6 papers
DMT-Dens: Density-preserving manifold visualization for biological data
Ruizhe Wang, Yixuan Dong, Bolin Yang +3
Motivation: Low-dimensional embeddings are widely used to explore cell-state heterogeneity in single-cell and other high-dimensional biological data. Although many methods preserve…
scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement
Xichen Yan, Zelin Zang, Changxi Chi +8
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While rec…
CellScientist: From Execution Feedback to Auditable Model-Revision Trajectories for Cellular Perturbation Prediction
Mengran Li, Bo Li, Jiaying Wang +13
Cellular perturbation-response modeling requires coordinated choices of representations, fusion mechanisms, objectives, and training procedures. Large language models (LLMs) can pr…
MAT-Cell: A Multi-Agent Tree-Structured Reasoning Framework for Batch-Level Single-Cell Annotation
Yehui Yang, Zelin Zang, Xienan Zheng +9
Automated single-cell annotation is difficult when the most abundant genes are not the most discriminative ones, or when a target state is poorly covered by a fixed reference atlas…
A Medical Multimodal Diagnostic Framework Integrating Vision-Language Models and Logic Tree Reasoning
Zelin Zang, Wenyi Gu, Siqi Ma +6
With the rapid growth of large language models (LLMs) and vision-language models (VLMs) in medicine, simply integrating clinical text and medical imaging does not guarantee reliabl…
The Dawn of Agentic EDA: A Survey of Autonomous Digital Chip Design
Zelin Zang, Yuhang Song, Aili Wang +6
The semiconductor industry faces a critical "Productivity Gap" where design complexity outpaces human capacity. While the "AI for EDA" revolution (L2) successfully optimized specif…