Add function to drop zero-positive rows and update CSV export logic in age-bin evaluation

evaluate_age.py

@@ -177,6 +177,7 @@ def _worker_eval_mcs_on_gpu(
 
         df_all = pd.concat(frames, ignore_index=True) if len(
             frames) else pd.DataFrame()
+        df_all = _drop_zero_positives_rows(df_all, "n_positives")
         df_all.to_csv(out_path, index=False)
         queue.put({"ok": True, "out_path": out_path})
     except Exception as e:
@@ -211,6 +212,20 @@ def build_criterion_and_out_dims(loss_type: str, n_disease: int, bin_edges, lamb
     raise ValueError(f"Unsupported loss_type: {loss_type}")
 
 
+def _drop_zero_positives_rows(df: pd.DataFrame, positive_col: str) -> pd.DataFrame:
+    """Drop rows where the provided positives column is <= 0.
+
+    Intended to reduce CSV size by omitting (cause, horizon, bin) rows that have
+    no positives, which otherwise yield undefined/NaN metrics.
+    """
+    if df is None or len(df) == 0:
+        return df
+    if positive_col not in df.columns:
+        return df
+    pos = pd.to_numeric(df[positive_col], errors="coerce")
+    return df[pos > 0].copy()
+
+
 def build_model(model_type: str, *, dataset: HealthDataset, cfg: dict):
     if model_type == "delphi_fork":
         return DelphiFork(
@@ -404,8 +419,10 @@ def main() -> None:
             device=device,
         )
 
-        df_by_bin.to_csv(out_bin, index=False)
+        df_by_bin_csv = _drop_zero_positives_rows(df_by_bin, "n_positives")
-        df_agg.to_csv(out_agg, index=False)
+        df_agg_csv = _drop_zero_positives_rows(df_agg, "n_positives_total_mean")
+        df_by_bin_csv.to_csv(out_bin, index=False)
+        df_agg_csv.to_csv(out_agg, index=False)
         print(f"Wrote: {out_bin}")
         print(f"Wrote: {out_agg}")
         return
@@ -464,8 +481,13 @@ def main() -> None:
     frames = [pd.read_csv(p) for p in tmp_paths if os.path.exists(p)]
     df_by_bin = pd.concat(frames, ignore_index=True) if len(
         frames) else pd.DataFrame()
+
+    # Ensure we don't keep zero-positive rows even if a temp file was produced
+    # by an older version of the worker.
+    df_by_bin = _drop_zero_positives_rows(df_by_bin, "n_positives")
     df_agg = aggregate_age_bin_results(df_by_bin)
 
+    df_agg = _drop_zero_positives_rows(df_agg, "n_positives_total_mean")
     df_by_bin.to_csv(out_bin, index=False)
     df_agg.to_csv(out_agg, index=False)
 

evaluation_age_time_dependent.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 import math
 from dataclasses import dataclass
-from typing import Dict, List, Optional, Sequence, Tuple
+from typing import Any, Dict, List, Optional, Sequence, Tuple
 
 import numpy as np
 import pandas as pd
@@ -23,6 +23,364 @@ from utils import (
 from torch_metrics import compute_binary_metrics_torch
 
