firthmodels 0.7.2__tar.gz → 0.8.0__tar.gz

{firthmodels-0.7.2 → firthmodels-0.8.0}/CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 title: firthmodels
 message: "If you use this software, please cite it as below."
 type: software
-version: 0.7.2
+version: 0.8.0
 doi: 10.5281/zenodo.17863280
 authors:
   - family-names: Luo

{firthmodels-0.7.2 → firthmodels-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: firthmodels
-Version: 0.7.2
+Version: 0.8.0
 Summary: Firth-penalized models in Python
 Project-URL: Homepage, https://github.com/jzluo/firthmodels
 Project-URL: Repository, https://github.com/jzluo/firthmodels
@@ -228,6 +228,10 @@ model.lrt_bse_         # Back-corrected standard errors (separate from Wald bse_
 Each feature requires a separate constrained model fit, so you can test selectively to
 avoid unnecessary computation. By default, LRT uses a warm start based on the full-model
 covariance to reduce Newton-Raphson iterations; pass `warm_start=False` to disable it.
+If the full-model fit does not converge, its likelihood is non-finite, or a constrained
+fit does not converge, a warning is emitted and the affected p-values and
+back-corrected standard errors remain `NaN`. A later explicit `lrt()` call retries
+failed constrained fits.
 
 ```python
 model.lrt(0)              # Single feature by index

{firthmodels-0.7.2 → firthmodels-0.8.0}/README.md

@@ -185,6 +185,10 @@ model.lrt_bse_         # Back-corrected standard errors (separate from Wald bse_
 Each feature requires a separate constrained model fit, so you can test selectively to
 avoid unnecessary computation. By default, LRT uses a warm start based on the full-model
 covariance to reduce Newton-Raphson iterations; pass `warm_start=False` to disable it.
+If the full-model fit does not converge, its likelihood is non-finite, or a constrained
+fit does not converge, a warning is emitted and the affected p-values and
+back-corrected standard errors remain `NaN`. A later explicit `lrt()` call retries
+failed constrained fits.
 
 ```python
 model.lrt(0)              # Single feature by index

{firthmodels-0.7.2 → firthmodels-0.8.0}/benchmarks/README.md

@@ -27,7 +27,7 @@ for Firth-penalized logistic regression.
 
 | Library | Version | BLAS |
 |---------|---------|------|
-| **firthmodels** | 0.7.2 | /usr/lib/x86_64-linux-gnu/openblas-pthread/ (openblas 0.3.26) |
+| **firthmodels** | 0.8.0 | /usr/lib/x86_64-linux-gnu/openblas-pthread/ (openblas 0.3.26) |
 | **brglm2** | 1.0.1 | /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 |
 | **logistf** | 1.26.1 | /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 |
 
@@ -56,16 +56,16 @@ Time to fit the model and perform Wald inference. Values are minimum time across
 
 | k | firthmodels<br>(numba) | firthmodels<br>(numpy) | brglm2<br>(AS-mean) | brglm2<br>(MPL_Jeffreys) | logistf |
 |--:|------:|------:|------------:|-------------:|--------:|
-|   5 | 0.5 | 1.4 | 4.2 | 4.2 | 2.0 |
-|  10 | 1.2 | 1.9 | 7.9 | 7.2 | 4.3 |
-|  15 | 1.2 | 1.9 | 8.2 | 8.2 | 7.6 |
-|  20 | 1.5 | 2.3 | 9.3 | 9.4 | 15.7 |
-|  25 | 1.8 | 2.7 | 11.7 | 11.7 | 24.2 |
-|  30 | 2.1 | 2.9 | 12.6 | 12.9 | 30.2 |
-|  35 | 2.3 | 3.4 | 14.9 | 14.8 | 42.0 |
-|  40 | 2.8 | 3.8 | 16.9 | 16.8 | 52.7 |
-|  45 | 3.9 | 4.6 | 18.6 | 19.8 | 70.3 |
-|  50 | 4.5 | 5.8 | 23.9 | 24.2 | 86.0 |
+|   5 | 0.5 | 1.4 | 4.2 | 4.3 | 2.1 |
+|  10 | 1.1 | 1.8 | 7.5 | 7.4 | 4.2 |
+|  15 | 1.2 | 2.0 | 8.4 | 8.5 | 6.8 |
+|  20 | 1.4 | 2.2 | 9.6 | 9.7 | 15.1 |
+|  25 | 1.7 | 2.7 | 12.0 | 12.0 | 23.2 |
+|  30 | 2.0 | 2.8 | 13.0 | 13.0 | 28.8 |
+|  35 | 2.1 | 3.2 | 15.5 | 15.4 | 40.5 |
+|  40 | 2.6 | 3.7 | 17.3 | 17.5 | 51.1 |
+|  45 | 3.3 | 4.6 | 19.1 | 19.3 | 67.9 |
+|  50 | 4.1 | 5.4 | 24.3 | 24.5 | 83.5 |
 
