diff --git a/FIDDLE/helpers.py b/FIDDLE/helpers.py index 6e2fef0..ca9138d 100644 --- a/FIDDLE/helpers.py +++ b/FIDDLE/helpers.py @@ -90,7 +90,7 @@ def get_frequent_numeric_variables(df_time_series, variables, threshold, args): T, dt = args.T, args.dt df_types = pd.read_csv(output_dir + 'value_types.csv').set_index(var_col)['value_type'] - numeric_vars = [col for col in variables if df_types[col] == 'Numeric'] + numeric_vars = [col for col in variables if df_types.get(col) == 'Numeric'] df_num_counts = calculate_variable_counts(df_time_series, df_population)[numeric_vars] #gets the count of each variable for each patient. variables_num_freq = df_num_counts.columns[df_num_counts.mean() >= threshold * np.floor(T/dt)] return variables_num_freq diff --git a/FIDDLE/steps.py b/FIDDLE/steps.py index 1ce2849..8f613db 100644 --- a/FIDDLE/steps.py +++ b/FIDDLE/steps.py @@ -72,6 +72,7 @@ def parse_variable_data_type(df_data, args): if len(var_names) == 0: # No hierarchical values pass else: + print('Parsing hierarchical values') for var_name in var_names: var_type = args.value_type_override[var_name] df_var = df.loc[df[var_col] == var_name, val_col] @@ -143,12 +144,12 @@ def parse_variable_data_type(df_data, args): var_names = [v for v, ty in data_types if 'numeric' not in ty.lower() and 'none' not in ty.lower()] df_non_num = df[df[var_col].isin(var_names)].copy() dup_ = df_non_num.duplicated(subset=[ID_col, t_col, var_col], keep=False) - df_non_num_dup = df_non_num[dup_] + df_non_num_dup = df_non_num[dup_].copy() dup_var_names = df_non_num_dup[var_col].unique() df_non_num_dup[var_col] = df_non_num_dup[var_col].astype(str) + ':' + df_non_num_dup[val_col].astype(str) df_non_num_dup[val_col] = 1 - df_non_num[dup_] = df_non_num_dup - df[df[var_col].isin(var_names)] = df_non_num + df_non_num.loc[dup_, :] = df_non_num_dup + df.loc[df[var_col].isin(var_names), :] = df_non_num return df, df_types['value_type'] diff --git a/tests/icd_test/Run.ipynb b/tests/icd_test/Run.ipynb index 1f903ba..3def364 100644 --- a/tests/icd_test/Run.ipynb +++ b/tests/icd_test/Run.ipynb @@ -76,19 +76,8 @@ "--------------------------------------------------------------------------------\n", "*) Detecting and parsing value types\n", "--------------------------------------------------------------------------------\n", + "Parsing hierarchical values\n", "Saved as: ./output-0/value_types.csv\n", - "/Users/shengputang/Developer/FIDDLE/FIDDLE/steps.py:148: SettingWithCopyWarning: \n", - "A value is trying to be set on a copy of a slice from a DataFrame.\n", - "Try using .loc[row_indexer,col_indexer] = value instead\n", - "\n", - "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - " df_non_num_dup[var_col] = df_non_num_dup[var_col].astype(str) + ':' + df_non_num_dup[val_col].astype(str)\n", - "/Users/shengputang/Developer/FIDDLE/FIDDLE/steps.py:149: SettingWithCopyWarning: \n", - "A value is trying to be set on a copy of a slice from a DataFrame.\n", - "Try using .loc[row_indexer,col_indexer] = value instead\n", - "\n", - "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - " df_non_num_dup[val_col] = 1\n", "\n", "--------------------------------------------------------------------------------\n", "*) Separate time-invariant and time-dependent\n", @@ -103,11 +92,11 @@ "--------------------------------------------------------------------------------\n", "(N × ^d) table :\t (200, 19)\n", "number of missing entries :\t 2816 out of 3800 total\n", - "Time elapsed: 0.012328 seconds\n", + "Time elapsed: 0.028853 seconds\n", "\n", "Output\n", "S_all, binary features :\t (200, 21)\n", - "Time elapsed: 0.101575 seconds\n", + "Time elapsed: 0.115737 seconds\n", "\n", "--------------------------------------------------------------------------------\n", "3-A) Post-filter time-invariant data\n", @@ -115,12 +104,13 @@ "Original : 21\n", "Nearly-constant: 0\n", "Correlated : 0\n", - "Time elapsed: 0.104368 seconds\n", + "Time elapsed: 0.120853 seconds\n", "\n", "Output\n", "S: shape=(200, 21), density=0.234\n", - "Total time: 0.106207 seconds\n", - "\n" + "Total time: 0.122271 seconds\n", + "\n", + "\u001b[0m" ] } ], @@ -172,7 +162,7 @@ " ICD9_CODE:290-319_value_1\n", " ICD9_CODE:320-389_value_1\n", " ICD9_CODE:390-459_value_1\n", - " ...\n", + " ICD9_CODE:460-519_value_1\n", " ICD9_CODE:520-579_value_1\n", " ICD9_CODE:580-629_value_1\n", " ICD9_CODE:680-709_value_1\n", @@ -222,7 +212,7 @@ " 1\n", " 0\n", " 0\n", - " ...\n", + " 0\n", " 1\n", " 0\n", " 0\n", @@ -246,7 +236,7 @@ " 1\n", " 1\n", " 1\n", - " ...\n", + " 1\n", " 0\n", " 0\n", " 1\n", @@ -270,7 +260,7 @@ " 0\n", " 0\n", " 1\n", - " ...\n", + " 0\n", " 0\n", " 0\n", " 0\n", @@ -294,7 +284,7 @@ " 0\n", " 0\n", " 0\n", - " ...\n", + " 0\n", " 0\n", " 0\n", " 0\n", @@ -318,7 +308,7 @@ " 1\n", " 0\n", " 1\n", - " ...\n", + " 0\n", " 0\n", " 1\n", " 0\n", @@ -366,7 +356,7 @@ " 0\n", " 0\n", " 1\n", - " ...\n", + " 0\n", " 0\n", " 1\n", " 0\n", @@ -390,7 +380,7 @@ " 0\n", " 1\n", " 1\n", - " ...\n", + " 0\n", " 1\n", " 0\n", " 0\n", @@ -414,7 +404,7 @@ " 0\n", " 0\n", " 0\n", - " ...\n", + " 0\n", " 0\n", " 0\n", " 0\n", @@ -438,7 +428,7 @@ " 0\n", " 0\n", " 1\n", - " ...\n", + " 1\n", " 1\n", " 0\n", " 0\n", @@ -462,7 +452,7 @@ " 1\n", " 1\n", " 1\n", - " ...\n", + " 1\n", " 0\n", " 0\n", " 0\n", @@ -536,49 +526,49 @@ "199634 0 0 \n", "199724 0 1 \n", "\n", - " ICD9_CODE:320-389_value_1 ICD9_CODE:390-459_value_1 ... \\\n", - "ID ... \n", - "100536 0 0 ... \n", - "101757 1 1 ... \n", - "102631 0 1 ... \n", - "103251 0 0 ... \n", - "104130 0 1 ... \n", - "... ... ... ... \n", - "197661 0 1 ... \n", - "198214 1 1 ... \n", - "198892 0 0 ... \n", - "199634 0 1 ... \n", - "199724 1 1 ... \n", - "\n", - " ICD9_CODE:520-579_value_1 ICD9_CODE:580-629_value_1 \\\n", + " ICD9_CODE:320-389_value_1 ICD9_CODE:390-459_value_1 \\\n", "ID \n", - "100536 1 0 \n", - "101757 0 0 \n", - "102631 0 0 \n", + "100536 0 0 \n", + "101757 1 1 \n", + "102631 0 1 \n", "103251 0 0 \n", "104130 0 1 \n", "... ... ... \n", "197661 0 1 \n", - "198214 1 0 \n", + "198214 1 1 \n", "198892 0 0 \n", - "199634 1 0 \n", - "199724 0 0 \n", + "199634 0 1 \n", + "199724 1 1 \n", "\n", - " ICD9_CODE:680-709_value_1 ICD9_CODE:710-739_value_1 \\\n", + " ICD9_CODE:460-519_value_1 ICD9_CODE:520-579_value_1 \\\n", "ID \n", - "100536 0 0 \n", + "100536 0 1 \n", "101757 1 0 \n", "102631 0 0 \n", "103251 0 0 \n", "104130 0 0 \n", "... ... ... \n", "197661 0 0 \n", + "198214 0 1 \n", + "198892 0 0 \n", + "199634 1 1 \n", + "199724 1 0 \n", + "\n", + " ICD9_CODE:580-629_value_1 ICD9_CODE:680-709_value_1 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 1 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 1 0 \n", "198214 0 0 \n", "198892 0 0 \n", - "199634 0 1 \n", + "199634 0 0 \n", "199724 0 0 \n", "\n", - " ICD9_CODE:740-759_value_1 ICD9_CODE:760-779_value_1 \\\n", + " ICD9_CODE:710-739_value_1 ICD9_CODE:740-759_value_1 \\\n", "ID \n", "100536 0 0 \n", "101757 0 0 \n", @@ -588,37 +578,51 @@ "... ... ... \n", "197661 0 0 \n", "198214 0 0 \n", - "198892 0 1 \n", - "199634 0 0 \n", + "198892 0 0 \n", + "199634 1 0 \n", "199724 0 0 \n", "\n", - " ICD9_CODE:780-799_value_1 ICD9_CODE:800-999_value_1 \\\n", + " ICD9_CODE:760-779_value_1 ICD9_CODE:780-799_value_1 \\\n", "ID \n", - "100536 0 1 \n", - "101757 1 0 \n", - "102631 0 1 \n", + "100536 0 0 \n", + "101757 0 1 \n", + "102631 0 0 \n", "103251 0 0 \n", - "104130 1 0 \n", + "104130 0 1 \n", "... ... ... \n", - "197661 0 1 \n", + "197661 0 0 \n", "198214 0 0 \n", - "198892 0 0 \n", + "198892 1 0 \n", "199634 0 0 \n", - "199724 0 1 \n", + "199724 0 0 \n", "\n", - " ICD9_CODE:E000-E999_value_1 ICD9_CODE:V01-V91_value_1 \n", - "ID \n", - "100536 1 0 \n", - "101757 0 1 \n", - "102631 0 0 \n", - "103251 0 0 \n", - "104130 0 1 \n", - "... ... ... \n", - "197661 0 0 \n", - "198214 0 0 \n", - "198892 0 1 \n", - "199634 0 1 \n", - "199724 0 0 \n", + " ICD9_CODE:800-999_value_1 ICD9_CODE:E000-E999_value_1 \\\n", + "ID \n", + "100536 1 1 \n", + "101757 0 0 \n", + "102631 1 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 1 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 1 0 \n", + "\n", + " ICD9_CODE:V01-V91_value_1 \n", + "ID \n", + "100536 0 \n", + "101757 1 \n", + "102631 0 \n", + "103251 0 \n", + "104130 1 \n", + "... ... \n", + "197661 0 \n", + "198214 0 \n", + "198892 1 \n", + "199634 1 \n", + "199724 0 \n", "\n", "[200 rows x 21 columns]" ] @@ -708,6 +712,7 @@ "--------------------------------------------------------------------------------\n", "*) Detecting and parsing value types\n", "--------------------------------------------------------------------------------\n", + "Parsing hierarchical values\n", "Saved as: ./output-1/value_types.csv\n", "\n", "--------------------------------------------------------------------------------\n", @@ -723,11 +728,11 @@ "--------------------------------------------------------------------------------\n", "(N × ^d) table :\t (200, 129)\n", "number of missing entries :\t 23337 out of 25800 total\n", - "Time elapsed: 0.034244 seconds\n", + "Time elapsed: 0.023302 seconds\n", "\n", "Output\n", "S_all, binary features :\t (200, 129)\n", - "Time elapsed: 0.558320 seconds\n", + "Time elapsed: 0.469013 seconds\n", "\n", "--------------------------------------------------------------------------------\n", "3-A) Post-filter time-invariant data\n", @@ -735,12 +740,13 @@ "Original : 129\n", "Nearly-constant: 0\n", "Correlated : 2\n", - "Time elapsed: 0.564048 seconds\n", + "Time elapsed: 0.542064 seconds\n", "\n", "Output\n", "S: shape=(200, 127), density=0.097\n", - "Total time: 0.567541 seconds\n", - "\n" + "Total time: 0.545616 seconds\n", + "\n", + "\u001b[0m" ] } ], @@ -792,7 +798,87 @@ " ICD9_CODE:130-136_value_1.0\n", " ICD9_CODE:140-239_value_1.0\n", " ICD9_CODE:150-159_value_1.0\n", + " ICD9_CODE:160-165_value_1.0\n", + " ICD9_CODE:179-189_value_1.0\n", + " ICD9_CODE:190-199_value_1.0\n", + " ICD9_CODE:200-209_value_1.0\n", + " ICD9_CODE:210-229_value_1.0\n", + " ICD9_CODE:235-238_value_1.0\n", + " ICD9_CODE:240-246_value_1.0\n", + " ICD9_CODE:240-279_value_1.0\n", + " ICD9_CODE:249-259_value_1.0\n", + " ICD9_CODE:260-269_value_1.0\n", + " ICD9_CODE:270-279_value_1.0\n", + " ICD9_CODE:280_value_1.0\n", + " ICD9_CODE:280-289_value_1.0\n", + " ICD9_CODE:281_value_1.0\n", + " ICD9_CODE:283_value_1.0\n", + " ICD9_CODE:284_value_1.0\n", + " ICD9_CODE:285_value_1.0\n", + " ICD9_CODE:286_value_1.0\n", + " ICD9_CODE:287_value_1.0\n", + " ICD9_CODE:288_value_1.0\n", + " ICD9_CODE:289_value_1.0\n", + " ICD9_CODE:290-294_value_1.0\n", + " ICD9_CODE:290-319_value_1.0\n", + " ICD9_CODE:295-299_value_1.0\n", + " ICD9_CODE:300-316_value_1.0\n", + " ICD9_CODE:320-327_value_1.0\n", + " ICD9_CODE:320-389_value_1.0\n", + " ICD9_CODE:330-337_value_1.0\n", + " ICD9_CODE:338-338_value_1.0\n", + " ICD9_CODE:340-349_value_1.0\n", + " ICD9_CODE:350-359_value_1.0\n", + " ICD9_CODE:360-379_value_1.0\n", + " ICD9_CODE:380-389_value_1.0\n", + " ICD9_CODE:390-459_value_1.0\n", + " ICD9_CODE:393-398_value_1.0\n", + " ICD9_CODE:401-405_value_1.0\n", + " ICD9_CODE:410-414_value_1.0\n", + " ICD9_CODE:415-417_value_1.0\n", + " ICD9_CODE:420-429_value_1.0\n", + " ICD9_CODE:430-438_value_1.0\n", " ...\n", + " ICD9_CODE:730-739_value_1.0\n", + " ICD9_CODE:740-759_value_1.0\n", + " ICD9_CODE:745_value_1.0\n", + " ICD9_CODE:746_value_1.0\n", + " ICD9_CODE:747_value_1.0\n", + " ICD9_CODE:752_value_1.0\n", + " ICD9_CODE:760-763_value_1.0\n", + " ICD9_CODE:760-779_value_1.0\n", + " ICD9_CODE:764-779_value_1.0\n", + " ICD9_CODE:780-789_value_1.0\n", + " ICD9_CODE:780-799_value_1.0\n", + " ICD9_CODE:790-796_value_1.0\n", + " ICD9_CODE:797-799_value_1.0\n", + " ICD9_CODE:800-804_value_1.0\n", + " ICD9_CODE:800-999_value_1.0\n", + " ICD9_CODE:805-809_value_1.0\n", + " ICD9_CODE:820-829_value_1.0\n", + " ICD9_CODE:850-854_value_1.0\n", + " ICD9_CODE:860-869_value_1.0\n", + " ICD9_CODE:870-879_value_1.0\n", + " ICD9_CODE:880-887_value_1.0\n", + " ICD9_CODE:900-904_value_1.0\n", + " ICD9_CODE:910-919_value_1.0\n", + " ICD9_CODE:920-924_value_1.0\n", + " ICD9_CODE:950-957_value_1.0\n", + " ICD9_CODE:958-959_value_1.0\n", + " ICD9_CODE:960-979_value_1.0\n", + " ICD9_CODE:990-995_value_1.0\n", + " ICD9_CODE:996-999_value_1.0\n", + " ICD9_CODE:E000-E999_value_1.0\n", + " ICD9_CODE:E810-E819_value_1.0\n", + " ICD9_CODE:E820-E825_value_1.0\n", + " ICD9_CODE:E846-E849_value_1.0\n", + " ICD9_CODE:E850-E858_value_1.0\n", + " ICD9_CODE:E870-E876_value_1.0\n", + " ICD9_CODE:E878-E879_value_1.0\n", + " ICD9_CODE:E880-E888_value_1.0\n", + " ICD9_CODE:E916-E928_value_1.0\n", + " ICD9_CODE:E930-E949_value_1.0\n", + " ICD9_CODE:E950-E959_value_1.0\n", " ICD9_CODE:E960-E969_value_1.0\n", " ICD9_CODE:V01-V09_value_1.0\n", " ICD9_CODE:V01-V91_value_1.0\n", @@ -827,6 +913,86 @@ " \n", " \n", " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -842,7 +1008,6 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -853,33 +1018,26 @@ " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 101757\n", + " 0\n", " 0\n", " 1\n", " 0\n", " 0\n", + " 1\n", " 0\n", " 0\n", - " 1\n", " 0\n", - " 1\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 1\n", - " 1\n", " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 102631\n", " 0\n", " 0\n", " 0\n", @@ -901,35 +1059,29 @@ " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 103251\n", " 0\n", " 0\n", " 0\n", " 0\n", + " 1\n", + " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", - " 1\n", - " 1\n", " 0\n", - " 1\n", - " 1\n", " 0\n", - " 1\n", " 0\n", " 1\n", - " \n", - " \n", - " 104130\n", + " 0\n", " 0\n", " 1\n", + " 0\n", + " 0\n", + " 0\n", " 1\n", " 0\n", " 0\n", @@ -938,55 +1090,33 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", - " 1\n", " 0\n", " 0\n", " 0\n", - " 1\n", + " 0\n", " 0\n", " 0\n", " 0\n", " \n", " \n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " \n", - " \n", - " 197661\n", + " 101757\n", + " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", + " 1\n", " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", + " 1\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -994,18 +1124,30 @@ " 0\n", " 0\n", " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 198214\n", + " 1\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 1\n", + " 0\n", + " 1\n", + " 0\n", + " 1\n", " 0\n", " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", + " 1\n", " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", @@ -1020,10 +1162,12 @@ " 0\n", " 0\n", " 0\n", + " 1\n", + " 1\n", + " 0\n", + " 0\n", + " 0\n", " 0\n", - " \n", - " \n", - " 198892\n", " 0\n", " 0\n", " 0\n", @@ -1034,47 +1178,35 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", - " 1\n", " 0\n", " 0\n", - " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 199634\n", " 0\n", - " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", - " 1\n", - " 1\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 1\n", + " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", - " 1\n", " 0\n", " 0\n", " \n", " \n", - " 199724\n", + " 102631\n", " 0\n", - " 1\n", - " 1\n", " 0\n", " 0\n", " 0\n", @@ -1082,7 +1214,6 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -1093,7 +1224,922 @@ " 0\n", " 0\n", " 0\n", - " \n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 1\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 1\n", + " 0\n", + " ...\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 1\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 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200 rows × 129 columns

