TAP-Path: Task-Adaptive Structural and Token Pruning for Efficient and Trustworthy Pathology Foundation Models

Pathology foundation models improve transferable representation learning for histopathology, but recent gains often rely on encoders with hundreds of millions of parameters and high inference cost. We propose TAP-Path, a task-adaptive compression framework that directly restructures a pretrained Virchow2 encoder rather than distilling it into a separate student. TAP-Path combines validation-driven transformer-block selection, physical removal of redundant blocks, input-adaptive patch-token pruning, multi-depth feature recovery, and a lightweight gated task head. The final model retains 24 of 32 transformer blocks and 70% of patch tokens after pruning, reducing encoder parameters by 24.96% (631.24M to 473.70M) and analytical encoder compute by 35.20% (340.13G to 220.40G FLOPs). Across three task-head optimization seeds, TAP-Path achieved $87.98 \pm 0.067%$ test accuracy, $81.26 \pm 0.49%$ balanced accuracy, and $82.38 \pm 0.48%$ macro-F1 on a 32-class histopathology benchmark, compared with 86.89% for full Virchow2 and 87.67% for UNI2-h. TAP-Path achieved a Brier score of $0.1800 \pm 0.0005$ and failure-detection AUROC of $0.9047 \pm 0.0060$. A validation-only rare-aware objective improved rare-class balanced accuracy in a secondary operating analysis. Frozen external evaluation on 433 CPTAC samples yielded $91.22 \pm 0.83%$ accuracy and $91.10 \pm 0.81%$ balanced accuracy. These results show that task-adaptive structural and token sparsification can improve the accuracy-efficiency trade-off of large pathology foundation models while preserving reliability under internal and external evaluation.

DistillPath: An Efficient 22M Distilled Pathology Encoder Approaching Large Foundation Model Performance

Many high-performing pathology tile encoders are now foundation models with hundreds of millions to over a billion parameters. Encoding and storing the thousands of tiles in each whole-slide image with such models is costly on commodity hardware, so compact encoders that retain useful downstream performance are a valuable alternative. We present DistillPath-KS16, which starts from the existing 22M kaiko ViT-S/16 encoder and improves it by distilling from released pathology encoders used as frozen teachers. The recipe reads only the teachers' final class and patch tokens and trains on 6,000 public slides, needing neither their DINO nor iBOT pretraining heads nor a billion-tile corpus, so it applies to any released encoder that exposes backbone tokens. We distill four teachers spanning 86M to 1.1B parameters into the same student. Every variant improves the kaiko baseline on all three benchmarks we use, EVA, HEST, and PLISM, and the strongest teacher is task-dependent. On the seven-task EVA mean, DistillPath-KS16-Virchow2 reaches $0.795$, within $0.015$ points of Virchow2, the top-scoring model in our evaluation, at about $29\times$ fewer parameters; it also scores above H0-mini and GPFM on this aggregate metric, though that advantage is task-concentrated rather than uniform. Because it remains a 22M ViT-S/16 with 384-dimensional features, DistillPath-KS16 runs more than $25\times$ faster than Virchow2. Code is available at https://github.com/RamonKaspar/DistillPath, and released model weights are available at https://huggingface.co/collections/RamonK/distillpath.

Gated Spatial Redundancy Projection for Pathology Transformer Attentions

Transformer models are increasingly used for whole-slide image analysis in computational pathology. Yet, WSIs differ fundamentally from natural images: neighbouring patches often contain highly similar tissue type, stain, texture, and cellular composition. We identify this local spatial redundancy as a pathology-specific failure mode of self-attention, where dominant neighbourhood features can be repeatedly mixed into patch-tokens and weaken subtle diagnostic or prognostic deviations. We propose Gated Spatial Redundancy Projection (Gated SRP), a lightweight drop-in correction module for self-attention layers. For each patch token and attention head, Gated SRP estimates a local redundancy axis from neighbouring value vectors, projects the attention output onto this axis, and applies a learned signed gate to correct the redundancy-aligned component geometrically. Across five TCGA survival cohorts, Gated SRP obtains the highest mean C-index among the compared attention variants in all cohorts, with an average improvement over the base attention, while adding only +0.02% parameters. Across five slide-level classification datasets, it improves the base attention on 12 of 16 reported metrics and achieves the best AUC on three datasets. Code is publicly available at https://github.com/AtlasAnalyticsLab/GatedSRP.