 #### Full Workflow (Fit + LRT + Profile CI)
 
@@ -73,16 +73,16 @@ Time to fit the model, compute penalized likelihood ratio test p-values for all
 
 | k | firthmodels<br>(numba) | firthmodels<br>(numpy) | logistf |
 |--:|------:|------:|--------:|
-|   5 | 4.9 | 10.6 | 13.6 |
-|  10 | 21.0 | 43.1 | 72.1 |
-|  15 | 32.6 | 68.1 | 157.6 |
-|  20 | 59.6 | 109.7 | 452.6 |
-|  25 | 98.5 | 175.4 | 931.5 |
-|  30 | 131.6 | 226.1 | 1350.4 |
-|  35 | 184.0 | 312.7 | 2322.4 |
-|  40 | 237.0 | 379.7 | 3334.4 |
-|  45 | 358.4 | 519.7 | 4692.8 |
-|  50 | 490.5 | 700.5 | 6501.0 |
+|   5 | 4.7 | 11.0 | 13.8 |
+|  10 | 19.4 | 40.0 | 81.4 |
+|  15 | 29.2 | 63.8 | 156.9 |
+|  20 | 45.8 | 89.8 | 438.5 |
+|  25 | 77.1 | 141.8 | 903.0 |
+|  30 | 110.6 | 183.6 | 1307.5 |
+|  35 | 138.3 | 236.3 | 2209.1 |
+|  40 | 199.7 | 314.7 | 3188.7 |
+|  45 | 266.0 | 405.1 | 4574.0 |
+|  50 | 370.9 | 532.9 | 6282.8 |
 
 
 ---
@@ -97,7 +97,7 @@ for Firth-penalized Cox proportional hazards regression.
 
 | Library | Version | BLAS |
 |---------|---------|------|
-| **firthmodels** | 0.7.2 | /usr/lib/x86_64-linux-gnu/openblas-pthread/ (openblas 0.3.26) |
+| **firthmodels** | 0.8.0 | /usr/lib/x86_64-linux-gnu/openblas-pthread/ (openblas 0.3.26) |
 | **coxphf** | 1.13.4 | /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 |
 
 ### Configuration
@@ -124,12 +124,12 @@ Time to fit the model and perform Wald inference. Values are minimum time across
 
 | k | firthmodels<br>(numba) | firthmodels<br>(numpy) | coxphf |
 |--:|------:|------:|-------:|
-|   5 | 1.8 | 4.3 | 3.5 |
-|  10 | 1.8 | 5.5 | 22.2 |
-|  15 | 2.2 | 7.1 | 49.9 |
-|  20 | 4.5 | 14.7 | 113.9 |
-|  25 | 5.9 | 35.9 | 225.5 |
-|  30 | 8.4 | 69.4 | 391.0 |
+|   5 | 1.1 | 1.8 | 4.3 |
+|  10 | 0.7 | 2.5 | 16.8 |
+|  15 | 0.9 | 3.6 | 49.8 |
+|  20 | 1.9 | 8.0 | 137.7 |
+|  25 | 2.6 | 11.1 | 268.9 |
+|  30 | 3.3 | 14.4 | 464.5 |
 
