Simple Token-Efficient Vision-Language Model for Case-level Pathology Synoptic Report Generation
Authors: Zhiyuan Yang, Jiahao Cheng, Vincent Quoc-Huy Trinh, Mahdi S. Hosseini
Abstract
Generating clinically useful pathology reports for pathology cases from whole-slide images (WSIs) is challenging due to gigapixel resolution, long visual-token sequences, and the complexity of case-level reasoning, where a single case may contain multiple WSIs with heterogeneous tissues and ambiguous findings. We present a simple token-efficient vision--language model for case-level synoptic report generation that remains practical under constrained GPU memory. Our architecture follows a minimal three-component design: a frozen pathology patch encoder, a lightweight two-layer MLP vision-language aligner, and a large language model decoder, with an explicit WSI marker token to separate slides within a case. Training proceeds in two supervised stages: (1) aligner-only WSI captioning using heterogeneous WSI-text pairs, and (2) case-level supervised fine-tuning on case-report pairs for structured report generation. To reduce sequence length, we represent each slide using 512×512 patches at 5× magnification, which reduces the average sequence length by up to 64× times compared to the commonly used 20× patches. Combined with efficient training techniques, we enable practical training with only half a NVIDIA H100 GPU. Across both training stages, our approach achieves high ROUGE-L/METEOR/BLEU-4 scores while being substantially more efficient in memory and runtime. In AI-based evaluations, our model is consistently preferred over strong baselines. Extensive ablations characterize performance-efficiency trade-offs and identify simple choices that improve robustness in multi-WSI settings. Overall, this work provides a strong, reproducible baseline for efficient pathology report generation, lowering the barrier to multi-WSI VLM research under limited compute.
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.
Whole-slide pathology images (WSIs) contain gigapixel-scale visual content, creating a major scalability challenge for slide-level multimodal large language models (MLLMs). Existing approaches process thousands of patch tokens and typically apply compression only after slide encoding, leaving multimodal attention computationally expensive. We introduce SLICEChat, a slide-level MLLM that integrates progressive token pruning within a hybrid Mamba--Transformer slide encoder. Mamba layers enable efficient long-range propagation, while Transformer layers preserve global interactions as the sequence is progressively shortened. Between stages, language-supervised, region-aware pruning removes spatially coherent low-utility regions under a controlled keep-rate schedule, producing compact slide representations before multimodal fusion. On SlideBench VQA, SLICEChat achieves 79.84% accuracy on TCGA and 59.09% on BCNB cohorts, outperforming prior slide-level pathology MLLMs, and achieves the highest overall WSI-Bench metrics. It also provides competitive memory usage and the inference latency among the evaluated models. These results demonstrate accurate and computationally efficient multimodal reasoning over gigapixel WSIs.
Ali Kerem Bozkurt, Baris Cem Bakay, Ibrahim Kulac +3
Gigapixel Whole-Slide Images (WSIs) present a fundamental computational bottleneck for vision-language models (VLMs) due to extreme sequence lengths. Existing approaches predominantly rely on spatial sampling or training-free pruning, which risk diluting weak but informative signals, leading to the loss of critical diagnostic evidence due to the spatially diffuse nature of pathological cues. We reformulate WSI token pruning as a sequential selection process, enabling the model to autonomously learn an optimal routing strategy rather than relying on static heuristics. We herein propose a decoupled routing framework integrated as an active plugin into the fully pre-trained SlideChat base model, leaving both the slide encoder and large language model frozen. To provide continuous gradients for the non-differentiable pruning operation during training, we introduce PathSelect. PathSelect employs a variance-preserving noise gate to modulate each patch's information flow via a differentiable Soft Top-K operator, paired with a diagonal-attention Denoiser that recovers the perturbed representations without semantic leakage. At inference, the PathSelect module is entirely detached. Relying solely on the trained Scorer, a deterministic Hard Top-K operator executes adaptive, data-dependent trajectory termination, significantly accelerating downstream generative processing with exceptionally low sequential token selection latency. Driven by an empirical average of only 44.86 tokens under a maximum constraint of K = 128, our framework achieves 74.00% overall accuracy on SlideBench (TCGA), representing an approximate 36.6x spatial token reduction relative to the uncompressed baseline average while consistently outperforming sampling-based counterparts.