diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e7338c6 --- /dev/null +++ b/.gitignore @@ -0,0 +1,126 @@ +# Specific folders +data/ + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don’t work, or not +# install all needed dependencies. +#Pipfile.lock + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ \ No newline at end of file diff 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VTQ_H.XPT \r", + "\r", + "Processing: WHQ.XPT \r", + "\r", + "Processing: WHQMEC_D.XPT \r", + "\r", + "Processing: WHQMEC_E.XPT \r", + "\r", + "Processing: WHQMEC_F.XPT \r", + "\r", + "Processing: WHQMEC_G.XPT \r", + "\r", + "Processing: WHQMEC_H.XPT \r", + "\r", + "Processing: WHQ_B.XPT \r", + "\r", + "Processing: WHQ_C.XPT \r", + "\r", + "Processing: WHQ_D.XPT \r", + "\r", + "Processing: WHQ_E.XPT \r", + "\r", + "Processing: WHQ_F.XPT \r", + "\r", + "Processing: WHQ_G.XPT \r", + "\r", + "Processing: WHQ_H.XPT" ] } ], "source": [ "ds = nhanes.Dataset(DATA_PATH)\n", - "ds.load_arthritis()\n", + "ds.load_cancer()\n", "n_fe = ds.features.shape[1]\n", "n_classes = 2\n", "\n", @@ -96,7 +19882,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -140,16 +19926,43 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "accu_tst_RFC 0.733\n", - "accu_tst_SVC 0.733\n", - "accu_tst_LR 0.738\n" + "accu_tst_RFC 0.727\n", + " precision recall f1-score support\n", + "\n", + " 0 0.71 0.77 0.74 500\n", + " 1 0.75 0.68 0.71 500\n", + "\n", + " micro avg 0.73 0.73 0.73 1000\n", + " macro avg 0.73 0.73 0.73 1000\n", + "weighted avg 0.73 0.73 0.73 1000\n", + "\n", + "accu_tst_SVC 0.726\n", + " precision recall f1-score support\n", + "\n", + " 0 0.71 0.76 0.74 500\n", + " 1 0.74 0.69 0.72 500\n", + "\n", + " micro avg 0.73 0.73 0.73 1000\n", + " macro avg 0.73 0.73 0.73 1000\n", + "weighted avg 0.73 0.73 0.73 1000\n", + "\n", + "accu_tst_LR 0.732\n", + " precision recall f1-score support\n", + "\n", + " 0 0.72 0.76 0.74 500\n", + " 1 0.74 0.71 0.73 500\n", + "\n", + " micro avg 0.73 0.73 0.73 1000\n", + " macro avg 0.73 0.73 0.73 1000\n", + "weighted avg 0.73 0.73 0.73 1000\n", + "\n" ] } ], @@ -160,22 +19973,28 @@ "accu = np.mean(preds_tst==targets_tst)\n", "print('accu_tst_RFC', accu)\n", "\n", + "print(classification_report(targets_tst, preds_tst))\n", + "\n", "clf = SVC(gamma='auto')\n", "clf.fit(features_trn, targets_trn)\n", "preds_tst = clf.predict(features_tst)\n", "accu = np.mean(preds_tst==targets_tst)\n", "print('accu_tst_SVC', accu)\n", "\n", + "print(classification_report(targets_tst, preds_tst))\n", + "\n", "clf = LogisticRegression(solver='lbfgs', max_iter=200)\n", "clf.fit(features_trn, targets_trn)\n", "preds_tst = clf.predict(features_tst)\n", "accu = np.mean(preds_tst==targets_tst)\n", - "print('accu_tst_LR', accu)\n" + "print('accu_tst_LR', accu)\n", + "\n", + "print(classification_report(targets_tst, preds_tst))\n" ] }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 16, "metadata": {}, "outputs": [ { @@ -184,12 +20003,12 @@ "text": [ " precision recall f1-score support\n", "\n", - " 0 0.73 0.76 0.74 500\n", - " 1 0.75 0.72 0.73 500\n", + " 0 0.73 0.79 0.76 500\n", + " 1 0.77 0.71 0.74 500\n", "\n", - " micro avg 0.74 0.74 0.74 1000\n", - " macro avg 0.74 0.74 0.74 1000\n", - "weighted avg 0.74 0.74 