 #### Full Workflow (Fit + LRT + Profile CI)
 
@@ -137,12 +137,12 @@ Time to fit the model, compute penalized likelihood ratio test p-values for all
 
 | k | firthmodels<br>(numba) | firthmodels<br>(numpy) | coxphf |
 |--:|------:|------:|-------:|
-|   5 | 4.4 | 18.2 | 23.8 |
-|  10 | 11.8 | 58.9 | 364.4 |
-|  15 | 32.9 | 159.1 | 1693.6 |
-|  20 | 105.3 | 473.2 | 5675.5 |
-|  25 | 173.4 | 2240.4 | 16062.0 |
-|  30 | 265.9 | 3846.8 | 34707.3 |
+|   5 | 2.6 | 12.9 | 26.9 |
+|  10 | 7.6 | 45.6 | 360.4 |
+|  15 | 18.7 | 115.3 | 2019.4 |
+|  20 | 52.4 | 294.7 | 6447.7 |
+|  25 | 100.1 | 535.3 | 16706.7 |
+|  30 | 148.2 | 870.7 | 34470.1 |
 
 
 ---

{firthmodels-0.7.2 → firthmodels-0.8.0}/benchmarks/benchmark_cox.py

@@ -92,7 +92,7 @@ def make_benchmark_data(
     T = -np.log(U) / (baseline_hazard * np.exp(eta))
 
     # Censoring to achieve target event rate
-    censor_quantile = 1 - event_rate
+    censor_quantile = event_rate
     censor_time = np.quantile(T, censor_quantile)
 
     time = np.minimum(T, censor_time)

firthmodels-0.8.0/benchmarks/cox_results.csv

@@ -0,0 +1,7 @@
+k,n,events,event_rate,numba_fit_ms,numpy_fit_ms,numba_full_ms,numpy_full_ms,coxphf_fit_ms,coxphf_full_ms,coxphf_fit_coef,coxphf_full_coef,coxphf_full_ci,coxphf_full_pval
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+15,500,100,0.2,0.8815601468086243,3.6000499967485666,18.663977039977908,115.33562699332833,49.821376,2019.3859889999999,"[-0.021324561738963754, -0.2051979392553246, 0.008685735819835219, 0.0226534916521478, -0.042279771057908956, 0.2721056818380464, 0.0597911603116723, -0.1620714049843953, 0.16879067038416407, -0.01978425826936327, 0.09253217243480237, 0.2505415436365788, 0.05525707566896529, 0.04693015459999141, 0.09502181087782054]","[-0.021324561738963754, -0.2051979392553246, 0.008685735819835219, 0.0226534916521478, -0.042279771057908956, 0.2721056818380464, 0.0597911603116723, -0.1620714049843953, 0.16879067038416407, -0.01978425826936327, 0.09253217243480237, 0.2505415436365788, 0.05525707566896529, 0.04693015459999141, 0.09502181087782054]","[[-0.2348936583341534, 0.19246585286399356], [-0.404111988991244, -0.005396170435751832], [-0.19729136004952588, 0.2153791626693171], [-0.17554870352129112, 0.22027575836240335], [-0.2534168687344002, 0.1695509723633138], [0.09136916113101086, 0.4523072729564928], [-0.1438614241820307, 0.26414488100595573], [-0.3713069248470362, 0.0479368670241594], [-0.039123420820662516, 0.3763243958058625], [-0.2163693111442772, 0.1794528517629138], [-0.10409695560264419, 0.2918728067431384], [0.05695926209742331, 0.444584890154318], [-0.13789943316063022, 0.24645664909363071], [-0.16405538666016936, 0.2581724307076542], [-0.10555710205579516, 0.2956170747444768]]","[0.8449513779008013, 0.0441414369314278, 0.9341810844177663, 0.822364776624329, 0.695228992402841, 0.0032077354790380763, 0.5653629569426026, 0.13004789642831083, 0.11152816054199877, 0.8446135919231629, 0.3578487262790535, 0.011186868561027685, 0.573520260722048, 0.6629391450495241, 0.35313773031598394]"
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{firthmodels-0.7.2 → firthmodels-0.8.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "firthmodels"
-version = "0.7.2"
+version = "0.8.0"
 description = "Firth-penalized models in Python"
 readme = "README.md"
 license = "MIT"

