TractoGraphVLM: A Unified Vision-Language Framework for White Matter Tractography

Vision language models have transformed 2D medical imaging, yet extending them to 3D white matter tractography remains challenging due to the complex topology of fiber bundles. We introduce TractoGraphVLM, a unified framework for four tasks, bundle classification, text-to-tract retrieval, anatomical captioning, and visual question answering, built on a shared GPS architecture, training procedure, and read-out design. Fiber bundles are represented as streamline graphs whose nodes encode 3D position and tangent orientation. A General, Powerful, Scalable (GPS) graph transformer produces bundle embeddings aligned with a frozen BiomedBERT text encoder via contrastive learning, while a BioGPT decoder with visual prefix tokens generates captions and answers. A single shared encoder and decoder is trained jointly across all four tasks and evaluated from one checkpoint. Trained on HCP Young Adult subjects, TractoGraphVLM achieves 91.8% bundle classification accuracy, 84.7% retrieval R@1, BLEU-4=20.1, ROUGE-L=66.8, and 66.4% VQA accuracy on a held-out test set. The same checkpoints transfer zero-shot to HCP Aging subjects, with a modest drop on discriminative tasks and a larger drop on generative tasks, showing robustness to age and acquisition shift. Language supervision yields richer representations than label-only training, recovering structure like hemisphere and fiber family, carried by captions but never given as a label. Swapping only the visual encoder, graphs preserving fiber orientation outperform volumetric baselines, with GPS giving the best balance. Generative metrics measure consistency with a structured knowledge base rather than independent clinical text; even so, TractoGraphVLM shows that classifying, retrieving, describing, and answering questions about a white matter bundle can be served by one jointly trained model that learns transferable neuroanatomy from language alone.

scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering

Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity. Despite the significant progress in scRNA-seq data clustering, we argue that current methods always ignore the sparsity and noise, as well as the complex intercellular structural information inherent in scRNA-seq data. Toward this end, in this paper, we propose a novel single-cell RNA-seq clustering framework via deep Siamese Graph Transformer Network (termed scGTN), which explicitly integrates gene expression profile and intercellular structural dependencies for cell clustering. In particular, we formulate scRNA-seq data as a graph and construct two augmented graph views that serve as dual views to capture complementary intercellular information. Then, a Siamese graph transformer network is employed to explicitly incorporate shortest-path information and node-wise distances for capturing richer structural relationships between cells. Finally, we employ an optimal transport strategy to guide the cell clustering in a self-supervised manner. Extensive experiments on multiple benchmark scRNA-seq datasets demonstrate that our scGTN consistently outperforms existing methods. Our code is available at https://github.com/W-RMSL/scGTN.