Kelley Yuan

All Publications

• Ensemble learning of pathology foundation models for precision oncology. Cancer cell Luo, X., Wang, X., Eweje, F., Zhang, X., Gomez Marti, J. L., Cascarino, S., Yang, S., Li, Y., Quinton, R., Xiang, J., Ji, Y., Li, Z., Chen, Y., Bergstrom, C., Kim, T., Olguin, F. M., Yuan, K., Abikenari, M., Heider, A., Willens, S., Rajaram, S., West, R., Neal, J., Schoenfeld, A., Diehn, M., Vanderbilt, C., Li, R. 2026

  Abstract

  Histopathology is essential for cancer diagnosis and treatment selection, and pathology foundation models learn visual representations from whole-slide images (WSIs). However, existing foundation models are trained on disparate datasets with varying strategies, leading to inconsistent performance and limited generalizability. Here, we introduce ELF (Ensemble Learning of Foundation models), which integrates five pretrained pathology foundation models into unified slide-level representations. Trained on 53,699 WSIs spanning 20 anatomical sites, ELF leverages ensemble learning to capture complementary information across models. ELF's slide-level architecture is designed for data-efficient downstream evaluation, including settings with limited data such as therapeutic response prediction. We evaluate ELF for disease classification and biomarker detection, as well as anticancer and immunotherapy response prediction across multiple cancer types. ELF achieves higher performance than the evaluated constituent and slide-level foundation models across the tested tasks, supporting further evaluation of ensemble learning for pathology applications in oncology.

  View details for DOI 10.1016/j.ccell.2026.08.008

  View details for PubMedID 42721959

  View details for PubMedCentralID PMC13564370

• Ensemble learning of foundation models for precision oncology Cancer Cell Luo, X., Wang, X., Eweje, F., Zhang, X., Yang, S., Quinton, R., Xiang, J., Li, Y., Ji, Y., Li, Z., Chen, Y., Bergstrom, C., Kim, T., Olguin, F. M., Yuan, K., Abikenari, M., Heider, A., Willens, S., Rajaram, S., West, R., Neal, J., Diehn, M., Li, R. 2026; 44: 1-16

  View details for DOI 10.1016/j.ccell.2026.08.008

• Artificial Intelligence-enabled Spatial Tumor Microenvironment Profiling Predicts Response to Immunotherapy in Invasive Breast Carcinoma Eweje, F., Li, Z., Yuan, K., Olguin, F., Bergstrom, C., Nirschl, J., Li, R. ELSEVIER SCIENCE INC. 2025

  View details for DOI 10.1016/j.labinv.2024.102367

  View details for Web of Science ID 001461740800025

• Clinical Optimization of Long-Read PCR-Based Oxford Nanopore Sequencing of CFTR in Dried Blood Spots Association for Molecular Pathology 2025 Yuan, K., Ho, C., Volkova, I., Chiang, T., Edwards, C., Suarez, C. J. 2025: S14
• Targeting the Platelet-Derived Growth Factor-beta Stimulatory Circuitry to Control Retinoblastoma Seeds INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE Goldsmith, Z. K., Coppess, W., Irvine, A. S., Yuan, K., Barsh, S. R., Ritter, M. K., McEwen, M. W., Flores-Otero, J., Garcia-Vargas, A., Martinez-Ferrer, M., Brennan, R. C., Morales-Tirado, V. M., Wilson, M. W. 2018; 59 (11): 4486-4495

  Abstract

  Vitreous seeding remains the primary reason for treatment failure in eyes with retinoblastoma (Rb). Systemic and intra-arterial chemotherapy, each with its own inherent set of complications, have improved salvage rates for eyes with advanced disease, but the location and biology of vitreous seeds present a fundamental challenge in developing treatments with minimal toxicity and risk. The aim of this study was to target the platelet-derived growth factor (PDGF)- PDGF-receptor β (PDGFRβ) signaling pathway and investigate its role in the growth of Rb seeds, apoptotic activity, and invasive potential.We performed ex vivo analyses on vitreous samples from Rb patients that underwent enucleation and from patient-derived xenografts. These samples were evaluated by quantitative PCR, immunohistochemistry, and ELISA. The effects of disruption of the PDGF-PDGFRβ signaling pathway, both by pharmacologic and genomic knockdown approaches, were evaluated in vitro by cell proliferation and apoptotic assays, quantitative PCR analyses, Western blotting, flow cytometry, and imaging flow cytometry. A three-dimensional cell culture system was generated for in-depth study of Rb seeds.Our results demonstrated that PDGFRβ signaling is active in the vitreous of Rb patients and patient-derived xenografts, sustaining growth and survival in an AKT-, MDM2-, and NF-κB-dependent manner. The novel three-dimensional cell culture system mimics Rb seeds, as the in vitro generated spheroids have similar morphologic features to Rb seeds and mimicked their natural physiology.Targeting the PDGFRβ pathway in vitro reduces Rb cell growth, survival, and invasiveness and could augment current therapies. This represents a novel signaling pathway for potential targeted therapy to further improve ocular survival in advanced Rb.

  View details for DOI 10.1167/iovs.18-24359

  View details for Web of Science ID 000443735600020

  View details for PubMedID 30193324

  View details for PubMedCentralID PMC6133233