{firthmodels-0.7.2 → firthmodels-0.8.0}/src/firthmodels/_lrt.py

@@ -1,6 +1,6 @@
 import math
 from dataclasses import dataclass
-from typing import Callable
+from typing import Callable, Literal
 
 import numpy as np
 import scipy
@@ -15,6 +15,9 @@ class LRTResult:
     chi2: float
     pvalue: float
     bse_backcorrected: float
+    valid: bool
+    n_iter: int
+    failure_reason: Literal["step_halving", "max_iter", "nonfinite"] | None = None
 
 
 @dataclass
@@ -24,6 +27,47 @@ class _SlicedQuantities:
     fisher_info: NDArray[np.float64]
 
 
+def lrt_result_from_loglik(
+    *,
+    beta: float,
+    loglik_full: float,
+    loglik_constrained: float,
+    converged: bool,
+    n_iter: int,
+    failure_reason: Literal["step_halving", "max_iter", "nonfinite"] | None = None,
+) -> LRTResult:
+    if not converged:
+        return LRTResult(
+            chi2=math.nan,
+            pvalue=math.nan,
+            bse_backcorrected=math.nan,
+            valid=False,
+            n_iter=n_iter,
+            failure_reason=failure_reason,
+        )
+
+    if not math.isfinite(loglik_full) or not math.isfinite(loglik_constrained):
+        return LRTResult(
+            chi2=math.nan,
+            pvalue=math.nan,
+            bse_backcorrected=math.nan,
+            valid=False,
+            n_iter=n_iter,
+            failure_reason="nonfinite",
+        )
+
+    chi2 = max(0.0, 2.0 * (loglik_full - loglik_constrained))
+    pval = scipy.stats.chi2.sf(chi2, df=1)
+    bse = abs(beta) / math.sqrt(chi2) if chi2 > 0 else math.inf
+    return LRTResult(
+        chi2=chi2,
+        pvalue=pval,
+        bse_backcorrected=bse,
+        valid=True,
+        n_iter=n_iter,
+    )
+
+
 def constrained_lrt_1df(
     *,
     idx: int,
@@ -78,6 +122,13 @@ def constrained_lrt_1df(
             p-value from chi-squared distribution with 1 degree of freedom.
         bse_backcorrected : float
             Back-corrected standard error, |beta[idx]| / sqrt(chi2).
+        valid : bool
+            Whether inference is valid. False if the constrained fit did not
+            converge or either penalized log-likelihood is non-finite.
+        n_iter : int
+            Number of constrained-fit Newton steps.
+        failure_reason : {'step_halving', 'max_iter', 'nonfinite'} or None
+            Reason inference was withheld when the constrained fit was invalid.
     """
     k = beta_hat_full.shape[0]
     free_indices = [i for i in range(k) if i != idx]
@@ -100,20 +151,36 @@ def constrained_lrt_1df(
             fisher_info=q.fisher_info[ix_grid],
         )
 
