From Patches to Patients: A study of the tile-to-slide performance transferability in Digital Pathology

Foundation Models (FMs) have recently redefined the state-of-the-art in histopathology by providing robust representations for whole-slide image (WSI) analysis. However, selecting the optimal foundation model (FM) for a specific clinical cohort currently requires multiple preprocessing steps, followed by computationally expensive feature extraction and the training of a Multiple Instance Learning (MIL) aggregator for every model. In this work, we investigate whether efficient tile-level linear probing can serve as a reliable proxy for slide-level performance, reducing the need to run full slide-level pipelines for every candidate encoder. We benchmark 19 state-of-the-art FMs on 42 slide-level and 16 tile-level tasks, comparing tile probing metrics against slide-level outcomes using ABMIL and Mean Pooling aggregations. We observe a high correlation between tile and slide performance across varying task difficulties, indicating that encoder representation quality is the primary determinant of WSI success. Sensitivity analyses show that transferability is stable across models and is more influenced by cohort sizes and numbers of tiles per slide than by average task difficulty. We also measure the agreement in best performing models between tile and slide-level tasks, showing tile benchmarks reliably shortlist strong candidates. Overall, our study indicates that tile-level benchmarking provides an efficient and practical first step for narrowing down candidate models, while slide-level evaluation remains essential for final validation on clinical tasks.

GD-MIL: Grade-Disentangled Multiple Instance Learning for Multimodal Biochemical Recurrence Prediction in Prostate Cancer

Biochemical recurrence (BCR) after radical prostatectomy is a critical endpoint in prostate cancer, yet risk stratification relies almost entirely on variables dominated by Gleason grade. Whether H&E whole slide images (WSIs) carry prognostic signal beyond grade, and whether multiple instance learning (MIL) can recover it, remains unsettled. A key obstacle is that many pipelines select model checkpoints on the evaluation fold, artificially inflating concordance. We construct a rigorous benchmark on TCGA-PRAD (487 patients, 101 BCR events) using strict out-of-fold scoring over five-fold cross-validation repeated across five seeds. The choice of MIL aggregator (ABMIL, CLAM, TransMIL, PatchGCN) has little effect (C-index 0.61-0.64 with UNI2-h), while the feature extractor is the dominant factor (ResNet50 0.566 versus pathology foundation models up to 0.639). A clinical Cox model on grade, stage, and age reaches 0.687; no imaging-only model significantly outperforms it (p > 0.10). We introduce Grade-Disentangled MIL (GD-MIL), a gated-attention MIL encoder trained with a gradient-reversal grade adversary that encourages the slide representation to be invariant to Gleason grade before late fusion with clinical variables. GD-MIL achieves C-index 0.704, significantly outperforming both the clinical baseline (delta-c = +0.029, p = 0.0005) and the best imaging-only model (delta-c = +0.062, p = 0.039), suggesting H&E morphology contains prognostic information complementary to grade. A median risk split yields log-rank p < 0.0001 separation in BCR-free survival (~20% vs ~70% at five years).

Democratising Camera Trap AI: An Open-Source Model for Detecting UK Mammals

Camera traps have become a cornerstone of biodiversity monitoring, but the artificial intelligence that turns vast quantities of images into usable ecological data is often locked behind commercial platforms or trained on fauna that does not match that of the British Isles. In an attempt to remove barriers and increase uptake, we release an open-source object detection model for 31 classes, 28 common UK mammal and bird species, plus utility classes for humans, calibration poles, and vehicles, drawn from a curated dataset of 48,165 labelled instances assembled from multiple sites over a decade of operational deployment through Conservation AI and its successor, Trap Tracker. The model, a YOLO26x detector trained and tested on an 80/10/10 class-stratified split, achieves a mean Average Precision of 0.984 at Intersection over Union (IoU) of 0.5 (0.956 at IoU 0.5-0.95) on the held-out validation set, with precision 0.988 and recall 0.965. On an unseen held-out test split, mean per-species confidence ranged from 0.96 to 0.99 across the 31 classes, with a 0.17% false-negative rate concentrated in difficult night-time, distant, or occluded images. These metrics are from data from the same pool of sites and cameras as training, so performance at entirely new sites is left to future work. We release the trained weights in ONNX format under a non-commercial licence, with local desktop and real-time camera support, aimed explicitly at ecologists with no machine-learning experience. This release is a deliberate counterweight to the multiple paid for models that have developed over the last decade.

