Paired Refinement Experiments
This directory evaluates masked diffusion as an enhancer refiner rather than as a pure de novo generator.
For each reference sequence x, the script creates edited variants x' under a mutation budget rho, scores both sequences with the trained DeepSTARR predictor, and reports:
delta = predictor(x') - predictor(x)
Experiments covered
- Paired delta distribution over
rho = 0.01, 0.03, 0.05, 0.10, 0.20. - Mask-selection strategy comparison:
random: randomly chosen editable positions.entropy: positions where the diffusion model is most uncertain.logit_gap: positions where the diffusion model most prefers a different base than the current base.
- Best-of-N refinement:
- sample multiple edits per sequence and keep the candidate with the largest predicted activity gain.
Outputs
The default output directory is:
${RESULT_ROOT}/refinement/paired_refinement_test
It contains:
refinement_details.jsonl
refinement_summary.json
paired_delta_by_mask_ratio.png
strategy_delta_violin.png
best_of_n_refinement_curve.png
Recommended command on the GPU server
Run from the repository root. Use explicit environment variables to avoid stale defaults from env.sh.
cd /inspire/hdd/project/intelligentcreativedesign/dangshengqi-253114050252/z-anna/genrl-enhancer-diffusion
PROJECT_ROOT=$(pwd) \
RUN_ROOT=$(pwd)/paper_runs \
DEEPSTARR_DIR=$(pwd)/datas/DeepSTARR-enhancer-activity \
GENERANNO_BASE_MODEL=$(pwd)/models/GENERanno-eukaryote-0.5b-base \
DIFFUSION_MODEL=$(pwd)/saved_model/deepstarr_discrete_diffusion \
PREDICTOR_MODEL=$(pwd)/paper_runs/results/deepstarr_regression/best_model \
REFINEMENT_SPLIT=test \
REFINEMENT_NUM_SEQUENCES=1024 \
REFINEMENT_NUM_SAMPLES=8 \
REFINEMENT_MASK_RATIOS="0.01 0.03 0.05 0.10 0.20" \
REFINEMENT_STRATEGIES="random entropy logit_gap" \
REFINEMENT_DIFFUSION_STEPS=32 \
REFINEMENT_BATCH_SIZE=16 \
PREDICTOR_SCORE_BATCH_SIZE=256 \
TRANSFORMERS_NO_TF=1 \
USE_TF=0 \
TOKENIZERS_PARALLELISM=false \
nohup bash scripts/11_refinement/run_paired_refinement.sh > paired_refinement.log 2>&1 &
For a fast smoke test:
PROJECT_ROOT=$(pwd) \
RUN_ROOT=$(pwd)/paper_runs \
DEEPSTARR_DIR=$(pwd)/datas/DeepSTARR-enhancer-activity \
GENERANNO_BASE_MODEL=$(pwd)/models/GENERanno-eukaryote-0.5b-base \
DIFFUSION_MODEL=$(pwd)/saved_model/deepstarr_discrete_diffusion \
PREDICTOR_MODEL=$(pwd)/paper_runs/results/deepstarr_regression/best_model \
REFINEMENT_SPLIT=valid \
REFINEMENT_NUM_SEQUENCES=64 \
REFINEMENT_NUM_SAMPLES=2 \
REFINEMENT_MASK_RATIOS="0.03 0.10" \
REFINEMENT_STRATEGIES="random logit_gap" \
REFINEMENT_DIFFUSION_STEPS=16 \
REFINEMENT_BATCH_SIZE=16 \
PREDICTOR_SCORE_BATCH_SIZE=128 \
TRANSFORMERS_NO_TF=1 \
USE_TF=0 \
TOKENIZERS_PARALLELISM=false \
nohup bash scripts/11_refinement/run_paired_refinement.sh > paired_refinement_smoke.log 2>&1 &