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Standard Errors of the Standard Deviation Above we explored how the spread in our estimates of the mean changed with sample size. We can similarly explore how our estimates of the standard deviation of the population change as we vary our sample size.
# the label arguments get used when we create a legend plt.hist(std25, normed=True, alpha=0.75, histtype="stepfilled", label="n=25") plt.hist(std50, normed=True, alpha=0.75, histtype="stepfilled", label="n=50") plt.hist(std100, normed=True, alpha=0.75, histtype="stepfilled", label="n=100") plt.hist(std200, normed=Tru...
Introduction-to-Simulation.ipynb
Bio204-class/bio204-notebooks
cc0-1.0
You can show mathematically for normally distributed data, that the expected Standard Error of the Standard Deviation is approximately $$ \mbox{Standard Error of Standard Deviation} \approx \frac{\sigma}{\sqrt{2(n-1)}} $$ where $\sigma$ is the population standard deviation, and $n$ is the sample size. Let's compare tha...
x = [25,50,100,200] y = [ss25,ss50,ss100,ss200] plt.scatter(x,y, label="Simulation estimates") plt.xlabel("Sample size") plt.ylabel("Std Error of Std Dev") theory = [np.std(popn)/(np.sqrt(2.0*(i-1))) for i in range(10,250)] plt.plot(range(10,250), theory, color='red', label="Theoretical expectation") plt.xlim(0,300) ...
Introduction-to-Simulation.ipynb
Bio204-class/bio204-notebooks
cc0-1.0
TensorFlow Model Analysis An Example of a Key TFX Library This example colab notebook illustrates how TensorFlow Model Analysis (TFMA) can be used to investigate and visualize the characteristics of a dataset and the performance of a model. We'll use a model that we trained previously, and now you get to play with the...
!pip install -q -U \ tensorflow==2.0.0 \ tfx==0.15.0rc0
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Import packages We import necessary packages, including standard TFX component classes.
import csv import io import os import requests import tempfile import zipfile from google.protobuf import text_format import tensorflow as tf import tensorflow_data_validation as tfdv import tensorflow_model_analysis as tfma from tensorflow_metadata.proto.v0 import schema_pb2 tf.__version__ tfma.version.VERSION_ST...
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Load The Files We'll download a zip file that has everything we need. That includes: Training and evaluation datasets Data schema Training results as EvalSavedModels Note: We are downloading with HTTPS from a Google Cloud server.
# Download the zip file from GCP and unzip it BASE_DIR = tempfile.mkdtemp() TFMA_DIR = os.path.join(BASE_DIR, 'eval_saved_models-2.0') DATA_DIR = os.path.join(TFMA_DIR, 'data') OUTPUT_DIR = os.path.join(TFMA_DIR, 'output') SCHEMA = os.path.join(TFMA_DIR, 'schema.pbtxt') response = requests.get('https://storage.googlea...
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Parse the Schema Among the things we downloaded was a schema for our data that was created by TensorFlow Data Validation. Let's parse that now so that we can use it with TFMA.
schema = schema_pb2.Schema() contents = tf.io.read_file(SCHEMA).numpy() schema = text_format.Parse(contents, schema) tfdv.display_schema(schema)
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Use the Schema to Create TFRecords We need to give TFMA access to our dataset, so let's create a TFRecords file. We can use our schema to create it, since it gives us the correct type for each feature.
datafile = os.path.join(DATA_DIR, 'eval', 'data.csv') reader = csv.DictReader(open(datafile)) examples = [] for line in reader: example = tf.train.Example() for feature in schema.feature: key = feature.name if len(line[key]) > 0: if feature.type == schema_pb2.FLOAT: example.features.feature[ke...
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Run TFMA and Render Metrics Now we're ready to create a function that we'll use to run TFMA and render metrics. It requires an EvalSavedModel, a list of SliceSpecs, and an index into the SliceSpec list. It will create an EvalResult using tfma.run_model_analysis, and use it to create a SlicingMetricsViewer using tfma....
def run_and_render(eval_model=None, slice_list=None, slice_idx=0): """Runs the model analysis and renders the slicing metrics Args: eval_model: An instance of tf.saved_model saved with evaluation data slice_list: A list of tfma.slicer.SingleSliceSpec giving the slices slice_idx: An integer index ...
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Slicing and Dicing We previously trained a model, and now we've loaded the results. Let's take a look at our visualizations, starting with using TFMA to slice along particular features. But first we need to read in the EvalSavedModel from one of our previous training runs. To define the slice you want to visualize ...
# Load the TFMA results for the first training run # This will take a minute eval_model_base_dir_0 = os.path.join(TFMA_DIR, 'run_0', 'eval_model_dir') eval_model_dir_0 = os.path.join(eval_model_base_dir_0, max(os.listdir(eval_model_base_dir_0))) eval_shared_model_0 = tfma.default_eval_sh...