Vector Map as Language: Toward Unified Remote Sensing Vector Mapping

Remote sensing vector mapping aims to generate structured maps of geospatial entities, such as buildings, roads, and water bodies, from remote sensing imagery. In practice, vector maps usually contain multiple category layers and heterogeneous entity structures, requiring a unified model for diverse mapping needs. However, existing methods typically represent vector objects as polygons or graphs, making them suitable only for specific categories: polygons poorly capture topological relations, while graphs often blur instance boundaries. We observe that language, as a natural medium for human communication, offers a flexible and expressive representation that can accommodate heterogeneous map elements, including geometry, semantics, and topolog. Motivated by this insight, we propose Vector Map as Language (VecLang), a unified paradigm that reformulates multiclass vector mapping as structured text generation. VecLang encodes the common elements of different geospatial entities into a GeoJSON-like vector language, enabling cross-category modeling within a shared textual format. To generate this language reliably, we design a progressive vision-language mapping framework that first localizes vectorization units and then generates structured map elements. We further introduce Hierarchical Vector Language Optimization, which uses reinforcement learning to improve syntax validity, content fidelity, and map executability. We also build VecMap-Bench with 54K images and 800K instances, supporting training and evaluation across standard and generalization settings. Extensive experiments demonstrate that VecLang handles both single-class and multiclass vector mapping while achieving strong cross-dataset and open-vocabulary generalization. The model and dataset are publicly available at https://github.com/yyyyll0ss/VecLang.

Self-Supervised Vision Transformers for CBCT-Based Detection of Temporomandibular Joint Osteoarthritis

Temporomandibular joint osteoarthritis (TMJ OA) is a prevalent degenerative condition whose osseous changes are often subtle on cone-beam CT (CBCT), making automated detection challenging. We study how well the DINO family of self-supervised vision transformers -- DINOv1, DINOv2, DINOv2+reg, and RAD-DINO (a radiology-pretrained variant) -- transfers to CBCT, asking how much backbone adaptation is needed and of what kind. We propose a simple slice-based pipeline using Vision Transformer (ViT) backbones: axial CBCT slices are encoded per-slice by a frozen or partially adapted ViT and aggregated via attention-based multiple instance learning (MIL) for patient-level binary OA/Normal classification. Through systematic ablation across unfreezing strategies and aggregation designs on a multi-source CBCT dataset, we find that partial unfreezing of the final two transformer blocks is the decisive factor, improving AUC from 0.671 (fully frozen DINOv2) to 0.902. This outperforms DINOv1 (0.867), DINOv2+reg (0.774), and a supervised ImageNet ViT-B/16 baseline (0.843). Our results provide practical guidance for adapting DINO-family foundation models in low-data medical imaging settings, showing that adaptation strategy is a stronger driver of performance than backbone choice alone.

LRMIL: Efficient Low-Resolution Multiple Instance Learning via High-Resolution Knowledge Distillation for Whole Slide Image Classification

Multiple instance learning (MIL) has become a standard paradigm for whole slide image (WSI) analysis in digital pathology, as it enables slide-level prediction without dense annotations. Existing MIL methods typically rely on exhaustive extraction and encoding of high-resolution patches. However, this practice suffers from two critical limitations in real-world clinical settings: it struggles to capture global visual cues at lower magnifications, and incurs substantial computational overhead due to the massive number of high-resolution patches per slide. To address these limitations, we propose an efficient low-resolution multiple instance learning (LRMIL) framework that transfers high-resolution knowledge to low-resolution representations. LRMIL adopts a two-stage distillation strategy. First, patch-level cross-resolution distillation aligns low-resolution patch embeddings with high-resolution representations. Second, slide-level knowledge distillation trains a low-resolution student MIL model under both slide-level supervision and teacher guidance. At inference time, LRMIL operates exclusively on low-resolution patches, substantially reducing data preprocessing and computational cost. Extensive experiments on multiple WSI benchmarks demonstrate that LRMIL consistently outperforms state-of-the-art MIL methods while achieving more efficient inference. These results highlight LRMIL as a practical and scalable solution for WSI analysis in clinical pathology.

