PurposeAccurate airway anatomical labeling is crucial for clinicians to identify and navigate complex bronchial structures during bronchoscopy. Automatic airway labeling is challenging due to significant anatomical variations. Previous methods are prone to generate inconsistent predictions, hindering preoperative planning and intraoperative navigation. This paper aims to enhance topological consistency and improve the detection of abnormal airway branches.MethodsWe propose a transformer-based framework incorporating two modules: the soft subtree consistency (SSC) and the abnormal branch saliency (ABS). The SSC module constructs a soft subtree to capture clinically relevant topological relationships, allowing for flexible feature aggregation within and across subtrees. The ABS module facilitates interaction between node features and prototypes to distinguish abnormal branches, preventing the erroneous features aggregation between normal and abnormal nodes.ResultsEvaluated on a challenging dataset characterized by severe airway deformities, our method achieves superior performance compared to state-of-the-art approaches. Specifically, it attains an 83.7% subsegmental accuracy, along with a 3.1% increase in segmental subtree consistency, a 45.2% increase in abnormal branch recall. Notably, the method demonstrates robust performance in cases with airway deformities, ensuring consistent and accurate labeling.ConclusionThe enhanced topological consistency and robust identification of abnormal branches provided by our method offer an accurate and robust solution for airway labeling, with potential to improve the precision and safety of bronchoscopy procedures.