Paper
- bioRxiv preprint: doi:10.64898/2026.05.16.725674v1
- Supplement (PDF): supplement.pdf
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-2026-08-04 |
Source-code snapshot |
results/K4-emwarm-top1000-2026-05-09 |
TKF-DP Kc=4 EM-warmup checkpoint (Pfam top-1000); backs the infinite-pair-HMM K=4 results |
results/paper2-coupling-rates-2026-08-04 |
Paper-2 coupled amino-acid substitution model rates (Exchangeable, Metropolis, Coupled, Metropolis-mixture) |
evoldoers/tkf-mixdom
| Tag | Contents |
|---|---|
results/mixdom-d3f1-perdomain-2026-08-04 |
MixDom-d3f1 (per-domain substitution matrices), Pfam v3 — current headline substitution-side model |
results/mixfrag-F2-pfam-2026-08-04 |
MixFrag ℱ=2 cherry-EM fit (TKF92 + 2-fragtype mixture) |
mixdom-checkpoints-2026-05 |
TKF92-K=20, CherryML-C=20 (and the earlier MixDom-d3f1) NPZ checkpoints |
Reproduction
The end-to-end recipe (training, evaluation, figure generation) lives at
REPRODUCTION_MANIFEST.md in the code repo.