{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# VAR inference on a Real Public Dataset, Herold et al. (2020)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In this example, we will be using the GP imputator on a dataset available at [Herold et al., 2020](https://doi.org/10.1038/s41467-020-19006-2) to imputate missing data. Then, we are going to use the VAR inference method to infer the causal relationships between the variables in the time series. " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "First, we will import the neccessary libraries and load the dataset." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "WARNING:tensorflow:From c:\\ProgramData\\anaconda3\\envs\\MIMIC\\Lib\\site-packages\\tf_keras\\src\\losses.py:2976: The name tf.losses.sparse_softmax_cross_entropy is deprecated. Please use tf.compat.v1.losses.sparse_softmax_cross_entropy instead.\n", "\n", "WARNING:tensorflow:From c:\\ProgramData\\anaconda3\\envs\\MIMIC\\Lib\\site-packages\\tensorflow_probability\\python\\internal\\backend\\numpy\\_utils.py:48: The name tf.logging.TaskLevelStatusMessage is deprecated. Please use tf.compat.v1.logging.TaskLevelStatusMessage instead.\n", "\n", "WARNING:tensorflow:From c:\\ProgramData\\anaconda3\\envs\\MIMIC\\Lib\\site-packages\\tensorflow_probability\\python\\internal\\backend\\numpy\\_utils.py:48: The name tf.control_flow_v2_enabled is deprecated. Please use tf.compat.v1.control_flow_v2_enabled instead.\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions.\n" ] } ], "source": [ "import matplotlib.pyplot as plt\n", "import numpy as np\n", "\n", "\n", "import pandas as pd\n", "import seaborn as sns\n", "\n", "\n", "from mimic.data_imputation.impute_GP import GPImputer\n", "from mimic.model_infer.infer_VAR_bayes import *" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | days | \n", "Acidimicrobium | \n", "Acinetobacter | \n", "Albidiferax | \n", "Candidatus Microthrix | \n", "Chitinophaga pinensis | \n", "Dechloromonas | \n", "Haliscomenobacter | \n", "Intrasporangium | \n", "Leptospira | \n", "Other | \n", "Xanthomonas | \n", "mean abundance < 2% | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "0.0 | \n", "8.322484 | \n", "0.791870 | \n", "6.383491 | \n", "26.180838 | \n", "7.055585 | \n", "4.998287 | \n", "15.142620 | \n", "11.445072 | \n", "4.742982 | \n", "2.357318 | \n", "0.853658 | \n", "11.725795 | \n", "
1 | \n", "1.0 | \n", "8.265177 | \n", "0.763703 | \n", "6.362575 | \n", "25.593890 | \n", "7.081694 | \n", "5.072711 | \n", "15.397948 | \n", "11.546582 | \n", "4.791269 | \n", "2.382206 | \n", "0.864697 | \n", "11.836536 | \n", "
2 | \n", "2.0 | \n", "8.180701 | \n", "0.781881 | \n", "6.330330 | \n", "25.226861 | \n", "7.127157 | \n", "5.147886 | \n", "15.663537 | \n", "11.636934 | \n", "4.833619 | \n", "2.399779 | \n", "0.879132 | \n", "11.947293 | \n", "
3 | \n", "3.0 | \n", "8.078737 | \n", "0.801890 | \n", "6.290243 | \n", "24.849371 | \n", "7.185821 | \n", "5.219273 | \n", "15.926969 | \n", "11.710476 | \n", "4.868031 | \n", "2.418784 | \n", "0.894873 | \n", "12.058067 | \n", "
4 | \n", "4.0 | \n", "7.969807 | \n", "0.823758 | \n", "6.246734 | \n", "24.505012 | \n", "7.249498 | \n", "5.280679 | \n", "16.172482 | \n", "11.759176 | \n", "4.892380 | \n", "2.438263 | \n", "0.909303 | \n", "12.168858 | \n", "
5 | \n", "5.0 | \n", "7.863614 | \n", "0.847488 | \n", "6.204391 | \n", "24.245813 | \n", "7.309111 | \n", "5.324508 | \n", "16.382314 | \n", "11.772278 | \n", "4.904550 | \n", "2.457029 | \n", "0.919595 | \n", "12.279667 | \n", "
6 | \n", "6.0 | \n", "7.770084 | \n", "0.873055 | \n", "6.167656 | \n", "24.127242 | \n", "7.355842 | \n", "5.342460 | \n", "16.538718 | \n", "11.737040 | \n", "4.902619 | \n", "2.473734 | \n", "0.923138 | \n", "12.390494 | \n", "
7 | \n", "7.0 | \n", "7.700314 | \n", "0.900405 | \n", "6.140528 | \n", "24.199845 | \n", "7.382293 | \n", "5.326927 | \n", "16.626579 | \n", "11.641157 | \n", "4.885061 | \n", "2.487002 | \n", "0.918012 | \n", "12.501338 | \n", "
8 | \n", "8.0 | \n", "7.664534 | \n", "0.911291 | \n", "6.125822 | \n", "23.641355 | \n", "7.383681 | \n", "5.273044 | \n", "16.636265 | \n", "11.476739 | \n", "4.850959 | \n", "2.520630 | \n", "0.903478 | \n", "12.612201 | \n", "
9 | \n", "9.0 | \n", "7.666801 | \n", "0.960073 | \n", "6.124129 | \n", "25.024940 | \n", "7.358852 | \n", "5.180566 | \n", "16.565955 | \n", "11.244474 | \n", "4.800196 | \n", "2.499159 | \n", "0.880339 | \n", "12.321359 | \n", "
10 | \n", "10.0 | \n", "7.701597 | \n", "0.992116 | \n", "6.133189 | \n", "25.753165 | \n", "7.310707 | \n", "5.055128 | \n", "16.422573 | \n", "10.955857 | \n", "4.733611 | \n", "2.497398 | \n", "0.851104 | \n", "12.030537 | \n", "
11 | \n", "11.0 | \n", "7.756540 | \n", "1.025393 | \n", "6.148177 | \n", "26.621835 | \n", "7.245802 | \n", "4.907436 | \n", "16.220878 | \n", "10.632238 | \n", "4.653122 | \n", "2.490776 | \n", "0.819790 | \n", "11.739731 | \n", "
12 | \n", "12.0 | \n", "7.816900 | \n", "1.059680 | \n", "6.162504 | \n", "27.550701 | \n", "7.173270 | \n", "4.751605 | \n", "15.981051 | \n", "10.301403 | \n", "4.561808 | \n", "2.479674 | \n", "0.791448 | \n", "11.448942 | \n", "
13 | \n", "13.0 | \n", "7.867041 | \n", "1.094721 | \n", "6.168573 | \n", "28.452806 | \n", "7.103389 | \n", "4.602845 | \n", "15.725567 | \n", "9.993155 | \n", "4.463977 | \n", "2.464200 | \n", "0.771427 | \n", "11.158170 | \n", "
14 | \n", "14.0 | \n", "7.890203 | \n", "1.130229 | \n", "6.158709 | \n", "29.247651 | \n", "7.046066 | \n", "4.475146 | \n", "15.476159 | \n", "9.734647 | \n", "4.365213 | \n", "2.444171 | \n", "0.764505 | \n", "10.867413 | \n", "