 
+def _nanmean_np(x: np.ndarray, axis: int = 0) -> np.ndarray:
+    with np.errstate(invalid="ignore"):
+        return np.nanmean(x, axis=axis)
+
+
+def _nanstd_np_ddof1(x: np.ndarray, axis: int = 0) -> np.ndarray:
+    """NaN-aware sample std (ddof=1), matching pandas std() semantics."""
+    x = np.asarray(x, dtype=float)
+    mask = np.isfinite(x)
+    cnt = mask.sum(axis=axis)
+    # mean over finite entries
+    x0 = np.where(mask, x, 0.0)
+    mean = x0.sum(axis=axis) / np.maximum(cnt, 1)
+    # sum of squared deviations over finite entries
+    dev2 = np.where(mask, (x - np.expand_dims(mean, axis=axis)) ** 2, 0.0)
+    ss = dev2.sum(axis=axis)
+    denom = cnt - 1
+    out = np.sqrt(ss / np.maximum(denom, 1))
+    out = np.where(denom > 0, out, np.nan)
+    return out
+
+
+def _weighted_mean_np(x: np.ndarray, w: np.ndarray, axis: int = 0) -> np.ndarray:
+    """NaN-aware weighted mean.
+
+    Only bins with finite x contribute to both numerator and denominator.
+    If denom==0 -> NaN.
+    """
+    x = np.asarray(x, dtype=float)
+    w = np.asarray(w, dtype=float)
+
+    if axis != 0:
+        raise ValueError("_weighted_mean_np currently supports axis=0 only")
+
+    # Broadcast weights along trailing dims of x.
+    while w.ndim < x.ndim:
+        w = w[..., None]
+    w = np.broadcast_to(w, x.shape)
+
+    mask = np.isfinite(x)
+    num = np.where(mask, x * w, 0.0).sum(axis=0)
+    denom = np.where(mask, w, 0.0).sum(axis=0)
+    return np.where(denom > 0.0, num / denom, np.nan)
+
+
+def _blocks_to_df_by_bin(
+    blocks: List[Dict[str, Any]],
+    *,
+    topk_percents: np.ndarray,
+) -> pd.DataFrame:
+    """Convert per-block column vectors into the long-format per-bin DataFrame.
+
+    This does a single vectorized reshape per block (cause-major ordering), and
+    concatenates columns once at the end.
+    """
+    if len(blocks) == 0:
+        return pd.DataFrame(
+            columns=[
+                "mc_idx",
+                "age_bin_id",
+                "age_bin_low",
+                "age_bin_high",
+                "horizon_tau",
+                "topk_percent",
+                "cause_id",
+                "n_samples",
+                "n_positives",
+                "auc",
+                "auprc",
+                "recall_at_K",
+                "precision_at_K",
+                "brier_score",
+            ]
+        )
+
+    P = int(topk_percents.size)
+
+    cols: Dict[str, List[np.ndarray]] = {
+        "mc_idx": [],
+        "age_bin_id": [],
+        "age_bin_low": [],
+        "age_bin_high": [],
+        "horizon_tau": [],
+        "topk_percent": [],
+        "cause_id": [],
+        "n_samples": [],
+        "n_positives": [],
+        "auc": [],
+        "auprc": [],
+        "recall_at_K": [],
+        "precision_at_K": [],
+        "brier_score": [],
+    }
+
+    for blk in blocks:
+        cause_id = np.asarray(blk["cause_id"], dtype=int)
+        K = int(cause_id.size)
+        n_rows = K * P
+
+        cols["mc_idx"].append(np.full(n_rows, int(blk["mc_idx"]), dtype=int))
+        cols["age_bin_id"].append(
+            np.full(n_rows, int(blk["age_bin_id"]), dtype=int))
+        cols["age_bin_low"].append(
+            np.full(n_rows, float(blk["age_bin_low"]), dtype=float))
+        cols["age_bin_high"].append(
+            np.full(n_rows, float(blk["age_bin_high"]), dtype=float))
+        cols["horizon_tau"].append(
+            np.full(n_rows, float(blk["horizon_tau"]), dtype=float))
+
+        cols["cause_id"].append(np.repeat(cause_id, P))
+        cols["topk_percent"].append(np.tile(topk_percents.astype(float), K))
