Nabin K. Malakar, Ph.D.

I am a computational physicist working on societal applications of machine-learning techniques.

Research Links

My research interests span multi-disciplinary fields involving Societal applications of Machine Learning, Decision-theoretic approach to automated Experimental Design, Bayesian statistical data analysis and signal processing.


Interested about the picture? Autonomous experimental design allows us to answer the question of where to take the measurements. More about it is here...


I addition to the research, I also like to hike, bike, read and play with water color.

Thanks for the visit. Please feel free to visit my Weblogs.

Welcome to Please visit again.

Wednesday, October 6, 2010

Cleaning the 16inch Telescope Mirror

Thanks to Prof. Delano, we were able to bring the 16-inch lens down.
It requires some cleaning up after about 40 5/6 years. The controller was also not functioning properly. The previous posts on observatory can be found here...
Follow AlbanyStargaze @twitter.
 The concave reflector. Yes, it needed cleaning!
BARSKA 40070 Starwatcher Compact Refractor Telescope with Table Top Tripod And Carrying Case National Geographic Backyard Guide to the Night SkyThe Night Sky 40°-50° (Large) Star Finder

Sunday, September 26, 2010

How to inspire your students?

It is said that it takes a whole village to raise kids...
The statement reflects the power a teacher has during the grooming of the kids in the classroom and beyond.

Some teachers took the parabolic flight, defying gravity and doing the experiments designed by their kids.

I think in the wake interest in increasing the number of students in STEM, one can devise NSF projects for such fun and inspiring projects.

How do you inspire your students?

Teaching Outside the Box: How to Grab Your Students By Their BrainsTeaching to Change Lives: Seven Proven Ways to Make Your Teaching Come AliveFirst Year Teacher's Survival Guide: Ready-To-Use Strategies, Tools & Activities for Meeting the Challenges of Each School Day (J-B Ed: Survival Guides)

Tuesday, September 21, 2010

What is Information?

What is Information?
Is it the data that you collect? Is it the statement that your mother makes when advising not to go outside in the dark? Or is it what you think on what you know about what you are thinking?
Defining information is not so trivial.
Try it, feel free to share on comments.

Friday, September 10, 2010

Seaswarm: Autonomous Oil absorbing robot

When the Gulf oil spill occured, attempts were made to clean it manually. It required deploying thousands of workers and still only few percentage of the spill was collected.  The spill had very bad effects on the environment. Just google gulf oil spill in pictures.
Now researchers at MIT have come up with an autonomous robot to collect the oil from such spill. The video below shows how swarm of networked robots can be used to collect such spill.
The idea is nice because it does not need human intervention. Once left on the spill site, it can work spontaneously.
The Exxon Valdez's Deadly Oil Spill (Code Red)The Basics of Oil Spill Cleanup, Second EditionDisaster in the Gulf - British Petroleum (BP) Deepwater Horizon Oil Spill in the Gulf of Mexico: Impacts on Wildlife, Fisheries, Cleanup Efforts, Investigation (Ringbound Book and DVD-ROM)

Thursday, August 12, 2010

Nepali Physics Students Departing from Nepal: Fall 2010.

This year about 25+-5 Nepali physics students departed aboard to pursue the PhD degree. There are more than 200 physicists aboard now!.
The name and university are listed below:

  • Binod Manandhar- University of Wisconsin Milwaukee
  • Santosh Sharma- University of Memphis, Tennessee
  • Shreedhar Pant- Texas Christian University
  • Navaraj subedi- Mississippi State University
  • Kamal Chapagain- Western Illinois University
  • Dipendra Adhikari- University of New Mexico, NM
  • Tej Nath Lamichhane- University of Texas, Arlington
  • Keshav Sapkota- Catholic University of America
  • Bijaya Thapa - University of Utah
  • Binod Rai- University of Memphis, Tennesse
  • Kamal Dhakal- University of Rhode Island
  • Disoj Neupane- New Mexico State University, NM
  • Takat Rawal- University of Central Florida
  • Raj Dahal- University of Memphis, Tennesse
  • Keshav Shrestha- University of Houston, TX
  • Nabaraj Sapkota- University of Utah
  • Tara Acharya- University of Utah

Please let us know if you are missing on the list.

Thanks to Sanjiv G.


Tuesday, August 10, 2010

Helmet Teachers and +2 Colleges in Nepal

Fuel Gloss Black X-Large Triple Vented Modular Full Face HelmetIn the recent edition of online Himalkhabar, there was a panel discussion on  "which kind of teachers are good". Of course, there was a recurring topic of "Helmet Teachers" as expressed by the participants.
"Helmet Teacher" (HT) in Kathmandu valley is the name given to the teachers who are the visiting teachers without full time commitment to the institution. Helmet teachers are basically invited to teach one or two classes. Since they usually have to cover many such campuses, they usually come in motor-bike (and thus with helmet in hand); teach and go.
Raider Deluxe Gloss Black Small Helmet
The bike Helmets can be lost in critical time, or traffic jam can prevent on-time arrival of such teachers.
Since HT are not fully responsible, the load shift from class to class can disrupt the learning environment. Even some of the time, the fulltime teachers may have to share the load for HT's absence.

10+2 should be obliged to hire certain number of full time committed faculties.
HSEB is now a very big institution. I wonder why it is still not going under hiring HSEB branded teachers. With proper training and HSEB affiliation, the quality of teacher can be assured (if there is any question on it).

The rest is out for discussion. One needs to note that planting the guilt into somebody does not solve the problem.

