Data Profiling in Python

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With every data analytics and data science project, one of the first tasks to that everyone needs to do is to profile the data sets. Data profiling allows you to get an initial picture of the data set, see data distributions and relationships. Additionally it allows us to see what kind of data cleaning and data transformations are necessary.

Most data analytics tools and languages have some functionality available to help you. Particular the various data science/machine learning products have this functionality built-in them and can do a lot of the data profiling automatically for you. But if you don’t use these tools/products, then you are probably using R and/or Python to profile your data.

With Python you will be working with the data set loaded into a Pandas data frame. From there you will be using various statistical functions and graphing functions (and libraries) to create a data profile. From there you will probably create a data profile report.

But one of the challenges with doing this in Python is having different coding for handling numeric and character based attributes/features. The describe function in Python (similar to the summary function in R) gives some statistical summaries for numeric attributes/features. A different set of functions are needed for character based attributes. The Python Library repository (https://pypi.org/) contains over 200K projects. But which ones are really useful and will help with your data science projects. Especially with new projects and libraries being released on a continual basis? This is a major challenge to know what is new and useful.

For example the followings shows loading the titanic data set into a Pandas data frame, creating a subset and using the describe function in Python.

import pandas as pd

df = pd.read_csv("/Users/brendan.tierney/Dropbox/4-Datasets/titanic/train.csv")

df.head(5)

Screenshot 2019-11-22 16.58.39

df2 = df.iloc[:,[1,2,4,5,6,7,8,10,11]]
df2.head(5)

Screenshot 2019-11-22 16.59.30

df2.describe()

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You will notice the describe function has only looked at the numeric attributes.

One of those 200+k Python libraries is one called pandas_profiling. This will create a data audit report for both numeric and character based attributes. This most be good, Right?  Let’s take a look at what it does.

For each column the following statistics – if relevant for the column type – are presented in an interactive HTML report:

  • Essentials: type, unique values, missing values
  • Quantile statistics like minimum value, Q1, median, Q3, maximum, range, interquartile range
  • Descriptive statistics like mean, mode, standard deviation, sum, median absolute deviation, coefficient of variation, kurtosis, skewness
  • Most frequent values
  • Histogram
  • Correlations highlighting of highly correlated variables, Spearman, Pearson and Kendall matrices
  • Missing values matrix, count, heatmap and dendrogram of missing values

The first step is to install the pandas_profiling library.

pip3 install pandas_profiling

Now run the pandas_profiling report for same data frame created and used, see above.

import pandas_profiling as pp

df2.profile_report()

The following images show screen shots of each part of the report. Click and zoom into these to see more details.

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Always watching, always listening. Be careful with your data

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The saying ‘Big Brother is Watching’ has been around a long time and typically gets associated with government organisations. But over the past few years we have a few new Big Brothers appearing. These are in the form of Google and Facebook and a few others.

These companies gather lots and lots. Some companies gather enormous amounts of data. This data will include details of your interactions with the companies through various websites, applications, etc. But some are gathering data in ways that you might not be aware. For example, take this following video. Data is being gathered about what you do and where you go even if you have disconnected your phone.

Did you know this kind of data was being gathered about you?

Just think of what they could be doing with that data, that data you didn’t know they were gathering about you. Companies like these generate huge amounts of income from selling advertisements and the more data they have about individuals the more the can understand what they might be interested. The generate customer profiles and sell expensive advertising based on having these very detailed customer profiles.

But it doesn’t stop there. Recently Google bought Fitbit. Just think about what they can do now. Combining their existing profiles of you as a person with you activities throughout every day, week and month. Just think about how various health and insurance companies would love to have this data. Yes they would and companies like Google would be able to charge these companies even more money for this level of detail on individuals/customers.

But it doesn’t stop there. There have been lots of reports of various apps sharing health and other related data with various companies, without their customers being aware this is happening.

What about Google Assistant? In a recent article by MIT Technology Review title Inside Amazon’s plan for Alexa to run your entire life, they discuss how Alexa can be used to control virtually everything. In this article Alexa’s cheif scientist say “plan is for the voice assistant to move from passive to proactive interactions. Rather than wait for and respond to requests, Alexa will anticipate what the user might want. The idea is to turn Alexa into an omnipresent companion that actively shapes and orchestrates your life. This will require Alexa to get to know you better than ever before.”  When combined with other products this will allow “these new products let Alexa listen to and log data about a dramatically larger portion of your life“.

Just imagine if Google did the same with their Google Assistant!  Big Brother isn’t just Watching, they are also Listening!

There has been some recent report of Google looking to get into Banking by offering checking accounts. The project, code-named Cache, is due to launch in 2020. Google has partnered with Citigroup and a credit union at Stanford University, which will administer the accounts. Users will be able to access their accounts through Google’s digital payment platform, Google Pay.

And there are the reports of Google having access to the health records of over 50 million people. In addition to this, Google has signed a deal with Ascension, the second-largest hospital system in the US, to collect and analyze millions of Americans’ personal health data. Ascension operates in 150 hospitals in 21 states.

