Cross-Modal Prototype Allocation: Unsupervised Slide Representation Learning via Patch-Text Contrast in Computational Pathology

With the rapid advancement of pathology foundation models (FMs), the representation learning of whole slide images (WSIs) attracts increasing attention. Existing studies develop high-quality patch feature extractors and employ carefully designed aggregation schemes to derive slide-level representations. However, mainstream weakly supervised slide representation learning methods, primarily based on multiple instance learning (MIL), are tailored to specific downstream tasks, which limits their generalizability. To address this issue, some studies explore unsupervised slide representation learning. However, these approaches focus solely on the visual modality of patches, neglecting the rich semantic information embedded in textual data. In this work, we propose ProAlign, a cross-modal unsupervised slide representation learning framework. Specifically, we leverage a large language model (LLM) to generate descriptive text for the prototype types present in a WSI, introducing patch-text contrast to construct initial prototype embeddings. Furthermore, we propose a parameter-free attention aggregation strategy that utilizes the similarity between patches and these prototypes to form unsupervised slide embeddings applicable to a wide range of downstream tasks. Extensive experiments on four public datasets show that ProAlign outperforms existing unsupervised frameworks and achieves performance comparable to some weakly supervised models.

Multimodal Distillation-Driven Ensemble Learning for Long-Tailed Histopathology Whole Slide Images Analysis

Multiple Instance Learning (MIL) plays a significant role in computational pathology, enabling weakly supervised analysis of Whole Slide Image (WSI) datasets. The field of WSI analysis is confronted with a severe long-tailed distribution problem, which significantly impacts the performance of classifiers. Long-tailed distributions lead to class imbalance, where some classes have sparse samples while others are abundant, making it difficult for classifiers to accurately identify minority class samples. To address this issue, we propose an ensemble learning method based on MIL, which employs expert decoders with shared aggregators and consistency constraints to learn diverse distributions and reduce the impact of class imbalance on classifier performance. Moreover, we introduce a multimodal distillation framework that leverages text encoders pre-trained on pathology-text pairs to distill knowledge and guide the MIL aggregator in capturing stronger semantic features relevant to class information. To ensure flexibility, we use learnable prompts to guide the distillation process of the pre-trained text encoder, avoiding limitations imposed by specific prompts. Our method, MDE-MIL, integrates multiple expert branches focusing on specific data distributions to address long-tailed issues. Consistency control ensures generalization across classes. Multimodal distillation enhances feature extraction. Experiments on Camelyon+-LT and PANDA-LT datasets show it outperforms state-of-the-art methods.

Can We Simplify Slide-level Fine-tuning of Pathology Foundation Models?

The emergence of foundation models in computational pathology has transformed histopathological image analysis, with whole slide imaging (WSI) diagnosis being a core application. Traditionally, weakly supervised fine-tuning via multiple instance learning (MIL) has been the primary method for adapting foundation models to WSIs. However, in this work we present a key experimental finding: a simple nonlinear mapping strategy combining mean pooling and a multilayer perceptron, called SiMLP, can effectively adapt patch-level foundation models to slide-level tasks without complex MIL-based learning. Through extensive experiments across diverse downstream tasks, we demonstrate the superior performance of SiMLP with state-of-the-art methods. For instance, on a large-scale pan-cancer classification task, SiMLP surpasses popular MIL-based methods by 3.52%. Furthermore, SiMLP shows strong learning ability in few-shot classification and remaining highly competitive with slide-level foundation models pretrained on tens of thousands of slides. Finally, SiMLP exhibits remarkable robustness and transferability in lung cancer subtyping. Overall, our findings challenge the conventional MIL-based fine-tuning paradigm, demonstrating that a task-agnostic representation strategy alone can effectively adapt foundation models to WSI analysis. These insights offer a unique and meaningful perspective for future research in digital pathology, paving the way for more efficient and broadly applicable methodologies.

