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## Taught Bio-Informatics (UG)

I am in the process of winding up taking a basic course on Bio-Informatics, it is offered as an elective subject for final year under-graduate Information Technology students.  I preferred taking this course as a visiting faculty on weekends as managing time in the week is hard (though i did take some classes on weekdays).

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[Gene Clustering : (a) shows clusters (b) uses hierarchical clustering (c) uses k-means (d)  SOM finds clusters which are arranged in grids. Source : Nature Biotechnology 23, 1499 – 1501 (2005) by Patrick D’haeseleer]

Why Bio-Informatics?

The course (out of the ones offered in Fall) I would have preferred taking the most would have been a course on AI. There is no course on Machine Learning or Pattern Recognition at the UG level here, and the course on AI comes closest as it has sufficient weight given to Neural Nets and Bayesian Learning.

The only subject that comes nearest to my choice as AI was not available, was Bio-Informatics as about 60 percent of the syllabus was Machine Learning, Data Mining and Pattern Recognition. And it being a basic course gave me the liberty to take these parts in much more detail as compared to the other parts. And that’s exactly why taking up Bio-Informatics even though it’s not directly my area was not a bad bargain!

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The Joys of Teaching:

This is the first time that I have formally taken a complete course, I have taken work-shops and given talks quite a few times before. But never taken a complete course.

I have always enjoyed teaching. When I say I enjoy teaching, I don’t necessarily mean something academic. I like discussing ideas in general

If I try to put down why I enjoy teaching, there might be some reasons:

• There is an obvious inherent joy in teaching that few activities have for me. When i say teaching here, like I said before I don’t just mean to talk about formal teaching, but rather the more general meaning of the term.
• It’s said that there is no better way to learn than to teach. Actually that was the single largest motivation that prompted me to take that offer.
• Teaching gives me a high! The time I get to discuss what I like (and teach), I forget things that might be pressing me at other times of the day. I tend to become a space-cadet when into teaching. It’s such a wonderful experience!
• One more reason that i think i like teaching is this : I have a wide range of reading (or atleast am interested in) and I have noticed that the best way it gets connected and in most unexpected ways is in discussions. You don’t get people who would be interested in involved discussions very often, also being an introvert means the problem is further compounded. Teaching gives me a platform to engage in such discussions. Some of the best ideas that I have got, borrowing from a number of almost unrelated areas is while discussing/teaching. And this course gave me a number of ideas that I would do something about if I get the chance and the resources.
• Teaching also gives you the limits of your own reading and can inspire you to plug the deficiencies in your knowledge.
• Other than that, I take teaching or explaining things as a challenge. I enjoy it when I find out that I can explain pion exchanges to friends who have not seen a science book after grade 10. Teaching is a challenge well worth taking for a number of reasons!

From this specific course the most rewarding moment was when a couple of groups approached me after the conclusion of classes to help them a little with their projects. Since their projects are of moderate difficulty and from pattern recognition, I did take that up as a compliment for sure! Though I can not say I can “help” them,  I don’t like using that word, it sounds pretentious, I would definitely like to work with them on their projects and hopefully would learn something new about the area.

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Course:

I wouldn’t be putting up my notes for the course, but the topics I covered included:

1. Introduction to Bio-Informatics, Historical Overview, Applications, Major Databases, Data Management, Analysis and Molecular Biology.

2. Sequence Visualization, structure visualization, user interface, animation verses simulation, general purpose technologies, statistical concepts, microarrays, imperfect data, quantitative randomness, data analysis, tool selection, statistics of alignment, clustering and classification, regression analysis.

3. Data Mining Methods & Technology overview, infrastructure, pattern recognition & discovery, machine learning methods, text mining & tools, dot matrix analysis, substitution metrics, dynamic programming, word methods, Bayesian methods, multiple sequence alignment, tools for pattern matching.

4. Introduction, working with FASTA, working with BLAST, filtering and capped BLAST, FASTA & BLAST algorithms & comparison.

Like I said earlier, my focus was on dynamic programming, clustering, regression (linear, locally weighted), Logistic regression, support vector machines, Neural Nets, an overview of Bayesian Learning. And then introduced all the other aspects as applications subsequently and covered the necessary theory then!

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Resources:

All my notes for the course were hand-made and not on $\LaTeX$, so it would be impossible to put them up now (they were basically made from a number of books and the MIT-OCW).

H0wever I would update this space soon enough linking to all the resources I would recommend.

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I am looking forward to taking a course on Digital Image Processing and Labs the next semester, which begins December onwards (again as a visiting instructor)! Since Image Processing is closer to the area I am interested in deeply (Applied Machine Learning – Computer Vision), I am already very excited about the possibility!

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### 7 Responses

1. Hi,

Great post! I completely agree on all the benefits of teaching you’ve mentioned.

It would be really nice if you could scan your handwritten notes and upload them.

Thanks!

2. Thanks Sumeet for the kudos!

Scanning all notes would be a little difficult (my handwriting is not that legible too). But I would try my best to do so.

Respect,
– Shubhenud

3. Great post, I agree fully with your points and its good to see you interested in Bio-Informatics.

4. Namaste. Teaching is a joy only if your students make a real effort. I’ve got a hard time just teaching English to adolescents (and my pay is not the most attractive at present). They really need to learn more about the world than just what they see on TV. But I’m glad you enjoy it so. You must have really good karma, sir.

5. @Manjil

Sorry for the extremely late reply. I was on a hiatus. Now back on the scene.

Thanks for the kudos! :) And an interest in Machine Learning opens up a good number of interest areas as the basic tools remain the same. I find population genetics very exciting, as exciting as vision (in which I have projects).

@Yours Truly.

Namaste _||_ (^_^)

Again apologize for the delayed reply. I was on a hiatus of sorts. Back now.

I agree with you. It is indeed difficult to handle un-motivated students, and I indeed think I was lucky to get a good set of students.
Giving in your best efforts to teach and not seeing much enthusiasm can be very disappointing. All the best with your teaching. I might be taking another class the next semester. I will write in case I get as excited as I got this time or have some interesting observation.

Respect to both,
– S

6. hi , great to see u teaching and enjoying it too !