Zhuoyang Lyu

Syed Asad Rizvi, Nazreen Pallikkavaliyaveetil, David Zhang et al.

Foundation models have achieved remarkable success across many domains, relying on pretraining over vast amounts of data. Graph-structured data often lacks the same scale as unstructured data, making the development of graph foundation models challenging. In this work, we propose Foundation-Informed Message Passing (FIMP), a Graph Neural Network (GNN) message-passing framework that leverages pretrained non-textual foundation models in graph-based tasks. We show that the self-attention layers of foundation models can effectively be repurposed on graphs to perform cross-node attention-based message-passing. Our model is evaluated on a real-world image network dataset and two biological applications (single-cell RNA sequencing data and fMRI brain activity recordings) in both finetuned and zero-shot settings. FIMP outperforms strong baselines, demonstrating that it can effectively leverage state-of-the-art foundation models in graph tasks.

Zhuoyang Lyu, Yiyang Zhang, Tongxin Wang et al.

Ultrasound foundation models have achieved strong performance on structured prediction tasks but remain exclusively vision-based, limiting zero-shot and few-shot transfer to novel tasks where task-specific annotation is scarce. We address this gap with EchoCare-CLIP, a CLIP-style dual-encoder contrastive framework that aligns ultrasound images with clinical text in a shared embedding space. We curate a multi-organ corpus of over 16K image-text pairs spanning breast, liver, lung, and thyroid, with over 78% of captions derived from expert-annotated reports, and complement the remainder with a three-tier template-based and LLM-based caption generation pipeline. We evaluate model configurations spanning two text encoder families (CLIP, BioClinicalBERT) and two caption strategies (template-based, LLM-generated) against OpenAI CLIP and BiomedCLIP baselines. Our trained models consistently improve cross-modal alignment over baselines, with the best configuration achieving a paired alignment score of 0.682. However, stronger alignment does not guarantee better downstream performance: CLIP-based variants with partial fine-tuning achieve the strongest zero-shot classification on external held-out datasets (0.709 on BUSI; 0.626 on AULI), while full end-to-end fine-tuning degrades transfer due to overfitting. On linear probing and few-shot adaptation, model rankings are dataset-dependent, reflecting a trade-off between domain adaptation and representational generalizability. We further show that template-based captions match or outperform LLM-generated captions, suggesting lexical diversity is not a proxy for caption quality. Taken together, our results demonstrate that ultrasound vision-language alignment is achievable from public data alone, but robust clinical transfer requires careful balancing of domain adaptation, encoder capacity, and caption supervision quality.