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Prateek Prasanna

Publications and source records attributed to Prateek Prasanna.

At least 19 recordsLinked to original sources
arXiv2026

Semantic Context-aware mOdality fUsion Transformer (SCOUT): A Context-Aware Multimodal Transformer for Concept-Grounded Pathology Report Generation

Whole-slide pathology report generation requires models to integrate localized histomorphology, global tissue context, and diagnostically relevant semantic information, yet existing approaches typically rely on fixed pretrained visual representations and may fail to represent key diagnostic concepts. Here we present SCOUT: Semantic Context-aware mOdality fUsion Transformer, a concept-grounded multimodal framework that integrates local histological patterns, whole-slide context, and expert-curated diagnostic concepts. SCOUT maintains an evolving visual representation together with recursively updated slide- and concept-conditioned representations, allowing visual and contextual information to iteratively co-evolve across encoder depth. During decoding, separate attention pathways attend to these complementary streams before an adaptive multimodal fusion module combines them for each generated token. We evaluated SCOUT on TCGA-BRCA, HistAI, and REG-2025, comprising more than 20,900 WSI-report pairs across more than seven cancer types. Using common CONCHv1.5 features and evaluation protocols, SCOUT outperformed WSI-Caption, HistGen, and Bi-Gen, improving BLEU scores by 9.6% on average, METEOR by 11.0%, and ROUGE-L by 3.6% relative to the strongest competing method. On REG-2025, SCOUT additionally improved the Clinical Report Quality Score by 5.6%, indicating better preservation of clinically relevant report attributes beyond lexical similarity. Ablations showed complementary contributions from iterative context refinement and adaptive fusion, while learned gates provided inspectable token-level estimates of modality use. Our results suggest that progressive contextual conditioning is effective across heterogeneous pathology report generation settings and provides a flexible framework for integrating domain knowledge into vision-language models for computational pathology.

cs.CV↗
arXiv2026

Benchmarking Vision-Language Models for Automated Pathology Diagnosis and Report Generation

The rapid advancement of vision-language models (VLMs) has accelerated progress in computational pathology; however, whole-slide image (WSI)-based pathology report generation remains limited by the scarcity of large-scale WSI--report datasets and the complexity of mapping spatially distributed visual patterns to structured clinical text. To address this, we introduce a clinically curated Pan-Asia WSI--report dataset of approximately 10,500 pairs from five institutions and establish the REG 2025 benchmark through a MICCAI challenge for systematic evaluation of multimodal models. We analyze submitted methods spanning pretrained VLMs, multiple-instance learning frameworks, hierarchical expert models, retrieval-augmented generation, and cross-modal Transformers. Rather than indicating that VLM use alone was sufficient for superior performance, the results suggest that top-performing methods benefited from structured report representations, hierarchical diagnostic decomposition, and effective multimodal grounding. We identify key limitations, including instability in quantitative attribute estimation (e.g., numeric hallucination) and a tendency toward diagnostic overspecification, with some errors resembling known diagnostic pitfalls in routine pathology. These findings establish REG 2025 as a benchmark for evaluating WSI-based structured report generation and vision-language understanding in computational pathology, providing insights for the design of clinically grounded multimodal pathology models.

cs.CV↗
arXiv2026

RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses challenges due to inherent spatial distortions and modality-specific variations. Existing methods largely rely on direct alignment, which often fails to capture complex cross-modal relationships. To address these limitations, we propose a novel framework that aligns gene and image features using a ranking-based alignment loss, preserving relative similarity across modalities and enabling robust multi-scale alignment. To further enhance the alignment's stability, we employ self-supervised knowledge distillation with a teacher-student network architecture, which serves as an intra-modal stability regularizer that prevents image-representation drift during cross-modal alignment. Extensive experiments on seven public datasets that encompass gene expression prediction, slide-level classification, and survival analysis demonstrate the efficacy of our method, showing improved alignment and predictive performance over existing methods. Code is available at https://github.com/winston52/RankByGene.

eess.IV↗
arXiv2026

GazeLT: Visual attention-guided long-tailed disease classification in chest radiographs