+        cols["n_samples"].append(
+            np.full(n_rows, int(blk["n_samples"]), dtype=int))
+
+        n_pos = np.asarray(blk["n_positives"], dtype=int)
+        cols["n_positives"].append(np.repeat(n_pos, P))
+
+        auc = np.asarray(blk["auc"], dtype=float)
+        auprc = np.asarray(blk["auprc"], dtype=float)
+        brier = np.asarray(blk["brier_score"], dtype=float)
+        cols["auc"].append(np.repeat(auc, P))
+        cols["auprc"].append(np.repeat(auprc, P))
+        cols["brier_score"].append(np.repeat(brier, P))
+
+        # precision/recall are stored as (P,K); we want cause-major rows, i.e.
+        # (K,P) then flatten.
+        prec = np.asarray(blk["precision_at_K"], dtype=float)
+        rec = np.asarray(blk["recall_at_K"], dtype=float)
+        if prec.shape != (P, K) or rec.shape != (P, K):
+            raise ValueError(
+                f"Expected precision/recall shapes (P,K)=({P},{K}); got {prec.shape} and {rec.shape}"
+            )
+        cols["precision_at_K"].append(prec.T.reshape(-1))
+        cols["recall_at_K"].append(rec.T.reshape(-1))
+
+    out = {k: np.concatenate(v, axis=0) for k, v in cols.items()}
+    return pd.DataFrame(out)
+
+
+def aggregate_metrics_columnar(
+    blocks: List[Dict[str, Any]],
+    *,
+    topk_percents: np.ndarray,
+    cause_id: np.ndarray,
+) -> pd.DataFrame:
+    """Aggregate per-bin results across age bins (macro/weighted) and MC (mean/std).
+
+    This is a vectorized, columnar replacement for the old pandas groupby/apply.
+    Semantics match the previous implementation:
+      - bins with n_samples==0 are excluded from bin-aggregation
+      - macro: unweighted mean over bins (NaN-aware)
+      - weighted: weighted mean over bins using weights=n_samples (NaN-aware)
+      - across MC: mean/std (ddof=1), NaN-aware
+    """
+    if len(blocks) == 0:
+        return pd.DataFrame(
+            columns=[
+                "agg_type",
+                "horizon_tau",
+                "topk_percent",
+                "cause_id",
+                "n_mc",
+                "n_bins_used_mean",
+                "n_samples_total_mean",
+                "n_positives_total_mean",
+                "auc_mean",
+                "auc_std",
+                "auprc_mean",
+                "auprc_std",
+                "recall_at_K_mean",
+                "recall_at_K_std",
+                "precision_at_K_mean",
+                "precision_at_K_std",
+                "brier_score_mean",
+                "brier_score_std",
+            ]
+        )
+
+    P = int(topk_percents.size)
+    cause_id = np.asarray(cause_id, dtype=int)
+    K = int(cause_id.size)
+
+    # Group blocks by (mc_idx, horizon_tau)
+    keys: List[Tuple[int, float]] = []
+    grouped: Dict[Tuple[int, float], List[Dict[str, Any]]] = {}
+    for blk in blocks:
+        key = (int(blk["mc_idx"]), float(blk["horizon_tau"]))
+        if key not in grouped:
+            grouped[key] = []
+            keys.append(key)
+        grouped[key].append(blk)
+
+    mc_vals = sorted({k[0] for k in keys})
+    tau_vals = sorted({k[1] for k in keys})
+    M = len(mc_vals)
+    T = len(tau_vals)
+
+    mc_index = {mc: i for i, mc in enumerate(mc_vals)}
+    tau_index = {tau: i for i, tau in enumerate(tau_vals)}
+
+    # Per (agg_type, mc, tau): store arrays
+    # metrics: (M,T,K) and (M,T,P,K)
+    auc_macro = np.full((M, T, K), np.nan, dtype=float)
+    auc_weighted = np.full((M, T, K), np.nan, dtype=float)
+    ap_macro = np.full((M, T, K), np.nan, dtype=float)