0.74 1000\n", + " micro avg 0.75 0.75 0.75 1000\n", + " macro avg 0.75 0.75 0.75 1000\n", + "weighted avg 0.75 0.75 0.75 1000\n", "\n" ] } @@ -198,6 +20017,13 @@ "print(classification_report(targets_tst, preds_tst))" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "code", "execution_count": null, @@ -222,7 +20048,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.8" + "version": "3.6.7" } }, "nbformat": 4, diff --git a/nhanes.py b/nhanes.py index 301ae83..4bd6100 100644 --- a/nhanes.py +++ b/nhanes.py @@ -10,12 +10,13 @@ import matplotlib.pyplot as plt import scipy.stats import sklearn.feature_selection +from random import choices class FeatureColumn: - def __init__(self, category, field, preprocessor, args=None, cost=None): + def __init__(self, category, field, preprocessors, args=None, cost=None): self.category = category self.field = field - self.preprocessor = preprocessor + self.preprocessors = preprocessors self.args = args self.data = None self.cost = cost @@ -77,8 +78,10 @@ def process(self): field = fe_col.field fe_col.data = df[field].copy() # do preprocessing - if fe_col.preprocessor is not None: - prepr_col = fe_col.preprocessor(df[field], fe_col.args) + if fe_col.preprocessors is not None: + prepr_col = df[field] + for x in range(len(fe_col.preprocessors)): + prepr_col = fe_col.preprocessors[x](prepr_col, fe_col.args[x]) else: prepr_col = df[field] # handle the 1 to many @@ -95,6 +98,20 @@ def process(self): def preproc_onehot(df_col, args=None): return pd.get_dummies(df_col, prefix=df_col.name, prefix_sep='#') +def preproc_map_mode(df_col, args=None): + if args is None: + args={'cutoff':np.inf} + df_col[df_col > args['cutoff']] = np.nan + df_col[pd.isna(df_col)] = df_col.mode() + return df_col + +def preproc_map_median(df_col, args=None): + if args is None: + args={'cutoff':np.inf} + df_col[df_col > args['cutoff']] = np.nan + df_col[pd.isna(df_col)] = df_col.median() + return df_col + def preproc_real(df_col, args=None): if args is None: args={'cutoff':np.inf} @@ -106,6 +123,52 @@ def preproc_real(df_col, args=None): df_col = (df_col-df_col.mean()) / df_col.std() return df_col +def preproc_real_mapped(df_col, args): + if args is None or not 'mappedValue' in args: + raise Exception("Missing required argument 'mappedValue'!") + if not 'cutoff' in args: + args['cutoff'] = np.inf + if not 'normalize' in args: + args['normalize'] = True + + # other answers as nan + df_col[df_col > args['cutoff']] = np.nan + # nan replaced by mappedValue + df_col[pd.isna(df_col)] = args['mappedValue'] + # statistical normalization + if args['normalize'] == True: + df_col = (df_col-df_col.mean()) / df_col.std() + return df_col + +def preproc_real_transform(df_col, args): + if args is None or not 'toTransform' in args: + raise Exception("Missing required argument 'toTransform'!") + if not 'cutoff' in args: + args['cutoff'] = np.inf + if not 'useOldMean' in args: + args['useOldMean'] = True + if not 'normalize' in args: + args['normalize'] = True + + # other answers as nan + df_col[df_col > args['cutoff']] = np.nan + old_mean = df_col.mean() + + # replace certain values with other values + for x in args['toTransform']: + df_col[df_col == x['selectValue']] = x['mappedValue'] + + if 'mappedValue' in args: + # nan replaced by mappedValue + df_col[pd.isna(df_col)] = args['mappedValue'] + else: + # nan replaced by mean + df_col[pd.isna(df_col)] = df_col.mean() if args['useOldMean'] == False else old_mean + # statistical normalization + if args['normalize'] == True: + df_col = (df_col-df_col.mean()) / df_col.std() + return df_col + def preproc_impute(df_col, args=None): # nan replaced by mean df_col[pd.isna(df_col)] = df_col.mean() @@ -113,14 +176,29 @@ def preproc_impute(df_col, args=None): def preproc_cut(df_col, bins): # limit values to the bins range - df_col = df_col[df_col >= bins[0]] - df_col = df_col[df_col <= bins[-1]] - return pd.cut(df_col.iloc[:,0], bins, labels=False) + #df_col = df_col[df_col >= bins[0]] + #df_col = df_col[df_col <= bins[-1]] + #return pd.cut(df_col.iloc[:,0], bins, labels=False) + return pd.cut(df_col, bins, labels=False) def preproc_dropna(df_col, args=None): df_col.dropna(axis=0, how='any', inplace=True) return df_col +def preproc_cutoff(df_col, args=None): + if args is None: + args={'cutoff':np.inf} + df_col[df_col > args['cutoff']] = np.nan + return df_col + +def preproc_probfill(df_col, args=None): + tmp = df_col.dropna(axis=0, how='any') + prob = tmp.value_counts(normalize=True) + c = df_col.isna().sum() + new_vals = choices(prob.index.tolist(), prob.values.tolist(), k=c) + df_col[pd.isna(df_col)] = new_vals + return df_col + #### Add your own preprocessing functions #### # Dataset loader @@ -142,83 +220,236 @@ def __init__(self, data_path=None): self.targets = None self.costs = None - def load_arthritis(self, opts=None): + def load_cancer(self, opts=None): columns = [ - # TARGET: systolic BP average + # TARGET: cancer/malignance diagnosis FeatureColumn('Questionnaire', 'MCQ220', None, None), + + ### DEMOGRAPHIC INFO - POTENTIAL CLUSTERING TARGET + # Gender FeatureColumn('Demographics', 'RIAGENDR', - preproc_real, None), - # Age at time of screening + [preproc_real_mapped, preproc_onehot], [{'cutoff':2, 'mappedValue': 2, 'normalize': False}, None]), + + # Age at time of screening (in years) FeatureColumn('Demographics', 'RIDAGEYR', - preproc_real, None), - FeatureColumn('Demographics', 'RIDRETH3', - preproc_onehot, None), + [preproc_real], [{'cutoff':85}]), + # Race/ethnicity - FeatureColumn('Demographics', 'RIDRETH1', - preproc_onehot, None), + FeatureColumn('Demographics', 'RIDRETH3', + [preproc_real_mapped], [{'mappedValue': 3, 'normalize': False}]), + + # Citizenship status + FeatureColumn('Demographics', 'DMDCITZN', + [preproc_real_mapped, preproc_onehot], [{'cutoff':2, 'mappedValue': 1, 'normalize': False}, None]), + # Annual household income + #FeatureColumn('Demographics', 'INDHHINC', + #[preproc_real_transform, preproc_map_median], [{'toTransform': [{'selectValue': 13, 'mappedValue': 3}], 'normalize': False}, {'cutoff': 11}]), FeatureColumn('Demographics', 'INDHHINC', - preproc_real, {'cutoff':11}), + [preproc_real_transform, preproc_cutoff, preproc_probfill], [{'toTransform': [{'selectValue': 13, 'mappedValue': 3}], 'normalize': False}, {'cutoff': 11}, None]), + # Education level + #FeatureColumn('Demographics', 'DMDEDUC2', + #[preproc_map_median], [{'cutoff':5}]), + # LESS THAN 50% OF DATA PRESENT FeatureColumn('Demographics', 