-    reduced_result = newton_raphson(
-        compute_quantities=constrained_quantities,
-        n_features=k - 1,
-        max_iter=max_iter,
-        max_step=max_step,
-        max_halfstep=max_halfstep,
-        gtol=gtol,
-        xtol=xtol,
-        beta_init=beta_init_free,
+    converged = True
+    n_iter = 0
+    failure_reason = None
+
+    if k == 1:
+        # No nuisance parameters remain, so the constrained model is specified by
+        # beta[idx] = 0 and there is nothing to optimize
+        loglik_constrained = compute_quantities_full(beta_full).loglik
+    else:
+        reduced_result = newton_raphson(
+            compute_quantities=constrained_quantities,
+            n_features=k - 1,
+            max_iter=max_iter,
+            max_step=max_step,
+            max_halfstep=max_halfstep,
+            gtol=gtol,
+            xtol=xtol,
+            beta_init=beta_init_free,
+            warn_on_failure=False,
+        )
+        loglik_constrained = reduced_result.loglik
+        converged = reduced_result.converged
+        n_iter = reduced_result.n_iter
+        failure_reason = reduced_result.failure_reason
+
+    return lrt_result_from_loglik(
+        beta=beta_hat_full[idx],
+        loglik_full=loglik_full,
+        loglik_constrained=loglik_constrained,
+        converged=converged,
+        n_iter=n_iter,
+        failure_reason=failure_reason,
     )
-
-    chi2 = max(0.0, 2.0 * (loglik_full - reduced_result.loglik))
-    pval = scipy.stats.chi2.sf(chi2, df=1)
-
-    # back-corrected SE: |beta|/sqrt(chi2), ensures (beta/SE)^2 = chi2
-    bse = abs(beta_hat_full[idx]) / math.sqrt(chi2) if chi2 > 0 else math.inf
-    return LRTResult(chi2=chi2, pvalue=pval, bse_backcorrected=bse)

{firthmodels-0.7.2 → firthmodels-0.8.0}/src/firthmodels/_numba/cox.py

@@ -518,7 +518,7 @@ def newton_raphson_cox(
     if status != 0:
         return beta, loglik, fisher_info, 0, status
 
-    for iteration in range(1, max_iter + 1):
+    for iteration in range(max_iter + 1):
         fisher_work[:] = fisher_info
 
         info = dpotrf(fisher_work)
@@ -537,6 +537,9 @@ def newton_raphson_cox(
         if max_score < gtol and max_delta < xtol:
             return beta, loglik, fisher_info, iteration, _STATUS_CONVERGED
 
+        if iteration == max_iter:
+            break
+
         if max_delta > max_step:
             scale = max_step / max_delta
             for i in range(k):
@@ -702,8 +705,10 @@ def constrained_lrt_1df_cox(
     )
     if status != 0:
         return loglik, 0, status
+    if free_k == 0:
+        return loglik, 0, _STATUS_CONVERGED
 
-    for iteration in range(1, max_iter + 1):
+    for iteration in range(max_iter + 1):
         for i in range(free_k):
             score_free[i] = modified_score[free_idx[i]]
 
@@ -734,6 +739,9 @@ def constrained_lrt_1df_cox(
         if max_score < gtol and max_delta < xtol:
             return loglik, iteration, _STATUS_CONVERGED
 
+        if iteration == max_iter:
+            break
+
         if max_delta > max_step:
             scale = max_step / max_delta
             for i in range(free_k):
@@ -910,7 +918,7 @@ def profile_ci_bound_cox(
     temp = np.empty(k, dtype=np.float64)
 
     # Appendix steps 4-9: Modified Newton-Raphson
-    for iteration in range(1, max_iter + 1):
+    for iteration in range(max_iter + 1):
         # Appendix step 4: compute score and Hessian at theta(i)
         loglik, status = compute_cox_quantities(
             X=X,
@@ -942,6 +950,9 @@ def profile_ci_bound_cox(
         if max_abs(F) <= tol:
             return theta[idx], _STATUS_CONVERGED, iteration
 
+        if iteration == max_iter:
+            break
+
         # D = d2l/dtheta2 at current theta (Appendix step 4)
         for i in range(k):
             for j in range(k):

