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c622c085c04eadc473f08541b255320e-Supplemental.pdf
The positive with the lowest rankx1 has a gradient in the good direction, since it leads to increasex1'sscore because the correct ordering is not reached (the negativeinstance WecanseeinFig.2bthatthis change enables tohavegradients inthecorrect directions forthetwopositiveinstancesx1 and x2 (tending to increase their scores), and for the negative instancex3 (tending to decrease its score). However there is still vanishing gradients. Overall, LSupAP has all the desired properties: i) A correct gradient flow during training, ii) No vanishing gradients while the correct ranking isnot reached, iii)Being anupper bound onthe AP lossLAP. We now write that each positive instance that respects the constraint ofLcalibr. A.3 Choiceofδ In the main paper we introduceδ in Eq. (4) to defineH .
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Harmonizing Community Science Datasets to Model Highly Pathogenic Avian Influenza (HPAI) in Birds in the Subantarctic
Littauer, Richard, Bubendorfer, Kris
Community science observational datasets are useful in epidemiology and ecology for modeling species distributions, but the heterogeneous nature of the data presents significant challenges for standardization, data quality assurance and control, and workflow management. In this paper, we present a data workflow for cleaning and harmonizing multiple community science datasets, which we implement in a case study using eBird, iNaturalist, GBIF, and other datasets to model the impact of highly pathogenic avian influenza in populations of birds in the subantarctic. We predict population sizes for several species where the demographics are not known, and we present novel estimates for potential mortality rates from HPAI for those species, based on a novel aggregated dataset of mortality rates in the subantarctic.
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Climbing the label tree: Hierarchy-preserving contrastive learning for medical imaging
Medical image labels are often organized by taxonomies (e.g., organ - tissue - subtype), yet standard self-supervised learning (SSL) ignores this structure. We present a hierarchy-preserving contrastive framework that makes the label tree a first-class training signal and an evaluation target. Our approach introduces two plug-in objectives: Hierarchy-Weighted Contrastive (HWC), which scales positive/negative pair strengths by shared ancestors to promote within-parent coherence, and Level-Aware Margin (LAM), a prototype margin that separates ancestor groups across levels. The formulation is geometry-agnostic and applies to Euclidean and hyperbolic embeddings without architectural changes. Across several benchmarks, including breast histopathology, the proposed objectives consistently improve representation quality over strong SSL baselines while better respecting the taxonomy. We evaluate with metrics tailored to hierarchy faithfulness: HF1 (hierarchical F1), H-Acc (tree-distance-weighted accuracy), and parent-distance violation rate. We also report top-1 accuracy for completeness. Ablations show that HWC and LAM are effective even without curvature, and combining them yields the most taxonomy-aligned representations. Taken together, these results provide a simple, general recipe for learning medical image representations that respect the label tree and advance both performance and interpretability in hierarchy-rich domains.