- Compare the definition of best matches and weak best matches:
- Check whether every best match in (N, σ) is also a weak best match. Test this computationally, but also try to give a formal argument.
- Check if a modified version of the BIC-cherry + expansion procedure yields networks that explain weak best match graphs.
- Find a way to edit the explaining networks for (weak) best matches to become more tree like.
| Todo | Name | Tested | Done |
|---|---|---|---|
| Hybrid-Node-Insertion (0) | Lenny | ❗ NO | ❗ NO |
| Unit tests for algos (ongoing, 1c) | OPEN | ❗ NO | ❗ NO |
| GraphOperations: "Pull-Up", "Pull-down", "Delete redundant nodes" (2c) | OPEN | ❗ NO | ❗ NO |
| Test if 1b is explanation for wbm Graphs (1d == Obj. 1b?) | OPEN | ❗ NO | ❗ NO |
| Finished Tasks | Name | Tested (as in 1c?) | Done |
|---|---|---|---|
| LEAH GITHUB SSH AUTH | ALL | ❗ YES | ✅ |
| Keep Distance attribute in gene tree | Lenny | ❗ YES | ✅ |
| Implement wbmg_from_network() | Leo | YES?(1) | ✅ |
| Implement bmg_from_network() | Leo | YES?(1) | ✅ |
| Test (bm = weak bm?) with python (Obj. 1a) | Leo | Yes | Yes |
| BIC Cherry Expansion (1a) | Leo | Yes (basic cases work) | ❗ NO-on random examples results are not consistently correct! (see the failing test) :/ |
| BIC Cherry Expansion - restricted to accepting edges (1b) | Leo | Yes | Yes |
- how to run project: uv
uv run main.py
or
uv run pytest
for testing