+    ap_weighted = np.full((M, T, K), np.nan, dtype=float)
+    brier_macro = np.full((M, T, K), np.nan, dtype=float)
+    brier_weighted = np.full((M, T, K), np.nan, dtype=float)
+
+    prec_macro = np.full((M, T, P, K), np.nan, dtype=float)
+    prec_weighted = np.full((M, T, P, K), np.nan, dtype=float)
+    rec_macro = np.full((M, T, P, K), np.nan, dtype=float)
+    rec_weighted = np.full((M, T, P, K), np.nan, dtype=float)
+
+    n_bins_used = np.zeros((M, T), dtype=float)
+    n_samples_total = np.zeros((M, T), dtype=float)
+    n_pos_total = np.zeros((M, T, K), dtype=float)
+
+    for (mc, tau), blks in grouped.items():
+        mi = mc_index[mc]
+        ti = tau_index[tau]
+
+        # keep only bins with n_samples>0
+        blks_nz = [b for b in blks if int(b["n_samples"]) > 0]
+        if len(blks_nz) == 0:
+            n_bins_used[mi, ti] = 0.0
+            n_samples_total[mi, ti] = 0.0
+            n_pos_total[mi, ti, :] = 0.0
+            continue
+
+        w = np.asarray([int(b["n_samples"])
+                       for b in blks_nz], dtype=float)  # (B,)
+        n_bins_used[mi, ti] = float(len(w))
+        n_samples_total[mi, ti] = float(w.sum())
+
+        npos = np.stack([np.asarray(b["n_positives"], dtype=float)
+                        for b in blks_nz], axis=0)  # (B,K)
+        n_pos_total[mi, ti, :] = npos.sum(axis=0)
+
+        auc_b = np.stack([np.asarray(b["auc"], dtype=float)
+                         for b in blks_nz], axis=0)  # (B,K)
+        ap_b = np.stack([np.asarray(b["auprc"], dtype=float)
+                        for b in blks_nz], axis=0)
+        brier_b = np.stack([np.asarray(b["brier_score"], dtype=float)
+                           for b in blks_nz], axis=0)
+
+        auc_macro[mi, ti, :] = _nanmean_np(auc_b, axis=0)
+        ap_macro[mi, ti, :] = _nanmean_np(ap_b, axis=0)
+        brier_macro[mi, ti, :] = _nanmean_np(brier_b, axis=0)
+
+        auc_weighted[mi, ti, :] = _weighted_mean_np(auc_b, w, axis=0)
+        ap_weighted[mi, ti, :] = _weighted_mean_np(ap_b, w, axis=0)
+        brier_weighted[mi, ti, :] = _weighted_mean_np(brier_b, w, axis=0)
+
+        prec_b = np.stack([np.asarray(b["precision_at_K"], dtype=float)
+                          for b in blks_nz], axis=0)  # (B,P,K)
+        rec_b = np.stack([np.asarray(b["recall_at_K"], dtype=float)
+                         for b in blks_nz], axis=0)
+
+        # macro mean over bins
+        prec_macro[mi, ti, :, :] = _nanmean_np(prec_b, axis=0)
+        rec_macro[mi, ti, :, :] = _nanmean_np(rec_b, axis=0)
+
+        # weighted mean over bins (weights along bin axis)
+        w3 = w.reshape(-1, 1, 1)
+        prec_weighted[mi, ti, :, :] = _weighted_mean_np(prec_b, w3, axis=0)
+        rec_weighted[mi, ti, :, :] = _weighted_mean_np(rec_b, w3, axis=0)
+
+    # Across-MC aggregation (mean/std), then emit long-format df keyed by
+    # (agg_type, horizon_tau, topk_percent, cause_id)
+    rows: Dict[str, List[np.ndarray]] = {
+        "agg_type": [],
+        "horizon_tau": [],
+        "topk_percent": [],
+        "cause_id": [],
+        "n_mc": [],
+        "n_bins_used_mean": [],
+        "n_samples_total_mean": [],
+        "n_positives_total_mean": [],
+        "auc_mean": [],
+        "auc_std": [],
+        "auprc_mean": [],
+        "auprc_std": [],
+        "recall_at_K_mean": [],
+        "recall_at_K_std": [],
+        "precision_at_K_mean": [],
+        "precision_at_K_std": [],
+        "brier_score_mean": [],
+        "brier_score_std": [],
+    }
+
+    cause_long = np.repeat(cause_id, P)
+    topk_long = np.tile(topk_percents.astype(float), K)
