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Fix icml2026 #9

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Merged
yanagis merged 4 commits into from
Jul 3, 2026
Merged

Fix icml2026 #9

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815fa81
remove asserts
yanagis Jul 3, 2026
476c611
fix warnings
yanagis Jul 3, 2026
fb0234b
add IC-cal
yanagis Jul 3, 2026
51f3de0
fix bug
yanagis Jul 3, 2026
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12 changes: 6 additions & 6 deletions notebooks/kaplan_meier.ipynb
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Expand Up @@ -10,7 +10,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 7,
"id": "075dad06",
"metadata": {},
"outputs": [
Expand All @@ -30,7 +30,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"id": "6649f9d0",
"metadata": {},
"outputs": [],
Expand All @@ -53,7 +53,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 9,
"id": "09c2011b",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -124,14 +124,14 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 10,
"id": "f7c08980",
"metadata": {},
"outputs": [],
"source": [
"import cenreg.model.nonparametric\n",
"\n",
"dist = cenreg.model.nonparametric.kaplan_meier_estimator(df[\"time\"].values, df[\"event\"].values)"
"dist = cenreg.model.nonparametric.kaplan_meier_estimator(df[\"time\"].values.astype(float), df[\"event\"].values)"
]
},
{
Expand All @@ -144,7 +144,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 11,
"id": "7aebf393",
"metadata": {},
"outputs": [
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19 changes: 5 additions & 14 deletions notebooks/li_watkins_yu.ipynb
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Expand Up @@ -10,19 +10,10 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 1,
"id": "458fd7ec",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The autoreload extension is already loaded. To reload it, use:\n",
" %reload_ext autoreload\n"
]
}
],
"outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2"
Expand All @@ -38,7 +29,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 2,
"id": "1615397c",
"metadata": {},
"outputs": [],
Expand All @@ -59,7 +50,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 3,
"id": "bf0a7543",
"metadata": {},
"outputs": [],
Expand All @@ -79,7 +70,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 4,
"id": "8c73dfeb",
"metadata": {},
"outputs": [
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31 changes: 11 additions & 20 deletions notebooks/nn_ic_log.ipynb
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Expand Up @@ -10,27 +10,18 @@
},
{
"cell_type": "code",
"execution_count": 103,
"execution_count": 1,
"id": "34da57fc",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The autoreload extension is already loaded. To reload it, use:\n",
" %reload_ext autoreload\n"
]
}
],
"outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "code",
"execution_count": 104,
"execution_count": 2,
"id": "0371fda9",
"metadata": {},
"outputs": [],
Expand All @@ -57,7 +48,7 @@
},
{
"cell_type": "code",
"execution_count": 105,
"execution_count": 3,
"id": "cabba736",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -101,7 +92,7 @@
},
{
"cell_type": "code",
"execution_count": 106,
"execution_count": 4,
"id": "1385c74b",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -155,7 +146,7 @@
},
{
"cell_type": "code",
"execution_count": 107,
"execution_count": 5,
"id": "4c810bf4",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -215,7 +206,7 @@
},
{
"cell_type": "code",
"execution_count": 108,
"execution_count": 6,
"id": "65de15bf",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -247,7 +238,7 @@
},
{
"cell_type": "code",
"execution_count": 109,
"execution_count": 7,
"id": "d57af800",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -281,7 +272,7 @@
},
{
"cell_type": "code",
"execution_count": 110,
"execution_count": 8,
"id": "596ac944",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -330,7 +321,7 @@
},
{
"cell_type": "code",
"execution_count": 111,
"execution_count": 9,
"id": "2c9d35a4",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -361,7 +352,7 @@
},
{
"cell_type": "code",
"execution_count": 114,
"execution_count": 10,
"id": "a7f84c10",
"metadata": {},
"outputs": [
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22 changes: 6 additions & 16 deletions notebooks/sc_net.ipynb
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Expand Up @@ -350,7 +350,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 10,
"id": "b050886e",
"metadata": {},
"outputs": [
Expand All @@ -361,20 +361,10 @@
