Softplus shape nonlinearity, rho=-10 null marks, and cleanup#2
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Softplus shape nonlinearity, rho=-10 null marks, and cleanup#2
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Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com>
Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com>
Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com>
…dal_diag.py Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com>
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[WIP] Retrain full pipelines in easier oracle mode
Diagnose Phase II bootstrap instability: easy-setting retraining + oracle warm-start experiment
Mar 19, 2026
…ase_np95_pihat95) Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com>
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Diagnose Phase II bootstrap instability: easy-setting retraining + oracle warm-start experiment
Parameterized experiment framework for gaubump case studies with Phase II optimizer restart
Mar 19, 2026
The shape function now uses softplus(rho) * exp(...) instead of rho * exp(...). Null marks use rho=-10 (softplus(-10) ≈ 4.5e-5) instead of rho=0, giving real background-like noise and allowing the model to represent 'zero' with a smooth gradient signal. Changes applied consistently across: - model.py (shape_fn, compute_X, compute_X_batched, sampling) - run_modal_experiment.py (inline copies, diagnostics, plots) - train.py (diagnostics, NaN replacement) - run_modal.py, run_modal_easy.py, run_modal_oracle.py, run_modal_diag.py Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com>
…t 0.95) The softplus(rho) nonlinearity completely resolves the Phase II bootstrap instability. Post-Phase-I frac=0.956 stays stable throughout 150k Phase II steps, finishing at 0.952. Compare with old linear model where frac degraded from 0.858 to 0.358. Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com>
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Parameterized experiment framework for gaubump case studies with Phase II optimizer restart
softplus(rho) shape nonlinearity with rho=-10 null marks
Mar 19, 2026
…gn doc Deleted: - results/case_np95_pihat95/ (pre-softplus experiment) - All root-level results (diag_*, easy_*, oracle_*, main pipeline outputs) - run_modal.py, run_modal_diag.py, run_modal_easy.py, run_modal_oracle.py (all superseded by the parameterized run_modal_experiment.py) - DETAILED_PLAN.md (pre-softplus design notes) Updated README.md to document: - Softplus shape function and rho=-10 null marks - Streamlined file listing (4 Python files + results/) - How to run experiments and configure cases - Current results (case_softplus_np95_pihat95) Co-authored-by: jacksonloper <2056977+jacksonloper@users.noreply.github.com> Agent-Logs-Url: https://github.com/prob-ml/admixture-identifiability/sessions/c51e3074-02a8-4128-ab3a-c8c53608aa7c
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softplus(rho) shape nonlinearity with rho=-10 null marks
Softplus shape nonlinearity, rho=-10 null marks, and cleanup
Mar 20, 2026
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Phase II bootstrap was unstable due to the hard zero at rho=0. This PR introduces
softplus(rho) * exp(...)as the shape function and moves null marks from rho=0 to rho=-10, giving smooth gradients near zero and faint background noise instead of exact silence.Shape function change
Applied in
shape_fn,compute_X,compute_X_batchedinmodel.pyand the inline copies inrun_modal_experiment.py.Null marks: rho=0 → rho=-10
rho=-10instead ofrho=0for null marks (softplus(-10) ≈ 4.5e-5)jnp.array([-10.0, 0.0])instead of0.0frac(softplus(rho) < 0.1)instead offrac(|rho| < 0.1)Results
Phase II bootstrap is now stable: frac holds at ~0.95 through 150k iterations (previously degraded 0.858 → 0.358).
Cleanup
run_modal.py,run_modal_diag.py,run_modal_easy.py,run_modal_oracle.py) — all superseded byrun_modal_experiment.pyDETAILED_PLAN.mdand all pre-softplus result filesREADME.mdto document current architecture and experiment workflow📱 Kick off Copilot coding agent tasks wherever you are with GitHub Mobile, available on iOS and Android.