In this work, we present GazeLT, a human visual attention integration-disintegration approach for long-tailed disease classification. A radiologist's eye gaze has distinct patterns that capture both fine-grained and coarser level disease related information. While interpreting an image, a radiologist's attention varies throughout the duration; it is critical to incorporate this into a deep learning framework to improve automated image interpretation. Another important aspect of visual attention is that apart from looking at major/obvious disease patterns, experts also look at minor/incidental findings (few of these constituting long-tailed classes) during the course of image interpretation. GazeLT harnesses the temporal aspect of the visual search process, via an integration and disintegration mechanism, to improve long-tailed disease classification. We show the efficacy of GazeLT on two publicly available datasets for long-tailed disease classification, namely the NIH-CXR-LT (n=89237) and the MIMIC-CXR-LT (n=111898) datasets. GazeLT outperforms the best long-tailed loss by 4.1% and the visual attention-based baseline by 21.7% in average accuracy metrics for these datasets. Our code is available at https://github.com/lordmoinak1/gazelt.

cs.CV↗
arXiv2026

Pathologist Attention-Aligned Report Generation for Prostate Histopathology

The allocation of visual attention by pathologists during cancer diagnosis is a highly selective process that critically shapes the information extracted from whole-slide images (WSIs). Human attention helps medical imaging tasks such as classification and segmentation, and becomes a strong semantic cue for identifying diagnostically informative regions for report generation. In this paper, we introduce human attention into the training of pathologist report generation models. To this end, we collected a multimodal human-attention dataset of 121 prostate WSIs annotated with pathologists' multi-scale viewport trajectories synchronized with the pathologists' verbal descriptions and cursor movements for five clinically relevant components (e.g., Gleason patterns). Using this dataset, we finetune two report generation models with an attention-alignment loss that regularizes the model attention over image patches to match the distribution of pathologist attention. We evaluate our approach on prostate cancer report generation and visual question answering using two models with different internal attention mechanisms (i.e., how image tokens are integrated into the language decoder). Experiments show average gains of 10.9% on NLP-based metrics and 19.3% in accuracy across five clinically relevant report components. Further, model attention maps extracted at inference time, with minimal computational overhead, align more closely with pathologist attention, providing stronger visual support for the generated reports by highlighting the regions that most influence the output.

cs.CV↗
arXiv2026

PathReportEval: A Systematic Benchmark for Pathology Report Generation

Pathology report generation from whole-slide images (WSIs) is a rapidly growing multimodal learning problem, yet progress is difficult to measure because existing studies use heterogeneous datasets, model settings, visual encoders, and evaluation protocols. Moreover, commonly used natural language generation metrics, including BLEU, ROUGE, and METEOR, primarily reward lexical similarity and often fail to detect clinically consequential errors such as omitted diagnoses, hallucinated findings, or discordant tumor attributes. We present a standardized benchmark and evaluation framework for pathology report generation. The benchmark evaluates four representative methods across three datasets (TCGA, HistAI, and REG 2025) using three pathology foundation encoders (CONCHv1.5, UNI2-h, and H-Optimus-1). Our framework standardizes preprocessing, feature extraction, training, decoding, and evaluation, enabling fair comparison across models while providing a modular platform for integrating new methods, datasets, and encoders. A central contribution is the Clinical Report Quality Score (CRQS), a clinically grounded metric for evaluating factual correctness. CRQS maps reference and generated reports into structured clinical attributes and measures four complementary dimensions: clinical fact coverage, key information recall, hallucination rate, and clinical discordance, producing both an overall score and interpretable sub-scores. Experiments demonstrate that conventional language-generation metrics are weakly aligned with clinical correctness and frequently overestimate report quality. In contrast, CRQS reveals clinically meaningful differences between models and encoders that lexical metrics fail to capture. Together, the benchmark, public plug-and-play framework, and CRQS establish a reproducible foundation for rigorous evaluation of pathology report generation.

