Alexey Pchelnikov

Dmitry Nechaev, Alexey Pchelnikov, Ekaterina Ivanova

Recent advancements in Digital Pathology (DP), particularly through artificial intelligence and Foundation Models, have underscored the importance of large-scale, diverse, and richly annotated datasets. Despite their critical role, publicly available Whole Slide Image (WSI) datasets often lack sufficient scale, tissue diversity, and comprehensive clinical metadata, limiting the robustness and generalizability of AI models. In response, we introduce the HISTAI dataset, a large, multimodal, open-access WSI collection comprising over 60,000 slides from various tissue types. Each case in the HISTAI dataset is accompanied by extensive clinical metadata, including diagnosis, demographic information, detailed pathological annotations, and standardized diagnostic coding. The dataset aims to fill gaps identified in existing resources, promoting innovation, reproducibility, and the development of clinically relevant computational pathology solutions. The dataset can be accessed at https://github.com/HistAI/HISTAI.

Dmitry Nechaev, Alexey Pchelnikov, Ekaterina Ivanova

Advancing AI in computational pathology requires large, high-quality, and diverse datasets, yet existing public datasets are often limited in organ diversity, class coverage, or annotation quality. To bridge this gap, we introduce SPIDER (Supervised Pathology Image-DEscription Repository), the largest publicly available patch-level dataset covering multiple organ types, including Skin, Colorectal, Thorax, and Breast with comprehensive class coverage for each organ. SPIDER provides high-quality annotations verified by expert pathologists and includes surrounding context patches, which enhance classification performance by providing spatial context. Alongside the dataset, we present baseline models trained on SPIDER using the Hibou-L foundation model as a feature extractor combined with an attention-based classification head. The models achieve state-of-the-art performance across multiple tissue categories and serve as strong benchmarks for future digital pathology research. Beyond patch classification, the model enables rapid identification of significant areas, quantitative tissue metrics, and establishes a foundation for multimodal approaches. Both the dataset and trained models are publicly available to advance research, reproducibility, and AI-driven pathology development. Access them at: https://github.com/HistAI/SPIDER

Alexey Pchelnikov, Aleksei Pchelnikov

Training AI models for computational pathology currently requires access to expensive whole-slide-image datasets, GPU infrastructure, deep expertise in machine learning, and substantial engineering effort. We present CellDX AI Autopilot, a platform that lets users -- from pathologists with no ML background to ML practitioners running many parallel experiments -- train, evaluate, and deploy whole-slide image classifiers through natural language interaction with an AI agent. The platform provides a structured set of agent skills that guide the user through dataset curation, automated hyperparameter tuning, multi-strategy model comparison, and human-in-the-loop deployment, all on a pre-built dataset of over 32,000 cases and 66,000 H&E-stained whole-slide images with pre-extracted features. We describe the agent skill architecture, the underlying Multiple Instance Learning (MIL) training framework supporting four classification strategies, and an iterative pairwise hyperparameter search (grid or seeded random) that reduces tuning cost by over 30x compared to exhaustive search. CellDX AI Autopilot is, to our knowledge, the first system to expose pathology-specialized agent skills and a pathology-specialized training platform to general-purpose AI agents (e.g. any LLM-based agent runtime), delivering end-to-end automated model training without requiring the agent itself to be domain-specific. The platform addresses both the ML-expertise bottleneck that limits adoption in diagnostic pathology and the engineering bottleneck that limits how many experiments a researcher can run cost-effectively.

Dmitry Nechaev, Alexey Pchelnikov, Ekaterina Ivanova

Pathology, the microscopic examination of diseased tissue, is critical for diagnosing various medical conditions, particularly cancers. Traditional methods are labor-intensive and prone to human error. Digital pathology, which converts glass slides into high-resolution digital images for analysis by computer algorithms, revolutionizes the field by enhancing diagnostic accuracy, consistency, and efficiency through automated image analysis and large-scale data processing. Foundational transformer pretraining is crucial for developing robust, generalizable models as it enables learning from vast amounts of unannotated data. This paper introduces the Hibou family of foundational vision transformers for pathology, leveraging the DINOv2 framework to pretrain two model variants, Hibou-B and Hibou-L, on a proprietary dataset of over 1 million whole slide images (WSIs) representing diverse tissue types and staining techniques. Our pretrained models demonstrate superior performance on both patch-level and slide-level benchmarks, surpassing existing state-of-the-art methods. Notably, Hibou-L achieves the highest average accuracy across multiple benchmark datasets. To support further research and application in the field, we have open-sourced the Hibou models, which can be accessed at https://github.com/HistAI/hibou.