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Slices Overview The default visualization is the Slices Overview when the number of slices is small. It shows the values of metrics for each slice. Since we've selected trip_start_hour above, it's showing us metrics like accuracy and AUC for each hour, which allows us to look for issues that are specific to some hours ...
slices = [tfma.slicer.SingleSliceSpec(columns=['trip_start_hour']), tfma.slicer.SingleSliceSpec(columns=['trip_start_day']), tfma.slicer.SingleSliceSpec(columns=['trip_start_month'])] run_and_render(eval_model=eval_shared_model_0, slice_list=slices, slice_idx=0)
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
You can create feature crosses to analyze combinations of features. Let's create a SliceSpec to look at a cross of trip_start_day and trip_start_hour:
slices = [tfma.slicer.SingleSliceSpec(columns=['trip_start_day', 'trip_start_hour'])] run_and_render(eval_shared_model_0, slices, 0)
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Crossing the two columns creates a lot of combinations! Let's narrow down our cross to only look at trips that start at noon. Then let's select accuracy from the visualization:
slices = [tfma.slicer.SingleSliceSpec(columns=['trip_start_day'], features=[('trip_start_hour', 12)])] run_and_render(eval_shared_model_0, slices, 0)
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Tracking Model Performance Over Time Your training dataset will be used for training your model, and will hopefully be representative of your test dataset and the data that will be sent to your model in production. However, while the data in inference requests may remain the same as your training data, in many cases i...
def get_eval_result(base_dir, run_name, data_loc, slice_spec): eval_model_base_dir = os.path.join(base_dir, run_name, "eval_model_dir") versions = os.listdir(eval_model_base_dir) eval_model_dir = os.path.join(eval_model_base_dir, max(versions)) output_dir = os.path.join(base_dir, "output", run_name) eval_shar...
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Next, let's use TFMA to see how these runs compare using render_time_series. How does it look today? First, we'll imagine that we've trained and deployed our model yesterday, and now we want to see how it's doing on the new data coming in today. We can specify particular slices to look at. Let's compare our training r...
output_dirs = [os.path.join(TFMA_DIR, "output", run_name) for run_name in ("run_0", "run_1", "run_2")] eval_results_from_disk = tfma.load_eval_results( output_dirs[:2], tfma.constants.MODEL_CENTRIC_MODE) tfma.view.render_time_series(eval_results_from_disk, slices[0])
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Now we'll imagine that another day has passed and we want to see how it's doing on the new data coming in today, compared to the previous two days. Again add AUC and average loss by using the "Add metric series" menu:
eval_results_from_disk = tfma.load_eval_results( output_dirs, tfma.constants.MODEL_CENTRIC_MODE) tfma.view.render_time_series(eval_results_from_disk, slices[0])
tfx_labs/Lab_6_Model_Analysis.ipynb
tensorflow/workshops
apache-2.0
Several Useful Functions These are functions that I reuse often to encode the feature vector (FV).
# These are several handy functions that I use in my class: # Encode a text field to dummy variables def encode_text_dummy(df,name): dummies = pd.get_dummies(df[name]) for x in dummies.columns: dummy_name = "{}-{}".format(name,x) df[dummy_name] = dummies[x] df.drop(name, axis=1, inplace=Tru...
tf_kdd99.ipynb
jbliss1234/ML
apache-2.0
Read in Raw KDD-99 Dataset
# This file is a CSV, just no CSV extension or headers # Download from: http://kdd.ics.uci.edu/databases/kddcup99/kddcup99.html df = pd.read_csv("/Users/jeff/Downloads/data/kddcup.data_10_percent", header=None) print("Read {} rows.".format(len(df))) # df = df.sample(frac=0.1, replace=False) # Uncomment this line to s...
tf_kdd99.ipynb
jbliss1234/ML
apache-2.0
Encode the feature vector Encode every row in the database. This is not instant!
# Now encode the feature vector encode_numeric_zscore(df, 'duration') encode_text_dummy(df, 'protocol_type') encode_text_dummy(df, 'service') encode_text_dummy(df, 'flag') encode_numeric_zscore(df, 'src_bytes') encode_numeric_zscore(df, 'dst_bytes') encode_text_dummy(df, 'land') encode_numeric_zscore(df, 'wrong_fragme...
tf_kdd99.ipynb
jbliss1234/ML
apache-2.0
Train the Neural Network
# Break into X (predictors) & y (prediction) x, y = to_xy(df,'outcome') # Create a test/train split. 25% test # Split into train/test x_train, x_test, y_train, y_test = train_test_split( x, y, test_size=0.25, random_state=42) # Create a deep neural network with 3 hidden layers of 10, 20, 10 classifier = skflow.T...
tf_kdd99.ipynb
jbliss1234/ML
apache-2.0
nltk Si vous utilisez la librairie nltk pour la première fois, il est nécessaire d'utiliser la commande suivante. Cette commande permet de télécharger de nombreux corpus de texte, mais également des informations grammaticales sur différentes langues. Information notamment nécessaire à l'étape de racinisation.