cs.CL↗
arXiv2026

Gaze2Report: Radiology Report Generation via Visual-Gaze Prompt Tuning of LLMs

Existing deep learning methods for radiology report generation enhance diagnostic efficiency but often overlook physician-informed medical priors. This leads to a suboptimal alignment between the structured explanations and disease manifestations. Eye gaze data provides critical insights into a radiologist's visual attention, enhancing the relevance and interpretability of extracted features while aligning with human decision-making processes. However, despite its promising potential, the integration of eye gaze information into AI-driven medical imaging workflows is impeded by challenges such as the complexity of multimodal data fusion and the high cost of gaze acquisition, particularly its absence during inference, limiting its practical applicability in real-world clinical settings. To address these issues, we introduce Gaze2Report, a framework which leverages a scanpath prediction module and Graph Neural Network (GNN) to generate joint visual-gaze tokens. Combined with instruction and report tokens, these form a multimodal prompt used to fine-tune LoRA layers of large language models (LLMs) for autoregressive report generation. Gaze2Report enhances report quality through eye-gaze-guided visual learning and incorporates on-the-fly scanpath prediction, enabling the model to operate without gaze input during inference.

q-bio.TO↗
arXiv2026

Vessel-Aware Deep Learning for OCTA-Based Detection of AMD

Age-related macular degeneration (AMD) is characterized by early micro-vascular alterations that can be captured non-invasively using optical coherence tomography angiography (OCTA), yet most deep learning (DL) models rely on global features and fail to exploit clinically meaningful vascular biomarkers. We introduce an external multiplicative attention framework that incorporates vessel-specific tortuosity maps and vasculature dropout maps derived from arteries, veins, and capillaries. These biomarker maps are generated from vessel segmentations and smoothed across multiple spatial scales to highlight coherent patterns of vascular remodeling and capillary rarefaction. Tortuosity reflects abnormalities in vessel geometry linked to impaired auto-regulation, while dropout maps capture localized perfusion deficits that precede structural retinal damage. The maps are fused with the OCTA projection to guide a deep classifier toward physiologically relevant regions. Arterial tortuosity provided the most consistent discriminative value, while capillary dropout maps performed best among density-based variants, especially at larger smoothing scales. Our proposed method offers interpretable insights aligned with known AMD pathophysiology.

cs.CV↗
arXiv2026

Structure-Guided Histopathology Synthesis via Dual-LoRA Diffusion

Histopathology image synthesis plays an important role in tissue restoration, data augmentation, and modeling of tumor microenvironments. However, existing generative methods typically address restoration and generation as separate tasks, although both share the same objective of structure-consistent tissue synthesis under varying degrees of missingness, and often rely on weak or inconsistent structural priors that limit realistic cellular organization. We propose Dual-LoRA Controllable Diffusion, a unified centroid-guided diffusion framework that jointly supports Local Structure Completion and Global Structure Synthesis within a single model. Multi-class nuclei centroids serve as lightweight and annotation-efficient spatial priors, providing biologically meaningful guidance under both partial and complete image absence. Two task-specific LoRA adapters specialize the shared backbone for local and global objectives without retraining separate diffusion models. Extensive experiments demonstrate consistent improvements over state-of-the-art GAN and diffusion baselines across restoration and synthesis tasks. For local completion, LPIPS computed within the masked region improves from 0.1797 (HARP) to 0.1524, and for global synthesis, FID improves from 225.15 (CoSys) to 76.04, indicating improved structural fidelity and realism. Our approach achieves more faithful structural recovery in masked regions and substantially improved realism and morphology consistency in full synthesis, supporting scalable pan-cancer histopathology modeling.

cs.CV↗
arXiv2025

TICON: A Slide-Level Tile Contextualizer for Histopathology Representation Learning