'DMDEDUC2', - preproc_real, {'cutoff':5}), + [preproc_cutoff, preproc_probfill], [{'cutoff':5}, None]), + + # Total # of People in the Household + FeatureColumn('Demographics', 'DMDHHSIZ', + [preproc_map_mode], [{'cutoff':7}]), + + ### EXAMINATION INFO - POTENTIAL CLUSTERING TARGET + + ## Potential Targets: BIX, BMX, BPX, CVX, DEX, DXX, MGX, PAXRAW + ## Non-Targets: ARX, AUX.., BAX, CSX, DXXAG, DXXFEM, DXXFRX, DXXSPN, DXXV, DXXVFA, ENX, LEXAB, LEXABPI, LEXPN, MSX, OHX..., OPX... + + # Body Fat Percentage + # LESS THAN 50% OF DATA PRESENT + FeatureColumn('Examination', 'BIDPFAT', + [preproc_real], [None]), # BMI FeatureColumn('Examination', 'BMXBMI', - preproc_real, None), + [preproc_real], [None]), # Waist FeatureColumn('Examination', 'BMXWAIST', - preproc_real, None), - # Height - FeatureColumn('Examination', 'BMXHT', - preproc_real, None), - # Upper Leg Length - FeatureColumn('Examination', 'BMXLEG', - preproc_real, None), - # Weight - FeatureColumn('Examination', 'BMXWT', - preproc_real, None), + [preproc_real], [None]), + + # Blood Pressure - Systolic + FeatureColumn('Examination', 'BPXSY2', + [preproc_real], [None]), + + # Blood Pressure - Diastolic + FeatureColumn('Examination', 'BPXDI2', + [preproc_real], [None]), + + # V02 Max + # LESS THAN 30% OF DATA PRESENT + FeatureColumn('Examination', 'CVDESVO2', + [preproc_real], [None]), + + # Fitness level + #FeatureColumn('Examination', 'CVDFITLV', + #[preproc_real_mapped], [{'mappedValue': 1, 'normalize': False}]), + # LESS THAN 30% OF DATA PRESENT + FeatureColumn('Examination', 'CVDFITLV', + [preproc_probfill], [None]), + + # Fitzpatrick Skin Type + #FeatureColumn('Examination', 'DEX1FITZ', + #[preproc_real_mapped], [{'cutoff':6, 'mappedValue': 3, 'normalize': False}]), + + # LESS THAN 30% OF DATA PRESENT + FeatureColumn('Examination', 'DEX1FITZ', + [preproc_cutoff, preproc_probfill], [{'cutoff':6}, None]), + + # Grip Strength + FeatureColumn('Examination', 'MGDCGSZ', + [preproc_real], [None]), + + ### LABORATORY INFO - POTENTIAL CLUSTERING TARGET + + ## Potential Targets: AMDGYB, APOB, BIOPRO, CAFE, CBC, DEET, HCAA..., HDL, L13..., L18..., L25..., L40..., LAB10, LAB13, LAB18, LAB25, TB, TFA, TCHOL, TRIGLY + ## Non-Targets: AL_IGE, ALB_CR, ALCR, ALDUST, B12, B27, BFRPOL, CARB, CHLM..., CMV, COT..., CRCO, CRP, CUSEZN, DOXPOL, EPH, EPP, FASTQX, FERTIN, FETIB, FLDEP, FLDEW, FOL..., GHB, GLU, HCY, HEP..., HIV, HP..., HSV, HUKM, HULT, IHG..., INS, L02..., L03..., L04..., L05..., L06..., L09..., L10..., L11..., L16..., L17..., L19..., L20..., L24..., L26..., L28..., L31..., L34..., L35..., L36..., L37..., L39..., L43..., L45..., L52..., LAB02, LAB03, LAB04, LAB05, LAB06, LAB07, LAB09, LAB11, LAB16, LAB17, LAB18-22, LAB26, LAB28, OGTT, OHPV, OPD, ORHPV, PAH, PBCD, PCBPOL, PERNT, PFAS, PFC, PH..., POOLTF, PP, PSA, PSTPOL, PTH, SER, SSAFB, SSAMH, SS..., SW..., TELO, TFR, TGEMA, THYROD, TRICH, TST, U..., VIT, VOC, WPIN + + # Acrylamide + FeatureColumn('Laboratory', 'LBXACR', + [preproc_real], [None]), + # Caffeine + # LESS THAN 30% OF DATA PRESENT + FeatureColumn('Laboratory', 'URXAMU', + [preproc_real], [None]), + # White Blood Cells + FeatureColumn('Laboratory', 'LBXWBCSI', + [preproc_real], [None]), + # Red Blood Cells + FeatureColumn('Laboratory', 'LBXRBCSI', + [preproc_real], [None]), + # Hemoglobin + FeatureColumn('Laboratory', 'LBXHGB', + [preproc_real], [None]), + # Platelets + FeatureColumn('Laboratory', 'LBXPLTSI', + [preproc_real], [None]), + # DEET + # LESS THAN 30% OF DATA PRESENT + FeatureColumn('Laboratory', 'URXDEE', + [preproc_real], [None]), + # HDL Cholesterol + FeatureColumn('Laboratory', 'LBDHDD', + [preproc_real], [None]), # Total Cholesterol FeatureColumn('Laboratory', 'LBXTC', - preproc_real, None), - # Alcohol consumption - FeatureColumn('Questionnaire', 'ALQ101', - preproc_real, {'cutoff':2}), + [preproc_real], [None]), + # Triglycerides + # LESS THAN 40% OF DATA PRESENT + FeatureColumn('Laboratory', 'LBXTR', + [preproc_real], [None]), + # LDL Cholesterol + # LESS THAN 40% OF DATA PRESENT + FeatureColumn('Laboratory', 'LBDLDL', + [preproc_real], [None]), + + ### QUESTIONNAIRE INFO - POTENTIAL CLUSTERING TARGET + + ## Potential Targets: ACQ, ALQ, AQQ, BPQ, CBQ, CDQ, DBQ, DEQ, DUQ, FSQ, HOQ, HUQ, INQ, MCQ, MPQ, OCQ, PAQ, PFQ, PUQ, RXQ, SLQ, SMQ, TBQ, WHQ + ## Non-Targets: AGQ, ARQ, AUQ, BAQ, BHQ, CFQ, CIQ..., CKQ, CSQ, DIQ, DLQ, DPQ, ECQ, HCQ, HEQ, HIQ, HSQ, IMO, KIQ, OHQ, OSQ, PSQ, RDQ, RHQ, SSQ, SXQ, VIQ, VTQ, Y... + + # 1+ Alcoholic Drink + # LESS THAN 40% OF DATA PRESENT FeatureColumn('Questionnaire', 'ALQ120Q', - preproc_real, {'cutoff':365}), - # Vigorous work activity - FeatureColumn('Questionnaire', 'PAQ605', - preproc_real, {'cutoff':2}), - FeatureColumn('Questionnaire', 'PAQ620', - preproc_real, {'cutoff':2}), - FeatureColumn('Questionnaire', 'PAQ180', - preproc_real, {'cutoff':4}), - FeatureColumn('Questionnaire', 'PAD615', - preproc_real, {'cutoff':780}), - # Doctor told overweight (risk factor) - FeatureColumn('Questionnaire', 'MCQ160J', - preproc_onehot, {'cutoff':2}), - # Sleep + [preproc_real], [{'cutoff':365}]), + + # 5+ Alcoholic Drinks + # LESS THAN 30% OF DATA PRESENT + FeatureColumn('Questionnaire', 'ALQ140Q', + [preproc_real], [{'cutoff':365}]), + + # Home Meals + FeatureColumn('Questionnaire', 'CBQ190', + [preproc_real], [{'cutoff':35}]), + + # Restaurant Meals + FeatureColumn('Questionnaire', 'DBD090', + [preproc_real_transform], [{'cutoff':21, 'toTransform': [{'selectValue': 6666, 'mappedValue': 0.5}], 'useOldMean': False}]), + + # Melanoma Close Relative + #FeatureColumn('Questionnaire', 'DEQ050', + #[preproc_real_mapped, preproc_onehot], [{'cutoff':2, 'mappedValue': 2, 'normalize': False}, None]), + FeatureColumn('Questionnaire', 'DEQ050', + [preproc_cutoff, preproc_probfill, preproc_onehot], [{'cutoff':2}, None, None]), + + # Age of Home + #FeatureColumn('Questionnaire', 'HOD040', + #[preproc_real_mapped], [{'cutoff':6, 'mappedValue': 2, 'normalize': False}]), + FeatureColumn('Questionnaire', 'HOD040', + [preproc_cutoff, preproc_probfill], [{'cutoff':6}, None]), + + # Health Condition + #FeatureColumn('Questionnaire', 'HUQ010', + #[preproc_real_mapped], [{'cutoff':5, 'mappedValue': 2, 'normalize': False}]), + FeatureColumn('Questionnaire', 'HUQ010', + [preproc_cutoff, preproc_probfill], [{'cutoff':5}, None]), + + # Medical Treament Frequency + #FeatureColumn('Questionnaire', 'HUQ050', + #[preproc_real_mapped], [{'cutoff':5, 'mappedValue': 1, 'normalize': False}]), + FeatureColumn('Questionnaire', 