May 6 11:39 Refresh figure data: drop Archived/, refresh Candidate_Analysis with rescored hits Removed 56 files in Generation_Model/End2end/Archived/ (legacy single-run experiments, not used by current figures). Removed obsolete Candidate_Analysis/AMP_{active_druglike,potent_druglike}.csv, replaced by AMP_active.csv (39,891 active candidates) + AMP_hit.csv (799 hits, triple filter) generated after the AMP ensemble retrain on MIC-only DBAASP. All other per-stage and end-to-end metrics re-uploaded; LFS dedup keeps unchanged content. Apr 5 14:59 data: update Candidate_Analysis (AMP_potent→AMP_active rename, updated eval_report) Apr 1 18:51 chore: upload raw.jsonl replacing raw.json (Flat/run5) 18:51 chore: upload raw.jsonl replacing raw.json (Flat/run4) 18:51 chore: upload raw.jsonl replacing raw.json (Flat/run3) 18:51 chore: upload raw.jsonl replacing raw.json (Flat/run2) 18:51 chore: upload raw.jsonl replacing raw.json (Flat/run1) 18:51 chore: remove old raw.json (Flat/run5) 18:51 chore: remove old raw.json (Flat/run4) 18:51 chore: remove old raw.json (Flat/run3) 18:51 chore: remove old raw.json (Flat/run2) 18:51 chore: remove old raw.json (Flat/run1) 18:51 chore: update eval_report.json with per_type_nn_distance (Flat/run5) 18:51 chore: update eval_report.json with per_type_nn_distance (Flat/run4) 18:51 chore: update eval_report.json with per_type_nn_distance (Flat/run3) 18:51 chore: update eval_report.json with per_type_nn_distance (Flat/run2) 18:51 chore: update eval_report.json with per_type_nn_distance (Flat/run1) 18:51 chore: update eval_report.json with per_type_nn_distance (Cascade/run5) 18:50 chore: update eval_report.json with per_type_nn_distance (Cascade/run4) 18:50 chore: update eval_report.json with per_type_nn_distance (Cascade/run3) 18:50 chore: update eval_report.json with per_type_nn_distance (Cascade/run2) 18:50 chore: update eval_report.json with per_type_nn_distance (Cascade/run1) 13:37 chore: remove script from Data directory (run_comparison.py) 13:37 chore: remove script from Data directory (prepare_constraints.py) 13:37 chore: remove script from Data directory (Infilling_Generation.ipynb) 13:37 chore: remove script from Data directory (constrained_generation.ipynb) 13:37 chore: remove script from Data directory (flat_cascade_multirun.ipynb) Mar 16 14:36 refactor: convert raw.json to raw.jsonl for consistency 10:05 Remove Archived directory (not needed for reproduction) 10:04 Restructure: all figure data under Data/ prefix 10:02 Delete batch 2 (200 files) 10:02 Delete batch 1 (200 files) 10:00 Restructure: all figure data under Data/ prefix Mar 13 12:10 Add eval data (eval_test.json + metrics.json) for paper figure reproduction 
