Pathology foundation models (PFMs) have emerged as powerful tools for analyzing whole slide images (WSIs). However, adapting these pretrained PFMs for specific clinical tasks presents considerable challenges, primarily due to the availability of only weak (WSI-level) labels for gigapixel images, necessitating multiple instance learning (MIL) paradigm for effective WSI analysis. This paper proposes a novel approach for single-GPU \textbf{T}ask \textbf{A}daptation of \textbf{PFM}s (TAPFM) that uses vision transformer (\vit) attention for MIL aggregation while optimizing both for feature representations and attention weights. The proposed approach maintains separate computational graphs for MIL aggregator and the PFM to create stable training dynamics that align with downstream task objectives during end-to-end adaptation. Evaluated on mutation prediction tasks for bladder cancer and lung adenocarcinoma across institutional and The Cancer Genome Atlas (TCGA) cohorts, TAPFM consistently outperforms conventional approaches, with H-Optimus-0 (TAPFM) outperforming the benchmarks. TAPFM effectively handles multi-label classification of actionable mutations as well. Thus, TAPFM makes adaptation of powerful pre-trained PFMs practical on standard hardware for various clinical applications.

Clustering graphs under the Stochastic Block Model (SBM) and extensions are well studied. Guarantees of correctness exist under the assumption that the data is sampled from a model. In this paper, we propose a framework, in which we obtain "correctness" guarantees without assuming the data comes from a model. The guarantees we obtain depend instead on the statistics of the data that can be checked. We also show that this framework ties in with the existing model-based framework, and that we can exploit results in model-based recovery, as well as strengthen the results existing in that area of research.

We provide theoretical insights that support our method's alignment with standard preference alignment objectives.

We provide theoretical insights that support our method's alignment with standard preference alignment objectives.

Finding communities in networks is a problem that remains difficult, in spite of the amount of attention it has recently received. The Stochastic Block-Model (SBM) is a generative model for graphs with "communities" for which, because of its simplicity, the theoretical understanding has advanced fast in recent years. In particular, there have been various results showing that simple versions of spectral clustering using the Normalized Laplacian of the graph can recover the communities almost perfectly with high probability. Here we show that essentially the same algorithm used for the SBM and for its extension called Degree-Corrected SBM, works on a wider class of Block-Models, which we call Preference Frame Models, with essentially the same guarantees. Moreover, the parametrization we introduce clearly exhibits the free parameters needed to specify this class of models, and results in bounds that expose with more clarity the parameters that control the recovery error in this model class.

Hematoxylin and eosin-stained mitotic figure (MF) counts are essential for tumor evaluation, serving both as stan-dalone and component grades in malignancy assessment (1). Mitotic figures are broadly classified into typical and atypical variants, with atypical forms--characterized by dysregulated chromatin aggregation and reflecting ge-nomic instabilities such as chromosomal instability and aneuploidy--demonstrating independent prognostic value in cancers like breast carcinoma (2, 3). However, manual enumeration and discrimination of MF variants are time-consuming and subject to substantial inter-observer variability. To address these challenges, we present a two-stage framework for automated MF classification in the MIDOG2025 Track 2 challenge (4). First, we performed parameter-efficient fine-tuning of multiple Pathology Foundation Models (PFMs) using low-rank adaptation (LoRA) (5). Training incorporated fisheye augmentation to emphasize central mi-toses (6) and Fourier Domain Adaptation (FDA) for unsupervised style transfer with ImageNet images (7). We further enhanced domain generalization by augmenting the MI-DOG2025 set with an external labeled MF dataset (8). Second, we ensembled the adapted PFMs and ConvNeXt V2 (9) to integrate complementary morphological insights into a unified classification decision (10). Our method achieved a high balanced accuracy on validation splits and also demonstrated strong performance on the Preliminary Evaluation Phase dataset, underscoring its potential for reliable, automated MF analysis.

Computational pathology, which involves analyzing whole slide images for automated cancer diagnosis, relies on multiple instance learning, where performance depends heavily on the feature extractor and aggregator. Recent Pathology Foundation Models (PFMs), pretrained on large-scale histopathology data, have significantly enhanced both the extractor and aggregator, but they lack a systematic analysis framework. In this survey, we present a hierarchical taxonomy organizing PFMs through a top-down philosophy applicable to foundation model analysis in any domain: model scope, model pretraining, and model design. Additionally, we systematically categorize PFM evaluation tasks into slide-level, patch-level, multimodal, and biological tasks, providing comprehensive benchmarking criteria. Our analysis identifies critical challenges in both PFM development (pathology-specific methodology, end-to-end pretraining, data-model scalability) and utilization (effective adaptation, model maintenance), paving the way for future directions in this promising field. Resources referenced in this survey are available at https://github.com/BearCleverProud/AwesomeWSI.

The goal is to obtain such guarantees with quantities that can be computed from the data and the output of the clustering algorithms being compared. Providing such model free theoretical guarantees for clustering is of importance for both theoretical and practical purposes. Given that Spectral Clutering works well for all the models specified, why not use the same model estimator? In particular, it is not clear why the Laplacian is used for PFM while the adjacency matrix is used for the SBM. Also, the results for PFM is for weighted ME whereas for SBM it is in terms of ME.

Etruscan mirrors constitute a significant category in Etruscan art, characterized by elaborate figurative illustrations featured on their backside. A laborious and costly aspect of their analysis and documentation is the task of manually tracing these illustrations. In previous work, a methodology has been proposed to automate this process, involving photometric-stereo scanning in combination with deep neural networks. While achieving quantitative performance akin to an expert annotator, some results still lack qualitative precision and, thus, require annotators for inspection and potential correction, maintaining resource intensity. In response, we propose a deep neural network trained to interactively refine existing annotations based on human guidance. Our human-in-the-loop approach streamlines annotation, achieving equal quality with up to 75% less manual input required. Moreover, during the refinement process, the relative improvement of our methodology over pure manual labeling reaches peak values of up to 26%, attaining drastically better quality quicker. By being tailored to the complex task of segmenting intricate lines, specifically distinguishing it from previous methods, our approach offers drastic improvements in efficacy, transferable to a broad spectrum of applications beyond Etruscan mirrors.

We present Preference Flow Matching (PFM), a new framework for preference-based reinforcement learning (PbRL) that streamlines the integration of preferences into an arbitrary class of pre-trained models. Existing PbRL methods require fine-tuning pre-trained models, which presents challenges such as scalability, inefficiency, and the need for model modifications, especially with black-box APIs like GPT-4. In contrast, PFM utilizes flow matching techniques to directly learn from preference data, thereby reducing the dependency on extensive fine-tuning of pre-trained models. By leveraging flow-based models, PFM transforms less preferred data into preferred outcomes, and effectively aligns model outputs with human preferences without relying on explicit or implicit reward function estimation, thus avoiding common issues like overfitting in reward models. We provide theoretical insights that support our method's alignment with standard PbRL objectives. Experimental results indicate the practical effectiveness of our method, offering a new direction in aligning a pre-trained model to preference.