The interpretation of small tiles in large whole slide images (WSI) often needs a larger image context. We introduce TICON, a transformer-based tile representation contextualizer that produces rich, contextualized embeddings for ''any'' application in computational pathology. Standard tile encoder-based pipelines, which extract embeddings of tiles stripped from their context, fail to model the rich slide-level information essential for both local and global tasks. Furthermore, different tile-encoders excel at different downstream tasks. Therefore, a unified model is needed to contextualize embeddings derived from ''any'' tile-level foundation model. TICON addresses this need with a single, shared encoder, pretrained using a masked modeling objective to simultaneously unify and contextualize representations from diverse tile-level pathology foundation models. Our experiments demonstrate that TICON-contextualized embeddings significantly improve performance across many different tasks, establishing new state-of-the-art results on tile-level benchmarks (i.e., HEST-Bench, THUNDER, CATCH) and slide-level benchmarks (i.e., Patho-Bench). Finally, we pretrain an aggregator on TICON to form a slide-level foundation model, using only 11K WSIs, outperforming SoTA slide-level foundation models pretrained with up to 350K WSIs.

cs.CV↗
arXiv2025

PixCell: A generative foundation model for digital histopathology images

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, there are unique problems in pathology, such as annotated data scarcity, privacy regulations in data sharing, and inherently generative tasks like virtual staining. Generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address these problems through image synthesis. We introduce PixCell, the first generative foundation model for histopathology images. PixCell is a diffusion model trained on PanCan-30M, a large, diverse dataset derived from 69,184 H&E-stained whole slide images of various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any human-annotated data. By conditioning on real slides, the synthetic images capture the properties of the real data and can be used as data augmentation for small-scale datasets to boost classification performance. We prove the foundational versatility of PixCell by applying it to two generative downstream tasks: privacy-preserving synthetic data generation and virtual IHC staining. PixCell's high-fidelity conditional generation enables institutions to use their private data to synthesize highly realistic, site-specific surrogate images that can be shared in place of raw patient data. Furthermore, using datasets of roughly paired H&E-IHC tiles, we learn to translate PixCell's conditioning from H&E to multiple IHC stains, allowing the generation of IHC images from H&E inputs. Our trained models are publicly released to accelerate research in computational pathology.

eess.IV↗
arXiv2025

PEaRL: Pathway-Enhanced Representation Learning for Gene and Pathway Expression Prediction from Histology

Integrating histopathology with spatial transcriptomics (ST) provides a powerful opportunity to link tissue morphology with molecular function. Yet most existing multimodal approaches rely on a small set of highly variable genes, which limits predictive scope and overlooks the coordinated biological programs that shape tissue phenotypes. We present PEaRL (Pathway Enhanced Representation Learning), a multimodal framework that represents transcriptomics through pathway activation scores computed with ssGSEA. By encoding biologically coherent pathway signals with a transformer and aligning them with histology features via contrastive learning, PEaRL reduces dimensionality, improves interpretability, and strengthens cross-modal correspondence. Across three cancer ST datasets (breast, skin, and lymph node), PEaRL consistently outperforms SOTA methods, yielding higher accuracy for both gene- and pathway-level expression prediction (up to 58.9 percent and 20.4 percent increase in Pearson correlation coefficient compared to SOTA). These results demonstrate that grounding transcriptomic representation in pathways produces more biologically faithful and interpretable multimodal models, advancing computational pathology beyond gene-level embeddings.

cs.CV↗
arXiv2025

Anatomy-DT: A Cross-Diffusion Digital Twin for Anatomical Evolution

Accurately modeling the spatiotemporal evolution of tumor morphology from baseline imaging is a pre-requisite for developing digital twin frameworks that can simulate disease progression and treatment response. Most existing approaches primarily characterize tumor growth while neglecting the concomitant alterations in adjacent anatomical structures. In reality, tumor evolution is highly non-linear and heterogeneous, shaped not only by therapeutic interventions but also by its spatial context and interaction with neighboring tissues. Therefore, it is critical to model tumor progression in conjunction with surrounding anatomy to obtain a comprehensive and clinically relevant understanding of disease dynamics. We introduce a mathematically grounded framework that unites mechanistic partial differential equations with differentiable deep learning. Anatomy is represented as a multi-class probability field on the simplex and evolved by a cross-diffusion reaction-diffusion system that enforces inter-class competition and exclusivity. A differentiable implicit-explicit scheme treats stiff diffusion implicitly while handling nonlinear reaction and event terms explicitly, followed by projection back to the simplex. To further enhance global plausibility, we introduce a topology regularizer that simultaneously enforces centerline preservation and penalizes region overlaps. The approach is validated on synthetic datasets and a clinical dataset. On synthetic benchmarks, our method achieves state-of-the-art accuracy while preserving topology, and also demonstrates superior performance on the clinical dataset. By integrating PDE dynamics, topology-aware regularization, and differentiable solvers, this work establishes a principled path toward anatomy-to-anatomy generation for digital twins that are visually realistic, anatomically exclusive, and topologically consistent.