# nltk.download("all")
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Les données Dans le dossier Cdiscount/data de ce répértoire vous trouverez les fichiers suivants : cdiscount_test.csv.zip: Fichier d'apprentissage constitué de 1.000.000 de lignes cdisount_test: Fichier test constitué de 50.000 lignes ### Read & Split Dataset On définit une fonction permettant de lire le fichier d'ap...
def split_dataset(input_path, nb_line, tauxValid): data_all = pd.read_csv(input_path,sep=",", nrows=nb_line) data_all = data_all.fillna("") data_train, data_valid = scv.train_test_split(data_all, test_size = tauxValid) time_end = time.time() return data_train, data_valid
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Bien que déjà réduit par rapport au fichier original du concours, contenant plus de 15M de lignes, le fichier cdiscount_test.csv.zip, contenant 1M de lignes est encore volumineux. Nous allons charger en mémoire qu'une partie de ce fichier grace à l'argument nb_line afin d'éviter des temps de calcul trop couteux. Nous...
input_path = "data/cdiscount_train.csv.zip" nb_line=100000 # part totale extraite du fichier initial ici déjà réduit tauxValid = 0.05 data_train, data_valid = split_dataset(input_path, nb_line, tauxValid) # Cette ligne permet de visualiser les 5 premières lignes de la DataFrame N_train = data_train.shape[0] N_valid =...
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
La commande suivante permet d'afficher les premières lignes du fichiers. Vous pouvez observer que chaque produit possède 3 niveaux de Catégories, qui correspondent au différents niveaux de l'arborescence que vous retrouverez sur le site. Il y a 44 catégories de niveau 1, 428 de niveau 2 et 3170 de niveau 3. Dans ce T...
data_train.head(5)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
La commande suivante permet d'afficher un exemple de produits pour chaque Catégorie de niveau 1.
data_train.groupby("Categorie1").first()[["Description","Libelle","Marque"]]
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Distribution des classes
#Count occurence of each Categorie data_count = data_train["Categorie1"].value_counts() #Rename index to add percentage new_index = [k+ ": %.2f%%" %(v*100/N_train) for k,v in data_count.iteritems()] data_count.index = new_index fig=plt.figure(figsize= (10,10)) ax = fig.add_subplot(1,1,1) data_count.plot.barh(logx = Fa...
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Q Que peut-on dire sur la distribution de ces classes? Sauvegarde des données On sauvegarde dans des csv les fichiers train et validation afin que ces mêmes fichiers soit ré-utilisés plus tard dans d'autre calepin
data_valid.to_csv("data/cdiscount_valid.csv", index=False) data_train.to_csv("data/cdiscount_train_subset.csv", index=False)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Nettoyage des données Afin de limiter la dimension de l'espace des variables ou features (i.e les mots présents dans le document), tout en conservant les informations essentielles, il est nécessaire de nettoyer les données en appliquant plusieurs étapes: Chaque mot est écrit en minuscule. Les termes numériques, de pon...
i = 0 description = data_train.Description.values[i] print("Original Description : " + description)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Suppression des posibles balises HTML dans la description Les descriptions produits étant parfois extraites d'autres sites commerçant, des balises HTML peuvent être incluts dans la description. La librairie 'BeautifulSoup' permet de supprimer ces balises
from bs4 import BeautifulSoup #Nettoyage d'HTML txt = BeautifulSoup(description,"html.parser",from_encoding='utf-8').get_text() print(txt)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Conversion du texte en minuscule Certaines mots peuvent être écrits en majuscule dans les descriptions textes, cela à pour conséquence de dupliquer le nombre de features et une perte d'information.
txt = txt.lower() print(txt)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Remplacement de caractères spéciaux Certains caractères spéciaux sont supprimés comme par exemple : \u2026: … \u00a0: NO-BREAK SPACE Cette liste est non exhaustive et peut être etayée en fonction du jeu de donées étudié, de l'objectif souhaité ou encore du résultat de l'étude explorative.
txt = txt.replace(u'\u2026','.') txt = txt.replace(u'\u00a0',' ') print(txt)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Suppression des accents
txt = unicodedata.normalize('NFD', txt).encode('ascii', 'ignore').decode("utf-8") print(txt)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Supprime les caractères qui ne sont ne sont pas des lettres minuscules Une fois ces premières étapes passées, on supprime tous les caractères qui sont pas des lettres minusculres, c'est à dire les signes de ponctuation, les caractères numériques etc...
txt = re.sub('[^a-z_]', ' ', txt) print(txt)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Remplace la description par une liste de mots (tokens), supprime les mots de moins de 2 lettres ainsi que les stopwords On va supprimer maintenant tous les mots considérés comme "non-informatif". Par exemple : "le", "la", "de" ... Des listes contenants ces mots sont proposés dans des libraires tels que nltk ou encore l...
