Guanghua Xiao

Ran Xu, Yuchen Zhuang, Yishan Zhong et al. · gatech

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129 categories derived from 12 authentic real-world biomedical scenarios. Tasks are encapsulated within executable sandbox environments, each featuring detailed task specifications, interactive feedback mechanisms, verifiable ground truth annotations, and scalable training trajectory generation. Extensive benchmarking of 29 LLMs reveals substantial performance disparities in biomedical data science between commercial and open-source LLMs. Leveraging efficient multi-threaded and multi-turn trajectory sampling in MedAgentGym, Med-Copilot achieves performance gains of +43.02% and +45.28% from offline and online reinforcement learning, respectively, demonstrating MedAgentGym as an effective training ground while establishing itself as a cost-effective, privacy-preserving alternative competitive with proprietary LLMs (gpt-4o). By offering a unified execution environment with a comprehensive benchmark and accessible, extensible training resources, MedAgentGym delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical data science.

Esteban Fernández Morales, Cong Zhang, Guanghua Xiao et al.

With the advanced imaging technology, digital pathology imaging of tumor tissue slides is becoming a routine clinical procedure for cancer diagnosis. This process produces massive imaging data that capture histological details in high resolution. Recent developments in deep-learning methods have enabled us to automatically detect and characterize the tumor regions in pathology images at large scale. From each identified tumor region, we extracted 30 well-defined descriptors that quantify its shape, geometry, and topology. We demonstrated how those descriptor features were associated with patient survival outcome in lung adenocarcinoma patients from the National Lung Screening Trial (n=143). Besides, a descriptor-based prognostic model was developed and validated in an independent patient cohort from The Cancer Genome Atlas Program program (n=318). This study proposes new insights into the relationship between tumor shape, geometrical, and topological features and patient prognosis. We provide software in the form of R code on GitHub: https://github.com/estfernandez/Slide_Image_Segmentation_and_Extraction.

Peiran Quan, Zifan Gu, Zhuo Zhao et al.

Foundation models (FMs) have transformed computational pathology by providing powerful, general-purpose feature extractors. However, adapting and benchmarking individual FMs for specific diagnostic tasks is often time-consuming and resource-intensive, especially given their scale and diversity. To address this challenge, we introduce Group-Aggregative Selection Multi-Instance Learning (GAS-MIL), a flexible ensemble framework that seamlessly integrates features from multiple FMs, preserving their complementary strengths without requiring manual feature selection or extensive task-specific fine-tuning. Across classification tasks in three cancer datasets-prostate (PANDA), ovarian (UBC-OCEAN), and breast (TCGA-BrCa)-GAS-MIL consistently achieves superior or on-par performance relative to individual FMs and established MIL methods, demonstrating its robustness and generalizability. By enabling efficient integration of heterogeneous FMs, GAS-MIL streamlines model deployment for pathology and provides a scalable foundation for future multimodal and precision oncology applications.

Chul Moon, Qiwei Li, Guanghua Xiao

Tumor shape is a key factor that affects tumor growth and metastasis. This paper proposes a topological feature computed by persistent homology to characterize tumor progression from digital pathology and radiology images and examines its effect on the time-to-event data. The proposed topological features are invariant to scale-preserving transformation and can summarize various tumor shape patterns. The topological features are represented in functional space and used as functional predictors in a functional Cox proportional hazards model. The proposed model enables interpretable inference about the association between topological shape features and survival risks. Two case studies are conducted using consecutive 133 lung cancer and 77 brain tumor patients. The results of both studies show that the topological features predict survival prognosis after adjusting clinical variables, and the predicted high-risk groups have worse survival outcomes than the low-risk groups. Also, the topological shape features found to be positively associated with survival hazards are irregular and heterogeneous shape patterns, which are known to be related to tumor progression.

Shidan Wang, Tao Wang, Lin Yang et al.

The spatial distributions of different types of cells could reveal a cancer cell growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key hallmarks of cancer. However, manually recognizing and localizing all the cells in pathology slides are almost impossible. In this study, we developed an automated cell type classification pipeline, ConvPath, which includes nuclei segmentation, convolutional neural network-based tumor, stromal and lymphocytes classification, and extraction of tumor microenvironment related features for lung cancer pathology images. The overall classification accuracy is 92.9% and 90.1% in training and independent testing datasets, respectively. By identifying cells and classifying cell types, this pipeline can convert a pathology image into a spatial map of tumor, stromal and lymphocyte cells. From this spatial map, we can extracted features that characterize the tumor micro-environment. Based on these features, we developed an image feature-based prognostic model and validated the model in two independent cohorts. The predicted risk group serves as an independent prognostic factor, after adjusting for clinical variables that include age, gender, smoking status, and stage.