docs: update citation with live bioRxiv DOI 10.64898/2026.05.29.728379

refresh: rename class_names inactive -> background in eval JSONs

Remove stale connection_type_coverage.json (no longer generated by candidate analysis pipeline)

Refresh figure data: drop Archived/, refresh Candidate_Analysis with rescored hits

docs: UTF-8 author name

docs: bioRxiv citation with DOI placeholder

fix: use @misc citation (pre-bioRxiv)

docs: update title and citation to bioRxiv preprint format

docs: update Corresponding Figures table and fix Connection dir name

data: update Candidate_Analysis (AMP_potent→AMP_active rename, updated eval_report)

docs: update README — rename Potent→Active, fix ratios, remove connection_type_coverage

docs: add dataset card with file structure, figure mapping, and quick start

chore: upload raw.jsonl replacing raw.json (Flat/run5)

chore: upload raw.jsonl replacing raw.json (Flat/run4)

chore: upload raw.jsonl replacing raw.json (Flat/run3)

chore: upload raw.jsonl replacing raw.json (Flat/run2)

chore: upload raw.jsonl replacing raw.json (Flat/run1)

chore: remove old raw.json (Flat/run5)

chore: remove old raw.json (Flat/run4)

chore: remove old raw.json (Flat/run3)

chore: remove old raw.json (Flat/run2)

chore: remove old raw.json (Flat/run1)

chore: update eval_report.json with per_type_nn_distance (Flat/run5)

chore: update eval_report.json with per_type_nn_distance (Flat/run4)

chore: update eval_report.json with per_type_nn_distance (Flat/run3)

chore: update eval_report.json with per_type_nn_distance (Flat/run2)

chore: update eval_report.json with per_type_nn_distance (Flat/run1)

chore: update eval_report.json with per_type_nn_distance (Cascade/run5)

chore: update eval_report.json with per_type_nn_distance (Cascade/run4)

chore: update eval_report.json with per_type_nn_distance (Cascade/run3)

chore: update eval_report.json with per_type_nn_distance (Cascade/run2)

chore: update eval_report.json with per_type_nn_distance (Cascade/run1)

chore: remove script from Data directory (run_comparison.py)

chore: remove script from Data directory (prepare_constraints.py)

chore: remove script from Data directory (Infilling_Generation.ipynb)

chore: remove script from Data directory (constrained_generation.ipynb)

chore: remove script from Data directory (flat_cascade_multirun.ipynb)

refactor: convert raw.json to raw.jsonl for consistency

Add pre-computed connection type coverage stats

Remove Archived directory (not needed for reproduction)

Restructure: all figure data under Data/ prefix

Delete batch 4 (73 files)

Delete batch 3 (200 files)

Delete batch 2 (200 files)

Delete batch 1 (200 files)

Restructure: all figure data under Data/ prefix

Add eval data (eval_test.json + metrics.json) for paper figure reproduction

Upload README.md with huggingface_hub

Upload Candidate_Analysis/eval_report.json with huggingface_hub

Upload Candidate_Analysis/AMP_potent_druglike.csv with huggingface_hub