CytoDINO: Risk-Aware and Biologically-Informed Adaptation of DINOv3 for Bone Marrow Cytomorphology

TL;DR

CytoDINO is a biologically-informed, risk-aware adaptation of DINOv3 that improves bone marrow cell classification accuracy while explicitly penalizing dangerous misdiagnoses, enabling efficient clinical application with minimal computational resources.

Contribution

It introduces a Hierarchical Focal Loss with Critical Penalties and demonstrates effective, resource-efficient fine-tuning of DINOv3 for cytomorphology analysis.

Findings

Achieves 88.2% weighted F1 score on the MLL dataset.

Enables high-accuracy predictions with only 8% trainable parameters.

Provides a confidence-based prediction system with 99.5% accuracy on certain samples.

Abstract

Bone marrow cell cytomorphology analysis is critical for the diagnosis of hematological malignancies but remains a labor-intensive process subject to significant inter-observer variability. While recent foundation models have shown promise in computational pathology, they often require extensive computational resources and fail to account for the asymmetric risks associated with clinical misdiagnosis. We introduce CytoDINO, a framework that achieves state-of-the-art performance on the Munich Leukemia Laboratory (MLL) dataset by fine-tuning DINOv3 using Low-Rank Adaptation (LoRA). Our primary contribution is a novel Hierarchical Focal Loss with Critical Penalties, which encodes biological relationships between cell lineages and explicitly penalizes clinically dangerous misclassifications (e.g., classifying blasts as normal cells). CytoDINO achieves an 88.2% weighted F1 score and 76.5% macro F1 on a held-out test set of 21 cell classes. By utilizing parameter-efficient fine-tuning with only 8% trainable parameters on a single NVIDIA RTX 5080, we demonstrate that consumer-grade hardware can match specialized infrastructure. Furthermore, confidence-based selective prediction yields 99.5% accuracy on 67% of samples, suggesting a viable pathway for clinical deployment where high-uncertainty cases are flagged for expert review