BioM-JEPA: joint-embedding prediction of graph-connected gene blocks in single cells

Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence. A student network infers each target-block representation from the remaining genes in a cell, while a slowly updated teacher supplies the corresponding target from the full observed gene set. Under the reported extraction procedure, block-level prediction produced embeddings with higher effective rank and weaker association with detected-gene depth in the tested diagnostics than token-prediction, random-block and reconstruction controls. Across CellBench tasks, frozen BioM-JEPA embeddings retained expression, pathway and neighbourhood information and achieved the lowest aggregate perturbation-response error among the evaluated models. Representation diagnostics were also consistent with canonical pancreatic programmes and compositional relationships between genetic perturbations. Linear attention avoids constructing a quadratic gene-by-gene attention matrix; in a matched one-epoch hPancreas experiment at batch size 8, BioM-JEPA provided 5.75-fold higher fine-tuning throughput and 3.76-fold higher held-out embedding throughput than scFoundation. Together, these results support graph-connected gene blocks as useful prediction units for JEPA-style representation learning in single-cell biology.

CARVE: Cross-Slice Anisotropic Reallocation of Visual Evidence for Efficient 3D Medical Volume Understanding

Slice-based MLLMs leverage mature 2D encoders by representing 3D volumes as sequences of 2D slices. However, this slice-wise formulation produces thousands of visual tokens that burden the LLM backbone, many of which capture overlapping visual evidence across adjacent slices. To understand how effectively a growing visual token budget improves performance, we perform scaling analyses on two 3D medical VQA benchmarks and find diminishing returns: cost keeps rising while accuracy saturates, and improving in-plane resolution is more effective than adding slices at comparable budgets. The budget should therefore be allocated more selectively rather than simply enlarged, yet most token compression methods are designed for 2D images or videos, where redundancy arises from spatial layout or temporal motion rather than from near-duplicate content along the depth axis. We present CARVE, a training-free framework that compresses visual tokens prior to LLM inference and casts token reduction as budget-constrained 2.5D allocation. CARVE partitions the depth axis into coherent windows and allocates tokens non-uniformly according to normalized cross-slice evidence. Under a shared budget, CARVE builds spatial anchors on representative slices and retrieves locally varying evidence from the full volume, then merges remaining eligible tokens into nearby anchors within each window. Removing roughly 80% of the visual tokens on Hulu-Med-7B, CARVE leads all compression baselines on every AMOS-MM report-generation metric, with 6.2 points higher retention of full-token quality than the strongest baseline, and preserves 98.1% of full-token performance across three VQA benchmarks.

EvtGraph: Event-Adaptive Compression for Sparse Temporal Graph Learning in Multimodal Time Series

Multimodal temporal data are inherently irregular and uneven in information density, yet most models rely on uniform discretization, leading to inefficient representations. We propose \textbf{EvtGraph}, a unified framework that aligns computation with temporal salience under explicit budget constraints. EvtGraph reparameterizes sequences into event-level tokens via event-adaptive compression (EAMC), selects a compact subset with a node budget (NBC), and performs temporally constrained sparse graph reasoning (T2SG). This transforms dense sequences into structured computation over salient events, reducing complexity while preserving critical transitions. We show that this design provides a practical mechanism for allocating representational capacity under a fixed budget, yielding a consistent performance--efficiency trade-off, where a small budget is often sufficient in practice. Experiments on multimodal clinical (MIMIC-IV + CXR) and cross-domain benchmarks demonstrate that EvtGraph outperforms both Transformer-based and recurrent baselines while significantly improving efficiency. These results suggest that budget-constrained event-centric representation provides a general paradigm for learning from high-redundancy temporal data.