## listes de mots à supprimer dans la description des produits ## Depuis NLTK nltk_stopwords = nltk.corpus.stopwords.words('french') ## Depuis Un fichier externe. lucene_stopwords =open("data/lucene_stopwords.txt","r").read().split(",") #En local ## Union des deux fichiers de stopwords stopwords = list(set(nltk_stopw...
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
On applique également la suppression des accents à cette liste
stopwords = [unicodedata.normalize('NFD', sw).encode('ascii', 'ignore').decode("utf-8") for sw in stopwords] stopwords[:10]
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Enfin on crée des tokens, liste de mots dans la description produit, en supprimant les éléments de notre description produit qui sont présent dans la liste de stopword.
tokens = [w for w in txt.split() if (len(w)>2) and (w not in stopwords)] remove_words = [w for w in txt.split() if (len(w)<2) or (w in stopwords)] print(tokens) print(remove_words)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Racinisation (Stem) chaque tokens Pour chaque mot de notre liste de token, on va ramener ce mot à sa racine au sens de l'algorithme de Snowball présent dans la librairie nltk. Cette liste de mots néttoyé et racinisé va constitué les features de cette description produits.
## Fonction de setmming de stemming permettant la racinisation stemmer=nltk.stem.SnowballStemmer('french') tokens_stem = [stemmer.stem(token) for token in tokens] print(tokens_stem)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Fonction de nettoyage de texte On définit une fonction clean-txt qui prend en entrée un texte de description produit et qui retourne le texte nettoyé en appliquant successivement les étapes présentés précedemment. On définit également une fonction clean_marque qui contient signifcativement moins d'étape de nettoyage.
# Fonction clean générale def clean_txt(txt): ### remove html stuff txt = BeautifulSoup(txt,"html.parser",from_encoding='utf-8').get_text() ### lower case txt = txt.lower() ### special escaping character '...' txt = txt.replace(u'\u2026','.') txt = txt.replace(u'\u00a0',' ') ### remove a...
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Applique le nettoyage sur toutes les lignes de la DataFrame et créé deux nouvelles Dataframe (avant et sans l'étape de racinisation).
# fonction de nettoyage du fichier(stemming et liste de mots à supprimer) def clean_df(input_data, column_names= ['Description', 'Libelle', 'Marque']): nb_line = input_data.shape[0] print("Start Clean %d lines" %nb_line) # Cleaning start for each columns time_start = time.time() clean_list=[]...
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Nettoyage des DataFrames
# Take approximately 2 minutes fors 100.000 rows warnings.filterwarnings("ignore") data_valid_clean, data_valid_clean_stem = clean_df(data_valid) warnings.filterwarnings("ignore") data_train_clean, data_train_clean_stem = clean_df(data_train)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Affiche les 5 premières lignes de la DataFrame d'apprentissage après nettoyage.
data_train_clean.head(5) data_train_clean_stem.head(5)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Taille du dictionnaire de mots pour le dataset avant et après la racinisation.
concatenate_text = " ".join(data_train["Description"].values) list_of_word = concatenate_text.split(" ") N = len(set(list_of_word)) print(N) concatenate_text = " ".join(data_train_clean["Description"].values) list_of_word = concatenate_text.split(" ") N = len(set(list_of_word)) print(N) concatenate_text = " ".join(da...
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Wordcloud Les représentations Wordcloud permettent des représentations de l'ensemble des mots d'un corpus de documents. Dans cette représentation plus un mot apparait de manière fréquent dans le corpus, plus sa taille sera grande dans la représentation du corpus.
from wordcloud import WordCloud A=WordCloud(background_color="black") A.generate_from_text?
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Wordcloud de l'ensemble des description à l'état brut.
all_descr = " ".join(data_valid.Description.values) wordcloud_word = WordCloud(background_color="black", collocations=False).generate_from_text(all_descr) plt.figure(figsize=(10,10)) plt.imshow(wordcloud_word,cmap=plt.cm.Paired) plt.axis("off") plt.show()
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Wordcloud après racinisation et nettoyage
all_descr_clean_stem = " ".join(data_valid_clean_stem.Description.values) wordcloud_word = WordCloud(background_color="black", collocations=False).generate_from_text(all_descr_clean_stem) plt.figure(figsize=(10,10)) plt.imshow(wordcloud_word,cmap=plt.cm.Paired) plt.axis("off") plt.show()
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Vous pouvez observer que les mots "voir et "present" sont les plus représentés. Cela est du au fait que la pluspart des descriptions se terminent par "Voir la présentation". C'est deux mots ne sont donc pas informatif car présent dans beaucoup de catégorie différente. C'est une bon exemple de stopword propre à un probl...