"CJD-Brier 0.9616783072036734\n",
"CJD-Logarithmic 3.6927649835189023\n",
"CJD-KS 0.2863711858453328\n",
"NLL-SC 4.885996452186602\n",
"Cen-log 0.4838524\n",
"D-calibration 0.7879467415784499\n"
]
},
{
"ename": "AttributeError",
"evalue": "module 'cenreg.metric.cdf' has no attribute 'km_calibration'",
"output_type": "error",
"traceback": [
"\u001b[31m---------------------------------------------------------------------------\u001b[39m",
"\u001b[31mAttributeError\u001b[39m Traceback (most recent call last)",
"\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[12]\u001b[39m\u001b[32m, line 38\u001b[39m\n\u001b[32m 35\u001b[39m \u001b[38;5;28mprint\u001b[39m(\u001b[33m\"\u001b[39m\u001b[33mD-calibration\u001b[39m\u001b[33m\"\u001b[39m, dcal)\n\u001b[32m 37\u001b[39m \u001b[38;5;66;03m# Compute KM-calibration\u001b[39;00m\n\u001b[32m---> \u001b[39m\u001b[32m38\u001b[39m kmcal = \u001b[43mcenreg\u001b[49m\u001b[43m.\u001b[49m\u001b[43mmetric\u001b[49m\u001b[43m.\u001b[49m\u001b[43mcdf\u001b[49m\u001b[43m.\u001b[49m\u001b[43mkm_calibration\u001b[49m(list_t_dist[\u001b[32m1\u001b[39m], observed_times, events, bins_np)\n\u001b[32m 39\u001b[39m \u001b[38;5;28mprint\u001b[39m(\u001b[33m\"\u001b[39m\u001b[33mKM-calibration\u001b[39m\u001b[33m\"\u001b[39m, kmcal)\n",
"\u001b[31mAttributeError\u001b[39m: module 'cenreg.metric.cdf' has no attribute 'km_calibration'"
"NLL-SC 4.8859964377774485\n",
"Cen-log 0.37202982911557014\n",
"D-calibration 0.0005720768376036918\n",
"KM-calibration 3.5778655806086626\n"
]
}
],
Expand Down Expand Up @@ -422,7 +412,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 11,
"id": "543f50f2",
"metadata": {},
"outputs": [
Expand Down
41 changes: 25 additions & 16 deletions notebooks/ts_brier.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -10,18 +10,27 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 12,
"id": "5d7b84bc",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The autoreload extension is already loaded. To reload it, use:\n",
" %reload_ext autoreload\n"
]
}
],
"source": [
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 13,
"id": "ae19496a",
"metadata": {},
"outputs": [],
Expand All @@ -48,7 +57,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 14,
"id": "d9d1e139",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -108,7 +117,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 15,
"id": "b4f78464",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -185,7 +194,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 16,
"id": "c8ba9e12",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -214,7 +223,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 17,
"id": "c4d5ce80",
"metadata": {},
"outputs": [],
Expand All @@ -230,16 +239,16 @@
"\n",
"# preparation for PyTorch training\n",
"sdm = SurvDataModule(128)\n",
"train_dataloader = sdm.train_dataloader(x_train, df_train[\"time\"].values, df_train[\"event\"].values)\n",
"train_dataloader = sdm.train_dataloader(x_train, df_train[\"time\"].values.astype(float), df_train[\"event\"].values)\n",
"num_bins = 32\n",
"bins = torch.tensor(cenreg.utils.create_bins(df[\"time\"].max(), 0.0, num_bins))\n",
"bins = torch.tensor(cenreg.utils.create_bins(df[\"time\"].max().astype(float), 0.0, num_bins))\n",
"loss_fn = Brier(bins, 2)\n",
"model = MLP(x_train.shape[1], num_bins*2, 64)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 18,
"id": "2e5f8205",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -285,7 +294,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 19,
"id": "3429b83c",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -321,7 +330,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 20,
"id": "62b4f42e",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -390,7 +399,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 21,
"id": "a3cbdc55",
"metadata": {},
"outputs": [
Expand All @@ -401,7 +410,7 @@
"CJD-Brier 0.6394180830320167\n",
"CJD-Logarithmic 2.379232\n",
"CJD-KS 0.1807599546171742\n",
"NLL-SC 6.258204767185328\n"
"NLL-SC 6.533535194080549\n"
]
}
],
Expand All @@ -411,7 +420,7 @@
"import cenreg.model.copula_np\n",
"\n",
"cjd_pred = cjd_pred.reshape(-1, num_bins * 2)\n",
"observed_times = df_test['time'].values\n",
"observed_times = df_test['time'].values.astype(float)\n",
"events = df_test[\"event\"].astype(bool).values\n",
"bins_np = bins.detach().cpu().numpy()\n",
"\n",
Expand All @@ -436,7 +445,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 22,
"id": "5a6a98f6",
"metadata": {},
"outputs": [
Expand Down
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