In-Context Multiple Instance Learning

Multiple Instance Learning (MIL) addresses problems where supervision is available at the level of bags of instances and has been successfully applied in fields ranging from computational pathology to satellite imagery. Nevertheless, existing algorithms struggle in the low-label regime that characterizes many real-world applications. Flexible models overfit and rigid ones fail to adapt to the task at hand. We show that pretraining an in-context learner with a Perceiver-style architecture on synthetic data yields a model that can solve new tasks from a handful of labeled bags. At inference time, classification happens in a single forward pass and requires no gradient updates. We propose and investigate different synthetic data generators for bag-structured data and find that they capture complementary inductive biases. A model pretrained on a mixture of these generators inherits their per-task strengths and achieves the best average performance across twelve MIL benchmarks, outperforming supervised baselines that require task-specific training.

DALE-CT: Depth-Aware Foundation Models for Computed Tomography

Recent breakthroughs in self-supervised learning (SSL), such as the Latent-Euclidean Joint-Embedding Predictive Architecture (LeJEPA), alongside successes in integrating visual encoders with language models, have driven the demand for adaptable, high-capacity vision encoders in Computed Tomography (CT). In this work, we explore 2D slice-based architectures as a flexible alternative to native 3D models for processing volumetric CT data. Using the CT-RATE dataset, we trained DALE-CT (Depth-Aware Latent-Euclidean Computed Tomography), a 2D model family built entirely from scratch using LeJEPA, and compared its performance against a continually pre-trained DINOv2 baseline. To enhance representation quality, we developed a novel 3D depth-aware pre-training strategy anchored by dense auxiliary supervision from both automated anatomical masks and human-annotated abnormalities. Under linear probe evaluation with Multiple Instance Learning (MIL) for multi-abnormality detection, the frozen backbone of this dual-supervised model (DALE-CT-2S) achieves a Macro AUROC of 0.833. This performance demonstrates near-parity with state-of-the-art 3D vision-language models, achieved entirely from scratch with significantly less data and no textual supervision. To ensure reproducibility, all training code, evaluation scripts, and model weights have been made publicly available.

Symb-xMIL: Symbolic Explanations for Multiple Instance Learning in Digital Pathology

Explanations of multiple instance learning (MIL) models are widely used for validation and discovery in digital histopathology. Existing methods primarily rely on heatmaps that highlight influential regions but do not explain how evidence from different tissue regions is combined to produce a prediction. This limits interpretability, especially when decisions depend on interactions between tissue features. We introduce Symbolic explainable MIL (Symb-xMIL), a post-hoc explanation framework that quantifies how a MIL model's behavior aligns with human-readable decision rules, expressed as logical relationships (e.g., AND, OR, NOT) between input features. These alignment scores reveal semantic patterns underlying the model's predictions. We evaluate Symb-xMIL on synthetic and real-world histopathology datasets. On synthetic MIL data, Symb-xMIL reliably recovers ground-truth logical rules. In a clinical tumor detection task, the best-aligned rules uncover heterogeneous decision patterns and expose hidden model errors. On an HPV-prediction task on TCGA-HNSCC, a cohort of head and neck cancer, our framework refines patient survival stratification beyond HPV status with potential clinical relevance. Overall, Symb-xMIL extends MIL explainability beyond visual attribution toward structured, rule-based reasoning, enabling more transparent and semantically grounded interpretation of model predictions.

Do Foundation Models See Biology? Evaluating Attention Coherence with Spatial Transcriptomics in Glioblastoma

Whether attention maps from pathology foundation models capture genuine biology remains unknown, yet this question is critical for clinical trust and regulatory approval. We propose a spatial transcriptomics-based framework for orthogonal, hypothesis-free evaluation of attention and apply it to five pathology foundation models (CONCH v1.5, UNI v2, Virchow2, GigaPath, H-Optimus-1) and a ResNet50 baseline. Using attention-based multiple instance learning, we train single-task and multi-task models to predict five molecular alterations in glioblastoma on the CPTAC cohort, validate on an independent TCGA cohort, and evaluate biological coherence of attention maps against 87 transcriptional signatures using co-registered Visium spatial transcriptomics data from 18 samples. Internally, no single encoder dominates across all tasks, and external validation inverts internal performance rankings. Attention maps show a five-fold enrichment gradient from pathways (Cohen's d=0.329) to individual genes (d=0.055), indicating that attention captures emergent multi-gene transcriptional programs rather than individual molecular events. Spatially smooth attention maps do not imply biological coherence, and different encoders attend to distinct biological compartments. Our framework provides objective, quantitative assessment of what foundation models learn from histopathology, moving the field beyond qualitative saliency map review.