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ICD9_CODE:130-136_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 1 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:140-239_value_1.0 ICD9_CODE:150-159_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 1 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:160-165_value_1.0 ICD9_CODE:179-189_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:190-199_value_1.0 ICD9_CODE:200-209_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:210-229_value_1.0 ICD9_CODE:235-238_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 1 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:240-246_value_1.0 ICD9_CODE:240-279_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 1 \n", + "... ... ... \n", + "197661 0 1 \n", + "198214 0 1 \n", + "198892 0 0 \n", + "199634 0 1 \n", + "199724 0 1 \n", + "\n", + " ICD9_CODE:249-259_value_1.0 ICD9_CODE:260-269_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 1 0 \n", + "198892 0 0 \n", + "199634 1 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:270-279_value_1.0 ICD9_CODE:280_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 1 0 \n", + "198214 1 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 1 0 \n", + "\n", + " ICD9_CODE:280-289_value_1.0 ICD9_CODE:281_value_1.0 \\\n", + "ID \n", + "100536 1 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 1 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:283_value_1.0 ICD9_CODE:284_value_1.0 \\\n", + "ID \n", + "100536 0 1 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:285_value_1.0 ICD9_CODE:286_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 1 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:287_value_1.0 ICD9_CODE:288_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:289_value_1.0 ICD9_CODE:290-294_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 1 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 1 \n", + "\n", + " ICD9_CODE:290-319_value_1.0 ICD9_CODE:295-299_value_1.0 \\\n", + "ID \n", + "100536 1 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 1 0 \n", + "\n", + " ICD9_CODE:300-316_value_1.0 ICD9_CODE:320-327_value_1.0 \\\n", + "ID \n", + "100536 1 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:320-389_value_1.0 ICD9_CODE:330-337_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 1 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 1 1 \n", + "\n", + " ICD9_CODE:338-338_value_1.0 ICD9_CODE:340-349_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 1 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:350-359_value_1.0 ICD9_CODE:360-379_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 1 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:380-389_value_1.0 ICD9_CODE:390-459_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 1 \n", + "102631 0 1 \n", + "103251 0 0 \n", + "104130 0 1 \n", + "... ... ... \n", + "197661 0 1 \n", + "198214 0 1 \n", + "198892 0 0 \n", + "199634 0 1 \n", + "199724 0 1 \n", + "\n", + " ICD9_CODE:393-398_value_1.0 ICD9_CODE:401-405_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 1 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 1 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 1 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:410-414_value_1.0 ICD9_CODE:415-417_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 1 0 \n", + "198214 1 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 1 0 \n", + "\n", + " ICD9_CODE:420-429_value_1.0 ICD9_CODE:430-438_value_1.0 ... \\\n", + "ID ... \n", + "100536 0 0 ... \n", + "101757 0 0 ... \n", + "102631 1 0 ... \n", + "103251 0 0 ... \n", + "104130 0 0 ... \n", + "... ... ... ... \n", + "197661 1 0 ... \n", + "198214 1 0 ... \n", + "198892 0 0 ... \n", + "199634 0 0 ... \n", + "199724 0 0 ... \n", + "\n", + " ICD9_CODE:730-739_value_1.0 ICD9_CODE:740-759_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:745_value_1.0 ICD9_CODE:746_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:747_value_1.0 ICD9_CODE:752_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:760-763_value_1.0 ICD9_CODE:760-779_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 1 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:764-779_value_1.0 ICD9_CODE:780-789_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", "101757 0 1 \n", "102631 0 0 \n", "103251 0 0 \n", @@ -1110,28 +2562,56 @@ "... ... ... \n", "197661 0 0 \n", "198214 0 0 \n", + "198892 1 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:780-799_value_1.0 ICD9_CODE:790-796_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 1 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", "198892 0 0 \n", - "199634 0 1 \n", - "199724 0 1 \n", + "199634 0 0 \n", + "199724 0 0 \n", "\n", - " ICD9_CODE:030-041_value_1.0 ICD9_CODE:042-042_value_1.0 \\\n", + " ICD9_CODE:797-799_value_1.0 ICD9_CODE:800-804_value_1.0 \\\n", "ID \n", - "100536 0 1 \n", + "100536 0 0 \n", "101757 0 0 \n", "102631 0 0 \n", "103251 0 0 \n", - "104130 1 0 \n", + "104130 0 0 \n", "... ... ... \n", "197661 0 0 \n", "198214 0 0 \n", "198892 0 0 \n", "199634 0 0 \n", - "199724 1 0 \n", + "199724 0 0 \n", "\n", - " ICD9_CODE:070-079_value_1.0 ICD9_CODE:080-088_value_1.0 \\\n", + " ICD9_CODE:800-999_value_1.0 ICD9_CODE:805-809_value_1.0 \\\n", "ID \n", "100536 1 0 \n", "101757 0 0 \n", + "102631 1 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 1 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 1 0 \n", + "\n", + " ICD9_CODE:820-829_value_1.0 ICD9_CODE:850-854_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", "102631 0 0 \n", "103251 0 0 \n", "104130 0 0 \n", @@ -1142,10 +2622,10 @@ "199634 0 0 \n", "199724 0 0 \n", "\n", - " ICD9_CODE:110-118_value_1.0 ICD9_CODE:130-136_value_1.0 \\\n", + " ICD9_CODE:860-869_value_1.0 ICD9_CODE:870-879_value_1.0 \\\n", "ID \n", "100536 0 0 \n", - "101757 1 0 \n", + "101757 0 0 \n", "102631 0 0 \n", "103251 0 0 \n", "104130 0 0 \n", @@ -1153,22 +2633,148 @@ "197661 0 0 \n", "198214 0 0 \n", "198892 0 0 \n", - "199634 0 1 \n", + "199634 0 0 \n", "199724 0 0 \n", "\n", - " ICD9_CODE:140-239_value_1.0 ICD9_CODE:150-159_value_1.0 ... \\\n", - "ID ... \n", - "100536 0 0 ... \n", - "101757 1 0 ... \n", - "102631 0 0 ... \n", - "103251 0 0 ... \n", - "104130 0 0 ... \n", - "... ... ... ... \n", - "197661 0 0 ... \n", - "198214 0 0 ... \n", - "198892 0 0 ... \n", - "199634 1 0 ... \n", - "199724 0 0 ... \n", + " ICD9_CODE:880-887_value_1.0 ICD9_CODE:900-904_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:910-919_value_1.0 ICD9_CODE:920-924_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:950-957_value_1.0 ICD9_CODE:958-959_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:960-979_value_1.0 ICD9_CODE:990-995_value_1.0 \\\n", + "ID \n", + "100536 1 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:996-999_value_1.0 ICD9_CODE:E000-E999_value_1.0 \\\n", + "ID \n", + "100536 0 1 \n", + "101757 0 0 \n", + "102631 1 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 1 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 1 0 \n", + "\n", + " ICD9_CODE:E810-E819_value_1.0 ICD9_CODE:E820-E825_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E846-E849_value_1.0 ICD9_CODE:E850-E858_value_1.0 \\\n", + "ID \n", + "100536 0 1 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E870-E876_value_1.0 ICD9_CODE:E878-E879_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E880-E888_value_1.0 ICD9_CODE:E916-E928_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E930-E949_value_1.0 ICD9_CODE:E950-E959_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", "\n", " ICD9_CODE:E960-E969_value_1.0 ICD9_CODE:V01-V09_value_1.0 \\\n", "ID \n", @@ -1328,6 +2934,7 @@ "--------------------------------------------------------------------------------\n", "*) Detecting