What if they also had access to your banking details and spending habits? Google is looking at different options to extend financial products from the google pay into more main stream banking. There has been some recent report of them looking at offering current accounts.

I won’t go discussing their attempts at Ethics and their various (failed) attempts at establishing and Ethics Advisory Board. This has been well documented elsewhere.

Things are getting a bit scary and the saying ‘Big Brother is Watching You’, is very, very true.

In the ever increasing connected world, all of us have a responsibility to know what data companies are gathering on us. We need to decide how comfortable we are with this and if you aren’t then you need to take steps to ensure you protect yourself. Maybe part of this protection requires us to become less connected, stop using some apps, turn off more notification, turn off updates, turn off tracking, etc

While taking each product or offering individually, it may seem ok to us for Google and other companies to offer such services and to analyze our data to provide a better service. But for most people the issues arise when each of these products start to be combined. By doing this they get to have greater access and understanding our our data and our behaviors. What role does (digital) ethics play in all of this? This is something for the company and the employees to decide where things should stop. But when/how do you decide this? when do you/they know things have gone too far? how can you undo some of this work to go back to an acceptable level? what is an acceptable level and how do you define this?

As yo can see there are lots of things to consider and a vital component is the role of (digital) ethics. All organizations who process and analyze data need to have an ethics board and ethics needs to be a core part of every project. To support this everyone needs more training and awareness of ethics and what is acceptable or not.

Demographics vs Psychographics for Machine Learning

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When preparing data for data science, data mining or machine learning projects you will create a data set that describes the various characteristics of the subject or case record. Each attribute will contain some descriptive information about the subject and is related to the target variable in some way.

In addition to these attributes, the data set will be enriched with various other internal/external data to complete the data set.

Some of the attributes in the data set can be grouped under the heading of Demographics. Demographic data contains attributes that explain or describe the person or event each case record is focused on. For example, if the subject of the case record is based on Customer data, this is the “Who” the demographic data (and features/attributes) will be about. Examples of demographic data include:

  • Age range
  • Marital status
  • Number of children
  • Household income
  • Occupation
  • Educational level

These features/attributes are typically readily available within your data sources and if they aren’t then these name be available from a purchased data set.

Additional feature engineering methods are used to generate new features/attributes that express meaning is different ways. This can be done by combining features in different ways, binning, dimensionality reduction, discretization, various data transformations, etc. The list can go on.

The aim of all of this is to enrich the data set to include more descriptive data about the subject. This enriched data set will then be used by the machine learning algorithms to find the hidden patterns in the data. The richer and descriptive the data set is the greater the likelihood of the algorithms in detecting the various relationships between the features and their values. These relationships will then be included in the created/generated model.

Another approach to consider when creating and enriching your data set is move beyond the descriptive features typically associated with Demographic data, to include Pyschographic data.

Psychographic data is a variation on demographic data where the feature are about describing the habits of the subject or customer.  Demographics focus on the “who” while psycographics focus on the “why”. For example, a common problem with data sets is that they describe subjects/people who have things in common. In such scenarios we want to understand them at a deeper level. Psycographics allows us to do this. Examples of Psycographics include:

  • Lifestyle activities
  • Evening activities
  • Purchasing interests – quality over economy,  how environmentally concerned are you
  • How happy are you with work, family, etc
  • Social activities and changes in these
  • What attitudes you have for certain topic areas
  • What are your principles and beliefs

The above gives a far deeper insight into the subject/person and helps to differentiate each subject/person from each other, when there is a high similarity between all subjects in the data set. For example, demographic information might tell you something about a person’s age, but psychographic information will tell you that the person is just starting a family and is in the market for baby products.

I’ll close with this. Consider the various types of data gathering that companies like Google, Facebook, etc perform. They gather lots of different types of data about individuals. This allows them to build up a complete and extensive profile of all activities for individuals. They can use this to deliver more accurate marketing and advertising. For example, Google gathers data about what places to visit throughout a data, they gather all your search results, and lots of other activities. They can do a lot with this data. but now they own Fitbit. Think about what they can do with that data and particularly when combined with all the other data they have about you. What if they had access to your medical records too!  Go Google this ! You will find articles about them now having access to your health records. Again combine all of the data from these different data sources. How valuable is that data?

 

Oracle Magazine articles

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Over the past few weeks I’ve had a couple of articles published with Oracle Magazine and these can be viewed on their website.

The first article is titled ‘Quickly Create Charts and Graphs of You Query Data‘ using Oracle Machine Learning Notebooks.

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The second article is titled ‘REST-Enabling Oracle Machine Learning Models‘.

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Click on the above links to check out those articles and check out the Oracle Magazine website for lots more articles and content.

There will be a few more Oracle Magazine articles coming out over the next few months.

 

Creating a VM on Oracle Always Free

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I’m going to create a new Cloud VM to host some of my machine learning work. The first step is to create the VM before installing the machine learning software.

That’s what I’m going to do in this blog post and the next blog post. In this blog post I’ll step through how to setup the VM using the Oracle Always Free cloud offering. In the next I’ll go through the machine learning software install and setup.

