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新论文 · v1arXiv:2611.17104

TuMAP：一种双视角、形态型感知的病理组学流程，用于量化肾小管重塑

TuMAP: A Dual-View, Morphotype-Aware Pathomics Pipeline for Quantifying Renal Tubular Remodeling

Ruijie Wu, Yuechen Yang, Yanfan Zhu, Yu Wang, Shilin Zhao, Ming-Tsun Tsai, Szu-Yuan Li, Shuo-Ming Ou 等 11 位作者

AI 速读 基于摘要

作者提出 TuMAP 流程，结合双视角基础模型表征、形态型标注与患者级统计推断，从 PAS 染色肾活检切片中量化肾小管形态型组成及形态型内差异。

cs.CV · eess.IV

arXiv ↗PDF ↗
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Quantifying disease-associated renal tubular remodeling is challenging because tubular appearances are heterogeneous. We introduce TuMAP (Tubular Morphotype-Aware Pathomics), a pipeline combining (1) dual-view foundation-model representations and provisional morphotype annotation, (2) compositional and within-morphotype pathomics, and (3) patient-level statistical inference. From 456,158 tubules in 358 PAS-stained kidney biopsy slides, TuMAP identified eight image-based morphotypes, seven of which showed stable subsampling assignments. Across 219 patients in six diagnostic groups, diabetic nephropathy (DN) and tubulointerstitial nephritis/acute tubular injury (TIN/ATI) each differed from minimal change disease in seven morphotype proportions, while IgA nephropathy differed in six. DN showed reduced nuclear solidity and increased eccentricity across all eight morphotypes. Area-normalized nuclear density exposed additional within-morphotype differences. TuMAP provides a framework for separating changes in tubular morphotype composition from phenotypic differences within morphotypes.

新论文 · v1arXiv:2611.07593

TACT-KV: Tri-Axis Cosine Transform for Compressing Volumetric KV Caches in Medical VLMs

Chongyu Qu, Ritchie Zhao, Yufan He, Dong Yang, Zhengyi Lu, Junchao Zhu, Tianyuan Yao, Juming Xiong 等 15 位作者

原文摘要

Vision-language models (VLMs) applied to 3D medical scans face a structural memory wall. A single CT or MRI volume produces tens of thousands of vision tokens, and the resulting key-value (KV) cache scales linearly with both batch and context. Existing KV compression methods operate on the cache's feature or token statistics, or apply 1D and 2D transforms, leaving the three-axis spatial structure in the cache unexploited. We propose TACT-KV (Tri-Axis Cosine Transform), a calibration-free KV compression method that exploits strong spatial correlations in visual KV states along all three anatomical axes of 3D scans. This correlation concentrates the KV cache energy under a frequency-domain transform. TACT-KV applies a separable 3D discrete cosine transform to the KV cache, allocates a per-layer bit budget across frequency bins via reverse water-filling (more bits to high-energy components), and quantizes each bin with a fixed scalar codebook. We derive a close-form relation: the distortion reduction from adaptive bit allocation is dominated by the spectral concentration of the transformed cache. Across six medical VLMs and two 3D CT benchmarks, TACT-KV achieves the lowest 1-bit prediction-flip rate on eleven of twelve model and dataset pairs in our main comparison. The same advantage reproduces on four general-purpose VLMs evaluated on video tasks, indicating that the benefit of exploiting three-axis structure generalizes beyond medical imaging. At equal high-bandwidth memory (HBM), TACT-KV scales the decoding batch size on a single GPU by up to $8\times$.

cs.CV · cs.LG

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arXiv ↗PDF ↗
新论文 · v1arXiv:2611.05925

3D Banff Glomerulitis Scoring for Kidney Transplant Pathology: Feasibility Study for Volumetric Quantification

Yanfan Zhu, Junchao Zhu, Ruining Deng, Shilin Zhao, Yu Wang, Yaohong Wang, Yuechen Yang, Chongyu Qu 等 15 位作者

原文摘要

Quantifying glomerular inflammation in kidney-transplant biopsies is traditionally performed on single whole-slide sections using the Banff "most-severe section" rule, despite the inherently three-dimensional nature of lesion distribution. This 2D based assessment might lead to instability when inflammation varies across slices. This paper reports a feasibility study examining the technical feasibility and clinical relevance of extending Banff scoring into three dimensions. To this end, we propose a 3D Banff lesion-scoring framework that aligns serial sections, reconstructs glomerular identities across depth, and integrates inflammatory-cell counts in 3D under three scoring strategies: Compatible, Volumetric, and Deduplicated Volumetric. In the experiments, glomerulitis (g-scores) was used as an example Banff metric and applied to multi-section renal allograft biopsies. Our findings indicate that 3D Banff g-scores are more consistent across sections and, under the semi-automatic setting, the Volumetric strategy correlates more strongly with clinical biomarkers than traditional 2D scores. These results show that 3D volumetric quantification offers promising added value, underscoring the potential benefit of 3D-aware Banff scoring for kidney transplant pathology.

cs.CV

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arXiv ↗PDF ↗
新论文 · v1arXiv:2610.39151

STRATA: Reinforcement-driven Active Sampling with Tri-paradigm Adaptation for Efficient 3D Spatial Transcriptomics

Junchao Zhu, Ruining Deng, Chongyu Qu, Zhengyi Lu, Yanfan Zhu, Yuechen Yang, Yu Wang, Shilin Zhao 等 10 位作者

原文摘要

Spatial transcriptomics (ST) enables joint characterization of tissue morphology and gene expression. However, 3D volumetric ST acquisition remains expensive. AI-driven methods offer a low-cost alternative but remain limited in accuracy, while recent 2D section-wise ST acquisition still rely on dense grid sampling, resulting in redundant measurements and undersampling of biologically informative regions. To bridge the gap, we propose STRATA, a reinforcement-driven active sampling framework with tri-paradigm adaptation for reconstructing dense 3D transcriptomic maps from sparse voxel-wise ST acquisition. STRATA constructs a 3D graph integrating H&E morphology with single-cell priors and employs a reinforcement learning agent to estimate morphological sparsity and transcriptomic informativeness, enabling budget-aware selection of informative spots. Given these sparse measurements, an adaptive tri-paradigm predictor combines retrieval, regression, and cross-layer imputation through lightweight fusion, dynamically weighting their contributions. Experiments across datasets demonstrate improved sampling efficiency and accuracy, particularly under low-budget settings. Code is available at https://github.com/Junchao-Zhu/STRATA.

cs.CV

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arXiv ↗PDF ↗