arXiv subjects

Yizhe Yuan

Publications and source records attributed to Yizhe Yuan.

3 recordsLinked to original sources

arXiv2026

Multi-Agent Closed-Loop Reasoning for Organic Structure Elucidation from Multimodal Spectra

Following the molecular discovery and synthesis revolutions, scalable automated structure elucidation from routine spectroscopic data remains an outstanding challenge. Despite decades of computational efforts, no existing system achieved reliable reasoning over unseen spectra. Here, we propose MACROS, a multi-agent system automating structure elucidation by emulating expert iterative hypothesis-testing. Trained on 100M simulated and 1.6M experimental spectra-molecule pairs, it natively supports arbitrary combinations of routine spectroscopic techniques. It achieves unprecedented zero-shot generalization to diverse real-world samples, correctly identifying synthetic compounds, natural products and metabolites above 500 Da with 1D NMR. Remarkably, MACROS spontaneously recovers textbook spectroscopic correlations from unassigned data and exhibits emergent chemical intuition such as a ring-first parsing preference, learning fundamental chemical principles rather than memorizing database patterns. MACROS augments chemists via collaboration to deliver sixfold faster, 40% more accurate elucidation. MACROS establishes a scalable foundation for fully automated structure elucidation, and catalyzes accelerated molecular discovery toward autonomous laboratories.

physics.chem-ph↗

arXiv2026

PPGL-Swarm: Integrated Multimodal Risk Stratification and Hereditary Syndrome Detection in Pheochromocytoma and Paraganglioma

Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors, of which 15-25% develop metastatic disease with 5-year survival rates reported as low as 34%. PPGL may indicate hereditary syndromes requiring stricter, syndrome-specific treatment and surveillance, but clinicians often fail to recognize these associations in routine care. Clinical practice uses GAPP score for PPGL grading, but several limitations remain for PPGL diagnosis: (1) GAPP scoring demands a high workload for clinician because it requires the manual evaluation of six independent components; (2) key components such as cellularity and Ki-67 are often evaluated with subjective criteria; (3) several clinically relevant metastatic risk factors are not captured by GAPP, such as SDHB mutations, which have been associated with reported metastatic rates of 35-75%. Agent-driven diagnostic systems appear promising, but most lack traceable reasoning for decision-making and do not incorporate domain-specific knowledge such as PPGL genotype information. To address these limitations, we present PPGL-Swarm, an agentic PPGL diagnostic system that generates a comprehensive report, including automated GAPP scoring (with quantified cellularity and Ki-67), genotype risk alerts, and multimodal report with integrated evidence. The system provides an auditable reasoning trail by decomposing diagnosis into micro-tasks, each assigned to a specialized agent. The gene and table agents use knowledge enhancement to better interpret genotype and laboratory findings, and during training we use reinforcement learning to refine tool selection and task assignment.

cs.CV↗

arXiv2025

PRINTER:Deformation-Aware Adversarial Learning for Virtual IHC Staining with In Situ Fidelity

Tumor spatial heterogeneity analysis requires precise correlation between Hematoxylin and Eosin H&E morphology and immunohistochemical (IHC) biomarker expression, yet current methods suffer from spatial misalignment in consecutive sections, severely compromising in situ pathological interpretation. In order to obtain a more accurate virtual staining pattern, We propose PRINTER, a weakly-supervised framework that integrates PRototype-drIven content and staiNing patTERn decoupling and deformation-aware adversarial learning strategies designed to accurately learn IHC staining patterns while preserving H&E staining details. Our approach introduces three key innovations: (1) A prototype-driven staining pattern transfer with explicit content-style decoupling; and (2) A cyclic registration-synthesis framework GapBridge that bridges H&E and IHC domains through deformable structural alignment, where registered features guide cross-modal style transfer while synthesized outputs iteratively refine the registration;(3) Deformation-Aware Adversarial Learning: We propose a training framework where a generator and deformation-aware registration network jointly adversarially optimize a style-focused discriminator. Extensive experiments demonstrate that PRINTER effectively achieves superior performance in preserving H&E staining details and virtual staining fidelity, outperforming state-of-the-art methods. Our work provides a robust and scalable solution for virtual staining, advancing the field of computational pathology.

cs.CV↗