Context-Aware Pseudo-Label Refinement for Source-Free Domain Adaptive Fundus Image Segmentation

In the domain adaptation problem, source data may be unavailable to the target client side due to privacy or intellectual property issues. Source-free unsupervised domain adaptation (SF-UDA) aims at adapting a model trained on the source side to align the target distribution with only the source model and unlabeled target data. The source model usually produces noisy and context-inconsistent pseudo-labels on the target domain, i.e., neighbouring regions that have a similar visual appearance are annotated with different pseudo-labels. This observation motivates us to refine pseudo-labels with context relations. Another observation is that features of the same class tend to form a cluster despite the domain gap, which implies context relations can be readily calculated from feature distances. To this end, we propose a context-aware pseudo-label refinement method for SF-UDA. Specifically, a context-similarity learning module is developed to learn context relations. Next, pseudo-label revision is designed utilizing the learned context relations. Further, we propose calibrating the revised pseudo-labels to compensate for wrong revision caused by inaccurate context relations. Additionally, we adopt a pixel-level and class-level denoising scheme to select reliable pseudo-labels for domain adaptation. Experiments on cross-domain fundus images indicate that our approach yields the state-of-the-art results. Code is available at https://github.com/xmed-lab/CPR.Comment: Accepted by MICCAI 2023, 11 page

GraphEcho: Graph-Driven Unsupervised Domain Adaptation for Echocardiogram Video Segmentation

Echocardiogram video segmentation plays an important role in cardiac disease diagnosis. This paper studies the unsupervised domain adaption (UDA) for echocardiogram video segmentation, where the goal is to generalize the model trained on the source domain to other unlabelled target domains. Existing UDA segmentation methods are not suitable for this task because they do not model local information and the cyclical consistency of heartbeat. In this paper, we introduce a newly collected CardiacUDA dataset and a novel GraphEcho method for cardiac structure segmentation. Our GraphEcho comprises two innovative modules, the Spatial-wise Cross-domain Graph Matching (SCGM) and the Temporal Cycle Consistency (TCC) module, which utilize prior knowledge of echocardiogram videos, i.e., consistent cardiac structure across patients and centers and the heartbeat cyclical consistency, respectively. These two modules can better align global and local features from source and target domains, improving UDA segmentation results. Experimental results showed that our GraphEcho outperforms existing state-of-the-art UDA segmentation methods. Our collected dataset and code will be publicly released upon acceptance. This work will lay a new and solid cornerstone for cardiac structure segmentation from echocardiogram videos. Code and dataset are available at: https://github.com/xmed-lab/GraphEchoComment: Accepted By ICCV 202

HiLM-D: Towards High-Resolution Understanding in Multimodal Large Language Models for Autonomous Driving

Autonomous driving systems generally employ separate models for different tasks resulting in intricate designs. For the first time, we leverage singular multimodal large language models (MLLMs) to consolidate multiple autonomous driving tasks from videos, i.e., the Risk Object Localization and Intention and Suggestion Prediction (ROLISP) task. ROLISP uses natural language to simultaneously identify and interpret risk objects, understand ego-vehicle intentions, and provide motion suggestions, eliminating the necessity for task-specific architectures. However, lacking high-resolution (HR) information, existing MLLMs often miss small objects (e.g., traffic cones) and overly focus on salient ones (e.g., large trucks) when applied to ROLISP. We propose HiLM-D (Towards High-Resolution Understanding in MLLMs for Autonomous Driving), an efficient method to incorporate HR information into MLLMs for the ROLISP task. Especially, HiLM-D integrates two branches: (i) the low-resolution reasoning branch, can be any MLLMs, processes low-resolution videos to caption risk objects and discern ego-vehicle intentions/suggestions; (ii) the high-resolution perception branch (HR-PB), prominent to HiLM-D,, ingests HR images to enhance detection by capturing vision-specific HR feature maps and prioritizing all potential risks over merely salient objects. Our HR-PB serves as a plug-and-play module, seamlessly fitting into current MLLMs. Experiments on the ROLISP benchmark reveal HiLM-D's notable advantage over leading MLLMs, with improvements of 4.8% in BLEU-4 for captioning and 17.2% in mIoU for detection