Dynamic Hypergraph Representation for Bone Metastasis Cancer Analysis

Bone metastasis analysis is a significant challenge in pathology and plays a critical role in determining patient quality of life and treatment strategies. The microenvironment and specific tissue structures are essential for pathologists to predict the primary bone cancer origins and primary bone cancer subtyping. By digitizing bone tissue sections into whole slide images (WSIs) and leveraging deep learning to model slide embeddings, this analysis can be enhanced. However, tumor metastasis involves complex multivariate interactions with diverse bone tissue structures, which traditional WSI analysis methods such as multiple instance learning (MIL) fail to capture. Moreover, graph neural networks (GNNs), limited to modeling pairwise relationships, are hard to represent high-order biological associations. To address these challenges, we propose a dynamic hypergraph neural network (DyHG) that overcomes the edge construction limitations of traditional graph representations by connecting multiple nodes via hyperedges. A low-rank strategy is used to reduce the complexity of parameters in learning hypergraph structures, while a Gumbel-Softmax-based sampling strategy optimizes the patch distribution across hyperedges. An MIL aggregator is then used to derive a graph-level embedding for comprehensive WSI analysis. To evaluate the effectiveness of DyHG, we construct two large-scale datasets for primary bone cancer origins and subtyping classification based on real-world bone metastasis scenarios. Extensive experiments demonstrate that DyHG significantly outperforms state-of-the-art (SOTA) baselines, showcasing its ability to model complex biological interactions and improve the accuracy of bone metastasis analysis.

Unlocking adaptive digital pathology through dynamic feature learning

Foundation models have revolutionized the paradigm of digital pathology, as they leverage general-purpose features to emulate real-world pathological practices, enabling the quantitative analysis of critical histological patterns and the dissection of cancer-specific signals. However, these static general features constrain the flexibility and pathological relevance in the ever-evolving needs of clinical applications, hindering the broad use of the current models. Here we introduce PathFiT, a dynamic feature learning method that can be effortlessly plugged into various pathology foundation models to unlock their adaptability. Meanwhile, PathFiT performs seamless implementation across diverse pathology applications regardless of downstream specificity. To validate PathFiT, we construct a digital pathology benchmark with over 20 terabytes of Internet and real-world data comprising 28 H\&E-stained tasks and 7 specialized imaging tasks including Masson's Trichrome staining and immunofluorescence images. By applying PathFiT to the representative pathology foundation models, we demonstrate state-of-the-art performance on 34 out of 35 tasks, with significant improvements on 23 tasks and outperforming by 10.20% on specialized imaging tasks. The superior performance and versatility of PathFiT open up new avenues in computational pathology.

Towards a Comprehensive Benchmark for Pathological Lymph Node Metastasis in Breast Cancer Sections

Advances in optical microscopy scanning have significantly contributed to computational pathology (CPath) by converting traditional histopathological slides into whole slide images (WSIs). This development enables comprehensive digital reviews by pathologists and accelerates AI-driven diagnostic support for WSI analysis. Recent advances in foundational pathology models have increased the need for benchmarking tasks. The Camelyon series is one of the most widely used open-source datasets in computational pathology. However, the quality, accessibility, and clinical relevance of the labels have not been comprehensively evaluated. In this study, we reprocessed 1,399 WSIs and labels from the Camelyon-16 and Camelyon-17 datasets, removing low-quality slides, correcting erroneous labels, and providing expert pixel annotations for tumor regions in the previously unreleased test set. Based on the sizes of re-annotated tumor regions, we upgraded the binary cancer screening task to a four-class task: negative, micro-metastasis, macro-metastasis, and Isolated Tumor Cells (ITC). We reevaluated pre-trained pathology feature extractors and multiple instance learning (MIL) methods using the cleaned dataset, providing a benchmark that advances AI development in histopathology.

Diagnostic Text-guided Representation Learning in Hierarchical Classification for Pathological Whole Slide Image

With the development of digital imaging in medical microscopy, artificial intelligent-based analysis of pathological whole slide images (WSIs) provides a powerful tool for cancer diagnosis. Limited by the expensive cost of pixel-level annotation, current research primarily focuses on representation learning with slide-level labels, showing success in various downstream tasks. However, given the diversity of lesion types and the complex relationships between each other, these techniques still deserve further exploration in addressing advanced pathology tasks. To this end, we introduce the concept of hierarchical pathological image classification and propose a representation learning called PathTree. PathTree considers the multi-classification of diseases as a binary tree structure. Each category is represented as a professional pathological text description, which messages information with a tree-like encoder. The interactive text features are then used to guide the aggregation of hierarchical multiple representations. PathTree uses slide-text similarity to obtain probability scores and introduces two extra tree specific losses to further constrain the association between texts and slides. Through extensive experiments on three challenging hierarchical classification datasets: in-house cryosectioned lung tissue lesion identification, public prostate cancer grade assessment, and public breast cancer subtyping, our proposed PathTree is consistently competitive compared to the state-of-the-art methods and provides a new perspective on the deep learning-assisted solution for more complex WSI classification.