data_valid_clean.to_csv("data/cdiscount_valid_clean.csv", index=False) data_train_clean.to_csv("data/cdiscount_train_clean.csv", index=False) data_valid_clean_stem.to_csv("data/cdiscount_valid_clean_stem.csv", index=False) data_train_clean_stem.to_csv("data/cdiscount_train_clean_stem.csv", index=False)
Cdiscount/Part1-1-AIF-PythonNltk-Explore&CleanText-Cdiscount.ipynb
wikistat/Ateliers-Big-Data
mit
Compilers: Numba and Cython Requirement To get Cython working, Winpython 3.7+ users should install "Microsoft Visual C++ Build Tools 2017" (visualcppbuildtools_full.exe, a 4 Go installation) at https://beta.visualstudio.com/download-visual-studio-vs/ To get Numba working, not-windows10 users may have to install "Micros...
# checking Numba JIT toolchain import numpy as np image = np.zeros((1024, 1536), dtype = np.uint8) #from pylab import imshow, show import matplotlib.pyplot as plt from timeit import default_timer as timer from numba import jit @jit def create_fractal(min_x, max_x, min_y, max_y, image, iters , mandelx): height = im...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Cython (a compiler for writing C extensions for the Python language) WinPython 3.5 and 3.6 users may not have mingwpy available, and so need "VisualStudio C++ Community Edition 2015" https://www.visualstudio.com/downloads/download-visual-studio-vs#d-visual-c
# Cython + Mingwpy compiler toolchain test %load_ext Cython %%cython -a # with %%cython -a , full C-speed lines are shown in white, slowest python-speed lines are shown in dark yellow lines # ==> put your cython rewrite effort on dark yellow lines def create_fractal_cython(min_x, max_x, min_y, max_y, image, iters , m...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Graphics: Matplotlib, Pandas, Seaborn, Holoviews, Bokeh, bqplot, ipyleaflet, plotnine
# Matplotlib 3.4.1 # for more examples, see: http://matplotlib.org/gallery.html from mpl_toolkits.mplot3d import axes3d import matplotlib.pyplot as plt from matplotlib import cm ax = plt.figure().add_subplot(projection='3d') X, Y, Z = axes3d.get_test_data(0.05) # Plot the 3D surface ax.plot_surface(X, Y, Z, rstride=...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Ipython Notebook: Interactivity & other
import IPython;IPython.__version__ # Audio Example : https://github.com/ipython/ipywidgets/blob/master/examples/Beat%20Frequencies.ipynb %matplotlib inline import matplotlib.pyplot as plt import numpy as np from ipywidgets import interactive from IPython.display import Audio, display def beat_freq(f1=220.0, f2=224.0):...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Mathematical: statsmodels, lmfit,
# checking statsmodels import numpy as np import matplotlib.pyplot as plt plt.style.use('ggplot') import statsmodels.api as sm data = sm.datasets.anes96.load_pandas() party_ID = np.arange(7) labels = ["Strong Democrat", "Weak Democrat", "Independent-Democrat", "Independent-Independent", "Independent-Republica...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
DataFrames: Pandas, Dask
#Pandas import pandas as pd import numpy as np idx = pd.date_range('2000', '2005', freq='d', closed='left') datas = pd.DataFrame({'Color': [ 'green' if x> 1 else 'red' for x in np.random.randn(len(idx))], 'Measure': np.random.randn(len(idx)), 'Year': idx.year}, index=idx.date) datas.head()
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Split / Apply / Combine Split your data into multiple independent groups. Apply some function to each group. Combine your groups back into a single data object.
datas.query('Measure > 0').groupby(['Color','Year']).size().unstack()
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Web Scraping: Beautifulsoup
# checking Web Scraping: beautifulsoup and requests import requests from bs4 import BeautifulSoup URL = 'http://en.wikipedia.org/wiki/Franklin,_Tennessee' req = requests.get(URL, headers={'User-Agent' : "Mining the Social Web"}) soup = BeautifulSoup(req.text, "lxml") geoTag = soup.find(True, 'geo') if geoTag and l...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Operations Research: Pulp
# Pulp example : minimizing the weight to carry 99 pennies # (from Philip I Thomas) # see https://www.youtube.com/watch?v=UmMn-N5w-lI#t=995 # Import PuLP modeler functions from pulp import * # The prob variable is created to contain the problem data prob = LpProblem("99_pennies_Problem",LpMinimiz...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Deep Learning: see tutorial-first-neural-network-python-keras Symbolic Calculation: sympy
# checking sympy import sympy a, b =sympy.symbols('a b') e=(a+b)**5 e.expand()
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
SQL tools: sqlite, Ipython-sql, sqlite_bro, baresql, db.py
# checking Ipython-sql, sqlparse, SQLalchemy %load_ext sql %%sql sqlite:///.baresql.db DROP TABLE IF EXISTS writer; CREATE TABLE writer (first_name, last_name, year_of_death); INSERT INTO writer VALUES ('William', 'Shakespeare', 1616); INSERT INTO writer VALUES ('Bertold', 'Brecht', 1956); SELECT * , sqlite_version()...