GL-Fusion: Global-Local Fusion Network for Multi-view Echocardiogram Video Segmentation

Cardiac structure segmentation from echocardiogram videos plays a crucial role in diagnosing heart disease. The combination of multi-view echocardiogram data is essential to enhance the accuracy and robustness of automated methods. However, due to the visual disparity of the data, deriving cross-view context information remains a challenging task, and unsophisticated fusion strategies can even lower performance. In this study, we propose a novel Gobal-Local fusion (GL-Fusion) network to jointly utilize multi-view information globally and locally that improve the accuracy of echocardiogram analysis. Specifically, a Multi-view Global-based Fusion Module (MGFM) is proposed to extract global context information and to explore the cyclic relationship of different heartbeat cycles in an echocardiogram video. Additionally, a Multi-view Local-based Fusion Module (MLFM) is designed to extract correlations of cardiac structures from different views. Furthermore, we collect a multi-view echocardiogram video dataset (MvEVD) to evaluate our method. Our method achieves an 82.29% average dice score, which demonstrates a 7.83% improvement over the baseline method, and outperforms other existing state-of-the-art methods. To our knowledge, this is the first exploration of a multi-view method for echocardiogram video segmentation. Code available at: https://github.com/xmed-lab/GL-FusionComment: Accepted By MICCAI 202

A reference-grade wild soybean genome

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs

A reference-grade wild soybean genome

Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci

Spatiotemporal characteristics and influencing factors of grain yield at the county level in Shandong Province, China

China's food security has always been a high priority issue on the political agenda with rapid urbanization affecting agricultural land, and it is challenged by several factors, such as human activities, social politics and policy. Shandong is an important grain-producing province and the second most populous province in China. In this paper, the spatiotemporal characteristics of grain yield and their potential influencing factors were explored at the county level in Shandong by using panel data over a 19-year period. The location Gini coefficient (L-Gini) and exploratory spatial data analysis (ESDA) were used to study the spatial agglomeration characteristics of grain yield, and spatial regression methods (SRMs) were used to analyse the influencing factors. The results indicated that grain yield increased from 38.3 million metric tons to 53.2 million metric tons in 2000-2018, with a growth rate of approximately 28.0%. The increase in grain yield in Shandong was due to the driving effect of radiation from high-yield counties to surrounding moderate-yield counties. This revealed an upward trend of spatial polarization in Shandong's grain yield. In 2000-2018, the L-Gini and global Moran's I increased from 0.330 to 0.479 and from 0.369 to 0.528, respectively. The number of counties in high-high (HH) and low-low (LL) agglomeration areas increased, and the spatial polarization effect was significant. SRMs analysis showed that irrigation investment and non-grain attention have significant positive and negative effects on grain production, respectively. The spatial relationship between grain yield and its influencing factors was explored to provide a reference for formulating scientific and rational agricultural policies

Free Lunch for Surgical Video Understanding by Distilling Self-Supervisions

Self-supervised learning has witnessed great progress in vision and NLP; recently, it also attracted much attention to various medical imaging modalities such as X-ray, CT, and MRI. Existing methods mostly focus on building new pretext self-supervision tasks such as reconstruction, orientation, and masking identification according to the properties of medical images. However, the publicly available self-supervision models are not fully exploited. In this paper, we present a powerful yet efficient self-supervision framework for surgical video understanding. Our key insight is to distill knowledge from publicly available models trained on large generic datasets4 to facilitate the self-supervised learning of surgical videos. To this end, we first introduce a semantic-preserving training scheme to obtain our teacher model, which not only contains semantics from the publicly available models, but also can produce accurate knowledge for surgical data. Besides training with only contrastive learning, we also introduce a distillation objective to transfer the rich learned information from the teacher model to self-supervised learning on surgical data. Extensive experiments on two surgical phase recognition benchmarks show that our framework can significantly improve the performance of existing self-supervised learning methods. Notably, our framework demonstrates a compelling advantage under a low-data regime. Our code is available at https://github.com/xmed-lab/DistillingSelf