MedARC: Training-Free Adaptive Redundancy Compression of Visual Tokens for 3D Medical Vision-Language Models

Integrating 3D medical images with vision-language models (VLMs) holds substantial promise for computer-aided diagnosis. However, volumetric images generate prohibitively long visual-token sequences with considerable spatial and inter-slice redundancy. Existing token compression methods typically apply uniform reduction or rely on a single importance signal, increasing the risk of removing regions that are clinically relevant to the query or structurally distinctive. To address this limitation, we propose MedARC, a unified, training-free framework for Adaptive Redundancy Compression of visual tokens in 3D medical VLMs. MedARC estimates token importance by integrating three complementary cues: self-attention from the VLM vision encoder, which reflects the model's intrinsic visual focus; similarity between projected visual tokens and text embeddings, which identifies query-relevant regions; and deviations of local visual foundation model features from the volume-level feature center, which highlight structurally distinctive anatomy. The resulting importance distribution guides a saliency-aware merging strategy that preserves informative tokens while consolidating redundant ones rather than simply discarding them. Experiments on CT-RATE and MR-RATE show that MedARC reduces visual-token overhead and inference time while preserving or improving diagnostic performance. Its multi-cue scoring cost is outweighed by the savings from processing fewer tokens, with greater benefits expected for larger language models.

qZACH-ViT: Quantization-Aware Intrinsic Explanations with Recursive Attribution-Stabilized Optimization

Compact medical-image classifiers need efficiency and interpretable evidence, yet these goals are often addressed separately. We introduce qZACH-ViT, a quantization-aware extension of the zero-token (CLS-token-free), position-free ZACH-ViT backbone with recursive intrinsic patch-level class evidence. We also introduce Recursive Attribution-Stabilized Optimization (RASO), which norm-matches classification and attribution gradients and removes attribution components that conflict with classification. We evaluate four controlled conditions on seven MedMNIST datasets using 50 training images per class and ten fixed seeds, completing 280 runs. All 210 qZACH-ViT checkpoints are converted to executable mixed-precision ONNX INT8 graphs containing 16 signed INT8 MatMulInteger projections with INT32 accumulation. Deployed mixed-precision INT8 qZACH-ViT with Adam improves the FP32 ZACH-ViT baseline mean on all seven datasets, with a mean paired gain of 0.0313 in the dataset-specific primary metric; qZACH-ViT with RASO yields a mean gain of 0.0368. Across 964,920 source-to-INT8 test comparisons, prediction agreement is 99.9751\%, with a mean absolute primary-metric change of 0.000133 and a maximum of 0.004386. Across 3,600 matched intrinsic maps, mean cosine similarity is 0.999955, mean rank correlation is 0.9944, and mean top-10\% overlap is 0.9692. ONNX artifacts are 70.0\% smaller than source checkpoints and provide $1.41\times$ and $2.39\times$ end-to-end CPU speedups with one and four threads. RASO significantly reduces sufficiency error and improves input-noise stability over Adam with the same attribution loss, but does not dominate every predictive or explainable artificial intelligence (XAI) metric. These results establish qZACH-ViT as a deployable compact intrinsically explainable model and RASO as a targeted stability-oriented optimization procedure.

CPR: Chained Perceptual Refinement for Coarse-to-Fine Medical Image Classification

High resolution medical images contain fine grained, spatially sparse cues that are critical for diagnosis, yet preserving full resolution incurs substantial computational and memory costs. Most deep models process images uniformly, leading to redundant computation or loss of diagnostic detail under downsampling. We propose Chained Perceptual Refinement, CPR, a coarse to fine framework that formulates medical image analysis as a sequential global to local decision process. Starting from a low resolution global view, CPR dynamically predicts the location and spatial extent of refinement regions, extracts high resolution evidence from the original image, and incrementally integrates it with global context. By keeping the backbone input size fixed while contracting the perceptual field, CPR preserves diagnostic fidelity with constant peak GPU memory. Extensive experiments on five medical imaging datasets and multiple backbone architectures demonstrate that CPR consistently outperforms both fixed resolution and multi scale state of the art baselines, achieving improvements of up to 2.27 percentage points over the second best method. It also achieves up to a 19.6 fold reduction in GFLOPs at matched accuracy, establishing a superior accuracy and efficiency trade off for high resolution medical image analysis. The code is available on GitHub.