diff --git a/.gitignore b/.gitignore index ad1d22e..8ebfa53 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,7 @@ # Large downloaded data files download/ + +# Python +__pycache__/ +*.egg-info/ diff --git a/README.md b/README.md index 9b7fd43..77ac2f9 100644 --- a/README.md +++ b/README.md @@ -20,3 +20,11 @@ conda env update --file environment.yml ``` Activate the environment by running `source activate cognoma-machine-learning` on Linux or OS X and `activate cognoma-machine-learning` on Windows. Once this environment is active in a terminal, run `jupyter notebook` to start a notebook server. + +## `cognoml` package + +This repository contains a python package named `cognoml`. For development, the package can be installed locally. First, make sure the `cognoma-machine-learning` environment is activated, so the `cognoml` is only installed for this environment. Then install using the following command from this repository's root directory: + +```sh +pip install --editable . +``` diff --git a/cognoml/__init__.py b/cognoml/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/cognoml/analysis.py b/cognoml/analysis.py new file mode 100644 index 0000000..c1ac5ad --- /dev/null +++ b/cognoml/analysis.py @@ -0,0 +1,114 @@ +import collections +import os +import warnings + +import pandas as pd +import numpy as np +import sklearn +from sklearn.model_selection import train_test_split + +from cognoml import utils +from cognoml.classifiers.logistic_regression import grid_search +from cognoml.figshare import download_files + +# expression_path = os.path.join('download', 'mutation-matrix.tsv.bz2') +data_directory = "download" + +def read_data(version=None): + """ + Read data. + """ + v_dir = download_files(directory=data_directory, article_id=3487685, version=version) + # Read expression data + path = os.path.join(v_dir, 'expression-matrix.tsv.bz2') + X = pd.read_table(path, index_col=0) + return X + +def classify(sample_id, mutation_status, data_version, **kwargs): + """ + Perform an analysis. + + Parameters + ---------- + sample_id : list + Sample IDs of the observations. + mutation_status : list + Mutation status (0 or 1) of each sample. + + Returns + ------- + results : dict + A JSON-serializable object. OrderedDicts are used for dictionaries to + enable reproducibile export. See `data/api/hippo-output-schema.json` + for JSON schema. + """ + results = collections.OrderedDict() + + obs_df = pd.DataFrame.from_items([ + ('sample_id', sample_id), + ('status', mutation_status), + ]) + + X_whole = read_data(version=data_version) + X = X_whole.loc[obs_df.sample_id, :] + y = obs_df.status + + X_train, X_test, y_train, y_test = train_test_split( + X, y, test_size=0.1, random_state=0, stratify=y) + obs_df['testing'] = obs_df.sample_id.isin(X_test.index).astype(int) + + grid_search.fit(X=X_train, y=y_train) + + predict_df = pd.DataFrame.from_items([ + ('sample_id', X_whole.index), + ('predicted_status', grid_search.predict(X_whole)), + ]) + if hasattr(grid_search, 'decision_function'): + predict_df['predicted_score'] = grid_search.decision_function(X_whole) + if hasattr(grid_search, 'predict_proba'): + predict_df['predicted_prob'] = grid_search.predict_proba(X_whole)[:, 1] + + # obs_df switches to containing non-selected samples + obs_df = obs_df.merge(predict_df, how='right', sort=True) + obs_df['selected'] = obs_df.sample_id.isin(sample_id).astype(int) + for column in 'status', 'testing', 'selected': + obs_df[column] = obs_df[column].fillna(-1).astype(int) + obs_train_df = obs_df.query("testing == 0") + obs_test_df = obs_df.query("testing == 1") + + #y_pred_train = obs_df.query("testing == 0").predicted_score + #y_pred_test = obs_df.query("testing == 1").predicted_score + + dimensions = collections.OrderedDict() + dimensions['observations_selected'] = sum(obs_df.selected == 1) + dimensions['observations_unselected'] = sum(obs_df.selected == 0) + dimensions['features'] = len(X.columns) + dimensions['positives'] = sum(obs_df.status == 1) + dimensions['negatives'] = sum(obs_df.status == 0) + dimensions['positive_prevalence'] = y.mean().round(5) + dimensions['training_observations'] = len(obs_train_df) + dimensions['testing_observations'] = len(obs_test_df) + results['dimensions'] = utils.value_map(dimensions, round, ndigits=5) + + performance = collections.OrderedDict() + for part, df in ('training', obs_train_df), ('testing', obs_test_df): + y_true = df.status + y_pred = df.predicted_status + metrics = utils.class_metrics(y_true, y_pred) + metrics.update(utils.threshold_metrics(y_true, y_pred)) + performance[part] = utils.value_map(metrics, round, ndigits=5) + performance['cv'] = {'auroc': round(grid_search.best_score_, 5)} + results['performance'] = performance + + gs = collections.OrderedDict() + gs['cv_scores'] = utils.cv_results_to_df(grid_search.cv_results_) + gs = utils.value_map(gs, utils.df_to_datatables) + results['grid_search'] = gs + + results['model'] = utils.model_info(grid_search.best_estimator_.steps[-1][1]) + + feature_df = utils.get_feature_df(grid_search, X.columns) + results['model']['features'] = utils.df_to_datatables(feature_df) + + results['observations'] = utils.df_to_datatables(obs_df) + return results diff --git a/cognoml/classifiers/__init__.py b/cognoml/classifiers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/cognoml/classifiers/logistic_regression.py b/cognoml/classifiers/logistic_regression.py new file mode 100644 index 0000000..aa958ce --- /dev/null +++ b/cognoml/classifiers/logistic_regression.py @@ -0,0 +1,28 @@ +import numpy as np +from sklearn.model_selection import GridSearchCV +from sklearn.pipeline import Pipeline +from sklearn.linear_model import SGDClassifier +from sklearn.feature_selection import VarianceThreshold +from sklearn.preprocessing import StandardScaler + +pipeline = Pipeline(steps=[ + ('select', VarianceThreshold()), + ('standardize', StandardScaler()), + ('classify', SGDClassifier()) +]) + +param_grid = { + 'classify__random_state': [0], + 'classify__class_weight': ['balanced'], + 'classify__loss': ['log'], + 'classify__penalty': ['elasticnet'], + 'classify__alpha': 10.0 ** np.linspace(-3, 1, 10), + 'classify__l1_ratio': [0.15], +} + +grid_search = GridSearchCV( + estimator=pipeline, + param_grid=param_grid, + n_jobs=-1, + scoring='roc_auc' +) diff --git a/cognoml/figshare.py b/cognoml/figshare.py new file mode 100644 index 0000000..c49a38d --- /dev/null +++ b/cognoml/figshare.py @@ -0,0 +1,62 @@ +import os +from urllib.request import urlretrieve +import json + +import requests + +def get_article_versions(article_id): + """ + Get version_to_url dictionary for a figshare article. + """ + url = 'https://api.figshare.com/v2/articles/{}/versions'.format(article_id) + response = requests.get(url) + version_to_url = {d['version']: d['url'] for d in response.json()} + return version_to_url + +def download_files(directory, article_id=3487685, version=None): + """ + Download files for a specific figshare article_id and version. Creates a + version-specific subdirectory in `directory` and downloads all files from + the figshare article into this subdirectory. + + Parameters + ---------- + directory : str + Directory to download files to. Files are written inside a versioned + directory (e.g. `v2`). + article_id : int + article_id on figshare + version : int or None + figshare version. `None` means latest. + + Returns + ------- + str + The version-specific DOI corresponding to the downloaded data. + """ + version_to_url = get_article_versions(article_id) + if version is None: + version = max(version_to_url.keys()) + url = version_to_url[version] + response = requests.get(url) + article = response.json() + version_directory = os.path.join(directory, 'v{}'.format(version)) + + if not os.path.exists(version_directory): + os.mkdir(version_directory) + + path = os.path.join(version_directory, 'info.json') + with open(path, 'w') as write_file: + json.dump(article, write_file, indent=2, ensure_ascii=False, sort_keys=True) + + # Download the files specified by the metadata + for file_info in article['files']: + name = file_info['name'] + path = os.path.join(version_directory, name) + if os.path.exists(path): + continue + url = file_info['download_url'] + print('Downloading {} to `{}`'.format(url, name)) + urlretrieve(url, path) + + return version_directory diff --git a/cognoml/main.py b/cognoml/main.py new file mode 100644 index 0000000..0d33aec --- /dev/null +++ b/cognoml/main.py @@ -0,0 +1,16 @@ +import json + +import requests + +from cognoml.analysis import classify +from cognoml import utils + +if __name__ == '__main__': + # Create a classifier using mock input. Print output to stdout. + url = 'https://github.com/cognoma/machine-learning/raw/876b8131bab46878cb49ae7243e459ec0acd2b47/data/api/hippo-input.json' + response = requests.get(url) + payload = response.json() + payload['data_version'] = 4 + results = classify(**payload) + json_results = json.dumps(results, indent=2, cls=utils.JSONEncoder) + print(json_results) diff --git a/cognoml/utils.py b/cognoml/utils.py new file mode 100644 index 0000000..31db796 --- /dev/null +++ b/cognoml/utils.py @@ -0,0 +1,132 @@ +import collections +import json + +import numpy as np +import pandas as pd +import sklearn + +def cv_results_to_df(cv_results): + """ + Convert a `sklearn.grid_search.GridSearchCV.cv_results_` attribute to a tidy + pandas DataFrame where each row is a hyperparameter combinatination. + """ + cv_results_df = pd.DataFrame(cv_results) + columns = [x for x in cv_results_df.columns if x.startswith('param_')] + columns += ['mean_train_score', 'mean_test_score', 'std_test_score'] + cv_results_df = cv_results_df[columns] + return cv_results_df + +def expand_grid(data_dict): + """ + Create a dataframe from every combination of given values. + """ + rows = itertools.product(*data_dict.values()) + grid_df = pd.DataFrame.from_records(rows, columns=data_dict.keys()) + return