{firthmodels-0.7.2 → firthmodels-0.8.0}/src/firthmodels/_numba/logistic.py

@@ -139,6 +139,19 @@ def compute_logistic_quantities(
         return loglik, 0
 
     info = dpotrf(fisher_info)
+    if info == 0:
+        # check pivots, dpotrf can return info=0 on a singular matrix on Accelerate
+        diag_max = fisher_info[0, 0]
+        diag_min = fisher_info[0, 0]
+        for i in range(1, k):
+            d = fisher_info[i, i]
+            if d > diag_max:
+                diag_max = d
+            if d < diag_min:
+                diag_min = d
+        chol_tol = np.sqrt(max(n, k) * np.finfo(np.float64).eps) * diag_max
+        if diag_min <= chol_tol:
+            info = 1
     if info == 0:
         logdet = 0.0
         for i in range(k):
@@ -286,7 +299,7 @@ def newton_raphson_logistic(
     if status != 0:
         return beta, loglik, fisher_info_aug, 0, status
 
-    for iteration in range(1, max_iter + 1):
+    for iteration in range(max_iter + 1):
         fisher_info[:, :] = fisher_info_aug
 
         info = dpotrf(fisher_info)
@@ -309,6 +322,9 @@ def newton_raphson_logistic(
         if max_score < gtol and max_delta < xtol:
             return beta, loglik, fisher_info_aug, iteration, _STATUS_CONVERGED
 
+        if iteration == max_iter:
+            break
+
         if max_delta > max_step:
             scale = max_step / max_delta
             for i in range(k):
@@ -426,8 +442,10 @@ def constrained_lrt_1df_logistic(
     )
     if status != 0:
         return loglik, 0, status
+    if free_k == 0:
+        return loglik, 0, _STATUS_CONVERGED
 
-    for iteration in range(1, max_iter + 1):
+    for iteration in range(max_iter + 1):
         for i in range(free_k):
             score_free[i] = modified_score[free_idx[i]]
 
@@ -460,6 +478,9 @@ def constrained_lrt_1df_logistic(
         if max_score < gtol and max_delta < xtol:
             return loglik, iteration, _STATUS_CONVERGED
 
+        if iteration == max_iter:
+            break
+
         if max_delta > max_step:
             scale = max_step / max_delta
             for i in range(free_k):
@@ -607,7 +628,7 @@ def profile_ci_bound_logistic(
     temp = np.empty(k, dtype=np.float64)
 
     # Appendix steps 4-9: Modified Newton-Raphson
-    for iteration in range(1, max_iter + 1):
+    for iteration in range(max_iter + 1):
         # Appendix step 4: compute score and Hessian at theta(i)
         loglik, status = compute_logistic_quantities(
             X, y, theta, sample_weight, offset, workspace, penalty_weight
@@ -627,6 +648,9 @@ def profile_ci_bound_logistic(
         if max_abs(F) <= tol:
             return theta[idx], _STATUS_CONVERGED, iteration
 
+        if iteration == max_iter:
+            break
+
         # D = d2l/dtheta2 at current theta (Appendix step 4)
         for i in range(k):
             for j in range(k):

{firthmodels-0.7.2 → firthmodels-0.8.0}/src/firthmodels/_profile_ci.py

@@ -112,7 +112,7 @@ def profile_ci_bound(
     theta = theta + h * tangent
 
     # Appendix steps 4-9: Modified Newton-Raphson
-    for iteration in range(1, max_iter + 1):
+    for iteration in range(max_iter + 1):
         # Appendix step 4: compute score and Hessian at theta(i)
         q = compute_quantities_full(theta)
 
@@ -131,6 +131,9 @@ def profile_ci_bound(
                 n_iter=iteration,
             )
 
+        if iteration == max_iter:
+            break
+
         # D = d2l/dtheta2 at current theta (Appendix step 4)
         D = -q.fisher_info
         G = D.copy(order="F")