| #!/bin/bash |
| |
| set -x |
| export PYTHONPATH=/root/patientphex/retrain_t1/code |
| export HF_HUB_OFFLINE=1 |
| export TRANSFORMERS_OFFLINE=1 |
| PY=/root/patientphex/judge_venv/bin/python |
| C=/root/patientphex/retrain_t1/code |
| R=$C/artifacts/b_retrain |
| B=/root/patientphex/PatientPheX-V1-B/PatientPheX-V1-B.jsonl |
|
|
| $PY $C/scripts/build_deployment_candidates.py \ |
| --train-data $C/artifacts/cleaned/PatientPheX-train.cleaned.jsonl \ |
| --predict-data $B \ |
| --ontology /root/patientphex/PatientPheX-V1-A/hp.obo \ |
| --bio-output $R/bio/B-bio.json \ |
| --phenotagger-output $R/pt-original/B-full.json \ |
| --output $R/B-candidates.json \ |
| --lexicon-threshold 0.55 \ |
| --phenotagger-threshold 0.50 || exit 1 |
| echo CANDIDATES_DONE |
|
|
| $PY /root/patientphex/check_count.py $R/B-candidates.json || true |
|
|
| pids="" |
| gpu=2 |
| for seed in 2026 2027 2028; do |
| CUDA_VISIBLE_DEVICES=$gpu nohup $PY $C/scripts/train_predict_candidate_verifier.py \ |
| --train-data $C/artifacts/cleaned/PatientPheX-train.cleaned.jsonl \ |
| --train-candidates $C/artifacts/candidates/oof-union-pheno.json \ |
| --predict-data $B \ |
| --predict-candidates $R/B-candidates.json \ |
| --model /root/patientphex/models/BiomedBERT-base-uncased-abstract-fulltext \ |
| --epochs 3 --batch-size 16 --learning-rate 2e-5 --max-length 256 --seed $seed \ |
| --output $R/verifier-seed$seed.json > $R/verifier-seed$seed.log 2>&1 & |
| pids="$pids $!" |
| gpu=$((gpu+1)) |
| done |
| fail=0 |
| for p in $pids; do wait $p || fail=1; done |
| [ $fail = 1 ] && { echo VERIFIER_FAIL; exit 2; } |
| echo VERIFIERS_DONE |
|
|
| CUDA_VISIBLE_DEVICES=1 $PY $C/scripts/assemble_task1_predictions.py \ |
| --data $B \ |
| --ontology /root/patientphex/PatientPheX-V1-A/hp.obo \ |
| --verifier-glob "$R/verifier-seed202[678].json" \ |
| --sapbert-model /root/patientphex/models/SapBERT-from-PubMedBERT-fulltext \ |
| --output $R/B-task1-ensemble-q3636.jsonl \ |
| --threshold 0.66 --target-fraction 0.3636 --lexicon-threshold 0.0 --phenotagger-threshold 0.90 || exit 3 |
| echo ASSEMBLE_DONE |
| wc -l $R/B-task1-ensemble-q3636.jsonl |
| echo CURRENT_CHAIN_DONE |
|
|
