Official public source carve-out for ABLE: Choosing Perturbation Experiments to Recover Gene Logic (AI for Science Workshop at ICML 2026).
ABLE recovers executable Boolean regulatory rules from perturbation-state transition data using a neural proposer, symbolic uniqueness checks, and active follow-up queries.
Throughout this codebase, paper31 refers to the 31 Biodivine Boolean Models (BBM) used in the paper's evaluation.
cd able-public
pip install -e .
# Optional symbolic baselines for the curated-biology comparison
pip install -e .[baselines]able-download-checkpoints --output-dir checkpoints
able-download-bbm --output-dir bbm_modelsCheckpoint artifacts are hosted on the public phuayj/able Hugging Face repo and require no authentication to download.
Reproduce CR Table 2 and Figure 2:
able-eval-biology --checkpoint checkpoints/checkpoint_n15_ncf_best.pt --output-dir results/biology
python scripts/gen_biology_table.py \
--input-json results/biology/baselines_bio_comparison.json \
--output results/tables/table2_biology.tex
python scripts/plot_bbm_bio_heatmap.py --output-dir results/figuresOutputs:
results/tables/table2_biology.texresults/figures/bbm_bio_heatmap_slim.pdf
Numerical/scripted tables:
- Table 2
tab:biology→results/tables/table2_biology.tex - Table 4
tab:local_obs_comparison→results/tables/table4_local_obs_comparison.tex - Table 5
tab:budget_sweep→results/tables/table5_budget_sweep.tex - Table 6
tab:omitted_audit→results/tables/table6_omitted_regulator_audit.tex - Table 7
tab:certifiability_diagnosis→results/tables/table7_certifiability_diagnosis.tex - Table 9
tab:adaptivity_collapse→results/tables/table9_adaptivity_collapse.tex - Table 11
tab:d4_bio_full→results/tables/table11_d4_cascade.tex - Table 12
tab:ablation_necessity→results/tables/table12_ablation_necessity.tex
Figures:
- Figure 1
fig:pipeline→results/figures/pipeline_overview.pdf - Figure 2
fig:bio_heatmap→results/figures/bbm_bio_heatmap_slim.pdf - Figure 3
fig:obs_comparison→results/figures/local_obs_comparison_vertical.pdf - Figure 4
fig:scaling_law_body→results/figures/fig_scaling_A.pdf - Figure 5
fig:bio_heatmap_full→results/figures/bbm_bio_heatmap_full.pdf - Figure 6
fig:active_crossover→results/figures/fig_active_crossover.pdf - Figure 7
fig:gating_tau→results/figures/gating_tau_sensitivity.pdf
Inline prose tables with no reproducer: Table 1 tab:liftcert_scope, Table 3 tab:capability_map, Table 8 tab:protocol_audit, and Table 10 tab:symbolic_comparison.
See docs/REPRODUCE.md for the section-by-section checklist with exact commands and rough wall-time estimates.
TBD