Recommending Bacterial Cultivation Conditions from 16S rRNA
Recommending bacterial cultivation conditions from sequence data is a challenging structured problem characterized by missing standardized benchmarks and limited use of sequence structure. To address this, we introduce DSNI, a benchmark of 65,023 bacterial strains with phylogeny-aware splits, pairing 16S rRNA sequences with four cultivation conditions (media, temperature, pH, oxygen). Exploiting the mosaic structure of 16S rRNA, where hypervariable regions support discrimination and conserved regions support primer design, we propose a Variability-Gated Encoder that learns position-dependent importance weights conditioned on biological features (region type, position, and local complexity...
| Authors | Juntang Wang, Hao Wu, Yihan Wang et al. |
|---|---|
| Primary category | cs.LG |
| Published | 20 October 2026 |
| Last updated at source | 20 October 2026 |
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