arXiv subjects

Anil Parwani

Publications and source records attributed to Anil Parwani.

7 recordsLinked to original sources

arXiv2026

Dino-NestedUNet: Unlocking Foundation Vision Encoders for Pathology Tumor Bulk Segmentation via Dense Decoding

Vision foundation models (VFMs), such as DINOv3, provide rich semantic representations that are promising for computational pathology. However, many current adaptations pair frozen VFMs with lightweight decoders, creating a capacity mismatch that often limits boundary fidelity for infiltrative tumor bulk segmentation. This paper presents Dino-NestedUNet, a framework that couples a pre-trained DINOv3 encoder with a Nested Dense Decoder. Instead of sparse skip connections and linear upsampling, the proposed decoder forms a dense grid of intermediate pathways to enable continuous feature reuse and multi-scale recalibration, aligning high-level semantics with low-level morphological textures during reconstruction. We evaluate Dino-NestedUNet on three histopathology cohorts (multi-center CHTN, institutional OSU, and CAMELYON16) and observe consistent improvements over UNet++ and standard Dino-UNet variants, particularly under cross-domain shift. To further assess external generalization, we perform zero-shot evaluation by training on CHTN and directly testing on unseen TIGER WSIBULK and OSU CRC cohorts without fine-tuning. These results suggest that dense decoding is a key ingredient for unlocking foundation encoders in boundary-sensitive pathology segmentation.

cs.CV↗

arXiv2026

Unified Multi-Foundation-Model Slide Representation for Pan-Cancer Recognition and Text-Guided Tumor Localization

The expanding ecosystem of pathology foundation models has produced powerful but fragmented tile-level representations, limiting their use in clinical tasks that require unified slide-level reasoning and interpretable linkage to clinically meaningful information. We present ASTRA, a pan-cancer framework that integrates heterogeneous foundation-model representations into a shared slide-level representation space and semantically grounds that space using structured pathology annotation fields, including classification category, cancer type, and anatomic site. ASTRA combines sparse mixture-of-experts contextualization, masked multi-model reconstruction, and contrastive alignment to structured pathology prompts to learn slide representations that support 4-category classification, 3-class solid tumor typing, 16-class cancer typing, and text-guided tumor localization without pixel-level supervision. Developed on a CHTN cohort of 10,359 whole-slide images (WSIs) spanning 16 tumor types, ASTRA consistently improves pan-cancer classification across four pathology foundation-model backbones, achieving up to 97.8% macro-AUC for 4-category classification, 99.7% for 3-class solid tumor typing, and 99.2% for 16-class cancer typing. For tumor localization, ASTRA achieves a mean Dice of 0.897 on an annotated in-domain CHTN subset (n = 380) spanning 16 cancer types and 0.738 on an external TCGA cohort (n = 1,686) spanning four cancer types. These results demonstrate that minimal structured pathology annotation fields derived from slide-level metadata can provide effective semantic supervision for unified slide representation learning, enabling both pan-cancer prediction and weakly supervised tumor localization within a single framework.

cs.CV↗

arXiv2026

MorphDistill: Distilling Unified Morphological Knowledge from Pathology Foundation Models for Colorectal Cancer Survival Prediction

Background: Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Accurate survival prediction is essential for treatment stratification, yet existing pathology foundation models often overlook organ-specific features critical for CRC prognostication. Methods: We propose MorphDistill, a two-stage framework that distills complementary knowledge from multiple pathology foundation models into a compact CRC-specific encoder. In Stage I, a student encoder is trained using dimension-agnostic multi-teacher relational distillation with supervised contrastive regularization on large-scale colorectal datasets. This preserves inter-sample relationships from ten foundation models without explicit feature alignment. In Stage II, the encoder extracts patch-level features from whole-slide images, which are aggregated via attention-based multiple instance learning to predict five-year survival. Results: On the Alliance/CALGB 89803 cohort (n=424, stage III CRC), MorphDistill achieves an AUC of 0.68 (SD 0.08), an approximately 8% relative improvement over the strongest baseline (AUC 0.63). It also attains a C-index of 0.661 and a hazard ratio of 2.52 (95% CI: 1.73-3.65), outperforming all baselines. On an external TCGA cohort (n=562), it achieves a C-index of 0.628, demonstrating strong generalization across datasets and robustness across clinical subgroups. Conclusion: MorphDistill enables task-specific representation learning by integrating knowledge from multiple foundation models into a unified encoder. This approach provides an efficient strategy for prognostic modeling in computational pathology, with potential for broader oncology applications. Further validation across additional cohorts and disease stages is warranted.

cs.CV↗

arXiv2026

PathoScribe: Transforming Pathology Data into a Living Library with a Unified LLM-Driven Framework for Semantic Retrieval and Clinical Integration