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
Qt libraries Demo See Dedicated Qt Libraries Demo Wrap-up
# optional scipy full test (takes up to 10 minutes) #!cmd /C start cmd /k python.exe -c "import scipy;scipy.test()" %pip list !jupyter labextension list !pip check !pipdeptree !pipdeptree -p pip
docs/Winpython_checker.ipynb
stonebig/winpython_afterdoc
mit
IP Addresses of Compute Nodes
ips = saz.arm.view_info()
ipynb/Use Case - NIST Pedestrian and Face Detection on Simple Azure (under development).ipynb
lee212/simpleazure
gpl-3.0
Load Ansible API with IPs
from simpleazure.ansible_api import AnsibleAPI ansible_client = AnsibleAPI(ips)
ipynb/Use Case - NIST Pedestrian and Face Detection on Simple Azure (under development).ipynb
lee212/simpleazure
gpl-3.0
Download Ansible Playbooks from Github The ansible scripts for Pedestrian and Face Detection is here: https://github.com/futuresystems/pedestrian-and-face-detection. We clone the repository using Github command line tools.
from simpleazure.github_cli import GithubCLI git_client = GithubCLI() git_client.set_repo('https://github.com/futuresystems/pedestrian-and-face-detection') git_client.clone()
ipynb/Use Case - NIST Pedestrian and Face Detection on Simple Azure (under development).ipynb
lee212/simpleazure
gpl-3.0
Install Software Stacks to Targeted VMs
ansible_client.playbook(git_client.path + "/site.yml") ansible_client.run()
ipynb/Use Case - NIST Pedestrian and Face Detection on Simple Azure (under development).ipynb
lee212/simpleazure
gpl-3.0
Check shed words pattern-matching requiremnts Ref: - Dodds, P. S., Harris, K. D., Kloumann, I. M., Bliss, C. A., & Danforth, C. M. (2011). Temporal patterns of happiness and information in a global social network: Hedonometrics and Twitter. PloS one, 6(12), e26752. Notes: - See 2.1 Algorithm for Hedonometer P3 - See...
""" Check all shed words """ if 1 == 1: ind_shed_word_dict = pd.read_pickle(config.IND_SHED_WORD_DICT_PKL) print(ind_shed_word_dict.values())
develop/20171019-daheng-build_shed_words_freq_dicts.ipynb
adamwang0705/cross_media_affect_analysis
mit
Build single shed words freq dict for topic_news docs Result single dict format (for all topic_news docs) {topic_ind_0: { news_native_id_0_0: {shed_word_0_ind: shed_word_0_freq, shed_word_1_ind: shed_word_1_freq, ...}, news_native_id_0_1: {shed_word_0_ind: shed_...
%%time """ Build single shed words freq dict for all topic_news docs Register TOPICS_NEWS_SHED_WORDS_FREQ_DICT_PKL = os.path.join(DATA_DIR, 'topics_news_shed_words_freq.dict.pkl') in config """ if 0 == 1: topics_news_shed_words_freq_dict = {} for topic_ind, topic in enumerate(config.MANUALLY_SELECTED_...
develop/20171019-daheng-build_shed_words_freq_dicts.ipynb
adamwang0705/cross_media_affect_analysis
mit
Check basic statistics
""" Print out sample news shed_words_freq_dicts inside single topic """ if 0 == 1: target_topic_ind = 0 with open(config.TOPICS_NEWS_SHED_WORDS_FREQ_DICT_PKL, 'rb') as f: topics_news_shed_words_freq_dict = pickle.load(f) count = 0 for news_native_id, news_doc_shed_words_freq_dict i...
develop/20171019-daheng-build_shed_words_freq_dicts.ipynb
adamwang0705/cross_media_affect_analysis
mit
Build shed words freq dicts for each topic_tweets doc separately Result dict format (for each given topic_tweets doc) {tweet_id_0_0: {shed_word_0_ind: shed_word_0_freq, shed_word_1_ind: shed_word_1_freq, ...}, tweet_id_0_1: {shed_word_0_ind: shed_word_0_freq, shed_word_1_i...
