arXiv subjects

Dongfang Wang

Publications and source records attributed to Dongfang Wang.

4 recordsLinked to original sources

arXiv2026

Querying structural and functional niches on spatial transcriptomics data

Cells in multicellular organisms coordinate to form structural and functional niches. With spatial transcriptomics (ST) enabling gene expression profiling in spatial contexts, it has been revealed that spatial niches serve as cohesive and recurrent units in physiological and pathological processes. These observations suggest universal tissue organization principles encoded by conserved niche patterns, and call for a query-based niche analytical paradigm beyond current computational tools. In this work, we defined the niche-query task, which is to identify similar niches across ST samples given a niche of interest (NOI). We further developed QueST, a specialized method for solving this task. QueST models each niche as a subgraph, uses contrastive learning to learn discriminative niche embeddings, and incorporates adversarial training to mitigate batch effects. In simulations and benchmark datasets, QueST outperformed existing methods repurposed for niche querying, accurately capturing niche structures in heterogeneous environments and demonstrating strong generalizability across diverse sequencing platforms. Applied to tertiary lymphoid structures in renal and lung cancers, QueST revealed functionally distinct niches associated with patient prognosis and uncovered conserved and divergent spatial architectures across cancer types. Applied to a combinatorial spatial perturbation dataset, QueST demonstrated a complete de novo discovery-oriented workflow, characterizing previously unresolved tumor nodules through querying. These results demonstrate that QueST enables systematic, quantitative profiling of spatial niches across samples, providing a powerful tool to dissect spatial tissue architecture in health and disease.

q-bio.QM↗

arXiv2025

Hierarchical Spatio-temporal Segmentation Network for Ejection Fraction Estimation in Echocardiography Videos

Automated segmentation of the left ventricular endocardium in echocardiography videos is a key research area in cardiology. It aims to provide accurate assessment of cardiac structure and function through Ejection Fraction (EF) estimation. Although existing studies have achieved good segmentation performance, their results do not perform well in EF estimation. In this paper, we propose a Hierarchical Spatio-temporal Segmentation Network (\ourmodel) for echocardiography video, aiming to improve EF estimation accuracy by synergizing local detail modeling with global dynamic perception. The network employs a hierarchical design, with low-level stages using convolutional networks to process single-frame images and preserve details, while high-level stages utilize the Mamba architecture to capture spatio-temporal relationships. The hierarchical design balances single-frame and multi-frame processing, avoiding issues such as local error accumulation when relying solely on single frames or neglecting details when using only multi-frame data. To overcome local spatio-temporal limitations, we propose the Spatio-temporal Cross Scan (STCS) module, which integrates long-range context through skip scanning across frames and positions. This approach helps mitigate EF calculation biases caused by ultrasound image noise and other factors.

cs.CV↗

arXiv2025

Recent advances in DNA origami-engineered nanomaterials and applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirits and asset that Seeman left for scientists will continue to bring inter-disciplinary innovations and useful applications to this field in the next decade.

physics.bio-ph↗

arXiv2025

Boosting Global-Local Feature Matching via Anomaly Synthesis for Multi-Class Point Cloud Anomaly Detection

Point cloud anomaly detection is essential for various industrial applications. The huge computation and storage costs caused by the increasing product classes limit the application of single-class unsupervised methods, necessitating the development of multi-class unsupervised methods. However, the feature similarity between normal and anomalous points from different class data leads to the feature confusion problem, which greatly hinders the performance of multi-class methods. Therefore, we introduce a multi-class point cloud anomaly detection method, named GLFM, leveraging global-local feature matching to progressively separate data that are prone to confusion across multiple classes. Specifically, GLFM is structured into three stages: Stage-I proposes an anomaly synthesis pipeline that stretches point clouds to create abundant anomaly data that are utilized to adapt the point cloud feature extractor for better feature representation. Stage-II establishes the global and local memory banks according to the global and local feature distributions of all the training data, weakening the impact of feature confusion on the establishment of the memory bank. Stage-III implements anomaly detection of test data leveraging its feature distance from global and local memory banks. Extensive experiments on the MVTec 3D-AD, Real3D-AD and actual industry parts dataset showcase our proposed GLFM's superior point cloud anomaly detection performance. The code is available at https://github.com/hustCYQ/GLFM-Multi-class-3DAD.

cs.CV↗