arXiv subjects

Jie-Fu Chen

Publications and source records attributed to Jie-Fu Chen.

3 recordsLinked to original sources

arXiv2026

Cross-Modal Contrastive Learning from Histopathology and CT for Automated Renal Cell Carcinoma Grading

Background: Clear cell renal cell carcinoma (ccRCC) exhibits substantial clinical heterogeneity, and accurate grade assessment is essential for risk stratification and treatment planning. However, conventional grading requires invasive tissue sampling. We developed RCC-Align, a cross-modal contrastive learning framework that leverages paired histopathology and computed tomography (CT) data during training to improve noninvasive CT-based ccRCC grade prediction. Methods: RCC-Align aligns paired whole-slide histopathology images (WSIs) and CT scans through contrastive cross-modal objectives, transferring grade-discriminative information from microscopic tissue morphology to macroscopic radiologic representations. The framework was trained and evaluated on paired TCGA and CPTAC cohorts using patient-level five-fold cross-validation. Performance for low- versus high-grade ccRCC classification was compared against CT-only baselines (DINOv2-Base and DINOv2-Finetuned) and a WSI-based reference model (GigaPath-Finetuned). Cross-modal alignment was assessed using cosine similarity analysis. Results: RCC-Align achieved an AUC of 0.601 (95% CI, 0.524-0.673) and AUPRC of 0.599 (95% CI, 0.541-0.676), outperforming DINOv2-Finetuned (AUC 0.545; AUPRC 0.543) with significantly improved low-grade prediction (p = 0.004). RCC-Align also demonstrated stronger paired WSI-CT embedding alignment compared with baselines. The WSI-based GigaPath reference achieved an AUC of 0.719. Conclusion: Pathology-guided contrastive learning improves CT-based ccRCC grading while requiring only CT at inference. This approach may complement tissue diagnosis when biopsy is unsafe, infeasible, or limited by intratumoral heterogeneity. Validation in larger, multi-institutional cohorts with external testing is needed before clinical translation.

cs.CV↗

arXiv2026

GOLDMARK: Governed Outcome-Linked Diagnostic Model Assessment Reference Kit

Computational biomarkers (CBs) are histopathology-derived patterns extracted from hematoxylin-eosin (H&E) whole-slide images (WSIs) using artificial intelligence (AI) to predict therapeutic response or prognosis. Recently, slide-level multiple-instance learning (MIL) with pathology foundation models (PFMs) has become the standard baseline for CB development. While these methods have improved predictive performance, computational pathology lacks standardized intermediate data formats, provenance tracking, checkpointing conventions, and reproducible evaluation metrics required for clinical-grade deployment. We introduce GOLDMARK (https://artificialintelligencepathology.org), a standardized benchmarking framework built on a curated TCGA cohort with clinically actionable OncoKB level 1-3 biomarker labels. GOLDMARK releases structured intermediate representations, including tile coordinate maps, per-slide feature embeddings from canonical PFMs, quality-control metadata, predefined patient-level splits, trained slide-level models, and evaluation outputs. Models are trained on TCGA and evaluated on an independent MSKCC cohort with reciprocal testing. Across 33 tumor-biomarker tasks, mean AUROC was 0.689 (TCGA) and 0.630 (MSKCC). Restricting to the eight highest-performing tasks yielded mean AUROCs of 0.831 and 0.801, respectively. These tasks correspond to established morphologic-genomic associations (e.g., LGG IDH1, COAD MSI/BRAF, THCA BRAF/NRAS, BLCA FGFR3, UCEC PTEN) and showed the most stable cross-site performance. Differences between canonical encoders were modest relative to task-specific variability. GOLDMARK establishes a shared experimental substrate for computational pathology, enabling reproducible benchmarking and direct comparison of methods across datasets and models.

cs.CV↗

arXiv2025

Single GPU Task Adaptation of Pathology Foundation Models for Whole Slide Image Analysis

Pathology foundation models (PFMs) have emerged as powerful tools for analyzing whole slide images (WSIs). However, adapting these pretrained PFMs for specific clinical tasks presents considerable challenges, primarily due to the availability of only weak (WSI-level) labels for gigapixel images, necessitating multiple instance learning (MIL) paradigm for effective WSI analysis. This paper proposes a novel approach for single-GPU \textbf{T}ask \textbf{A}daptation of \textbf{PFM}s (TAPFM) that uses vision transformer (\vit) attention for MIL aggregation while optimizing both for feature representations and attention weights. The proposed approach maintains separate computational graphs for MIL aggregator and the PFM to create stable training dynamics that align with downstream task objectives during end-to-end adaptation. Evaluated on mutation prediction tasks for bladder cancer and lung adenocarcinoma across institutional and TCGA cohorts, TAPFM consistently outperforms conventional approaches, with H-Optimus-0 (TAPFM) outperforming the benchmarks. TAPFM effectively handles multi-label classification of actionable mutations as well. Thus, TAPFM makes adaptation of powerful pre-trained PFMs practical on standard hardware for various clinical applications.

cs.CV↗