As an analyst, I spent a significant amount of time typing, all kinds of typing, writing code in Jupyter notebook, navigating through the servers within bash, browsing the internet or even just writing emails and text editing in general, or even right at this second, typing this blog up (I guess Jupyter notebook and blog writing both falls under the browser navigating). Most people might not have the opportunity or access to watching some of the best “typers” in a close distance, some of you who constantly do pair programmings with your coworkers, coaching your junior team members how to use linux, or even just by sitting in a meeting watching your someone sharing their screen, you can clearly tell a difference in people’s productivity not necessarily by people’s IQ, nor methodology, merely noticeable time saving/wasting led by operatational efficiencies introduce by how fast they can instruct the computer in general, or simply typing.

Blind Typing

To me, blind typing is as much a necessary skillset in the 21st century as driving to society after Ford commercialized automobiles. I happen to have the opportunity sit in several technical interviews with lots of candidates with various experiences based on their own claims, and various levels of experiences based on their own demonstration. I came across college students who navigate through stackoverflow and google like playing starcraft 2 with a 200APM cracking the coding interview like no one’s business, and at the same time, tortured by watching self-claimed decades of experience senior staff delete lines of text again and again because they made a typo in previous lines of code but unable to notice it till the very end because the attention is all on the keyboard to find the right key. People claim that writing or programming is only about typing, and many top notch programmers aren’t the fastest typers in the world, it is more about the logic, the ideas, which I fully agree and bear that philosophy deep in my heart.But in my humble opinion, having great logic and beautiful written code doesn’t conflict with you typing fast. Making blind typing your second nature with 60 words per minute minimum and decent amount of accuracy (no constant backspace) will certainly free your mind to focus more on thinking.

Lebron James might be an exception who is “allowed” to type using two index fingers but only because he doesn’t even need to look at his “monitor” when he does his job, let alone “keyboard”.

Shortcut

To me, this is the differentiator which many people got left behind because now they have a way of doing things. Theoretically, yes, having the keys, backspace and arrow keys can help you navigate through if not all, very majority of your tasks. It is more intuitive, “makes sense”, but it is those black magics that made your job unique, it is those mysteries that distinguish you from the rest. And shortcuts are certainly the key. It get you to a place faster, faster to allow to make more mistakes, faster to save time, faster to achieve more, and faster to level that quantitative difference one day will actually make a qualitative difference that people who watch your screen suddenly drops their jaw to the ground.

You can pretty much Google search “shortcuts of” with any softwares that you use at a day to day basis, conquer the inertia of doing it in the old way and soon you will learn it. However, on a software to software basis, sometimes the marginal benefit is fairly low because some shortcuts are not quite frequently used, and those shortcuts won’t work in other tools so it will be good to start analyzing people’s typing behavior and come up with a some of the most generic and beneficial shortcuts to get started.

There is no doubt of those usual suspects like C-c (Control +C), C-v and C-z, if you are not already familiar with. Here I want to share a few shortcuts specifically related to text editing that I wish someone told me when I first started my career, or back to when I was access computer since 12 years old. I do have to say, many of the short cuts were actually learned from when I started using Linux, which a mouse or even a GUI is not readily available. You need to figure out how to only use a keyboard to do everything you wanted text editing.

Control + E

C-e: go to the end of the current line, this one works EVERYWHERE, in the browser, in code editor, in terminal and pretty much everywhere that I know of texting editing. Can you use mouse? sure, can you hit the right arrow key until you get to the end of the text? yes, can you use down Arrow key and it will get to the end of the line if the line your are editing is indeed the last line? yes. Can you … I believe there are a dozens of ways of achieving go the end of the current line but to me. I will share when I use this functions the most.