+    n_mc_val = float(M)
+
+    for ti, tau in enumerate(tau_vals):
+        # scalar totals (repeat across causes/topk)
+        n_bins_mean = float(
+            np.mean(n_bins_used[:, ti])) if M > 0 else float("nan")
+        n_samp_mean = float(
+            np.mean(n_samples_total[:, ti])) if M > 0 else float("nan")
+        n_pos_mean = _nanmean_np(n_pos_total[:, ti, :], axis=0)  # (K,)
+
+        for agg_type in ("macro", "weighted"):
+            if agg_type == "macro":
+                auc_m = _nanmean_np(auc_macro[:, ti, :], axis=0)
+                auc_s = _nanstd_np_ddof1(auc_macro[:, ti, :], axis=0)
+                ap_m = _nanmean_np(ap_macro[:, ti, :], axis=0)
+                ap_s = _nanstd_np_ddof1(ap_macro[:, ti, :], axis=0)
+                brier_m = _nanmean_np(brier_macro[:, ti, :], axis=0)
+                brier_s = _nanstd_np_ddof1(brier_macro[:, ti, :], axis=0)
+                prec_m = _nanmean_np(prec_macro[:, ti, :, :], axis=0)  # (P,K)
+                prec_s = _nanstd_np_ddof1(prec_macro[:, ti, :, :], axis=0)
+                rec_m = _nanmean_np(rec_macro[:, ti, :, :], axis=0)
+                rec_s = _nanstd_np_ddof1(rec_macro[:, ti, :, :], axis=0)
+            else:
+                auc_m = _nanmean_np(auc_weighted[:, ti, :], axis=0)
+                auc_s = _nanstd_np_ddof1(auc_weighted[:, ti, :], axis=0)
+                ap_m = _nanmean_np(ap_weighted[:, ti, :], axis=0)
+                ap_s = _nanstd_np_ddof1(ap_weighted[:, ti, :], axis=0)
+                brier_m = _nanmean_np(brier_weighted[:, ti, :], axis=0)
+                brier_s = _nanstd_np_ddof1(brier_weighted[:, ti, :], axis=0)
+                prec_m = _nanmean_np(prec_weighted[:, ti, :, :], axis=0)
+                prec_s = _nanstd_np_ddof1(prec_weighted[:, ti, :, :], axis=0)
+                rec_m = _nanmean_np(rec_weighted[:, ti, :, :], axis=0)
+                rec_s = _nanstd_np_ddof1(rec_weighted[:, ti, :, :], axis=0)
+
+            n_rows = K * P
+            rows["agg_type"].append(np.full(n_rows, agg_type, dtype=object))
+            rows["horizon_tau"].append(np.full(n_rows, float(tau), dtype=float))
+            rows["topk_percent"].append(topk_long)
+            rows["cause_id"].append(cause_long)
+            rows["n_mc"].append(np.full(n_rows, n_mc_val, dtype=float))
+            rows["n_bins_used_mean"].append(
+                np.full(n_rows, n_bins_mean, dtype=float))
+            rows["n_samples_total_mean"].append(
+                np.full(n_rows, n_samp_mean, dtype=float))
+            rows["n_positives_total_mean"].append(np.repeat(n_pos_mean, P))
+
+            rows["auc_mean"].append(np.repeat(auc_m, P))
+            rows["auc_std"].append(np.repeat(auc_s, P))
+            rows["auprc_mean"].append(np.repeat(ap_m, P))
+            rows["auprc_std"].append(np.repeat(ap_s, P))
+            rows["brier_score_mean"].append(np.repeat(brier_m, P))
+            rows["brier_score_std"].append(np.repeat(brier_s, P))
+
+            rows["precision_at_K_mean"].append(prec_m.T.reshape(-1))
+            rows["precision_at_K_std"].append(prec_s.T.reshape(-1))
+            rows["recall_at_K_mean"].append(rec_m.T.reshape(-1))
+            rows["recall_at_K_std"].append(rec_s.T.reshape(-1))
+
+    out = {k: np.concatenate(v, axis=0) for k, v in rows.items()}
+    df = pd.DataFrame(out)
+    return df.sort_values(
+        ["agg_type", "horizon_tau", "topk_percent", "cause_id"], ignore_index=True
+    )
+
+
 def aggregate_age_bin_results(df_by_bin: pd.DataFrame) -> pd.DataFrame:
     """Aggregate per-bin age evaluation results.
 
