Paper
- bioRxiv preprint: doi:10.64898/2026.05.16.725674v1
- Supplement (PDF): supplement.pdf
- Supplement (browsable HTML): supplement/supplement.html
Code
- Reference implementation: github.com/evoldoers/tkfdp
- Companion library (TKF91 / TKF92 / MixDom in JAX): github.com/evoldoers/tkf-mixdom
- Dataset fetchers (Pfam / BAliBASE / OxBench): github.com/evoldoers/bio-datasets
Releases
evoldoers/tkfdp
| Tag | Contents |
|---|---|
code-2026-05-19 |
Source-code snapshot at the bioRxiv submission, packaged as a tarball |
results/K4-emwarm-top1000-2026-05-09 |
TKF-DP Kc=4 EM-warmup checkpoint (Pfam top-1000); backs Figs 3-5 and Table 1 row inf-PHMM-K=4 |
qprime-bali3pdbm-2026-05-16 |
Q′ caches (per-pair posteriors) for all 8 methods compared in Tables 1+2 (~3.6 GB across 8 tarballs) |
evoldoers/tkf-mixdom
| Tag | Contents |
|---|---|
mixdom-checkpoints-2026-05 |
MixDom-d3f1, TKF92-K=20, CherryML-C=20 NPZ checkpoints (3 files, ~210 KB total) |
Reproduction
The end-to-end recipe (training, evaluation, figure generation) lives at
REPRODUCTION_MANIFEST.md in the code repo.