For example, when I edit Python code, I tend to use Jupyter Notebook which whenever I type any type of closure, like left open parenthesis, left brackets, single/double/triple comma, it will auto complete with the pairing half and focus your cursor in the middle. This is a great feature to save you the effort of counting brackets or avoid error out of accidentally missing the closure or actually saved you half of the typing because when there is an open, there must be a closure. However, now you are in the middle, after you auto editing the content, there isn’t necessarily a way to get back outside so you can keep editing, most people now will use the Arrow key, or god forbid, mouse, to navigate back to where they wanted to edit. Here is where C-e comes in which directly navigate to the end of the line which you can keep editing. If you are comfortable using Control keys or Meta keys (Alt or Option), C-e literally feels like one keystroke. but instead of completely moving your right hand away, find arrow keys, push it several times, and then reposition your index finger on the J key now feels too much work all of a sudden. In this case, there is a easily 2x or 3x+ inefficiencies introduced by not using C-e, and imagine how many closures you have in your code? every function has a closure, every collection (list, dictionary) has some sort of closure, indexing slicing, ..etc.

I did a character count on all the Python files within one of the most popular libraries out there, sklearn. As you can tell, there are about ~ 3% of all your keystrokes that can benefit from this little shortcut.

People go to beginning of the line far less frequent than end of line as you right right beginning to ending! But if you do, which I use occasionally, C-a is the opposite of C-e.

Shift Click Selection

Sometimes, one needs to select a good chunk of text, copy and paste it somewhere. Have you had this experience that your selection is several pages and after you click your left mosue key, scrolling for pages after pages while holding that key down, only once in a while you accidentally let it go and you will have to scroll up and redo everything again? Sometime, we are talking about pages after pages. At least, I certainly remember the frustration when it happens and I have to hold my breath. There is a little trick that you can just click the start of the text that you want to copy, without holding anything, it is just like place a an invisible sign to mark the start of your selection, and then you can casually scroll down, and use “Shift + Click” to mark the end of the selection and everything will be selected! What is even better, after you mark the start, you can even use page up, page down, space and other keystrokes to navigate without even rolling that squeeky wheel on the poor mouse.

C-f/b better than Right/Left Arrow

As I have mentioned before, moving either of your hand away, so far away from the F and J key that you need to reposition should be avoided at all possible costs. Then people might ask, I need the Arrow keys to go forward and backward some certain characters like when there is a typo, missed typed several characters, or only when you noticed there is a typo in the middle of your line. Don’t worry, there are shortcuts too so you don’t have to use Arrow keys. You can use C-f to move your cursor forward by one character and C-b to move backward by one chart. holding those keys, just like using the arrow key will move as many characters as long as you are holding them down. This one took me a while to change the habit but once I get used to it – combination keys don’t slow me down anymore and reaching out to the arrow keys feel like a 5 hrs trip from LA to NY, again, reaching out to the mouse or trackpad is figuratively visiting India from NewYork, on an economy class in the middle seat with both of your neighbors need seat belt extension.

M-f/b faster than C-f/b

M is many contexts refers to the Meta (meta) key or the Alt key for your keyboard. If you are editing one line of texts and want to move way back or forard to make a change, holding down either arrow or C-f/b feels too long. Have you seen this before?

This is where some shortcuts conflict with each other and might be platform dependent as in Linux or Emac, it is M-f to move forward by a word and M-b to move backward by a word. In MacOS terminal, it is still the case, but certainly not the case in text editor. Instead it looks like Meta + Arrow keys to move by word just so everyone knows.

Tab

Many people know that tab means autocomplete, but the level of adoption certainly varies. I have seen people use tab merely as a suggestion, still prefers to type literally every character out one by one, also have seen people use the mouse to choose from the autocomplete, probably trained by years of experience using filters in Excel.

Others

Later on, I realized that many of the short comes from Linux and here is a Emac reference card which if not all, very majority of the shortcuts related to Motion and Editing are applicable in all text editor. Even Google search bar 🙂 I will keep adding to this posts about great shortcuts that I found and share with you. Also, the ultimate secret to take the shortcut is to a good trade off between exploration and exploitation. Can you turn a code snippet into a small framework or function, can you use others libraries.

refcard

In the data booming age, there is an unprecedented amount of demand for data processing, especially “big data scale” processing, something that you just know it won’t work on your laptop. A few common cases like parsing large amounts of HTML pages, preprocess millions of photos and many others. There are tools readily available if your data is fairly structured, like Hive, Impala but there are just those cases, which you need a bit more flexibility other than plain SQL. In this blog post, we will use one of the most popular frameworks Apache Spark, and share how to ship out your own Python environment without worrying at all about the Python dependency issues.

