Compositional data -- vectors encoding relative proportions -- arise across scientific domains, including ecology, geochemistry, and genomics. The features in these data often come with known hierarchical structure (e.
arXiv:2606. 11646v1 Announce Type: new Abstract: Compositional data -- vectors encoding relative proportions -- arise across scientific domains, including ecology, geochemistry, and genomics.
arXiv:2605. 13894v2 Announce Type: replace-cross Abstract: In this work, we introduce a Tropical Axial Attention neural reasoning architecture that replaces vanilla softmax dot-product attention with max-plus operators, inducing a piecewise-linear structure aligned with dynamic programming formulations.
arXiv:2607. 06224v1 Announce Type: new Abstract: Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering.
arXiv:2609.38506v1 Announce Type: new Abstract: Tree-like branching structures are common in nature, from botanical trees to neurons, blood vessels and respiratory trees. Their branching shape often...
arXiv:2603. 19636v2 Announce Type: replace Abstract: Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce.
arXiv:2602. 02320v4 Announce Type: replace-cross Abstract: Molecular function is largely determined by structure.
arXiv:2608. 04460v1 Announce Type: cross Abstract: The quantitative analysis of 3D neuronal morphologies requires capturing both graph topology and spatial geometry.
arXiv:2310.08774v3 Announce Type: replace-cross Abstract: Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history an...
arXiv:2607. 19376v1 Announce Type: cross Abstract: Machine learning models trained on biochemical data are routinely evaluated using splits that fail to account for relational structure, causing information leakage and over-optimistic performance estimates.
arXiv:2605.28868v2 Announce Type: replace-cross Abstract: Metagenomic taxonomic annotation is essential for interpreting complex microbial communities, yet reliable annotation remains challenging und...
arXiv:2607. 27258v1 Announce Type: cross Abstract: Plant biosynthetic gene clusters (BGCs) encode specialized-metabolite pathways, yet curated plant BGC labels remain scarce, hindering supervised discovery at genome scale.
Plant biosynthetic gene clusters (BGCs) encode specialized-metabolite pathways, yet curated plant BGC labels remain scarce, hindering supervised discovery at genome scale. Existing plant BGC mining tools are largely signature- and rule-driven and do not fully leverage recent advances in contextual representation learning for modeling long-range domain context and controlling false positives under strong domain shift.