# SLICEChat: Progressive In-Encoder Token Pruning for Whole-Slide Pathology Language Models

arXiv: https://arxiv.org/abs/2609.24894 · HTML: https://mlsanity.com/paper/2609.24894/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical vision-language models, one of 16 directions in Multimodal LLMs / vision-language models.
- Builds on 49 of its 60 references that are in the map.
- First posted on arXiv 21 Sep 2026.

## Placed in

- Multimodal LLMs / vision-language models / [Medical vision-language models](https://mlsanity.com/mllm/medical-vision-language-models/)
- State-space sequence models (S4, Mamba) / [Mamba for medical image analysis](https://mlsanity.com/ssm/mamba-for-medical-image-analysis/)
- Efficient LLM inference and serving / [Visual token pruning in multimodal models](https://mlsanity.com/inference/visual-token-pruning-in-multimodal-models/)

## Builds on (most cited first, 30 of 49)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation](https://mlsanity.com/paper/2201.12086/) (2022)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Transformers are SSMs: Generalized Models and Efficient Algorithms Through Structured State Space Duality](https://mlsanity.com/paper/2405.21060/) (2024)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Vision Mamba: Efficient Visual Representation Learning with Bidirectional State Space Model](https://mlsanity.com/paper/2401.09417/) (2024)
- [Token Merging: Your ViT But Faster](https://mlsanity.com/paper/2210.09461/) (2022)
- [DynamicViT: Efficient Vision Transformers with Dynamic Token Sparsification](https://mlsanity.com/paper/2106.02034/) (2021)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [Gated Delta Networks: Improving Mamba2 with Delta Rule](https://mlsanity.com/paper/2412.06464/) (2024)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [LLaVA-PruMerge: Adaptive Token Reduction for Efficient Large Multimodal Models](https://mlsanity.com/paper/2403.15388/) (2024)
- [Prismatic VLMs: Investigating the Design Space of Visually-Conditioned Language Models](https://mlsanity.com/paper/2402.07865/) (2024)
- [Gated Attention for Large Language Models: Non-linearity, Sparsity, and Attention-Sink-Free](https://mlsanity.com/paper/2505.06708/) (2025)
- [Rotary Position Embedding for Vision Transformer](https://mlsanity.com/paper/2403.13298/) (2024)
- [MambaVision: A Hybrid Mamba-Transformer Vision Backbone](https://mlsanity.com/paper/2407.08083/) (2024)
- [LongNet: Scaling Transformers to 1,000,000,000 Tokens](https://mlsanity.com/paper/2307.02486/) (2023)
- [Quilt-1M: One Million Image-Text Pairs for Histopathology](https://mlsanity.com/paper/2306.11207/) (2023)
- [DivPrune: Diversity-based Visual Token Pruning for Large Multimodal Models](https://mlsanity.com/paper/2503.02175/) (2025)
- [Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images](https://mlsanity.com/paper/2306.07831/) (2023)
- [Virchow: A Million-Slide Digital Pathology Foundation Model](https://mlsanity.com/paper/2309.07778/) (2023)
- [Quilt-LLaVA: Visual Instruction Tuning by Extracting Localized Narratives from Open-Source Histopathology Videos](https://mlsanity.com/paper/2312.04746/) (2023)

## Abstract (arXiv)

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.