'HUQ050', + [preproc_cutoff, preproc_probfill], [{'cutoff':5}, None]), + + # Blood Transfusion + #FeatureColumn('Questionnaire', 'MCQ092', + #[preproc_real_mapped, preproc_onehot], [{'cutoff':2, 'mappedValue': 2, 'normalize': False}, None]), + FeatureColumn('Questionnaire', 'MCQ092', + [preproc_cutoff, preproc_probfill, preproc_onehot], [{'cutoff':2}, None, None]), + + # Work Days Missed + #FeatureColumn('Questionnaire', 'MCQ245B', + #[preproc_real_mapped], [{'cutoff':365, 'mappedValue': 365}]), + FeatureColumn('Questionnaire', 'MCQ245B', + [preproc_real], [{'cutoff':365}]), + + # Hours Working + # LESS THAN 40% OF DATA PRESENT + FeatureColumn('Questionnaire', 'OCQ180', + [preproc_real], [{'cutoff':105}]), + + # Hours Sleeping FeatureColumn('Questionnaire', 'SLD010H', - preproc_real, {'cutoff':12}), - # Smoking + [preproc_real], [{'cutoff':12}]), + + # Restlessness + #FeatureColumn('Questionnaire', 'SLQ110', + #[preproc_real_mapped], [{'cutoff': 4, 'mappedValue': 0, 'normalize': False}]), + FeatureColumn('Questionnaire', 'SLQ110', + [preproc_cutoff, preproc_probfill], [{'cutoff': 4}, None]), + + # 100+ Cigarettes + #FeatureColumn('Questionnaire', 'SMQ020', + #[preproc_real_mapped, preproc_onehot], [{'cutoff':2, 'mappedValue': 2, 'normalize': False}, None]), + # LESS THAN 50% OF DATA PRESENT FeatureColumn('Questionnaire', 'SMQ020', - preproc_onehot, None), - FeatureColumn('Questionnaire', 'SMD030', - preproc_real, {'cutoff':72}), - # Blood relatives with arthritis - FeatureColumn('Questionnaire', 'MCQ250D', - preproc_onehot, {'cutoff':2}), - # joint pain/aching/stiffness in past year - FeatureColumn('Questionnaire', 'MPQ010', - preproc_onehot, {'cutoff':2}), - # symptoms began only because of injury - FeatureColumn('Questionnaire', 'MPQ030', - preproc_onehot, {'cutoff':2}), - # how long experiencing pain - FeatureColumn('Questionnaire', 'MPQ110', - preproc_real, {'cutoff':4}), + [preproc_cutoff, preproc_probfill, preproc_onehot], [{'cutoff':2}, None, None]), + + # 20+ Chewing Tobacco + #FeatureColumn('Questionnaire', 'SMQ210', + #[preproc_real_mapped, preproc_onehot], [{'cutoff':2, 'mappedValue': 2, 'normalize': False}, None]) + # LESS THAN 50% OF DATA PRESENT + FeatureColumn('Questionnaire', 'SMQ210', + [preproc_cutoff, preproc_probfill, preproc_onehot], [{'cutoff':2}, None, None]), + + # Anyone smoke in the home? + FeatureColumn('Questionnaire', 'SMD410', + [preproc_cutoff, preproc_probfill, preproc_onehot], [{'cutoff':2}, None, None]) + + # Prescription Medication Total + # THIS CAUSES ERROR WHEN LOADING + #FeatureColumn('Questionnaire', 'RXD295', + #preproc_real, None) + + ### DIETARY INFO - seems to be too specific to work with ### ] nhanes_dataset = NHANES(self.data_path, columns) df = nhanes_dataset.process() @@ -231,11 +462,12 @@ def load_arthritis(self, opts=None): target = target[inds_valid] # Put each person in the corresponding bin + #targets = np.zeros(target.shape[0]) targets = np.full((target.shape[0]), 3) - targets[target == 1] = 0 # yes arthritis - targets[target == 2] = 1 # no arthritis + targets[target == 1] = 0 # yes cancer + targets[target == 2] = 1 # no cancer - # random permutation + # random permutation perm = np.random.permutation(targets.shape[0]) self.features = features[perm] self.targets = targets[perm]