grid_df + +def df_to_datatables(df, double_precision=5, indent=2): + """ + Convert a pandas dataframe to a JSON object formatted for datatables input. + """ + dump_str = df.to_json(orient='split', double_precision=double_precision) + obj = json.loads(dump_str) + del obj['index'] + obj = collections.OrderedDict(obj) + obj.move_to_end('data') + return obj + +def json_sanitize(obj, object_pairs_hook=collections.OrderedDict): + """ + Sanitize an object containing pandas/numpy objects so it's JSON + serializable. Does not preserve order since `pandas.json.dumps()` does not + respect OrderedDict objects. Hence, it's recommended to just use the builtin + `json.dump` function with `cls=JSONEncoder`. + """ + obj_str = pd.json.dumps(obj) + print(obj_str) + obj = json.loads(obj_str, object_pairs_hook=object_pairs_hook) + return obj + +class JSONEncoder(json.JSONEncoder): + """ + A JSONEncoder that supports numpy types by converting them to standard + python types. + """ + + def default(self, o): + if type(o).__module__ == 'numpy': + return o.item() + return super().default(o) + +def value_map(dictionary, function, *args, **kwargs): + """ + Edits a dictionary-like object in place to apply a function to its values. + """ + for key, value in dictionary.items(): + dictionary[key] = function(value, *args, **kwargs) + return dictionary + +def class_metrics(y_true, y_pred): + metrics = collections.OrderedDict() + metrics['precision'] = sklearn.metrics.precision_score(y_true, y_pred) + metrics['recall'] = sklearn.metrics.recall_score(y_true, y_pred) + metrics['f1'] = sklearn.metrics.f1_score(y_true, y_pred) + metrics['accuracy'] = sklearn.metrics.accuracy_score(y_true, y_pred) + # See https://github.com/scikit-learn/scikit-learn/pull/6752 + metrics['balanced_accuracy'] = sklearn.metrics.recall_score( + y_true, y_pred, pos_label=None, average='macro') + return metrics + +def threshold_metrics(y_true, y_pred): + metrics = collections.OrderedDict() + metrics['auroc'] = sklearn.metrics.roc_auc_score(y_true, y_pred) + metrics['auprc'] = sklearn.metrics.average_precision_score(y_true, y_pred) + return metrics + +def model_info(estimator): + model = collections.OrderedDict() + model['class'] = type(estimator).__name__ + model['module'] = estimator.__module__ + model['parameters'] = sort_dict(estimator.get_params()) + return model + +def get_feature_df(grid_search, features): + """ + Return the feature names and coefficients from the final classifier of the + best pipeline found by GridSearchCV. See https://git.io/vPWLI. This function + assumes every selection step of the pipeline has a name starting with + `select`. + + Params + ------ + grid_search: GridSearchCV object + A post-fit GridSearchCV object where the estimator is a Pipeline. + features: list + initial feature names + + Returns + ------- + pandas.DataFrame + Dataframe of feature name and coefficient values + """ + features = np.array(features) + pipeline = grid_search.best_estimator_ + for name, transformer in pipeline.steps: + if name.startswith('select'): + X_index = np.arange(len(features)).reshape(1, -1) + indexes = transformer.transform(X_index).tolist() + features = features[indexes] + step_name, classifier = pipeline.steps[-1] + coefficients, = classifier.coef_ + feature_df = pd.DataFrame.from_items([ + ('feature', features), + ('coefficient', coefficients), + ]) + return feature_df + +def sort_dict(dictionary): + """ + Return a dictionary as an OrderedDict sorted by keys. + """ + items = sorted(dictionary.items()) + return 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PEP440. For a discussion on single-sourcing + # the version across setup.py and the project code, see + # https://packaging.python.org/en/latest/single_source_version.html + version='0.1.0', + + description='Machine learning for Project Cognoma', + + # The project's main homepage. + url='https://github.com/cognoma/machine-learning', + + # Author details + author='Project Cognoma', + + # Choose your license + license='BSD 3-Clause', + + # See https://pypi.python.org/pypi?%3Aaction=list_classifiers + classifiers=[ + # How mature is this project? Common values are + # 3 - Alpha + # 4 - Beta + # 5 - Production/Stable + 'Development Status :: 3 - Alpha', + + # Indicate who your project is intended for + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + + # Pick your license as you wish (should match "license" above) + 'License :: OSI Approved :: BSD License', + + # Specify the Python versions you support here. In particular, ensure + # that you indicate whether you support Python 2, Python 3 or both. + 'Programming Language :: Python :: 3 :: Only', + 'Programming Language :: Python :: 3.5', + ], + + # What does your project relate to? + keywords='cognoma machine learning cancer', + + # You can just specify the packages manually here if your project is + # simple. Or you can use find_packages(). + packages=['cognoml'], +)