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Improving Detection of Rare Nodes in Hierarchical Multi-Label Learning

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In hierarchical multi-label classification, a persistent challenge is enabling model predictions to reach deeper levels of the hierarchy for more detailed or fine-grained classifications. This difficulty partly arises from the natural rarity of certain classes (or hierarchical nodes) and the hierarchical constraint that ensures child nodes are almost always less frequent than their parents. To address this, we propose a weighted loss objective for neural networks that combines node-wise imbalance weighting with focal weighting components, the latter leveraging modern quantification of ensemble uncertainties. By emphasizing rare nodes rather than rare observations (data points), and focusing on uncertain nodes for each model output distribution during training, we observe improvements in recall by up to a factor of five on benchmark datasets, along with statistically significant gains in $F_{1}$ score. We also show our approach aids convolutional networks on challenging tasks, as in situations with suboptimal encoders or limited data.

Isaac Xu, Martin Gillis, Ayushi Sharma, Benjamin Misiuk, Craig J. Brown, Thomas Trappenberg• 2026

Related benchmarks

TaskDatasetResultRank
Multi-Label ClassificationENRON processed image data
F1 Score15.4
6
Multi-Label ClassificationDIATOM
F1 Score57.65
6
Hierarchical Multi-label ClassificationCELLCYCLE GO
F1 Score1.94
5
Hierarchical Multi-label ClassificationDERISI GO
F1 Score77
5
Hierarchical Multi-label ClassificationEISEN GO
F1 Score3.17
5
Hierarchical Multi-label ClassificationEXPR GO
F1 Score4.61
5
Hierarchical Multi-label ClassificationGASCH-1 GO
F1 Score266
5
Hierarchical Multi-label ClassificationGASCH GO 2
F1 Score1.84
5
Hierarchical Multi-label ClassificationSEQ (GO)
F1 Score4.46
5
Hierarchical Multi-label ClassificationSPO GO
F1 Score1.26
5
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