| --- |
| license: mit |
| tags: |
| - phylogenetics |
| - biology |
| --- |
| |
| # DeepPhylo checkpoints |
|
|
| Trained models for *Deep Generative Models for Phylogenetic Inference with |
| Complex Evolutionary Processes*. These are the exact checkpoints behind the |
| paper's NELBO bar chart and its RF-vs-sites / RF-vs-taxa figures. |
|
|
| Five methods (BU, MO, TD, PF2, QF) on three simulated datasets: `jc` (DNA, Jukes-Cantor), `cat` (amino |
| acids, CAT mixture), `indels` (DNA, GTR with indels and realignment). |
|
|
| | Directory | Method | Dataset | Step | Size | |
| |---|---|---|---|---| |
| | `BU_JC` | Bottom up | JC | 26,000 | 224 MiB | |
| | `MO_JC` | Middle out | JC | 26,000 | 224 MiB | |
| | `TD_JC` | Top down | JC | 22,000 | 224 MiB | |
| | `PF2_JC` | Phyloformer 2 (baseline) | JC | 16,000 | 299 MiB | |
| | `QF_JC` | QuartFormer (baseline) | JC | 56,000 | 26 MiB | |
| | `BU_CAT` | Bottom up | CAT | 26,000 | 224 MiB | |
| | `MO_CAT` | Middle out | CAT | 26,000 | 224 MiB | |
| | `TD_CAT` | Top down | CAT | 22,000 | 224 MiB | |
| | `PF2_CAT` | Phyloformer 2 (baseline) | CAT | 16,000 | 299 MiB | |
| | `QF_CAT` | QuartFormer (baseline) | CAT | 60,000 | 26 MiB | |
| | `BU_Indels` | Bottom up | Indels | 26,000 | 224 MiB | |
| | `MO_Indels` | Middle out | Indels | 24,000 | 224 MiB | |
| | `TD_Indels` | Top down | Indels | 22,000 | 224 MiB | |
| | `PF2_Indels` | Phyloformer 2 (baseline) | Indels | 14,000 | 299 MiB | |
| | `QF_Indels` | QuartFormer (baseline) | Indels | 50,000 | 26 MiB | |
|
|
| Each directory holds `model.ckpt` and the `config.yaml` of the run that produced |
| it, which is what the code reads to rebuild the model. |
|
|
| ## Usage |
|
|
| Clone [DeepPhylo](https://github.com/AlanNawzadAmin/DeepPhylo), then place a |
| directory here under `checkpoints/` and name it in `run=`: |
|
|
| ```bash |
| python sample.py run=BU_JC sampling.path=out.pkl |
| ``` |
|
|
| See the repository README for greedy vs. consensus decoding. |
|
|
| `MANIFEST.tsv` lists the training run id, step, size and SHA-256 of every file. |
|
|
