{
"cells": [
{
"cell_type": "markdown",
"id": "078900c6-d71d-44f0-9e76-cc5ce66f0ca9",
"metadata": {},
"source": [
"# Logistic regression: exploring bootstrapping\n",
"\n",
"Exploring different bootstrapping idea:\n",
"\n",
"* non-parametric with minimal constraint (no empty group)\n",
"* stratified non-parametric\n",
"* parametric boostrapping \n",
"* comparing distribution of boostrapped parameters with MLE asymptotic approx\n",
"\n",
"Ref:\n",
" * https://www.scirp.org/journal/paperinformation?paperid=70962"
]
},
{
"cell_type": "markdown",
"id": "e18cec5e",
"metadata": {},
"source": [
"## Common"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "3b351af7",
"metadata": {},
"outputs": [],
"source": [
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import scipy\n",
"\n",
"import pandas as pd\n",
"import os\n",
"\n",
"from sklearn import linear_model\n",
"\n",
"# our libs\n",
"from src import data_utils\n",
"from src import report_utils\n",
"from src import logit\n",
"\n",
"# testing multivariate normal\n",
"import pingouin as pg\n",
"from src import mvn"
]
},
{
"cell_type": "markdown",
"id": "e0de7f02-942b-42ff-874c-3c0e2ac1e0dc",
"metadata": {},
"source": [
"## Data"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "3373f87f",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"results_path = \"./results\"\n",
"if not os.path.exists(results_path): os.makedirs(results_path)\n",
"\n",
"data_path = \"../../data/\"\n",
"suv_filename = os.path.join(data_path, \"suv_percentilesSLOthenUWM.mat\")\n",
"flags_filename = os.path.join(data_path,\"flags_combined.mat\")\n",
"normal_range_filename = os.path.join(data_path, \"normal_range.mat\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "811d990d",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"\"\"\"\n",
"Loading all data\n",
"\"\"\"\n",
"suv_dict = scipy.io.loadmat(suv_filename)\n",
"flags_dict = scipy.io.loadmat(flags_filename)\n",
"normal_range_dict = scipy.io.loadmat(normal_range_filename)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "4a292c31",
"metadata": {},
"outputs": [],
"source": [
"# get data\n",
"perc = 95\n",
"organ = \"lung\"\n",
"x, y = data_utils.get_data(organ, perc, suv_dict, flags_dict)\n",
"\n",
"# number of boostrapping samples\n",
"n_boots = 10000"
]
},
{
"cell_type": "markdown",
"id": "35e9bb7b-5a50-4cae-9af4-261c11453dd4",
"metadata": {},
"source": [
"## Fit\n",
"\n",
"Ref: logistic regression documentation\n",
"* https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
"* https://stats.stackexchange.com/questions/186830/what-is-scikit-learns-logisticregression-minimizing"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "239ae789",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"pars = array([-11.68319035, 5.68708926])\n"
]
}
],
"source": [
"# fits\n",
"logr = linear_model.LogisticRegression(penalty = None)\n",
"pars = logit.logit_poly_fit(x, y, degree = 1, lm=logr)\n",
"print(f\"{pars = }\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "9cf6fec1",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"cov_pars = array([[12.31854544, -6.71118734],\n",
" [-6.71118734, 3.81820749]])\n"
]
}
],
"source": [
"# asymptotic covariance matrix of parameters\n",
"cov_pars = logit.logit_poly_cov(x, pars)\n",
"print(f\"{cov_pars = }\")"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "2359d3c1",
"metadata": {},
"outputs": [],
"source": [
"# defining twosided probabilities\n",
"alpha = 0.05 # significance level\n",
"probs = [alpha/2, 1 - alpha/2]"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "4ba4d5d4",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"pars_CI = array([[-18.5622299 , 1.85727375],\n",
" [ -4.80415081, 9.51690477]])\n"
]
}
],
"source": [
"# CI of params (assuming asymptotic distr of parameters)\n",
"pars_CI = logit.logit_poly_pars_quantiles_normal(probs, pars, cov_pars)\n",
"print(f\"{pars_CI = }\")"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "96acc3ab",
"metadata": {},
"outputs": [
{
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