eess.IV↗
arXiv2025

SoC-DT: Standard-of-Care Aligned Digital Twins for Patient-Specific Tumor Dynamics

Accurate prediction of tumor trajectories under standard-of-care (SoC) therapies remains a major unmet need in oncology. This capability is essential for optimizing treatment planning and anticipating disease progression. Conventional reaction-diffusion models are limited in scope, as they fail to capture tumor dynamics under heterogeneous therapeutic paradigms. There is hence a critical need for computational frameworks that can realistically simulate SoC interventions while accounting for inter-patient variability in genomics, demographics, and treatment regimens. We introduce Standard-of-Care Digital Twin (SoC-DT), a differentiable framework that unifies reaction-diffusion tumor growth models, discrete SoC interventions (surgery, chemotherapy, radiotherapy) along with genomic and demographic personalization to predict post-treatment tumor structure on imaging. An implicit-explicit exponential time-differencing solver, IMEX-SoC, is also proposed, which ensures stability, positivity, and scalability in SoC treatment situations. Evaluated on both synthetic data and real world glioma data, SoC-DT consistently outperforms classical PDE baselines and purely data-driven neural models in predicting tumor dynamics. By bridging mechanistic interpretability with modern differentiable solvers, SoC-DT establishes a principled foundation for patient-specific digital twins in oncology, enabling biologically consistent tumor dynamics estimation. Code will be made available upon acceptance.

cs.CV↗
arXiv2025

NeuroRAD-FM: A Foundation Model for Neuro-Oncology with Distributionally Robust Training

Neuro-oncology poses unique challenges for machine learning due to heterogeneous data and tumor complexity, limiting the ability of foundation models (FMs) to generalize across cohorts. Existing FMs also perform poorly in predicting uncommon molecular markers, which are essential for treatment response and risk stratification. To address these gaps, we developed a neuro-oncology specific FM with a distributionally robust loss function, enabling accurate estimation of tumor phenotypes while maintaining cross-institution generalization. We pretrained self-supervised backbones (BYOL, DINO, MAE, MoCo) on multi-institutional brain tumor MRI and applied distributionally robust optimization (DRO) to mitigate site and class imbalance. Downstream tasks included molecular classification of common markers (MGMT, IDH1, 1p/19q, EGFR), uncommon alterations (ATRX, TP53, CDKN2A/2B, TERT), continuous markers (Ki-67, TP53), and overall survival prediction in IDH1 wild-type glioblastoma at UCSF, UPenn, and CUIMC. Our method improved molecular prediction and reduced site-specific embedding differences. At CUIMC, mean balanced accuracy rose from 0.744 to 0.785 and AUC from 0.656 to 0.676, with the largest gains for underrepresented endpoints (CDKN2A/2B accuracy 0.86 to 0.92, AUC 0.73 to 0.92; ATRX AUC 0.69 to 0.82; Ki-67 accuracy 0.60 to 0.69). For survival, c-index improved at all sites: CUIMC 0.592 to 0.597, UPenn 0.647 to 0.672, UCSF 0.600 to 0.627. Grad-CAM highlighted tumor and peri-tumoral regions, confirming interpretability. Overall, coupling FMs with DRO yields more site-invariant representations, improves prediction of common and uncommon markers, and enhances survival discrimination, underscoring the need for prospective validation and integration of longitudinal and interventional signals to advance precision neuro-oncology.