%%time """ Build shed words freq dict for each topic separately Register TOPICS_TWEETS_SHED_WORDS_FREQ_DICT_PKLS_DIR = os.path.join(DATA_DIR, 'topics_tweets_shed_words_freq_dict_pkls') in config Note: - Number of tweets is large. Process each topic_tweets doc individually to avoid crash - Execute second time fo...
develop/20171019-daheng-build_shed_words_freq_dicts.ipynb
adamwang0705/cross_media_affect_analysis
mit
Check basic statistics
%%time """ Print out sample tweet shed_words_freq_dicts inside single topic """ if 0 == 1: target_topic_ind = 0 topic_tweets_shed_words_freq_dict_pkl_file = os.path.join(config.TOPICS_TWEETS_SHED_WORDS_FREQ_DICT_PKLS_DIR, '{}.updated.dict.pkl'.format(target_topic_ind)) with open(topic_tweets_shed_words...
develop/20171019-daheng-build_shed_words_freq_dicts.ipynb
adamwang0705/cross_media_affect_analysis
mit
Linear classifier on sensor data with plot patterns and filters Decoding, a.k.a MVPA or supervised machine learning applied to MEG and EEG data in sensor space. Fit a linear classifier with the LinearModel object providing topographical patterns which are more neurophysiologically interpretable [1]_ than the classifier...
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr> # Romain Trachel <trachelr@gmail.com> # Jean-Remi King <jeanremi.king@gmail.com> # # License: BSD (3-clause) import mne from mne import io, EvokedArray from mne.datasets import sample from mne.decoding import Vectorizer, get_coef...
0.14/_downloads/plot_linear_model_patterns.ipynb
mne-tools/mne-tools.github.io
bsd-3-clause
Set parameters
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif' event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif' tmin, tmax = -0.1, 0.4 event_id = dict(aud_l=1, vis_l=3) # Setup for reading the raw data raw = io.read_raw_fif(raw_fname, preload=True) raw.filter(.5, 25) events = mne.read...
0.14/_downloads/plot_linear_model_patterns.ipynb
mne-tools/mne-tools.github.io
bsd-3-clause
Decoding in sensor space using a LogisticRegression classifier
clf = LogisticRegression() scaler = StandardScaler() # create a linear model with LogisticRegression model = LinearModel(clf) # fit the classifier on MEG data X = scaler.fit_transform(meg_data) model.fit(X, labels) # Extract and plot spatial filters and spatial patterns for name, coef in (('patterns', model.patterns...
0.14/_downloads/plot_linear_model_patterns.ipynb
mne-tools/mne-tools.github.io
bsd-3-clause
Let's do the same on EEG data using a scikit-learn pipeline
X = epochs.pick_types(meg=False, eeg=True) y = epochs.events[:, 2] # Define a unique pipeline to sequentially: clf = make_pipeline( Vectorizer(), # 1) vectorize across time and channels StandardScaler(), # 2) normalize features across trials LinearModel(LogisticRegre...
0.14/_downloads/plot_linear_model_patterns.ipynb
mne-tools/mne-tools.github.io
bsd-3-clause
This cell can be used for all data sets except colon. colon is special because it has 3 types of events instead of just 2. Just change the first line to run a different data set.
#data = ds._pbc #data = ds._lung #data = ds._nwtco data = ds._flchain df = pd.read_csv(data['filename'][:-4] + "_org.csv", sep=None, engine='python') k = 4 # flchain has three guys at zero, remove them if 'flchain' in data['filename']: df = df[(df[data['timecol']] > 0)] # Need shape later n, d =...
DataSetStratification.ipynb
spacecowboy/article-annriskgroups-source
gpl-3.0
Print the labeled to data to a new file.
fname = data['filename'] print(fname) df.to_csv(fname, na_rep='NA', index=False)
DataSetStratification.ipynb
spacecowboy/article-annriskgroups-source
gpl-3.0
Colon Is kind of special. It has 3 events where two must be combined before stratification is possible.
data = ds._colon df = pd.read_csv(data['filename'], sep=None, engine='python') n, d = df.shape k = 4 # Construct lists of events, censored events = [] censored = [] for i in df['id'].unique(): x = ((df['id'] == i) & (df['etype'] == 1)) if df[x]['status'].sum() < 1: censored.append(i) else: ...
DataSetStratification.ipynb
spacecowboy/article-annriskgroups-source
gpl-3.0
Print data to file.