Pathology underpins modern diagnosis and cancer care, yet its most valuable asset, the accumulated experience encoded in millions of narrative reports, remains largely inaccessible. Although institutions are rapidly digitizing pathology workflows, storing data without effective mechanisms for retrieval and reasoning risks transforming archives into a passive data repository, where institutional knowledge exists but cannot meaningfully inform patient care. True progress requires not only digitization, but the ability for pathologists to interrogate prior similar cases in real time while evaluating a new diagnostic dilemma. We present PathoScribe, a unified retrieval-augmented large language model (LLM) framework designed to transform static pathology archives into a searchable, reasoning-enabled living library. PathoScribe enables natural language case exploration, automated cohort construction, clinical question answering, immunohistochemistry (IHC) panel recommendation, and prompt-controlled report transformation within a single architecture. Evaluated on 70,000 multi-institutional surgical pathology reports, PathoScribe achieved perfect Recall@10 for natural language case retrieval and demonstrated high-quality retrieval-grounded reasoning (mean reviewer score 4.56/5). Critically, the system operationalized automated cohort construction from free-text eligibility criteria, assembling research-ready cohorts in minutes (mean 9.2 minutes) with 91.3% agreement to human reviewers and no eligible cases incorrectly excluded, representing orders-of-magnitude reductions in time and cost compared to traditional manual chart review. This work establishes a scalable foundation for converting digital pathology archives from passive storage systems into active clinical intelligence platforms.

cs.CV↗

arXiv2026

HistoMet: A Pan-Cancer Deep Learning Framework for Prognostic Prediction of Metastatic Progression and Site Tropism from Primary Tumor Histopathology

Metastatic Progression remains the leading cause of cancer-related mortality, yet predicting whether a primary tumor will metastasize and where it will disseminate directly from histopathology remains a fundamental challenge. Although whole-slide images (WSIs) provide rich morphological information, prior computational pathology approaches typically address metastatic status or site prediction as isolated tasks, and do not explicitly model the clinically sequential decision process of metastatic risk assessment followed by downstream site-specific evaluation. To address this research gap, we present a decision-aware, concept-aligned MIL framework, HistoMet, for prognostic metastatic outcome prediction from primary tumor WSIs. Our proposed framework adopts a two-module prediction pipeline in which the likelihood of metastatic progression from the primary tumor is first estimated, followed by conditional prediction of metastatic site for high-risk cases. To guide representation learning and improve clinical interpretability, our framework integrates linguistically defined and data-adaptive metastatic concepts through a pretrained pathology vision-language model. We evaluate HistoMet on a multi-institutional pan-cancer cohort of 6504 patients with metastasis follow-up and site annotations. Under clinically relevant high-sensitivity screening settings (95 percent sensitivity), HistoMet significantly reduces downstream workload while maintaining high metastatic risk recall. Conditional on metastatic cases, HistoMet achieves a macro F1 of 74.6 with a standard deviation of 1.3 and a macro one-vs-rest AUC of 92.1. These results demonstrate that explicitly modeling clinical decision structure enables robust and deployable prognostic prediction of metastatic progression and site tropism directly from primary tumor histopathology.

cs.CV↗

arXiv2026

Inferring Clinically Relevant Molecular Subtypes of Pancreatic Cancer from Routine Histopathology Using Deep Learning

Molecular subtyping of PDAC into basal-like and classical has established prognostic and predictive value. However, its use in clinical practice is limited by cost, turnaround time, and tissue requirements, thereby restricting its application in the management of PDAC. We introduce PanSubNet, an interpretable deep learning framework that predicts therapy-relevant molecular subtypes directly from standard H&E-stained WSIs. PanSubNet was developed using data from 1,055 patients across two multi-institutional cohorts (PANCAN, n=846; TCGA, n=209) with paired histology and RNA-seq data. Ground-truth labels were derived using the validated Moffitt 50-gene signature refined by GATA6 expression. The model employs dual-scale architecture that fuses cellular-level morphology with tissue-level architecture, leveraging attention mechanisms for multi-scale representation learning and transparent feature attribution. On internal validation within PANCAN using five-fold cross-validation, PanSubNet achieved mean AUC of 88.5% with balanced sensitivity and specificity. External validation on the independent TCGA cohort without fine-tuning demonstrated robust generalizability (AUC 84.0%). PanSubNet preserved and, in metastatic disease, strengthened prognostic stratification compared to RNA-seq based labels. Prediction uncertainty linked to intermediate transcriptional states, not classification noise. Model predictions are aligned with established transcriptomic programs, differentiation markers, and DNA damage repair signatures. By enabling rapid, cost-effective molecular stratification from routine H&E-stained slides, PanSubNet offers a clinically deployable and interpretable tool for genetic subtyping. We are gathering data from two institutions to validate and assess real-world performance, supporting integration into digital pathology workflows and advancing precision oncology for PDAC.

cs.LG↗

arXiv2025

Eye-Tracking, Mouse Tracking, Stimulus Tracking,and Decision-Making Datasets in Digital Pathology

Interpretation of giga-pixel whole-slide images (WSIs) is an important but difficult task for pathologists. Their diagnostic accuracy is estimated to average around 70%. Adding a second pathologist does not substantially improve decision consistency. The field lacks adequate behavioral data to explain diagnostic errors and inconsistencies. To fill in this gap, we present PathoGaze1.0, a comprehensive behavioral dataset capturing the dynamic visual search and decision-making processes of the full diagnostic workflow during cancer diagnosis. The dataset comprises 18.69 hours of eye-tracking, mouse interaction, stimulus tracking, viewport navigation, and diagnostic decision data (EMSVD) collected from 19 pathologists interpreting 397 WSIs. The data collection process emphasizes ecological validity through an application-grounded testbed, called PTAH. In total, we recorded 171,909 fixations, 263,320 saccades, and 1,867,362 mouse interaction events. In addition, such data could also be used to improve the training of both pathologists and AI systems that might support human experts. All experiments were preregistered at https://osf.io/hj9a7, and the complete dataset along with analysis code is available at https://go.osu.edu/pathogaze.

cs.CV↗