and parsing value types\n", "--------------------------------------------------------------------------------\n", + "Parsing hierarchical values\n", "Saved as: ./output-2/value_types.csv\n", "\n", "--------------------------------------------------------------------------------\n", @@ -1343,11 +2950,11 @@ "--------------------------------------------------------------------------------\n", "(N × ^d) table :\t (200, 455)\n", "number of missing entries :\t 86795 out of 91000 total\n", - "Time elapsed: 0.092419 seconds\n", + "Time elapsed: 0.062218 seconds\n", "\n", "Output\n", "S_all, binary features :\t (200, 455)\n", - "Time elapsed: 1.690453 seconds\n", + "Time elapsed: 2.054338 seconds\n", "\n", "--------------------------------------------------------------------------------\n", "3-A) Post-filter time-invariant data\n", @@ -1355,12 +2962,13 @@ "Original : 455\n", "Nearly-constant: 0\n", "Correlated : 87\n", - "Time elapsed: 1.715216 seconds\n", + "Time elapsed: 2.169691 seconds\n", "\n", "Output\n", "S: shape=(200, 368), density=0.055\n", - "Total time: 1.719981 seconds\n", - "\n" + "Total time: 2.173815 seconds\n", + "\n", + "\u001b[0m" ] } ], @@ -1402,67 +3010,1139 @@ " \n", " \n", " \n", - " ICD9_CODE:001-009_value_1.0\n", - " ICD9_CODE:001-139_value_1.0\n", - " ICD9_CODE:008_value_1.0\n", - " ICD9_CODE:030-041_value_1.0\n", - " ICD9_CODE:038_value_1.0\n", - " ICD9_CODE:041_value_1.0\n", - " ICD9_CODE:042_value_1.0\n", - " ICD9_CODE:042-042_value_1.0\n", - " ICD9_CODE:070_value_1.0\n", - " ICD9_CODE:070-079_value_1.0\n", + " ICD9_CODE:001-009_value_1.0\n", + " ICD9_CODE:001-139_value_1.0\n", + " ICD9_CODE:008_value_1.0\n", + " ICD9_CODE:030-041_value_1.0\n", + " ICD9_CODE:038_value_1.0\n", + " ICD9_CODE:041_value_1.0\n", + " ICD9_CODE:042_value_1.0\n", + " ICD9_CODE:042-042_value_1.0\n", + " ICD9_CODE:070_value_1.0\n", + " ICD9_CODE:070-079_value_1.0\n", + " ICD9_CODE:079_value_1.0\n", + " ICD9_CODE:080-088_value_1.0\n", + " ICD9_CODE:088_value_1.0\n", + " ICD9_CODE:110-118_value_1.0\n", + " ICD9_CODE:112_value_1.0\n", + " ICD9_CODE:130-136_value_1.0\n", + " ICD9_CODE:135_value_1.0\n", + " ICD9_CODE:136_value_1.0\n", + " ICD9_CODE:140-239_value_1.0\n", + " ICD9_CODE:150-159_value_1.0\n", + " ICD9_CODE:153_value_1.0\n", + " ICD9_CODE:155_value_1.0\n", + " ICD9_CODE:157_value_1.0\n", + " ICD9_CODE:160-165_value_1.0\n", + " ICD9_CODE:162_value_1.0\n", + " ICD9_CODE:179-189_value_1.0\n", + " ICD9_CODE:185_value_1.0\n", + " ICD9_CODE:189_value_1.0\n", + " ICD9_CODE:190-199_value_1.0\n", + " ICD9_CODE:191_value_1.0\n", + " ICD9_CODE:194_value_1.0\n", + " ICD9_CODE:197_value_1.0\n", + " ICD9_CODE:198_value_1.0\n", + " ICD9_CODE:200_value_1.0\n", + " ICD9_CODE:200-209_value_1.0\n", + " ICD9_CODE:201_value_1.0\n", + " ICD9_CODE:202_value_1.0\n", + " ICD9_CODE:203_value_1.0\n", + " ICD9_CODE:210-229_value_1.0\n", + " ICD9_CODE:214_value_1.0\n", + " ICD9_CODE:216_value_1.0\n", + " ICD9_CODE:218_value_1.0\n", + " ICD9_CODE:225_value_1.0\n", + " ICD9_CODE:228_value_1.0\n", + " ICD9_CODE:235-238_value_1.0\n", + " ICD9_CODE:238_value_1.0\n", + " ICD9_CODE:240-246_value_1.0\n", + " ICD9_CODE:240-279_value_1.0\n", + " ICD9_CODE:242_value_1.0\n", + " ICD9_CODE:244_value_1.0\n", + " ...\n", + " ICD9_CODE:E916-E928_value_1.0\n", + " ICD9_CODE:E928_value_1.0\n", + " ICD9_CODE:E930-E949_value_1.0\n", + " ICD9_CODE:E931_value_1.0\n", + " ICD9_CODE:E932_value_1.0\n", + " ICD9_CODE:E933_value_1.0\n", + " ICD9_CODE:E934_value_1.0\n", + " ICD9_CODE:E935_value_1.0\n", + " ICD9_CODE:E939_value_1.0\n", + " ICD9_CODE:E942_value_1.0\n", + " ICD9_CODE:E950_value_1.0\n", + " ICD9_CODE:E950-E959_value_1.0\n", + " ICD9_CODE:E956_value_1.0\n", + " 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0\n", " 0\n", " 1\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", " 1\n", + " 0\n", " 1\n", - " 1\n", - " ...\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", " 0\n", " 0\n", " 0\n", @@ -1475,7 +4155,7 @@ " 0\n", " \n", " \n", - " 101757\n", + " 199634\n", " 0\n", " 1\n", " 0\n", @@ -1486,7 +4166,15 @@ " 0\n", " 0\n", " 0\n", - " ...\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 1\n", + " 1\n", + " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", @@ -1497,9 +4185,6 @@ " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 102631\n", " 0\n", " 0\n", " 0\n", @@ -1509,8 +4194,23 @@ " 0\n", " 0\n", " 0\n", + " 1\n", + " 1\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 1\n", + " 0\n", + " 0\n", + " ...\n", + " 0\n", + " 0\n", + " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -1521,12 +4221,10 @@ " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 103251\n", " 0\n", " 0\n", " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", @@ -1534,36 +4232,26 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", - " 1\n", - " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", - " 1\n", - " 1\n", - " \n", - " \n", - " 104130\n", " 0\n", - " 1\n", " 0\n", - " 1\n", " 0\n", - " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", " 0\n", + " 1\n", " 0\n", + " 1\n", " 0\n", " 0\n", " 0\n", @@ -1571,33 +4259,12 @@ " 0\n", " \n", " \n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " ...\n", - " \n", - " \n", - " 197661\n", + " 199724\n", " 0\n", + " 1\n", " 0\n", + " 1\n", + " 1\n", " 0\n", " 0\n", " 0\n", @@ -1606,7 +4273,6 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -1617,9 +4283,6 @@ " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 198214\n", " 0\n", " 0\n", " 0\n", @@ -1630,7 +4293,6 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -1641,20 +4303,20 @@ " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 198892\n", " 0\n", " 0\n", " 0\n", " 0\n", + " 1\n", + " 0\n", + " 0\n", + " ...\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -1665,11 +4327,7 @@ " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 199634\n", " 0\n", - " 1\n", " 0\n", " 0\n", " 0\n", @@ -1678,31 +4336,21 @@ " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", - " 1\n", " 0\n", - " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", - " \n", - " \n", - " 199724\n", " 0\n", - " 1\n", " 0\n", - " 1\n", - " 1\n", " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", - " ...\n", " 0\n", " 0\n", " 0\n", @@ -1722,52 +4370,556 @@ "text/plain": [ " ICD9_CODE:001-009_value_1.0 ICD9_CODE:001-139_value_1.0 \\\n", "ID \n", - "100536 0 1 \n", - "101757 0 1 \n", + "100536 0 1 \n", + "101757 0 1 \n", + "102631 0 0 \n", + "103251 0 0 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"198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E934_value_1.0 ICD9_CODE:E935_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E939_value_1.0 ICD9_CODE:E942_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E950_value_1.0 ICD9_CODE:E950-E959_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E956_value_1.0 ICD9_CODE:E960_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:E960-E969_value_1.0 ICD9_CODE:E966_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V01-V09_value_1.0 ICD9_CODE:V01-V91_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 1 \n", + "102631 0 0 \n", + "103251 1 1 \n", "104130 0 1 \n", "... ... ... \n", "197661 0 0 \n", "198214 0 0 \n", - "198892 0 0 \n", + "198892 0 1 \n", "199634 0 1 \n", - "199724 0 1 \n", + "199724 0 0 \n", "\n", - " ICD9_CODE:008_value_1.0 ICD9_CODE:030-041_value_1.0 \\\n", + " ICD9_CODE:V02_value_1.0 ICD9_CODE:V05_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 1 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V07_value_1.0 ICD9_CODE:V09_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V10_value_1.0 ICD9_CODE:V10-V19_value_1.0 \\\n", "ID \n", "100536 0 0 \n", - "101757 0 0 \n", + "101757 1 1 \n", "102631 0 0 \n", "103251 0 0 \n", - "104130 0 1 \n", + "104130 0 0 \n", "... ... ... \n", "197661 0 0 \n", "198214 0 0 \n", "198892 0 0 \n", "199634 0 0 \n", - "199724 0 1 \n", + "199724 0 0 \n", "\n", - " ICD9_CODE:038_value_1.0 ICD9_CODE:041_value_1.0 \\\n", + " ICD9_CODE:V12_value_1.0 ICD9_CODE:V13_value_1.0 \\\n", "ID \n", "100536 0 0 \n", "101757 0 0 \n", "102631 0 0 \n", "103251 0 0 \n", - "104130 0 1 \n", + "104130 0 0 \n", "... ... ... \n", "197661 0 0 \n", "198214 0 0 \n", "198892 0 0 \n", "199634 0 0 \n", - "199724 1 0 \n", + "199724 0 0 \n", "\n", - " ICD9_CODE:042_value_1.0 ICD9_CODE:042-042_value_1.0 \\\n", + " ICD9_CODE:V14_value_1.0 ICD9_CODE:V15_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V17_value_1.0 ICD9_CODE:V20-V29_value_1.0 \\\n", "ID \n", - "100536 1 1 \n", + "100536 0 0 \n", "101757 0 0 \n", "102631 0 0 \n", - "103251 0 0 \n", + "103251 0 1 \n", "104130 0 0 \n", "... ... ... \n", "197661 0 0 \n", @@ -1776,19 +4928,75 @@ "199634 0 0 \n", "199724 0 0 \n", "\n", - " ICD9_CODE:070_value_1.0 ICD9_CODE:070-079_value_1.0 ... \\\n", - "ID ... \n", - "100536 1 1 ... \n", - "101757 0 0 ... \n", - "102631 0 0 ... \n", - "103251 0 0 ... \n", - "104130 0 0 ... \n", - "... ... ... ... \n", - "197661 0 0 ... \n", - "198214 0 0 ... \n", - "198892 0 0 ... \n", - "199634 0 0 ... \n", - "199724 0 0 ... \n", + " ICD9_CODE:V29_value_1.0 ICD9_CODE:V30_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 1 1 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V30-V39_value_1.0 ICD9_CODE:V31_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 1 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 1 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V34_value_1.0 ICD9_CODE:V40-V49_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 1 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 1 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V42_value_1.0 ICD9_CODE:V43_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 0 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", + "\n", + " ICD9_CODE:V45_value_1.0 ICD9_CODE:V46_value_1.0 \\\n", + "ID \n", + "100536 0 0 \n", + "101757 0 0 \n", + "102631 0 0 \n", + "103251 0 0 \n", + "104130 1 0 \n", + "... ... ... \n", + "197661 0 0 \n", + "198214 0 0 \n", + "198892 0 0 \n", + "199634 0 0 \n", + "199724 0 0 \n", "\n", " ICD9_CODE:V49_value_1.0 ICD9_CODE:V50_value_1.0 \\\n", "ID \n", @@ -1891,7 +5099,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1905,7 +5113,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.9.7" } }, "nbformat": 4, diff --git a/tests/icd_time_test/Run.ipynb b/tests/icd_time_test/Run.ipynb new file mode 100644 index 0000000..bbac186 --- /dev/null +++ b/tests/icd_time_test/Run.ipynb @@ -0,0 +1,5108 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "!rm -rf output-*/" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Test: levels = [0]" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "!mkdir -p output-0" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Input:\n", + " Data : ./input/data.csv\n", + " Population: ./input/pop.csv\n", + " Config : ./input/config-0.yaml\n", + "\n", + "Output directory: ./output-0/\n", + "\n", + "Input arguments:\n", + " T = 4.0\n", + " dt = 1.0\n", + " θ₁ = 0.001\n", + " θ₂ = 0.001\n", + " θ_freq = 1.0\n", + " k = 3 ['min', 'max', 'mean']\n", + "\n", + "discretize = yes\n", + " S discretization bins: to be computed from data\n", + " X discretization bins: to be computed from data\n", + "\n", + "N = 200\n", + "L = 4\n", + "\n", + "\n", + "================================================================================\n", + "1) Pre-filter\n", + "================================================================================\n", + "Remove rows not in population\n", + "Remove rows with t outside of [0, 4]\n", + "Remove rare variables (<= 0.001)\n", + "Total variables : 1\n", + "Rare variables : 0\n", + "Remaining variables : 1\n", + "# rows (original) : 591\n", + "# rows (filtered) : 591\n", + "\n", + "================================================================================\n", + "2) Transform; 3) Post-filter\n", + "================================================================================\n", + "\n", + "--------------------------------------------------------------------------------\n", + "*) Detecting and parsing value types\n", + "--------------------------------------------------------------------------------\n", + "Parsing hierarchical values\n", + "Saved as: ./output-0/value_types.csv\n", + "\n", + "--------------------------------------------------------------------------------\n", + "*) Separate time-invariant and time-dependent\n", + "--------------------------------------------------------------------------------\n", + "Variables (time-invariant): 0\n", + "Variables (time-dependent): 1\n", + "# rows (time-invariant): 0\n", + "# rows (time-dependent): 591\n", + "\n", + "--------------------------------------------------------------------------------\n", + "2-B) Transform time-dependent data\n", + "--------------------------------------------------------------------------------\n", + "Total variables : 1\n", + "Frequent variables : []\n", + "M₁ = 0\n", + "M₂ = 1\n", + "k = 3 ['min', 'max', 'mean']\n", + "\n", + "Transforming each example...\n", + "Batches of size 100: 2\n", + "100%|█████████████████████████████████████████████| 2/2 [00:02<00:00, 1.14s/it]\n", + "\n", + "Parallel processing done\n", + "/data4/tangsp/FIDDLE/FIDDLE/steps.py:503: FutureWarning: Passing keywords other than 'data', 'dtype', 'copy', 'name', 'tupleize_cols' is deprecated and will raise TypeError in a future version. Use the specific Index subclass directly instead\n", + " index = pd.Index(index, names=['ID', 't_range'])\n", + "DONE: Transforming each example...\n", + "(freq) number of missing entries :\t 0.0 out of 200×4×0=0 total\n", + "(freq) number of imputed entries :\t 0.0\n", + "(freq) number of not imputed entries :\t 0.0\n", + "(non-freq) number of missing entries :\t 209 out of 200×4×1=800 total\n", + "\n", + "(N × L × ^D) table :\t (200, 4, 1)\n", + "Time elapsed: 2.817426 seconds\n", + "Discretizing features...\n", + "\n", + "Processing 1 non-boolean variable columns...\n", + " Computing bin edges for numeric variables...\n", + "100%|████████████████████████████████████████████| 1/1 [00:00<00:00, 129.38it/s]\n", + " Discretizing variables to binary features\n", + "100%|█████████████████████████████████████████████| 1/1 [00:00<00:00, 31.03it/s]\n", + "Finished discretizing features\n", + "\n", + "Output\n", + "X_all: shape=(200, 4, 18), density=0.041\n", + "Time elapsed: 3.262486 seconds\n", + "\n", + "--------------------------------------------------------------------------------\n", + "3-B) Post-filter time-dependent data\n", + "--------------------------------------------------------------------------------\n", + "(200, 4, 18) 0.041041666666666664\n", + "Original : 18\n", + "Nearly-constant: 0\n", + "*** time: 4.792196989059448\n", + "Correlated : 0\n", + "*** time: 7.208120822906494\n", + "\n", + "Output\n", + "X: shape=(200, 4, 18), density=0.041\n", + "(200, 4, 18) 0.041041666666666664\n", + "Time elapsed: 10.470810 seconds\n", + "\n", + "Output\n", + "X: shape=(200, 4, 18), density=0.041\n", + "Total time: 10.472504 seconds\n", + "\n", + "\u001b[0m" + ] + } + ], + "source": [ + "! PYTHONPATH=\"$PYTHONPATH:../../\" \\\n", + "python -m FIDDLE.run \\\n", + " --data_fname='./input/data.csv' \\\n", + " --population_fname='./input/pop.csv' \\\n", + " --config_fname='./input/config-0.yaml' \\\n", + " --output_dir='./output-0/' \\\n", + " --T=4 --dt=1.0 \\\n", + " --theta_1=0.001 --theta_2=0.001 --theta_freq=1 \\\n", + " --stats_functions 'min' 'max' 'mean'" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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ICD9_CODE_value_001-139ICD9_CODE_value_140-239ICD9_CODE_value_240-279ICD9_CODE_value_280-289ICD9_CODE_value_290-319ICD9_CODE_value_320-389ICD9_CODE_value_390-459ICD9_CODE_value_460-519ICD9_CODE_value_520-579ICD9_CODE_value_580-629ICD9_CODE_value_680-709ICD9_CODE_value_710-739ICD9_CODE_value_740-759ICD9_CODE_value_760-779ICD9_CODE_value_780-799ICD9_CODE_value_800-999ICD9_CODE_value_E000-E999ICD9_CODE_value_V01-V91