Step 1 – Create a ssh key/file

Whatever your preferred platform for your day to day computer there will be software available for you to generate a ssh key file. You will need this when creating the VM and for when you want to login in to VM on the command line. My day-to-day workhorse is a Mac, and I used the following command to create the ssh key file.

ssh-keygen -t rsa -N "" -b 2048 -C "myOracleCloudkey" -f myOracleCloudkey

Step 2 – Login and Select create VM

Log into your Oracle Cloud Always Free account.

Screenshot 2019-10-21 17.17.00

Select Create a VM Instance.

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Step 3 – Configure the VM

Give the instance a name. I called mine ‘b01-vm-1

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Expand the networks section by clicking on Show Shape, Network and Storage Options. Set the IP address to be public.

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Scroll down to the ssh section. Select the ssh file you created earlier.

Screenshot 2019-10-21 17.24.22

Click on the Create button.

That’s it, all done. Just wait for the VM to be created. This will takes a few seconds.

Screenshot 2019-10-21 17.26.15

After the VM is created the IP address will be listed on this screen. Take note of it.

Step 4 – Connect and log into the VM

We can not log into the VM using ssh, to prove that it exists, using the command

ssh -i <name of ssh file> opc@<ip address of VM>

When I use this command I get the following:

ssh -i XXXXXXXXXX opc@XXX.XXX.XXX.XXX
The authenticity of host 'XXX.XXX.XXX.XXX (XXX.XXX.XXX.XXX)' can't be established.
ECDSA key fingerprint is SHA256:fX417Z1yFoQufm7SYfxNi/RnMH5BvpvlOb2gOgnlSCs.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'XXX.XXX.XXX.XXX' (ECDSA) to the list of known hosts.
Enter passphrase for key 'XXXXXXXXXX': 
[opc@b1-vm-01 ~]$ pwd
/home/opc

[opc@b1-vm-01 ~]$ df
Filesystem   1K-blocks     Used Available Use%  Mounted on
devtmpfs        469092        0    469092   0%  /dev
tmpfs           497256        0    497256   0%  /dev/shm
tmpfs           497256     6784    490472   2%  /run
tmpfs           497256        0    497256   0%  /sys/fs/cgroup
/dev/sda3     40223552  1959816  38263736   5%  /
/dev/sda1       204580     9864    194716   5%  /boot/efi
tmpfs            99452        0     99452   0%  /run/user/1000

And there we have it. A VM setup on Oracle Always Free.

Next step is to install some Machine Learning software.

Changing PDB/CDB spfile parameters

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When working with a Oracle database hosted on the Oracle cloud (not an Autonomous DB), I recently had the need to change/increase the number of processes for the database. After a bit of researching it looked liked I just had to make the change to the SPFILE and that would be it.

I needed to change/increase the PROCESSES parameter for the CDB and the PDB. Following the multitude of advice on the internet, I ssh into the DB server, found the SPFILE and changed it.

I bounced the DB and when I connected to the PDB, I found the number for PROCESSES was still the same as the old/original value. Nothing had changed.

By default the initialization parameter for the PDB inherit the values from the parameters for the CDB. But this didn’t seem to be the case.

After a bit more research, I needed to set this parameter for the CDB and the PDB. But no luck finding a parameter file for the PDB. It turns out the parameters for the PDB are set at the metadata level, and I needed to change the parameter there.

What I had to do was to change the value when connected to it using SQL*Plus, SQL Dev etc.  So, How did I change the parameter value.

Using SQL Developer as my tool, I connected as SYSDBA to my PDB. Then ran,

alter session set container = cdb$root

Now change the parameter value.

alter system set processes = 1200 scope=both

I then bounced the database, logged back into my PDB as system and checked the parameter values. It worked. This was such a simple solution and it worked for me, but there was way too many articles, blog posts, etc out there that didn’t work. Something I’ll need to investigate later is, did I need to connect to the CDB? could I have just run the second command only?  I need to setup a different/test DB and see.

 

OML Workspace Permissions

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When working with Oracle Machine Learning (OML) you are creating notebooks which focus on a particular data exploration and possibly some machine learning. Despite it’s name, OML is used extensively for data discovery and data exploration.

One of the aims of using OML, or notebooks in general, is that these can be easily shared with other people either within the same team or beyond. Something to consider when sharing notebooks is what you are allowing other people do with your notebook. Without any permissions you are allowing people to inspect, run and modify the notebooks. This can be a problem because those people you are sharing with may or may not be allowed to make modification. Some people should be able to just view the notebook, and others should be able to more advanced tasks.

With OML Notebooks there are four primary types of people who can access Notebooks and these can have different privileges. These are defined as

  • Developer : Can create new notebooks withing a project and workspace but cannot create a workspace or a project. Can create and run a notebook as a scheduled job.
  • Viewer : They can just view projects, Workspaces and notebooks. They are not allowed to create or run anything.
  • Manager : can create new notebooks and projects. But only view Workspaces. Additionally they can schedule notebook jobs.
  • Administrators : Administrators of the OML environment do not have any edit capabilities on notebooks. But they can view them.

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