In most of the vanilla big data environment, HDFS is the still a common technology where data is stored. In Cloudera/Hortonworks distribution and cloud provider solutions like AWS EMR, they mostly YARN or Hadoop Next Gen. Even for an environment where Spark is installed, there are many users run Spark on top of YARN like this. As Python is the most commonly use language, Pyspark sounds like the best option.

Managing Python environment on your own laptop is already fun, managing multiple versions, multiple copies on a cluster that likely be shared with other users could be a disaster. If not otherwise configured, pySpark will use the default Python installed on each node. And your system admin certainly won’t let you mess with the server Python interpreter at all. So your cluster admin and you might come to a middle ground which a new Python, say Anaconda Python, can be installed on all the nodes using a network shared file system which you have more flexibility, as any installation can be mirrored to other nodes and the consistency is ensured. However, only after a few days that you noticed your colleagues accidentally “broke” the environment by upgrading certain libraries without you knowing, and now, you have to police that Python environment. After all, this comes to the question of how each user can customize their own Python environment and make sure it runs on the cluster. The answer to Python environment management is certainly Anaconda, and the answer to distributed shipment will be YARN archives argument.

The idea is that for any project, feel free to create your own conda environment and do the development within that environment, so in the end, you will use the Python at your own choice and a clean environment with all the necessary libraries only installed for this project. Like a uber jar idea of Java. Everything python related in one box. Then, we will submit our pyspark job first by shipping that environment to all the executors where the workload will be distributed, but then second, configuring each executor will use the Python that we shipped. All the resource management, fan out and pull back will be handled by Spark and YARN. So three steps in total, first being a conda environment, second being a Pyspark driver and last is the code submition.

In the following section, I will share how to distribute the HTML parsing in a Cloudera environment as an example, every single step is also available on Github in case you want to follow along.

Conda

If you are not already familiar with Conda, it is only one of the tools that many Python users live and breathe on a day to day basis.  You can learn more about Anaconda from here.

Driver.py

Run.sh

Reference:

[1] https://docs.cloudera.com/documentation/enterprise/5-14-x/topics/spark_python.html

[2] https://blog.cloudera.com/making-python-on-apache-hadoop-easier-with-anaconda-and-cdh/

Great video from Joe Collins introducing abut Pushd and Popd so you can find your way back in the linux directory navigation.

Recently I got access to a server that somehow all the ports got blocked except for SSH, instead of waiting for a few weeks until the IT freeze and ports got opened up, I found that you can access the other ports via a technique called SSH tunneling if you have admin rights on the remote host.

ssh -L 9191:localhost:9191 -L 8080:localhost:8080 -L 8088:localhost:8088 user@host

This will ssh into the remote host and keep those three ports mapped from local client to remote host. However, this is fragile as if your ssh is broken, all the ports will be broken, and if your terminal is idle with a broken pipe, your tunnel is also break. There are other flags like run in background as daemon but if you chose that route, make sure you kill the ssh process when done, otherwise, you will never get back to your own 9191 🙂

Now you can access the port in your client browser just like below.

There are plenty of images data out there that are of the format RGBA (Red Green Blue and Alpha), in which Alpha represents the transparency. By leaving RGB all empty and Alpha to store the information of the shape, the image itself is like a layer that you can add on top of any other photos that sort of “float around”, just like lots of icons out there. However, this type of photos aren’t necessarily friendly or ready to be directly fed into many of the machine learning frameworks which usually work with RGB or greyscale directly. This is a post to document what I did to convert some of this kind of alpha only images into RGB image.

First, there are plenty of libraries out there process images. I am merely sharing some of the work that I did without necessarily comparing the performance of different approaches. The libraries that I will cover in this post is imageio and Pillow. I have read htat imageio is supposed to be your first choice as it is well maintained while Pillow isn’t anymore. However, I found that imageio is very easy to use but its functionality is limited and not as diverse as Pillow. Imageio, as the name indicates, deals with read and write of images, while Pillow has more functionalities of dealing with images itself like channels, data manipulation, etc.

My very first try was to convert RGBA into a matrix that has (200, 200, 4) which my image already has the square size of 200×200. And then drop the last column which is alpha and then populate the RGB channel using the value of alpha channel. In that case, our RGB will be equally populated and our photo should look black and white.