cs.CV↗
arXiv2025

BrainMRDiff: A Diffusion Model for Anatomically Consistent Brain MRI Synthesis

Accurate brain tumor diagnosis relies on the assessment of multiple Magnetic Resonance Imaging (MRI) sequences. However, in clinical practice, the acquisition of certain sequences may be affected by factors like motion artifacts or contrast agent contraindications, leading to suboptimal outcome, such as poor image quality. This can then affect image interpretation by radiologists. Synthesizing high quality MRI sequences has thus become a critical research focus. Though recent advancements in controllable generative AI have facilitated the synthesis of diagnostic quality MRI, ensuring anatomical accuracy remains a significant challenge. Preserving critical structural relationships between different anatomical regions is essential, as even minor structural or topological inconsistencies can compromise diagnostic validity. In this work, we propose BrainMRDiff, a novel topology-preserving, anatomy-guided diffusion model for synthesizing brain MRI, leveraging brain and tumor anatomies as conditioning inputs. To achieve this, we introduce two key modules: Tumor+Structure Aggregation (TSA) and Topology-Guided Anatomy Preservation (TGAP). TSA integrates diverse anatomical structures with tumor information, forming a comprehensive conditioning mechanism for the diffusion process. TGAP enforces topological consistency during reverse denoising diffusion process; both these modules ensure that the generated image respects anatomical integrity. Experimental results demonstrate that BrainMRDiff surpasses existing baselines, achieving performance improvements of 23.33% on the BraTS-AG dataset and 33.33% on the BraTS-Met dataset. Code will be made publicly available soon.

eess.IV↗
arXiv2025

ImmunoDiff: A Diffusion Model for Immunotherapy Response Prediction in Lung Cancer

Accurately predicting immunotherapy response in Non-Small Cell Lung Cancer (NSCLC) remains a critical unmet need. Existing radiomics and deep learning-based predictive models rely primarily on pre-treatment imaging to predict categorical response outcomes, limiting their ability to capture the complex morphological and textural transformations induced by immunotherapy. This study introduces ImmunoDiff, an anatomy-aware diffusion model designed to synthesize post-treatment CT scans from baseline imaging while incorporating clinically relevant constraints. The proposed framework integrates anatomical priors, specifically lobar and vascular structures, to enhance fidelity in CT synthesis. Additionally, we introduce a novel cbi-Adapter, a conditioning module that ensures pairwise-consistent multimodal integration of imaging and clinical data embeddings, to refine the generative process. Additionally, a clinical variable conditioning mechanism is introduced, leveraging demographic data, blood-based biomarkers, and PD-L1 expression to refine the generative process. Evaluations on an in-house NSCLC cohort treated with immune checkpoint inhibitors demonstrate a 21.24% improvement in balanced accuracy for response prediction and a 0.03 increase in c-index for survival prediction. Code will be released soon.

eess.IV↗
arXiv2025

GECKO: Gigapixel Vision-Concept Contrastive Pretraining in Histopathology

Pretraining a Multiple Instance Learning (MIL) aggregator enables the derivation of Whole Slide Image (WSI)-level embeddings from patch-level representations without supervision. While recent multimodal MIL pretraining approaches leveraging auxiliary modalities have demonstrated performance gains over unimodal WSI pretraining, the acquisition of these additional modalities necessitates extensive clinical profiling. This requirement increases costs and limits scalability in existing WSI datasets lacking such paired modalities. To address this, we propose Gigapixel Vision-Concept Knowledge Contrastive pretraining (GECKO), which aligns WSIs with a Concept Prior derived from the available WSIs. First, we derive an inherently interpretable concept prior by computing the similarity between each WSI patch and textual descriptions of predefined pathology concepts. GECKO then employs a dual-branch MIL network: one branch aggregates patch embeddings into a WSI-level deep embedding, while the other aggregates the concept prior into a corresponding WSI-level concept embedding. Both aggregated embeddings are aligned using a contrastive objective, thereby pretraining the entire dual-branch MIL model. Moreover, when auxiliary modalities such as transcriptomics data are available, GECKO seamlessly integrates them. Across five diverse tasks, GECKO consistently outperforms prior unimodal and multimodal pretraining approaches while also delivering clinically meaningful interpretability that bridges the gap between computational models and pathology expertise. Code is made available at https://github.com/bmi-imaginelab/GECKO

cs.CV↗