# Dictionary-based Pathology Mining with Hard-instance-assisted Classifier Debiasing for Genetic Biomarker Prediction from WSIs

arXiv: https://arxiv.org/abs/2603.26809 · HTML: https://mlsanity.com/paper/2603.26809/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 64 references that are in the map.
- First posted on arXiv 26 Mar 2026.

## Builds on (most cited first, 22 of 22)

- [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)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification](https://mlsanity.com/paper/2203.12081/) (2022)
- [Whole Slide Images based Cancer Survival Prediction using Attention Guided Deep Multiple Instance Learning Networks](https://mlsanity.com/paper/2009.11169/) (2020)
- [Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology](https://mlsanity.com/paper/2408.00738/) (2024)
- [Whole Slide Images are 2D Point Clouds: Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks](https://mlsanity.com/paper/2107.13048/) (2021)
- [Interventional Bag Multi-Instance Learning On Whole-Slide Pathological Images](https://mlsanity.com/paper/2303.06873/) (2023)
- [A graph-transformer for whole slide image classification](https://mlsanity.com/paper/2205.09671/) (2022)
- [Multi-scale Domain-adversarial Multiple-instance CNN for Cancer Subtype Classification with Unannotated Histopathological Images](https://mlsanity.com/paper/2001.01599/) (2020)
- [Dynamic Graph Representation with Knowledge-aware Attention for Histopathology Whole Slide Image Analysis](https://mlsanity.com/paper/2403.07719/) (2024)
- [Transcending the Limit of Local Window: Advanced Super-Resolution Transformer with Adaptive Token Dictionary](https://mlsanity.com/paper/2401.08209/) (2024)
- [Multiple Instance Learning Framework with Masked Hard Instance Mining for Whole Slide Image Classification](https://mlsanity.com/paper/2307.15254/) (2023)
- [Bi-directional Weakly Supervised Knowledge Distillation for Whole Slide Image Classification](https://mlsanity.com/paper/2210.03664/) (2022)
- [DGMIL: Distribution Guided Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2206.08861/) (2022)
- [Rethinking Multiple Instance Learning for Whole Slide Image Classification: A Good Instance Classifier is All You Need](https://mlsanity.com/paper/2307.02249/) (2023)
- [When Dictionary Learning Meets Deep Learning: Deep Dictionary Learning and Coding Network for Image Recognition with Limited Data](https://mlsanity.com/paper/2005.10940/) (2020)
- [Rethinking Multiple Instance Learning for Whole Slide Image Classification: A Bag-Level Classifier is a Good Instance-Level Teacher](https://mlsanity.com/paper/2312.01099/) (2023)
- [Histopathological Image Classification using Discriminative Feature-oriented Dictionary Learning](https://mlsanity.com/paper/1506.05032/) (2015)
- [Prompting Whole Slide Image Based Genetic Biomarker Prediction](https://mlsanity.com/paper/2407.09540/) (2024)

## Abstract (arXiv)

Prediction of genetic biomarkers, e.g., microsatellite instability in colorectal cancer is crucial for clinical decision making. But, two primary challenges hamper accurate prediction: (1) It is difficult to construct a pathology-aware representation involving the complex interconnections among pathological components. (2) WSIs contain a large proportion of areas unrelated to genetic biomarkers, which make the model easily overfit simple but irrelative instances. We hereby propose a Dictionary-based hierarchical pathology mining with hard-instance-assisted classifier Debiasing framework to address these challenges, dubbed as D2Bio. Our first module, dictionary-based hierarchical pathology mining, is able to mine diverse and very fine-grained pathological contextual interaction without the limit to the distances between patches. The second module, hard-instance-assisted classfier debiasing, learns a debiased classifier via focusing on hard but task-related features, without any additional annotations. Experimental results on five cohorts show the superiority of our method, with over 4% improvement in AUROC compared with the second best on the TCGA-CRC-MSI cohort. Our analysis further shows the clinical interpretability of D2Bio in genetic biomarker diagnosis and potential clinical utility in survival analysis. Code will be available at https://github.com/DeepMed-Lab-ECNU/D2Bio.