IDt_range
100536[0.0, 1.0)000000000000000000
[1.0, 2.0)000000000000000100
[2.0, 3.0)100000000000000000
[3.0, 4.0)100000000000000000
101757[0.0, 1.0)000000000000000000
............................................................
199634[3.0, 4.0)000000010000000000
199724[0.0, 1.0)000000000000000000
[1.0, 2.0)100000000000000000
[2.0, 3.0)000000000000000100
[3.0, 4.0)000000100000000000
\n", + "

800 rows × 18 columns

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" + ], + "text/plain": [ + " ICD9_CODE_value_001-139 ICD9_CODE_value_140-239 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 1 0 \n", + " [3.0, 4.0) 1 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 1 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE_value_240-279 ICD9_CODE_value_280-289 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE_value_290-319 ICD9_CODE_value_320-389 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE_value_390-459 ICD9_CODE_value_460-519 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 1 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 1 0 \n", + "\n", + " ICD9_CODE_value_520-579 ICD9_CODE_value_580-629 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE_value_680-709 ICD9_CODE_value_710-739 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE_value_740-759 ICD9_CODE_value_760-779 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE_value_780-799 ICD9_CODE_value_800-999 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 1 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 1 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE_value_E000-E999 ICD9_CODE_value_V01-V91 \n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + "[800 rows x 18 columns]" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import numpy as np\n", + "import pandas as pd\n", + "import json\n", + "import sparse\n", + "\n", + "X = sparse.load_npz('output-0/X_all.npz')\n", + "X_names = json.load(open('output-0/X_all.feature_names.json', 'r'))\n", + "X_index = pd.read_csv('output-0/X.ID,t_range.csv').set_index(['ID', 't_range'])\n", + "df_X = pd.DataFrame(X.todense().reshape(X.shape[0]*X.shape[1], X.shape[2]), columns=X_names, index=X_index.index)\n", + "\n", + "display(df_X)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Test: levels = [0,1]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "!mkdir -p output-1" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Input:\n", + " Data : ./input/data.csv\n", + " Population: ./input/pop.csv\n", + " Config : ./input/config-1.yaml\n", + "\n", + "Output directory: ./output-1/\n", + "\n", + "Input arguments:\n", + " T = 4.0\n", + " dt = 1.0\n", + " θ₁ = 0.001\n", + " θ₂ = 0.001\n", + " θ_freq = 1.0\n", + " k = 3 ['min', 'max', 'mean']\n", + "\n", + "discretize = yes\n", + " S discretization bins: to be computed from data\n", + " X discretization bins: to be computed from data\n", + "\n", + "N = 200\n", + "L = 4\n", + "\n", + "\n", + "================================================================================\n", + "1) Pre-filter\n", + "================================================================================\n", + "Remove rows not in population\n", + "Remove rows with t outside of [0, 4]\n", + "Remove rare variables (<= 0.001)\n", + "Total variables : 1\n", + "Rare variables : 0\n", + "Remaining variables : 1\n", + "# rows (original) : 591\n", + "# rows (filtered) : 591\n", + "\n", + "================================================================================\n", + "2) Transform; 3) Post-filter\n", + "================================================================================\n", + "\n", + "--------------------------------------------------------------------------------\n", + "*) Detecting and parsing value types\n", + "--------------------------------------------------------------------------------\n", + "Parsing hierarchical values\n", + "Saved as: ./output-1/value_types.csv\n", + "\n", + "--------------------------------------------------------------------------------\n", + "*) Separate time-invariant and time-dependent\n", + "--------------------------------------------------------------------------------\n", + "Variables (time-invariant): 0\n", + "Variables (time-dependent): 97\n", + "# rows (time-invariant): 0\n", + "# rows (time-dependent): 1182\n", + "\n", + "--------------------------------------------------------------------------------\n", + "2-B) Transform time-dependent data\n", + "--------------------------------------------------------------------------------\n", + "Total variables : 97\n", + "Frequent variables : []\n", + "M₁ = 0\n", + "M₂ = 97\n", + "k = 3 ['min', 'max', 'mean']\n", + "\n", + "Transforming each example...\n", + "Batches of size 100: 2\n", + "100%|█████████████████████████████████████████████| 2/2 [00:02<00:00, 1.26s/it]\n", + "\n", + "Parallel processing done\n", + "/data4/tangsp/FIDDLE/FIDDLE/steps.py:503: FutureWarning: Passing keywords other than 'data', 'dtype', 'copy', 'name', 'tupleize_cols' is deprecated and will raise TypeError in a future version. Use the specific Index subclass directly instead\n", + " index = pd.Index(index, names=['ID', 't_range'])\n", + "DONE: Transforming each example...\n", + "(freq) number of missing entries :\t 0.0 out of 200×4×0=0 total\n", + "(freq) number of imputed entries :\t 0.0\n", + "(freq) number of not imputed entries :\t 0.0\n", + "(non-freq) number of missing entries :\t 76418 out of 200×4×97=77600 total\n", + "\n", + "(N × L × ^D) table :\t (200, 4, 97)\n", + "Time elapsed: 2.990010 seconds\n", + "Discretizing features...\n", + "\n", + "Processing 97 non-boolean variable columns...\n", + " Computing bin edges for numeric variables...\n", + "100%|██████████████████████████████████████████| 97/97 [00:00<00:00, 384.82it/s]\n", + " Discretizing variables to binary features\n", + "100%|██████████████████████████████████████████| 97/97 [00:00<00:00, 437.55it/s]\n", + "Finished discretizing features\n", + "\n", + "Output\n", + "X_all: shape=(200, 4, 97), density=0.015\n", + "Time elapsed: 3.860744 seconds\n", + "\n", + "--------------------------------------------------------------------------------\n", + "3-B) Post-filter time-dependent data\n", + "--------------------------------------------------------------------------------\n", + "(200, 4, 97) 0.015231958762886598\n", + "Original : 97\n", + "Nearly-constant: 0\n", + "*** time: 5.134121894836426\n", + "Correlated : 1\n", + "*** time: 8.108163118362427\n", + "\n", + "Output\n", + "X: shape=(200, 4, 96), density=0.015\n", + "(200, 4, 96) 0.015377604166666666\n", + "Time elapsed: 11.969133 seconds\n", + "\n", + "Output\n", + "X: shape=(200, 4, 96), density=0.015\n", + "Total time: 11.971706 seconds\n", + "\n", + "\u001b[0m" + ] + } + ], + "source": [ + "! PYTHONPATH=\"$PYTHONPATH:../../\" \\\n", + "python -m FIDDLE.run \\\n", + " --data_fname='./input/data.csv' \\\n", + " --population_fname='./input/pop.csv' \\\n", + " --config_fname='./input/config-1.yaml' \\\n", + " --output_dir='./output-1/' \\\n", + " --T=4 --dt=1.0 \\\n", + " --theta_1=0.001 --theta_2=0.001 --theta_freq=1 \\\n", + " --stats_functions 'min' 'max' 'mean'" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:288_value_1.0 ICD9_CODE:290-319_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:295-299_value_1.0 