<reponame>tylerashoff/paper_influence<gh_stars>0
import numpy as np
import pandas as pd
import csv
import os
from sklearn.model_selection import train_test_split
from sklearn import metrics
import xgboost as xgb
from sklearn.gaussian_process import GaussianProcessRegressor, GaussianProcessClassifier
from keras.models import Sequential
from keras.layers import Dense
from sklearn.ensemble import RandomForestRegressor, RandomForestClassifier


class analysis():

    def __init__(self, verbose=False):
        self.verbose = verbose
        pass

    def neural_network(self, x_train, x_test, y_train):
        '''
        build a dense neural network for citation prediction
        '''
        if self.verbose:
            print('neural network')
            pass

        model = Sequential()

        model.add(Dense(512, input_dim=x_train.shape[1], activation='relu'))

        model.add(Dense(512, activation='relu'))
        model.add(Dense(256, activation='relu'))
        model.add(Dense(128, activation='relu'))
        model.add(Dense(64, activation='relu'))
        model.add(Dense(32, activation='relu'))

        if not self.binary:
            model.add(Dense(1, activation='relu'))
            model.compile(
                loss='mean_squared_error',
                optimizer='adam',
                metrics=['mean_squared_error'])
            pass
        else:
            model.add(Dense(1, activation='sigmoid'))
            model.compile(
                loss='binary_crossentropy',
                optimizer='adam',
                metrics=['binary_accuracy'])
            pass

        model.fit(
            x_train,
            y_train,
            epochs=200,
            batch_size=32,
            validation_split=0.2,
            verbose=0)
        preds = model.predict(x_test)

        if not self.binary:
            return (preds.astype('float64').flatten())
        else:
            return (np.round(preds.flatten()))
        pass

    def random_forest(self, x_train, x_test, y_train):
        '''
        implementation of Random Forests for classification and regression
        '''
        if self.verbose:
            print('random forests')
            pass

        if not self.binary:
            model = RandomForestRegressor()
            pass
        else:
            model = RandomForestClassifier()
            pass

        model.fit(x_train, y_train)
        preds = model.predict(x_test)

        return (preds)

    def xgboost(self, x_train, x_test, y_train):
        '''
        implementation of XGBoost for classification and regression
        '''
        if self.verbose:
            print('xgboost')
            pass

        if not self.binary:
            obj = 'reg:squarederror'
            pass
        else:
            obj = 'binary:hinge'
            pass

        params = {
            'max_depth': 5,
            'eta': 0.5,
            'objective': obj,
            'eval_metric': ['logloss']
        }

        data_train = xgb.DMatrix(x_train, label=y_train)
        data_test = xgb.DMatrix(x_test, label=y_test)

        bst = xgb.train(params, data_train)
        preds = bst.predict(data_test)

        return (preds)

    def gaussian_process(self, x_train, x_test, y_train):
        '''
        implementation of a gaussian process for classification and regression
        '''
        if self.verbose:
            print('gaussian_process')
            pass

        if not self.binary:
            model = GaussianProcessRegressor()
            pass
        else:
            model = GaussianProcessClassifier()
            pass

        model.fit(x_train, y_train)
        preds = model.predict(x_test)

        return (preds)

    def scores(self, y_test, preds):
        '''
        calculate chosen metrics for regression and binary classification
        '''
        if not self.binary:
            mse = metrics.mean_squared_error(y_test, preds)
            r2 = np.corrcoef(y_test, preds)[0, 1]
            ev = metrics.explained_variance_score(y_test, preds)
            return (mse, r2, ev)
        else:
            fpr, tpr, threshs = metrics.roc_curve(y_test, preds)
            auc = metrics.auc(fpr, tpr)
            acc = metrics.accuracy_score(y_test, preds)
            f1 = metrics.f1_score(y_test, preds)
            return (auc, acc, f1)
        pass

    def write(self, model, scores):
        types = 'regression' if not self.binary else 'binary'
        csv.writer(open('results.csv', 'a')).writerow([
            str(self.embedding), types, model, scores[0], scores[1], scores[2]
        ])
        pass

    def main(self,
             x_train,
             x_test,
             y_train,
             y_test,
             binary=False,
             embedding=None):

        self.embedding = embedding
        self.binary = binary

        # XGBoost
        xg_preds = self.xgboost(x_train, x_test, y_train)
        xg_scores = self.scores(y_test, xg_preds)
        self.write('xgboost', xg_scores)
        print(xg_scores)

        # Random Forests
        rf_preds = self.random_forest(x_train, x_test, y_train)
        rf_scores = self.scores(y_test, rf_preds)
        self.write('random_forests', rf_scores)
        print(rf_scores)

        # Gaussian Process
        gp_preds = self.gaussian_process(x_train, x_test, y_train)
        gp_scores = self.scores(y_test, gp_preds)
        self.write('gaussian_process', gp_scores)
        print(gp_scores)

        # Neural Network
        nn_preds = self.neural_network(x_train, x_test, y_train)
        nn_scores = self.scores(y_test, nn_preds)
        self.write('neural_net', nn_scores)
        print(nn_scores)

        pass

    pass


# run all models for all embeddings

embeddings = ['spectral', 'isomap', 'varenc', None]

for embedding in embeddings:
    print(embedding)
    if embedding is None:
        filename = './datasets/full_data.csv'
        pass
    else:
        filename = './datasets/' + embedding + '_full_data.csv'
        pass

    df = pd.read_csv(filename).to_numpy()

    # split into 2020 and not
    dates = pd.to_datetime(df[:, 1])
    mask = dates >= pd.to_datetime('2020')
    df_2020 = df[mask, :]
    df = df[np.invert(mask), :]

    if embedding is None:
        vec_dim = 100
        pass
    else:
        vec_dim = 5
        pass
    end_ind = vec_dim + 8

    # set missing values
    df[:, 5:][np.isnan(list(df[:, 5:].flatten())).reshape(df[:, 5:].shape)] = 0
    df[:, 2][[isinstance(i, float) for i in df[:, 2]]] = 'NA'

    # enumerate journal entry
    journal_to_int = dict((c, i) for i, c in enumerate(np.unique(df[:, 2])))
    journal = np.array([journal_to_int[char] for char in df[:, 2]])

    # transforms
    small_const = 10**(-4)
    x = np.vstack([
        pd.to_datetime(df[:, 1]).year, journal,
        np.log(list(df[:, 5] + small_const)),
        np.log(list(df[:, 6] + small_const)), df[:, 7],
        np.log(list(df[:, end_ind + 1] + small_const)),
        np.log(list(df[:, end_ind + 2] + small_const)), df[:, end_ind + 3]
    ]).T.astype('float64')
    y = np.log(list(df[:, 3] + 10**(-4)))

    x_train, x_test, y_train, y_test = train_test_split(
        x, y, test_size=0.20, random_state=42)

    anlys = analysis(verbose=True)
    anlys.main(
        x_train, x_test, y_train, y_test, binary=False, embedding=embedding)

    # binary predictions above a given number of citations
    cut = 5
    y_train = y_train > np.log(cut)
    y_test = y_test > np.log(cut)
    #print('ratio: ', sum(y_test)/len(y_test))
    anlys.main(
        x_train, x_test, y_train, y_test, binary=True, embedding=embedding)

    pass