Agent Aggregator with Mask Denoise Mechanism for Histopathology Whole Slide Image Analysis

Histopathology analysis is the gold standard for medical diagnosis. Accurate classification of whole slide images (WSIs) and region-of-interests (ROIs) localization can assist pathologists in diagnosis. The gigapixel resolution of WSI and the absence of fine-grained annotations make direct classification and analysis challenging. In weakly supervised learning, multiple instance learning (MIL) presents a promising approach for WSI classification. The prevailing strategy is to use attention mechanisms to measure instance importance for classification. However, attention mechanisms fail to capture inter-instance information, and self-attention causes quadratic computational complexity. To address these challenges, we propose AMD-MIL, an agent aggregator with a mask denoise mechanism. The agent token acts as an intermediate variable between the query and key for computing instance importance. Mask and denoising matrices, mapped from agents-aggregated value, dynamically mask low-contribution representations and eliminate noise. AMD-MIL achieves better attention allocation by adjusting feature representations, capturing micro-metastases in cancer, and improving interpretability. Extensive experiments on CAMELYON-16, CAMELYON-17, TCGA-KIDNEY, and TCGA-LUNG show AMD-MIL's superiority over state-of-the-art methods.

MergeUp-augmented Semi-Weakly Supervised Learning for WSI Classification

Recent advancements in computational pathology and artificial intelligence have significantly improved whole slide image (WSI) classification. However, the gigapixel resolution of WSIs and the scarcity of manual annotations present substantial challenges. Multiple instance learning (MIL) is a promising weakly supervised learning approach for WSI classification. Recently research revealed employing pseudo bag augmentation can encourage models to learn various data, thus bolstering models' performance. While directly inheriting the parents' labels can introduce more noise by mislabeling in training. To address this issue, we translate the WSI classification task from weakly supervised learning to semi-weakly supervised learning, termed SWS-MIL, where adaptive pseudo bag augmentation (AdaPse) is employed to assign labeled and unlabeled data based on a threshold strategy. Using the "student-teacher" pattern, we introduce a feature augmentation technique, MergeUp, which merges bags with low-priority bags to enhance inter-category information, increasing training data diversity. Experimental results on the CAMELYON-16, BRACS, and TCGA-LUNG datasets demonstrate the superiority of our method over existing state-of-the-art approaches, affirming its efficacy in WSI classification.

Leveraging Pre-trained Models for FF-to-FFPE Histopathological Image Translation

The two primary types of Hematoxylin and Eosin (H&E) slides in histopathology are Formalin-Fixed Paraffin-Embedded (FFPE) and Fresh Frozen (FF). FFPE slides offer high quality histopathological images but require a labor-intensive acquisition process. In contrast, FF slides can be prepared quickly, but the image quality is relatively poor. Our task is to translate FF images into FFPE style, thereby improving the image quality for diagnostic purposes. In this paper, we propose Diffusion-FFPE, a method for FF-to-FFPE histopathological image translation using a pre-trained diffusion model. Specifically, we employ a one-step diffusion model as the generator and fine-tune it with LoRA adapters using adversarial learning objectives. To ensure that the model effectively captures both global structural information and local details, we propose a multi-scale feature fusion (MFF) module. This module utilizes two VAE encoders to extract features of varying image sizes and performs feature fusion before feeding them into the UNet. Furthermore, we utilize a pre-trained vision-language model for histopathology as the backbone for the discriminator to further improve performance We conducted FF-to-FFPE translation experiments on the TCGA-NSCLC datasets, and our method achieved better performance compared to other methods. The code and models are released at https://github.com/QilaiZhang/Diffusion-FFPE.