ICD9_CODE:300-316_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:320-389_value_1.0 ICD9_CODE:393-398_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:320-327_value_1.0 ICD9_CODE:330-337_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:340-349_value_1.0 ICD9_CODE:390-459_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 1 \n", + "\n", + " ICD9_CODE:401-405_value_1.0 ICD9_CODE:287_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:410-414_value_1.0 ICD9_CODE:415-417_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 1 0 \n", + "\n", + " ICD9_CODE:430-438_value_1.0 ICD9_CODE:440-449_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:500-508_value_1.0 ICD9_CODE:451-459_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:420-429_value_1.0 ICD9_CODE:460-519_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 1 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:480-488_value_1.0 ICD9_CODE:490-496_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 1 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:510-519_value_1.0 ICD9_CODE:520-579_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:550-553_value_1.0 ICD9_CODE:530-539_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:555-558_value_1.0 ICD9_CODE:560-569_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:570-579_value_1.0 ICD9_CODE:600-608_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:680-686_value_1.0 ICD9_CODE:580-629_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:590-599_value_1.0 ICD9_CODE:710-739_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:680-709_value_1.0 ICD9_CODE:580-589_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:745_value_1.0 ICD9_CODE:710-719_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:720-724_value_1.0 ICD9_CODE:740-759_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:746_value_1.0 ICD9_CODE:760-763_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:990-995_value_1.0 ICD9_CODE:860-869_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:820-829_value_1.0 ICD9_CODE:850-854_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:805-809_value_1.0 ICD9_CODE:870-879_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:996-999_value_1.0 ICD9_CODE:880-887_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 1 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:900-904_value_1.0 ICD9_CODE:790-796_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:910-919_value_1.0 ICD9_CODE:958-959_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:764-779_value_1.0 ICD9_CODE:760-779_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:E820-E825_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 \n", + " [1.0, 2.0) 0 \n", + " [2.0, 3.0) 0 \n", + " [3.0, 4.0) 0 \n", + "101757 [0.0, 1.0) 0 \n", + "... ... \n", + "199634 [3.0, 4.0) 0 \n", + 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+ " ICD9_CODE:E810-E819_value_1.0 ICD9_CODE:V20-V29_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:V40-V49_value_1.0 ICD9_CODE:V01-V91_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:V10-V19_value_1.0 ICD9_CODE:V50-V59_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:V30-V39_value_1.0 ICD9_CODE:V01-V09_value_1.0 \n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + "[800 rows x 97 columns]" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import numpy as np\n", + "import pandas as pd\n", + "import json\n", + "import sparse\n", + "\n", + "X = sparse.load_npz('output-1/X_all.npz')\n", + "X_names = json.load(open('output-1/X_all.feature_names.json', 'r'))\n", + "X_index = pd.read_csv('output-1/X.ID,t_range.csv').set_index(['ID', 't_range'])\n", + "df_X = pd.DataFrame(X.todense().reshape(X.shape[0]*X.shape[1], X.shape[2]), columns=X_names, index=X_index.index)\n", + "\n", + "display(df_X)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Test: levels = [0,1,2]" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [], + "source": [ + "!mkdir -p output-2" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Input:\n", + " Data : ./input/data.csv\n", + " Population: ./input/pop.csv\n", + " Config : ./input/config-2.yaml\n", + "\n", + "Output directory: ./output-2/\n", + "\n", + "Input arguments:\n", + " T = 4.0\n", + " dt = 1.0\n", + " θ₁ = 0.001\n", + " θ₂ = 0.001\n", + " θ_freq = 1.0\n", + " k = 3 ['min', 'max', 'mean']\n", + "\n", + "discretize = yes\n", + " S discretization bins: to be computed from data\n", + " X discretization bins: to be computed from data\n", + "\n", + "N = 200\n", + "L = 4\n", + "\n", + "\n", + "================================================================================\n", + "1) Pre-filter\n", + "================================================================================\n", + "Remove rows not in population\n", + "Remove rows with t outside of [0, 4]\n", + "Remove rare variables (<= 0.001)\n", + "Total variables : 1\n", + "Rare variables : 0\n", + "Remaining variables : 1\n", + "# rows (original) : 591\n", + "# rows (filtered) : 591\n", + "\n", + "================================================================================\n", + "2) Transform; 3) Post-filter\n", + "================================================================================\n", + "\n", + "--------------------------------------------------------------------------------\n", + "*) Detecting and parsing value types\n", + "--------------------------------------------------------------------------------\n", + "Parsing hierarchical values\n", + "Saved as: ./output-2/value_types.csv\n", + "\n", + "--------------------------------------------------------------------------------\n", + "*) Separate time-invariant and time-dependent\n", + "--------------------------------------------------------------------------------\n", + "Variables (time-invariant): 0\n", + "Variables (time-dependent): 273\n", + "# rows (time-invariant): 0\n", + "# rows (time-dependent): 1773\n", + "\n", + "--------------------------------------------------------------------------------\n", + "2-B) Transform time-dependent data\n", + "--------------------------------------------------------------------------------\n", + "Total variables : 273\n", + "Frequent variables : []\n", + "M₁ = 0\n", + "M₂ = 273\n", + "k = 3 ['min', 'max', 'mean']\n", + "\n", + "Transforming each example...\n", + "Batches of size 100: 2\n", + "100%|█████████████████████████████████████████████| 2/2 [00:02<00:00, 1.17s/it]\n", + "\n", + "Parallel processing done\n", + "/data4/tangsp/FIDDLE/FIDDLE/steps.py:503: FutureWarning: Passing keywords other than 'data', 'dtype', 'copy', 'name', 'tupleize_cols' is deprecated and will raise TypeError in a future version. Use the specific Index subclass directly instead\n", + " index = pd.Index(index, names=['ID', 't_range'])\n", + "DONE: Transforming each example...\n", + "(freq) number of missing entries :\t 0.0 out of 200×4×0=0 total\n", + "(freq) number of imputed entries :\t 0.0\n", + "(freq) number of not imputed entries :\t 0.0\n", + "(non-freq) number of missing entries :\t 216627 out of 200×4×273=218400 total\n", + "\n", + "(N × L × ^D) table :\t (200, 4, 273)\n", + "Time elapsed: 2.917234 seconds\n", + "Discretizing features...\n", + "\n", + "Processing 273 non-boolean variable columns...\n", + " Computing bin edges for numeric variables...