ADR-D23: LAFA submission strategy

Status:

Accepted

Date:

2026-05-05

Phase:

F-LAFA

Context

LAFA (functionbench.net) provides a public benchmark surface for protein function annotation methods, comparable in spirit to CAFA. PROTEA needs a credible adoption story; LAFA also exposes the method to comparison against external systems on identical evaluation conditions.

Decision

F-LAFA at the end of the timeline (~1.5 weeks). Three containers built on top of protea-method-runtime:

  • lafa_knn_v1 (one PLM, KNN baseline, GO propagation).

  • lafa_knn_8plm (ensemble across the eight PLMs).

  • lafa_v18 (full pipeline with selective re-ranking).

Each container submitted to the LAFA test suite per anphan0828/LAFA_container_guide.

Consequences

  • Reuses F-OPS deliverables (protea-method-runtime).

  • Material for chapter 7 conclusion: external adoption.

  • apps/lafa_container/ and protea-lafa-container/ (existing preliminaries) are not iterated on until F-LAFA opens; F-LAFA rewrites them on top of protea-method-runtime.

Resolution

Closed.