Machine Learning, python, research, resources

Deep Learning for Protein Function Prediction

Protein function prediction is taking information about a protein (such as its amino acid sequence, 2D and 3D structure etc.) and trying to predict which functions it will exhibit. This has implications in several areas of bioinformatics and affects how drugs are created and diseases are studied. This is typically an intensive task requiring inputs from biologists and computer experts alike and annotating newly found proteins requires empirical as well as computational results.

We, here at FAST NU, recently came up with a unique method (dubbed DeepSeq — since it’s based on Deep Learning and works on protein sequences!) for predicting functions of proteins using only the amino acid sequences. This is the information that is the first bit we get when a new protein is found and is thus readily available. (Other pieces require a lot more effort.)

We have successfully applied DeepSeq to predict protein function from sequences alone without requiring any input from domain experts. The paper isn’t peer reviewed yet but we have made the paper available as preprint and our full code on github so you can review it yourself.

We believe DeepSeq is going to be a breakthrough inshaallah in the field of bioinformatics and how function prediction is done. Let’s see if I can come up with an update about this in a year after the paper has been read a few times by domain experts and we have a detailed peer review.

DeepSeq

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Django, python, Tutorials

Row-level Permissions in Django Admin

So you’ve started working with Django and you love the admin interface that you get for free with your models. You deploy half of your app with the admin interface and are about to release when you figure out that anyone who can modify a model can do anything with it. There is no concept of “ownership” of records!

Let me give you an example. Let’s say we’re creating a little MIS for the computer science department where each faculty member can put in his courses and record the course execution (what was done per lecture). That would be a nice application. (In fact, it’s available open source on github and that is what this tutorial is referring to.) However, the issue is that all instructors can access all the course records and there is no way of ensuring that an instructor can modify only the courses that s/he taught. This isn’t easily possible because admin doesn’t not have “row-level permissions”.

Continue reading “Row-level Permissions in Django Admin”

Geek stuff, python, resources, Tutorials

AVL Tree in Python

I’ve been teaching “Applied Algorithms and Programming Techniques” and we just reached the topic of AVL Trees. Having taught half of the AVL tree concept, I decided to code it in python — my newest adventure. Bear in mind that I have never actually coded an AVL tree before and I’m not particularly comfortable with python. I thought it would be a good idea to experiment with both of them at the same time. So, I started up my python IDE (that’s Aptana Studio, btw) and started coding.

For the newbie programmer, the code itself may not be very useful since you can find better code online. The benefit is in being able to look at the process. You can take a look at the commits I made along the way over here on github. You can take a look at how I structured the code when I began and how I added bits and pieces. This abstraction should help in solving other problems as well. The final code (along with a rigorous unit test file) can be seen here: https://github.com/recluze/python-avl-tree