REPRODUCE.md

scFATE NeurIPS 2026 — Reproduce the Paper

This directory ships every checkpoint behind the paper's Table 1 + a reproduce.sh for each run. All 31 paper-headline runs are listed below.

0. Prerequisites

git clone https://huggingface.co/Angione-Lab/scFATE
cd scFATE/code  # source code is in scfate-code submodule
uv venv && uv pip install -e .  # or pip install -r requirements.txt

Then download datasets:

huggingface-cli download Angione-Lab/scFATE-datasets --local-dir datasets/scFATE/processed --repo-type dataset

1. Dependency graph

backbone (rotation autoencoder)         — hf-assets/checkpoints/<dataset>/
    └─→ flow head (s1, s2, s3)          — runs/<dataset>_flow_*/flow_best.pt
            └─→ reflow K=2 (K562)       — runs/*_reflow_K2_*_s1/flow_best.pt
            └─→ teachers ×18 (SciPlex3) — runs/*_priorkrr_V2B_s{1..9}, *_priornone_V2B_s{1..9}
                    └─→ student ×7     — runs/*_reflow_ensemble_mixed18_K16_V2B_s{1..7}

2. Per-run reproduction

Each runs/<run_dir>/ contains:

• flow_best.pt — checkpoint with embedded hparams (load via torch.load, look at top-level keys or ckpt['hparams'])
• config.json — extracted hparams + result-JSON pointer + dataset path
• reproduce.sh — exact training command, ready to run
• flow_metrics.jsonl — training trajectory
• krr_prior.pkl — KRR-init prior (if prior=krr)

3. Paper-headline runs

Paper row	Dataset	Run dir	Result JSON	Reproduce
Norman seed 1	CRISPRa Norman	runs/b200_norman_flow_e115_krrinit_s02_mask_30k	experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_K128.json	bash runs/b200_norman_flow_e115_krrinit_s02_mask_30k/reproduce.sh
Norman seed 2	CRISPRa Norman	runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2	experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed2.json	bash runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2/reproduce.sh
Norman seed 3	CRISPRa Norman	runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3	experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed3.json	bash runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3/reproduce.sh
RPE1 seed 1	Replogle RPE1	runs/b200_rpe1_flow_block_krrinit_mask_30k_s1	experiments/results/fair_comparison/rpe1_rotation_vs_direct__flow__b200_rpe1_flow_block_krrinit_mask_30k_s1_rpe1_block_K128.json	bash runs/b200_rpe1_flow_block_krrinit_mask_30k_s1/reproduce.sh
K562 base flow (teacher for reflow)	Replogle K562	runs/b200_k562_flow_bs2048_krrinit_mask_30k	experiments/results/fair_comparison/replogle_rotation_vs_direct__flow__b200_k562_flow_bs2048_krrinit_mask_30k_K128.json	bash runs/b200_k562_flow_bs2048_krrinit_mask_30k/reproduce.sh
K562 reflow K=2 (paper headline 81.2)	Replogle K562	runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1	experiments/results/fair_comparison/replogle_rotation_vs_direct__flow__b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1_reflow_K2_bracket1p0_ens5seed_sigmainf0p15_antithetic_Kper128.json	bash runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1/reproduce.sh
SciPlex3 priornone teacher s1	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/reproduce.sh
SciPlex3 priorkrr teacher s1	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/reproduce.sh
SciPlex3 priornone teacher s2	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/reproduce.sh
SciPlex3 priorkrr teacher s2	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/reproduce.sh
SciPlex3 priornone teacher s3	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/reproduce.sh
SciPlex3 priorkrr teacher s3	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/reproduce.sh
SciPlex3 priornone teacher s4	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/reproduce.sh
SciPlex3 priorkrr teacher s4	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/reproduce.sh
SciPlex3 priornone teacher s5	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/reproduce.sh
SciPlex3 priorkrr teacher s5	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/reproduce.sh
SciPlex3 priornone teacher s6	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/reproduce.sh
SciPlex3 priorkrr teacher s6	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/reproduce.sh
SciPlex3 priornone teacher s7	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/reproduce.sh
SciPlex3 priorkrr teacher s7	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/reproduce.sh
SciPlex3 priornone teacher s8	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/reproduce.sh
SciPlex3 priorkrr teacher s8	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/reproduce.sh
SciPlex3 priornone teacher s9	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/reproduce.sh
SciPlex3 priorkrr teacher s9	SciPlex3	runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9	—	bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/reproduce.sh
SciPlex3 mixed-18 K=16 student s1 (paper headline 70.0)	SciPlex3	runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s1	experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json	bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s1/reproduce.sh
SciPlex3 mixed-18 K=16 student s2 (paper headline 70.0)	SciPlex3	runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2	experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json	bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2/reproduce.sh
SciPlex3 mixed-18 K=16 student s3 (paper headline 70.0)	SciPlex3	runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3	experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json	bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3/reproduce.sh
SciPlex3 mixed-18 K=16 student s4 (paper headline 70.0)	SciPlex3	runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4	experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json	bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4/reproduce.sh
SciPlex3 mixed-18 K=16 student s5 (paper headline 70.0)	SciPlex3	runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5	experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json	bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5/reproduce.sh
SciPlex3 mixed-18 K=16 student s6 (paper headline 70.0)	SciPlex3	runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6	experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json	bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6/reproduce.sh
SciPlex3 mixed-18 K=16 student s7 (paper headline 70.0)	SciPlex3	runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7	experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json	bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7/reproduce.sh

4. Eval pipeline

.venv/bin/python scripts/eval_fair_comparison.py \\
    --dataset <dataset_name> --flow_ckpt <run_dir>/flow_best.pt \\
    --multiview data/gene_embeddings/<dataset>_multiview.pt --K_eval 128

5. Known caveats

• SciPlex3 paper-row cosine (0.491) and PDE (0.483) numbers in Table 1 are not in any saved results JSON; only mean DA = 0.700 reproduces from iter214_multi_metric_router_ensemble.json (metric_da.tanimoto_morgan2048). Re-eval needed before final submission.
• Norman cos/PDE in Table 1 differ by ~0.002 from *_K128.json (rounded).
• K562 reflow cos/PDE in Table 1 differ by ~0.007 from the saved ensemble JSON.