# TaxoMIL: Taxonomy-Constrained Learning for Hierarchical Whole Slide Image Analysis

arXiv: https://arxiv.org/abs/2606.31100 · HTML: https://mlsanity.com/paper/2606.31100/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 16 references that are in the map.
- First posted on arXiv 30 Jun 2026.

## Builds on (most cited first, 12 of 12)

- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images](https://mlsanity.com/paper/2111.04740/) (2021)
- [MambaMIL: Enhancing Long Sequence Modeling with Sequence Reordering in Computational Pathology](https://mlsanity.com/paper/2403.06800/) (2024)
- [SlideChat: A Large Vision-Language Assistant for Whole-Slide Pathology Image Understanding](https://mlsanity.com/paper/2410.11761/) (2024)
- [Structured State Space Models for Multiple Instance Learning in Digital Pathology](https://mlsanity.com/paper/2306.15789/) (2023)
- [WSI-VQA: Interpreting Whole Slide Images by Generative Visual Question Answering](https://mlsanity.com/paper/2407.05603/) (2024)
- [ViLa-MIL: Dual-scale Vision-Language Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2502.08391/) (2025)
- [HMIL: Hierarchical Multi-Instance Learning for Fine-Grained Whole Slide Image Classification](https://mlsanity.com/paper/2411.07660/) (2024)
- [CAMP: Continuous and Adaptive Learning Model in Pathology](https://mlsanity.com/paper/2407.09030/) (2024)
- [Hierarchical Classification for Improved Histopathology Image Analysis](https://mlsanity.com/paper/2603.00504/) (2026)

## Abstract (arXiv)

Whole slide image (WSI) analysis is central to computational pathology, with multiple instance learning (MIL) emerging as the standard pipeline for slide-level diagnosis. However, conventional approaches formulate WSI diagnosis as a flat classification task over discrete labels, contradicting the inherently hierarchical, coarse-to-fine nature of clinical reasoning. Although recent hierarchical classifiers and vision-language models (VLMs) have sought to address this structural gap, they either fail to capture semantic continuity between related diagnoses or suffer from unconstrained text generation that produces taxonomic hallucinations and parent-child label violations. To address these limitations, we propose TaxoMIL, a taxonomy-constrained framework that reformulates WSI diagnosis as a multi-granularity text generation task. TaxoMIL utilizes a dual-head Transformer decoder to generate coarse- and fine-level diagnostic text, and introduces taxonomy-guided objectives that explicitly structure the label embedding space and strictly ground slide-level visual representations within the clinical taxonomy. Extensive experiments across three diverse WSI datasets demonstrate that TaxoMIL consistently outperforms state-of-the-art MIL classifiers and VLM-based generative methods, yielding accurate and hierarchy-aware diagnostic predictions. The code is released at https://github.com/QuIIL/TaxoMIL