The code is simple, m is PIL.Image.imread returned object. I first resize it to be 256*256, which is more ML friendly. And then convert it into an array, data which has the shape of 40000, 4. After assigning RGB and dropping A, we call the reshape to turn it back into 256*256*4 and reconstruct the image “fromarray”. Here astype(np.unit8) caught me offguard a bit and there maybe one of the reasons that Pillow is not perfect due to the lack of maintenance. And the invert in the end will invert the color (black to white and white to black) so it has the background that I like.

The code is easy to understand but when I execute it, it was slow, I did not run any benchmark but it was noticeable slow comparing with some other preprocessing that I ran before.

In the end, I realize that there is already a built in function called getchannel so you can get a specific channel without dealing with arrays directly.

The convert_rgb_fast does the same thing as the function above but execute much faster, likely because I was doing lots of matrix assignment and index slicing which is not very efficient I guess.

Also, by using getchannel, you can easily convert it to have only one channel that is basically greyscale. All the channels don’t have name and RGBA is just convention, if you only have one channel, all the tools out there will assume it is greyscale.

Image preprocessing is likely as important as training the model itself, the easy part of image processing is that it can be easily distributed using frameworks like mapreduce, spark and others. Using Python is probably the easiest way for model data professionals and we will find an opportunity in the future to demonstrate how to speedup the data cleaning.

First, here is the proof that I got stylegan2 (using pre-trained model) working 🙂

Nvidia GPU can accelerate the computing dramatically, especially for training models, however, if not careful, all the time that you saved from training can be easily wasted on struggling with setting up the environment in the first place, if you can get it working.

The challenges here is that there are multiple nvidia related enviroment like the basic GPU driver, CUDA version, cudnn and others. For each of those, there is also different versions which you need to be careful about making sure they are consistent. That itself is already some pain that you want to go through. Last but certainly the least fun, is getting tensorflow itself not only working, but getting the tensorflow versions in alignment with the CUDA environment that you have, at the same time, using the tensorflow with the project that you likely did not write yourself but forked some other person’s github project. The odds of all of those steps working seamless will add no value to you as someone who just wanted to generate some images and serve no purpose but becoming frustrated.

I know that lots of the Python users out there use anaconda to manage their Python development environment, switching between different versions of Python at will, maintaining multiple environment with different versions of tensorflow if you want, and sometimes even have a completely new conda environment for each project just to keep things clean. In the world of getting github project up and running fast, I guess that workflow is not enough. There is much more than just Python so in the end, a tool like Docker is actually the panacea.

If you have not used Docker that much in the past, it is as easy as memorizing just a few command line instructions to start and stop the Docker container. This Tensorflow with Docker from Google is a fantastic tutorial to get started.

For stylegan2, here are some commands that might help you.

sudo docker build - < Dockerfile    # build the docker image using the Docker file from stylegan2
sudo docker image ls
docker tag 90bbdeb87871 datafireball/stylegan2:v0.1
sudo docker run --gpus all -it -rm -v `pwd`:/tmp -w /tmp datafireball/stylegan2:v0.1 bash # create a disposal working environment that will get deleted after logout that also map the current host working directory to the /tmp folder into the Docker
sudo docker run --gpus all -it -d -v `pwd`:/tmp -w /tmp datafireball/stylegan2:v0.1 bash # run it as a long running daemon like a development environment
sudo docker container ls 
sudo docker exec -it youthful_sammet /bin/bash # connect to the container and run bash command "like ssh"

I assure you, the pleasure from getting all the examples run AS-IS is unprecedented. I suddenly changed my view from “nothing F* works, what is wrong with these developers” to “the world is beautiful, I love the open source community”. 

You can use Docker to not only get Stylegan running, you can get the tensorflow-gpu-py3 working, and not meant to jump the gun for the rest of the development world, I bet there are plenty of other people who struggle to environment set up can benefit from using Docker, and there are equally amount of people out there who can make the world a better place by start his/her project with a docker image knowing that no one in the world, including the developer himself, how the environment is configured.