@@ -129,34 +487,79 @@ def aggregate_age_bin_results(df_by_bin: pd.DataFrame) -> pd.DataFrame:
             )
         )
 
+    # Kept for backward compatibility (e.g., if callers load a CSV and need to
+    # aggregate). Prefer `aggregate_metrics_columnar` during evaluation.
     group_keys = ["mc_idx", "horizon_tau", "topk_percent", "cause_id"]
 
-    gb = df_by_bin.groupby(group_keys)
+    df = df_by_bin[df_by_bin["n_samples"] > 0].copy()
+    if len(df) == 0:
+        return pd.DataFrame(
+            columns=[
+                "agg_type",
+                "horizon_tau",
+                "topk_percent",
+                "cause_id",
+                "n_mc",
+                "n_bins_used_mean",
+                "n_samples_total_mean",
+                "n_positives_total_mean",
+                "auc_mean",
+                "auc_std",
+                "auprc_mean",
+                "auprc_std",
+                "recall_at_K_mean",
+                "recall_at_K_std",
+                "precision_at_K_mean",
+                "precision_at_K_std",
+                "brier_score_mean",
+                "brier_score_std",
+            ]
+        )
 
-    try:
+    # Macro: mean over bins
-        df_mc_macro = gb.apply(
+    df_mc_macro = (
-            lambda g: _bin_aggregate(g, weighted=False), include_groups=False
+        df.groupby(group_keys, as_index=False)
-        ).reset_index()
+        .agg(
-    except TypeError:  # pandas<2.2 (no include_groups)
+            n_bins_used=("age_bin_id", "nunique"),
-        df_mc_macro = gb.apply(lambda g: _bin_aggregate(
+            n_samples_total=("n_samples", "sum"),
-            g, weighted=False)).reset_index()
+            n_positives_total=("n_positives", "sum"),
+            auc=("auc", "mean"),
+            auprc=("auprc", "mean"),
+            recall_at_K=("recall_at_K", "mean"),
+            precision_at_K=("precision_at_K", "mean"),
+            brier_score=("brier_score", "mean"),
+        )
+    )
     df_mc_macro["agg_type"] = "macro"
 
-    try:
+    # Weighted: weighted mean over bins with weights=n_samples, NaN-aware per metric
-        df_mc_weighted = gb.apply(
+    w = df["n_samples"].astype(float)
-            lambda g: _bin_aggregate(g, weighted=True), include_groups=False
+    df_w = df.copy()
-        ).reset_index()
+    for col in ["auc", "auprc", "recall_at_K", "precision_at_K", "brier_score"]:
-    except TypeError:  # pandas<2.2 (no include_groups)
+        m = df_w[col].astype(float)
-        df_mc_weighted = gb.apply(
+        ww = w.where(m.notna(), other=0.0)
-            lambda g: _bin_aggregate(g, weighted=True)).reset_index()
+        df_w[f"__num_{col}"] = (m.fillna(0.0) * w)
-    df_mc_weighted["agg_type"] = "weighted"
+        df_w[f"__den_{col}"] = ww
 
-    df_mc_binagg = pd.concat([df_mc_macro, df_mc_weighted], ignore_index=True)
+    df_mc_w = df_w.groupby(group_keys, as_index=False).agg(
+        n_bins_used=("age_bin_id", "nunique"),
+        n_samples_total=("n_samples", "sum"),
+        n_positives_total=("n_positives", "sum"),
+        **{f"__num_{c}": (f"__num_{c}", "sum") for c in ["auc", "auprc", "recall_at_K", "precision_at_K", "brier_score"]},
+        **{f"__den_{c}": (f"__den_{c}", "sum") for c in ["auc", "auprc", "recall_at_K", "precision_at_K", "brier_score"]},
+    )
+    for col in ["auc", "auprc", "recall_at_K", "precision_at_K", "brier_score"]:
+        num = df_mc_w[f"__num_{col}"].astype(float)
+        den = df_mc_w[f"__den_{col}"].astype(float)
+        df_mc_w[col] = (num / den).where(den > 0.0, other=float("nan"))
+        df_mc_w.drop(columns=[f"__num_{col}", f"__den_{col}"], inplace=True)
+    df_mc_w["agg_type"] = "weighted"
+
+    df_mc_binagg = pd.concat([df_mc_macro, df_mc_w], ignore_index=True)
 
