| --- |
| license: cc-by-4.0 |
| tags: |
| - biology |
| - gene-regulatory-network |
| - foundation-model |
| - cross-species-transfer |
| - plant |
| - Nicotiana-benthamiana |
| --- |
| |
| # nbgrn-transfer — cross-species gene-regulatory-network transfer to *Nicotiana benthamiana* |
|
|
| Models, data, and inferred networks for the paper |
| **"Conditioning a gene-regulatory foundation model on transcription-factor sequence enables ortholog-free cross-species transfer: the *Nicotiana benthamiana* network from soybean and Arabidopsis."** |
|
|
| A masked-expression gene-regulatory foundation model (**GRN-FM**) with a single explicit |
| TF×target weight tensor **W** is trained in a data-rich source species (soybean or Arabidopsis) |
| and transferred **zero-shot** to data-poor *N. benthamiana* — either through reciprocal-best-hit |
| orthologs, or, with **no ortholog lookup for the regulators**, by a **sequence-conditioned** model |
| whose TF rows are generated from ESM-2 protein embeddings (`W = φ(ESM(TF))·Vᵀ`). Transfer is scored |
| by relatedness-aware **leave-study-out** prediction of tobacco's own held-out-study expression |
| (no regulatory gold standard is used). |
|
|
| ## Contents |
|
|
| ### `models/` |
| | file | description | |
| |---|---| |
| | `arabidopsis_grn_fm_W.npz` | Arabidopsis GRN-FM explicit weight tensor W (source) | |
| | `arabidopsis_grn_fm_seq_d256.pt` | Arabidopsis **sequence-conditioned** GRN-FM (φ + V, rank d=256; ESM-2 `esm2_t12_35M_UR50D`) | |
| | `soybean_grn_fm_W.npz` | Soybean GRN-FM weight tensor W (source; same model as the companion `dirmy/soygrn`) | |
| | `tobacco_within_grn_fm_W.npz` | Within-species tobacco GRN-FM W (upper-bound reference) | |
|
|
| ### `data/` |
| | file | description | |
| |---|---| |
| | `tobacco_gene_tpm.npz` | *N. benthamiana* compendium: 56,738 genes × 1,540 samples (NbT2T reference) | |
| | `tobacco_sample_meta.csv` | per-sample SRA Study/BioProject metadata (153 studies) | |
| | `tobacco_protein_esm2.npz` | ESM-2 mean-pooled embeddings of tobacco proteins | |
| | `tobacco_tf_genes.txt` | 1,203 ortholog-defined candidate tobacco TFs | |
| | `tobacco_to_arabidopsis_rbh.tsv` | tobacco↔Arabidopsis reciprocal-best-hit orthologs (12,773) | |
| | `tobacco_to_soybean_rbh.tsv` | tobacco↔soybean reciprocal-best-hit orthologs (13,981) | |
|
|
| ### `networks/` |
| Inferred TF→target edge lists (columns: `TF`, `target`, `score`): |
| `tobacco_within_clr.tsv`, `tobacco_within_grnboost2.tsv`, `tobacco_within_fm.tsv` |
| (within-species), and `tobacco_transfer_from_arabidopsis.tsv` (zero-shot Arabidopsis→tobacco transfer). |
|
|
| ## Reproduce |
|
|
| Code: **https://github.com/k821209/nbgrn-transfer** |
| ``` |
| python src/grn_transfer_eval.py # ortholog transfer (soybean/Arabidopsis → tobacco) |
| python src/grn_transfer_seq.py # sequence-conditioned, ortholog-free transfer |
| python src/grn_fewshot.py # within-species data-efficiency curve |
| ``` |
|
|
| ## Companion |
|
|
| Within-species soybean GRN benchmark: **`dirmy/soygrn`** (DOI 10.57967/hf/9365). |
|
|
| ## Citation |
|
|
| Kang, Y. *Conditioning a gene-regulatory foundation model on transcription-factor sequence |
| enables ortholog-free cross-species transfer.* (2026). Data & models: this repository. |
|
|
| License: CC-BY-4.0. |
|
|