\n", + "100%|████████████████████████████████████████| 273/273 [00:00<00:00, 383.46it/s]\n", + " Discretizing variables to binary features\n", + "100%|████████████████████████████████████████| 273/273 [00:01<00:00, 186.25it/s]\n", + "Finished discretizing features\n", + "\n", + "Output\n", + "X_all: shape=(200, 4, 273), density=0.008\n", + "Time elapsed: 5.639386 seconds\n", + "\n", + "--------------------------------------------------------------------------------\n", + "3-B) Post-filter time-dependent data\n", + "--------------------------------------------------------------------------------\n", + "(200, 4, 273) 0.008118131868131867\n", + "Original : 273\n", + "Nearly-constant: 0\n", + "*** time: 9.159954071044922\n", + "Correlated : 34\n", + "*** time: 13.995959758758545\n", + "\n", + "Output\n", + "X: shape=(200, 4, 239), density=0.009\n", + "(200, 4, 239) 0.008823221757322176\n", + "Time elapsed: 19.635627 seconds\n", + "\n", + "Output\n", + "X: shape=(200, 4, 239), density=0.009\n", + "Total time: 19.639108 seconds\n", + "\n", + "\u001b[0m" + ] + } + ], + "source": [ + "! PYTHONPATH=\"$PYTHONPATH:../../\" \\\n", + "python -m FIDDLE.run \\\n", + " --data_fname='./input/data.csv' \\\n", + " --population_fname='./input/pop.csv' \\\n", + " --config_fname='./input/config-2.yaml' \\\n", + " --output_dir='./output-2/' \\\n", + " --T=4 --dt=1.0 \\\n", + " --theta_1=0.001 --theta_2=0.001 --theta_freq=1 \\\n", + " --stats_functions 'min' 'max' 'mean'" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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ICD9_CODE:436_value_1.0 ICD9_CODE:433_value_1.0 ... \\\n", + "ID t_range ... \n", + "100536 [0.0, 1.0) 0 0 ... \n", + " [1.0, 2.0) 0 0 ... \n", + " [2.0, 3.0) 0 0 ... \n", + " [3.0, 4.0) 0 0 ... \n", + "101757 [0.0, 1.0) 0 0 ... \n", + "... ... ... ... \n", + "199634 [3.0, 4.0) 0 0 ... \n", + "199724 [0.0, 1.0) 0 0 ... \n", + " [1.0, 2.0) 0 0 ... \n", + " [2.0, 3.0) 0 0 ... \n", + " [3.0, 4.0) 0 0 ... \n", + "\n", + " ICD9_CODE:873_value_1.0 ICD9_CODE:881_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:880-887_value_1.0 ICD9_CODE:882_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 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"100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:959_value_1.0 ICD9_CODE:710-719_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:965_value_1.0 ICD9_CODE:967_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 1 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:969_value_1.0 ICD9_CODE:990-995_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:996_value_1.0 ICD9_CODE:995_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:998_value_1.0 ICD9_CODE:997_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:999_value_1.0 ICD9_CODE:740-759_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 1 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:E812_value_1.0 ICD9_CODE:E810-E819_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:E820-E825_value_1.0 ICD9_CODE:7456_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:E821_value_1.0 ICD9_CODE:E880-E888_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:E888_value_1.0 ICD9_CODE:E916_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:E916-E928_value_1.0 ICD9_CODE:E950_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:E950-E959_value_1.0 ICD9_CODE:V01-V09_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:V05_value_1.0 ICD9_CODE:V10_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:482_value_1.0 ICD9_CODE:V12_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:V20-V29_value_1.0 ICD9_CODE:V30_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:774_value_1.0 ICD9_CODE:V29_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:787_value_1.0 ICD9_CODE:V34_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:780-789_value_1.0 ICD9_CODE:V40-V49_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:V42_value_1.0 ICD9_CODE:V50_value_1.0 \\\n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + " ICD9_CODE:V50-V59_value_1.0 ICD9_CODE:V46_value_1.0 \n", + "ID t_range \n", + "100536 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "101757 [0.0, 1.0) 0 0 \n", + "... ... ... \n", + "199634 [3.0, 4.0) 0 0 \n", + "199724 [0.0, 1.0) 0 0 \n", + " [1.0, 2.0) 0 0 \n", + " [2.0, 3.0) 0 0 \n", + " [3.0, 4.0) 0 0 \n", + "\n", + "[800 rows x 273 columns]" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import numpy as np\n", + "import pandas as pd\n", + "import json\n", + "import sparse\n", + "\n", + "X = sparse.load_npz('output-2/X_all.npz')\n", + "X_names = json.load(open('output-2/X_all.feature_names.json', 'r'))\n", + "X_index = pd.read_csv('output-2/X.ID,t_range.csv').set_index(['ID', 't_range'])\n", + "df_X = pd.DataFrame(X.todense().reshape(X.shape[0]*X.shape[1], X.shape[2]), columns=X_names, index=X_index.index)\n", + "\n", + "display(df_X)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "FIDDLE-py36", + "language": "python", + "name": "fiddle-py36" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.13" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/tests/icd_time_test/input/config-0.yaml b/tests/icd_time_test/input/config-0.yaml new file mode 100644 index 0000000..03044b4 --- /dev/null +++ b/tests/icd_time_test/input/config-0.yaml @@ -0,0 +1,5 @@ +hierarchical_sep: ':' +hierarchical_levels: [0] + +value_types: + ICD9_CODE: hierarchical_ICD9 diff --git a/tests/icd_time_test/input/config-1.yaml b/tests/icd_time_test/input/config-1.yaml new file mode 100644 index 0000000..2c6ecce --- /dev/null +++ b/tests/icd_time_test/input/config-1.yaml @@ -0,0 +1,2 @@ +hierarchical_sep: ':' +hierarchical_levels: [0,1] diff --git a/tests/icd_time_test/input/config-2.yaml b/tests/icd_time_test/input/config-2.yaml new file mode 100644 index 0000000..9c6d4af --- /dev/null +++ b/tests/icd_time_test/input/config-2.yaml @@ -0,0 +1,2 @@ +hierarchical_sep: ':' +hierarchical_levels: [0,1,2] diff --git a/tests/icd_time_test/input/data.csv b/tests/icd_time_test/input/data.csv new file mode 100644 index 0000000..be35491 --- /dev/null +++ b/tests/icd_time_test/input/data.csv @@ -0,0 +1,1862 @@ +ID,t,variable_name,variable_value +172335,1.0,ICD9_CODE,40301 +172335,2.0,ICD9_CODE,486 +172335,3.0,ICD9_CODE,58281 +172335,4.0,ICD9_CODE,5855 +172335,5.0,ICD9_CODE,4254 +172335,6.0,ICD9_CODE,2762 +172335,7.0,ICD9_CODE,7100 +172335,8.0,ICD9_CODE,2767 +172335,9.0,ICD9_CODE,7243 +172335,10.0,ICD9_CODE,45829 +172335,11.0,ICD9_CODE,2875 +172335,12.0,ICD9_CODE,28521 +172335,13.0,ICD9_CODE,28529 +172335,14.0,ICD9_CODE,27541 +173633,1.0,ICD9_CODE,40301 +173633,2.0,ICD9_CODE,5856 +173633,3.0,ICD9_CODE,58381 +173633,4.0,ICD9_CODE,7100 +173633,5.0,ICD9_CODE,5589 +173633,6.0,ICD9_CODE,2875 +173633,7.0,ICD9_CODE,28521 +173633,8.0,ICD9_CODE,45829 +173633,9.0,ICD9_CODE,32723 +173633,10.0,ICD9_CODE,22804 +173633,11.0,ICD9_CODE,33829 +173633,12.0,ICD9_CODE,78900 +173633,13.0,ICD9_CODE,79092 +173633,14.0,ICD9_CODE,V4511 +174105,1.0,ICD9_CODE,53100 +174105,2.0,ICD9_CODE,41071 +174105,3.0,ICD9_CODE,2859 +174105,4.0,ICD9_CODE,41401 +174105,5.0,ICD9_CODE,725 +109976,1.0,ICD9_CODE,1915 +109976,2.0,ICD9_CODE,3314 +109976,3.0,ICD9_CODE,53081 +178393,1.0,ICD9_CODE,41401 +178393,2.0,ICD9_CODE,4111 +178393,3.0,ICD9_CODE,48283 +178393,4.0,ICD9_CODE,2859 +178393,5.0,ICD9_CODE,2720 +178393,6.0,ICD9_CODE,3051 +114585,1.0,ICD9_CODE,1940 +114585,2.0,ICD9_CODE,1977 +114585,3.0,ICD9_CODE,2553 +114585,4.0,ICD9_CODE,4240 +114585,5.0,ICD9_CODE,5845 +114585,6.0,ICD9_CODE,99859 +114585,7.0,ICD9_CODE,6822 +114585,8.0,ICD9_CODE,5119 +114585,9.0,ICD9_CODE,5990 +114585,10.0,ICD9_CODE,4280 +114585,11.0,ICD9_CODE,34982 +114585,12.0,ICD9_CODE,4019 +114585,13.0,ICD9_CODE,V1000 +114585,14.0,ICD9_CODE,V453 +114585,15.0,ICD9_CODE,V5865 +114585,16.0,ICD9_CODE,0413 +114585,17.0,ICD9_CODE,2518 +114585,18.0,ICD9_CODE,E9320 +127203,1.0,ICD9_CODE,V3001 +127203,2.0,ICD9_CODE,V053 +127203,3.0,ICD9_CODE,V290 +140784,1.0,ICD9_CODE,5715 +140784,2.0,ICD9_CODE,7895 +140784,3.0,ICD9_CODE,07054 +140784,4.0,ICD9_CODE,2875 +140784,5.0,ICD9_CODE,4280 +140784,6.0,ICD9_CODE,2851 +140784,7.0,ICD9_CODE,2765 +140784,8.0,ICD9_CODE,4019 +140784,9.0,ICD9_CODE,25000 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