     df_agg = (
         df_mc_binagg.groupby(
-            ["agg_type", "horizon_tau", "topk_percent", "cause_id"], as_index=False
+            ["agg_type", "horizon_tau", "topk_percent", "cause_id"], as_index=False)
-        )
         .agg(
             n_mc=("mc_idx", "nunique"),
             n_bins_used_mean=("n_bins_used", "mean"),
@@ -173,10 +576,7 @@ def aggregate_age_bin_results(df_by_bin: pd.DataFrame) -> pd.DataFrame:
             brier_score_mean=("brier_score", "mean"),
             brier_score_std=("brier_score", "std"),
         )
-        .sort_values(
+        .sort_values(["agg_type", "horizon_tau", "topk_percent", "cause_id"], ignore_index=True)
-            ["agg_type", "horizon_tau", "topk_percent", "cause_id"],
-            ignore_index=True,
-        )
     )
     return df_agg
 
@@ -193,6 +593,7 @@ class EvalAgeConfig:
     n_mc: int = 5
     seed: int = 0
     cause_ids: Optional[Sequence[int]] = None
+    store_per_cause: bool = True
 
 
 @torch.inference_mode()
@@ -247,12 +648,17 @@ def evaluate_time_dependent_age_bins(
     if cfg.cause_ids is None:
         cause_ids = None
         n_causes_eval = int(n_disease)
+        cause_id_vec = np.arange(n_causes_eval, dtype=int)
     else:
         cause_ids = torch.tensor(
             list(cfg.cause_ids), dtype=torch.long, device=device)
         n_causes_eval = int(cause_ids.numel())
+        cause_id_vec = np.asarray(list(cfg.cause_ids), dtype=int)
 
-    rows_by_bin: List[Dict[str, float | int]] = []
+    topk_percents_np = np.asarray(topk_percents, dtype=float)
+
+    # Columnar per-(mc,tau,bin) blocks; avoids Python per-row dict appends.
+    blocks: List[Dict[str, Any]] = []
 
     for mc_idx in range(int(cfg.n_mc)):
         global_mc_idx = int(mc_offset) + int(mc_idx)
@@ -354,27 +760,25 @@ def evaluate_time_dependent_age_bins(
         for h_idx, tau_y in enumerate(horizons_years):
             for bin_idx, (a_lo, a_hi) in enumerate(age_bins):
                 if len(y_true_mc[h_idx][bin_idx]) == 0:
-                    # No samples in this bin for this (mc, tau)
+                    # No samples in this bin for this (mc, tau): store a single
-                    for cause_k in range(n_causes_eval):
+                    # block with NaN metric vectors.
-                        cause_id = int(cause_k) if cause_ids is None else int(
+                    K = int(n_causes_eval)
-                            cfg.cause_ids[cause_k])
+                    P = int(topk_percents_np.size)
-                        for k_percent in topk_percents:
+                    blocks.append(
-                            rows_by_bin.append(
                         dict(
                             mc_idx=global_mc_idx,
                             age_bin_id=bin_idx,
                             age_bin_low=float(a_lo),
                             age_bin_high=float(a_hi),
                             horizon_tau=float(tau_y),
-                                    topk_percent=float(k_percent),
-                                    cause_id=cause_id,
                             n_samples=0,
-                                    n_positives=0,
+                            cause_id=cause_id_vec,
-                                    auc=float("nan"),
+                            n_positives=np.zeros((K,), dtype=int),
-                                    auprc=float("nan"),
+                            auc=np.full((K,), np.nan, dtype=float),
-                                    recall_at_K=float("nan"),
+                            auprc=np.full((K,), np.nan, dtype=float),
-                                    precision_at_K=float("nan"),
+                            brier_score=np.full((K,), np.nan, dtype=float),
-                                    brier_score=float("nan"),
+                            precision_at_K=np.full((P, K), np.nan, dtype=float),
+                            recall_at_K=np.full((P, K), np.nan, dtype=float),
                         )
                     )
                     continue
@@ -397,40 +801,52 @@ def evaluate_time_dependent_age_bins(
                     compute_ici=False,
                 )
 
