to reduce the reliance on labeled data (e.g., semi-supervised or unsupervised learning, few-shot learning), the complex nature of geographic data such as spatial heterogeneity still requires sufficient training labels when transferring a pre-trained model from one region to another. On the other hand, it is often much easier to collect lower-quality training labels with imperfect alignment with earth imagery pixels (e.g., through interpreting coarse imagery by non-expert volunteers). However, directly training a deep neural network on imperfect labels with geometric annotation errors could significantly impact model performance. Existing research that overcomes imperfect training labels either focuses on errors in label class semantics or characterizes label location errors at the pixel level. These methods do not fully incorporate the geometric properties of label location errors in the vector representation. To fill the gap, this article proposes a weakly supervised learning framework to simultaneously update deep learning model parameters and infer hidden true vector label locations. Specifically, we model label location errors in the vector representation to partially reserve geometric properties (e.g., spatial contiguity within line segments). Evaluations on real-world datasets in the National Hydrography Dataset (NHD) refinement application illustrate that the proposed framework outperforms baseline methods in classification accuracy. 

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5. Blind Primed Supervised (BLIPS) Learning for MR Image Reconstrution

   Lahiri, Anish; Wang, Guanhua; Ravishankar, Saiprasad; Fessler, Jeffrey (January 2021, International Society for Magnetic Resonance in Medicine)

   The work examines a combined supervised-unsupervised framework involving dictionary-based blind learning and deep supervised learning or MR image reconstruction from under-sampled k-space data. A major focus of the work is to investigate the possible synergy of learned features in traditional shallow reconstruction using sparsity-based priors and deep prior-based reconstruction. Specifically, we propose a framework that uses an unrolled network to refine a blind dictionary learning based reconstruction. we compare the proposed method with strictly supervised deep learning-based reconstruction approaches on several datasets of varying sized and anatomies. 

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