Life is short, use [Python inside a docker] 🙂

A big problem of many machine learning techniques is the difficulty of interpreting the model and explaining why things are predicted in certain ways. For simple models like linear regression, one can sort of justify using the concepts of slope for every change in x lead to certain amount change in y. Decision Tree can be plotted to explain to users how a leaf got reached based on the split conditions. However, neural network is notoriously difficult to explain and tree based ensembles are also complex, let alone other techniques. Lime is a pretty commonly used technique that is capable of serving some explanations for the prediction given by any model, hence the name, model-agnostic.

The rough idea is that you start with a prediction made by a trained model. The model is supposedly trained by the whole training dataset and capable of recognizing the real underlying pattern, eg. if we assume there are two numerical inputs x1, x2 and one numerical outputs y, the underlying relationship could be a deterministic function that you can visualize in a 3D space y = x1^2 + 3*x2^2. A good supervised machine learning technique is supposed to accurately capture the function from lots of data points and generalize to the mapping shape in its model. When the model is making a prediction, LIME will intelligently generate several data points around the input neighbourhood, if the neighbour is small enough, we should be able to reach a smooth surface and accurately build a model, a linear model to describe the effect of each of the input variables. Once you calculate the gradients, you can interpret the gradient as the partial derivatives with meaningful interpretations like the final prediction score was made up of all the inputs weighted in certain ways.

You can read more about LIME through its Github page, this paper or this blog.

In this blog post, we will dig through its source code and browse through some of the key functions being used in LIME to better understand how the idea got implemented. As we are not looking at any computer vision related machine learning applications, like CNN, we will focus on these two following files which also turned out to be the latest maintained files, lime_base.py and lime_tabular.py.

LIME_BASE

lime_base.py is a very small file that only includes the LimeBase class.

As in the file doc, the lime_base class contains abstract functionality for learning locally linear sparse model. The explain_instance_with_data is the starting point which pretty much captured the gist of the whole LIME package.

One can learn more about Ridge and Lasso in this blog post.

Feature selection is a very important step during this approximation process and it is adopting several different techniques that are well explained in its comments.

However, understanding feature selection is beyond the scope of this post but I highly recommend you read more about these techniques as it is not only used in LIME but also generalizes to the whole machine learning realm. Here we will only take a glimpse into the forward_selection method is a pretty straight forward feature selection process.

random.rand

random_state is a class from the numpy package which can generate random number following many types of distributions. In this case, the author used the random_state.rand(d0) to generate a one dimension array that has as many elements as n_total_samples, in which each value is between 0 and 1.

Meanwhile, they also prepopulate the sample_mask which has the same shape as the rand variable with 0s.

Then during the for loop, they decide if they want to mask each sample from 0 to 1 using a pretty interesting condition.

rand[i] * (n_total_samples – i) < (n_total_in_bag – n_bagged)

or if we rearrange to be like:

rand[i]  < (n_total_in_bag – n_bagged) / (n_total_samples – i)

n_total_in_bag – n_bagged => how many remaining need to be bagged

n_total_samples – i => how many total samples to be considered

At the beginning of numerator is large and will decrease as we switch more masks, and the denominator is also large and also decrease as we continue. n_bagged will start at 0 and as i increase, the threshold will keep increasing and the probability that rand[i] is smaller actually will increase. And when the condition is met, we will flag it as masked and add 1 to the n_bagged. And we will continue until n_bagged equals to n_total_in_bag. In that case, the threshold will become literally 0 and the condition will never be met because the random number generator only spit out numbers between [0,1). Also, if there are more remaining need to be bagged than total left to be considered, the threshold will be strictly greater than 1 and it will definitely will masked which probably happens a lot at the beginning.

mask

Here is a screenshot to demonstrate how np.array indexing mask works. As you can see, they support boolean type and numeric index slicing. However, there is one operator which is the “~” sign which our Python users might not come across very often. It is actually the invert operator.

yeah, this is exactly what I mean by inversion!

Joke aside, “~” is the same as the operator.__invert__. Regarding bitwise operations, you can find the definitions from the Python wiki bitwise operations documentation here. “~x” is basically the same as -x-1. Like ~3 => -4 and ~-4 => 3.

You can also find more information about indexing from ndarray indexing documentation.