fname = data['filename'][:-8] + '.csv' print(fname) df.to_csv(fname, na_rep='NA', index=False)
DataSetStratification.ipynb
spacecowboy/article-annriskgroups-source
gpl-3.0
Model results Rule learning and rule application in the matching task Rule Learning > Rule Application
l1cope="3" l2cope="1" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule Application > Rule Learning
l1cope="3" l2cope="1" l3cope="1" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule Learning > Baseline
l1cope="2" l2cope="1" l3cope="1" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Baseline > Rule Learning
l1cope="2" l2cope="1" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule Application > Baseline
l1cope="1" l2cope="1" l3cope="1" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Baseline > Rule Application
l1cope="1" l2cope="1" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() Image(sliced_img) render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule learning and rule application in the classification task Rule Learning > Rule Application
l1cope="3" l2cope="2" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule Learning > Baseline
l1cope="2" l2cope="2" l3cope="1" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Baseline > Rule Learning
l1cope="2" l2cope="2" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule Application > Baseline
l1cope="1" l2cope="2" l3cope="1" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Baseline > Rule Application
l1cope="1" l2cope="2" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule learning in the matching and classification tasks Matching > Classification
l1cope="2" l2cope="3" l3cope="1" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Classification > Matching
l1cope="2" l2cope="3" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Rule application in the matching and classification tasks Matching > Classification
l1cope="1" l2cope="3" l3cope="1" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Classification > Matching
l1cope="1" l2cope="3" l3cope="2" sliced_img,wb_img,cluster_corr,tstat_img,html_cl,html_t = paths() render(html_cl,[wb_img,cluster_corr])
thresholded_results/RulesFPC/model_1_FPC/model_1_FPC.ipynb
dpaniukov/RulesFPC
mit
Define path to data: (It's a good idea to put it in a subdirectory of your notebooks folder, and then exclude that directory from git control by adding it to .gitignore.)
path = "data/dogscats/" #path = "data/dogscats/sample/"
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
We have created a file most imaginatively called 'utils.py' to store any little convenience functions we'll want to use. We will discuss these as we use them.
import utils; reload(utils) from utils import plots
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
Use a pretrained VGG model with our Vgg16 class Our first step is simply to use a model that has been fully created for us, which can recognise a wide variety (1,000 categories) of images. We will use 'VGG', which won the 2014 Imagenet competition, and is a very simple model to create and understand. The VGG Imagenet t...
# As large as you can, but no larger than 64 is recommended. # If you have an older or cheaper GPU, you'll run out of memory, so will have to decrease this. batch_size=64 # Import our class, and instantiate import vgg16; reload(vgg16) from vgg16 import Vgg16 vgg = Vgg16() # Grab a few images at a time for training a...
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
(BTW, when Keras refers to 'classes', it doesn't mean python classes - but rather it refers to the categories of the labels, such as 'pug', or 'tabby'.) Batches is just a regular python iterator. Each iteration returns both the images themselves, as well as the labels.
imgs,labels = next(batches)
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
That shows all of the steps involved in using the Vgg16 class to create an image recognition model using whatever labels you are interested in. For instance, this process could classify paintings by style, or leaves by type of disease, or satellite photos by type of crop, and so forth. Next up, we'll dig one level deep...
from numpy.random import random, permutation from scipy import misc, ndimage from scipy.ndimage.interpolation import zoom import keras from keras import backend as K from keras.utils.data_utils import get_file from keras.models import Sequential, Model from keras.layers.core import Flatten, Dense, Dropout, Lambda from...
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
Let's import the mappings from VGG ids to imagenet category ids and descriptions, for display purposes later.
FILES_PATH = 'http://files.fast.ai/models/'; CLASS_FILE='imagenet_class_index.json' # Keras' get_file() is a handy function that downloads files, and caches them for re-use later fpath = get_file(CLASS_FILE, FILES_PATH+CLASS_FILE, cache_subdir='models') with open(fpath) as f: class_dict = json.load(f) # Convert diction...
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
Here's a few examples of the categories we just imported:
classes[:5]
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
Model creation Creating the model involves creating the model architecture, and then loading the model weights into that architecture. We will start by defining the basic pieces of the VGG architecture. VGG has just one type of convolutional block, and one type of fully connected ('dense') block. Here's the convolution...
def ConvBlock(layers, model, filters): for i in range(layers): model.add(ZeroPadding2D((1,1))) model.add(Convolution2D(filters, 3, 3, activation='relu')) model.add(MaxPooling2D((2,2), strides=(2,2)))
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
...and here's the fully-connected definition.
def FCBlock(model): model.add(Dense(4096, activation='relu')) model.add(Dropout(0.5))
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
When the VGG model was trained in 2014, the creators subtracted the average of each of the three (R,G,B) channels first, so that the data for each channel had a mean of zero. Furthermore, their software that expected the channels to be in B,G,R order, whereas Python by default uses R,G,B. We need to preprocess our data...
# Mean of each channel as provided by VGG researchers vgg_mean = np.array([123.68, 116.779, 103.939]).reshape((3,1,1)) def vgg_preprocess(x): x = x - vgg_mean # subtract mean return x[:, ::-1] # reverse axis bgr->rgb
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0
Now we're ready to define the VGG model architecture - look at how simple it is, now that we have the basic blocks defined!
def VGG_16(): model = Sequential() model.add(Lambda(vgg_preprocess, input_shape=(3,224,224))) ConvBlock(2, model, 64) ConvBlock(2, model, 128) ConvBlock(3, model, 256) ConvBlock(3, model, 512) ConvBlock(3, model, 512) model.add(Flatten()) FCBlock(model) FCBlock(model) model...
deeplearning1/nbs/lesson1.ipynb
sainathadapa/fastai-courses
apache-2.0