-                # Move just the metric vectors to CPU once per (mc, tau, bin)
+                # Collect a single columnar block (vectors, not per-row dicts).
-                # for DataFrame construction.
+                blocks.append(
-                auc = metrics.auc_per_cause.detach().cpu().numpy()
-                auprc = metrics.ap_per_cause.detach().cpu().numpy()
-                brier = metrics.brier_per_cause.detach().cpu().numpy()
-                n_pos = metrics.n_pos_per_cause.detach().cpu().numpy()
-                prec_at_k = metrics.precision_at_k.detach().cpu().numpy()  # (P,K)
-                rec_at_k = metrics.recall_at_k.detach().cpu().numpy()  # (P,K)
-
-                for cause_k in range(n_causes_eval):
-                    cause_id = int(cause_k) if cause_ids is None else int(
-                        cfg.cause_ids[cause_k])
-                    for p_idx, k_percent in enumerate(topk_percents):
-                        rows_by_bin.append(
                     dict(
                         mc_idx=global_mc_idx,
                         age_bin_id=bin_idx,
                         age_bin_low=float(a_lo),
                         age_bin_high=float(a_hi),
                         horizon_tau=float(tau_y),
-                                topk_percent=float(k_percent),
+                        n_samples=int(n_samples),
-                                cause_id=cause_id,
+                        cause_id=cause_id_vec,
-                                n_samples=n_samples,
+                        n_positives=metrics.n_pos_per_cause.detach().cpu().numpy().astype(int),
-                                n_positives=int(n_pos[cause_k]),
+                        auc=metrics.auc_per_cause.detach().cpu().numpy().astype(float),
-                                auc=float(auc[cause_k]),
+                        auprc=metrics.ap_per_cause.detach().cpu().numpy().astype(float),
-                                auprc=float(auprc[cause_k]),
+                        brier_score=metrics.brier_per_cause.detach().cpu().numpy().astype(float),
-                                recall_at_K=float(rec_at_k[p_idx, cause_k]),
+                        precision_at_K=metrics.precision_at_k.detach().cpu().numpy().astype(float),
-                                precision_at_K=float(prec_at_k[p_idx, cause_k]),
+                        recall_at_K=metrics.recall_at_k.detach().cpu().numpy().astype(float),
-                                brier_score=float(brier[cause_k]),
                     )
                 )
 
-    df_by_bin = pd.DataFrame(rows_by_bin)
+    # Aggregation is computed from columnar blocks (fast, no pandas apply).
+    df_agg = aggregate_metrics_columnar(
+        blocks,
+        topk_percents=topk_percents_np,
+        cause_id=cause_id_vec,
+    )
 
-    df_agg = aggregate_age_bin_results(df_by_bin)
+    if bool(cfg.store_per_cause):
+        df_by_bin = _blocks_to_df_by_bin(blocks, topk_percents=topk_percents_np)
+    else:
+        df_by_bin = pd.DataFrame(
+            columns=[
+                "mc_idx",
+                "age_bin_id",
+                "age_bin_low",
+                "age_bin_high",
+                "horizon_tau",
+                "topk_percent",
+                "cause_id",
+                "n_samples",
+                "n_positives",
+                "auc",
+                "auprc",
+                "recall_at_K",
+                "precision_at_K",
+                "brier_score",
+            ]
+        )
 
     return df_by_bin, df_agg