Saturday, August 7, 2010

My Favorite Ten Nepali Blog posts

Blogging Heroes: Interviews with 30 of the World's Top BloggersOne of the Suggestion on Third Nepali Blogger Bhela was to have a post of 10 fav. posts by Nepali bloggers. This is not top ten blog list. Just ten posts that I liked and remembered as nice posts by fellow bloggers. Posting such favorite posts may help to cross correlate the feelings among the bloggers. 

Amazingly, it ranges from politics, satire, fun, travel diary to daily life instances captured in the words of the bloggers. 

My source of updated nepali blogs is hamrocircle. However, I do wander out of circle and find blogs that are equally compelling.

I have many posts that I like a lot, and selecting 10 is hard job.
However, My Favorite Ten Nepali Blog posts are:

अनन्त बाँदर सिद्धान्त

भेजिटेरीएन माछाको कथा

Why the hell can’t we follow any rules?

भूकम्प-अब हाम्रै पालो त होईन?

वाह ! दृष्टि

विकल्प @ कोपनहेगन

Time For Kids Go Back To School (After Dashain Holiday)

Having Nepali flag on the Blog

A Google Widget for Nepali Bloggers

तपाईं किन कमेन्ट गर्नुहुन्न?

and a bonus!!
SLC को रिजल्ट

Congratulations to for organizing third successful Global Nepali Blogger Bhela.
All the best to Nepali Bloggers.

PS: please feel free to post your favorite ten in your blog. Please do leave some comments :)

Friday, August 6, 2010

Packing for Mars?

This is definitely not a book review, just my wild speculations into travel into Mars.

When you travel for cross Atlantic travel, how cozy was it? Seating at one confined place while waiting for long destination has so many side effects. Physical, psychological so and so.
Well, we are talking about months of isolations and painful travel. This should shakedown your enthusiasm for space travel. :P  
How about adding some humor to the pain? 
It is said that
"Pain + time = humor".

Packing for Mars: The Curious Science of Life in the Void

"Packing for Mars: The Curious Science of Life in the Void" by Mary Roach should be a good read. I would definitely love to have a chance to read it. Actually, I have added it to my wish list@Amazon. ;) Reviews are saying that there are a lot of LOL moments in the book.

I know the saying, "No pain, no gain". However, I am curious why send humans to the deep space? The recent advancement in robotics allows us to do the same thing at less cost and less insurance value than pushing humans to such harsh environments and posing fatal risks involved.

Side note:
Download the pdf to have some idea on how tricky it is to travel to sister planet Mars:

Thursday, August 5, 2010

Bayes' Theorem in \LATEX

I am learning Latex. Using Texnic Center and other similar softwares. I wish that Kile was available on Windows...
Anyways, everytime I start a new file, I have to search for the barebone of the file which needs to be there before anything can be done.
So, here I am collecting some skeleton for latex files:
I think they are free from any (c).

\usepackage{amsmath} % need for subequations
\usepackage{hyperref} % use for hypertext links, including those to external documents and URLs
\title{Your Title Here}
\author{Your Name here \thanks{Email:}
Abstract goes here...
\tableofcontents{} % comment: just in case... it can be commented
Here we start...
Oh, why not start by writing Bayes Theorem in Latex ?
... we use Bayesian method to infer the model parameters in question. We learn from the available data. The process of arriving at the posterior from the prior in the light of given data can be accomplished by using Bayes' theorem.
As a general statement, we can state Baye's theorem as follows\\
P(\theta|\textbf{D}) = P(\theta ) \frac{P(\textbf{D} |\theta)}{P(\textbf{D})} ~~~~~|| I,
where we have adopted Skilling--Gull convention of writing $I$ as the generally accepted term in the conditionals. The data are represented by \textbf{D} and parameters are represented by $\theta$.

Thanks to the Blogger platform which do not convert latex command into symbols. (That was a satire :P )
Note to self: I believe I have seen Gull using the conditional out of bracket... where, where ???

Sunday, August 1, 2010

Bus Resistance of a Code or Program

Last year I was on a training for a operating computations on grid at Cornell. Our instructor from Texas threw a Joke: "Do you know the bus resistance of your code?"
Everyone was surprised to hear the question. The Joke is interesting because it indicates one thing and tells you something else. While some people were thinking of how the string of 1's and 0's that travel through the computer data bus might come across such bus resistance, he explained in a funny way.

Here we go:
Imagine one fine friday evening you are grabbing a beer and walking down the road, and you are hit by a bus. What happens to your code? The next day the project manager decides to give your code to your colleague to continue the project. If your code is not properly commented, he will be completely lost in there. 
So, the bus resistance is given by the amount of comments in a code and the readability of your code by someone else.
Let us wish that this happens to no one. However, for the continuity of the project in your lab, your code must have very high bus resistance value.
The moral is: comment your code as much as you can.
Beginning C++ Through Game Programming, Second EditionPython Programming: An Introduction to Computer Science 2nd EditionC Programming Language (2nd Edition)

Are your codes bus resistant?

Wednesday, July 28, 2010

Congratulations to recent Nepali Physics PhD graduates

Wishing all the best to the recent Physics PhD graduates.

Dr. Hikmat BC
New Mexico State University 

Dr. Shyam Badu
University at Albany

Dr. Madhav Neupane
Boston College

Dr. Pashupati Dhakal 
Boston College

Dr. Mukti Aryal
UT Dallas 

Locating Nepali Physicists on Google map LINK here:

Please join us to congratulate Nepali Physicists graduating with PhD degree. The Google group of Nepal Physical Society LINK here.

Tuesday, July 20, 2010

Collective Behavior in Animals

Feel like yawning? Look around, someone near you might also be yawning!

The so called collective behavior such as yawning might be an urban myth but a recent studies have attempted to model such collective behavior. The modal system they considered consists of an example of collective behavior of cows. Such theories have not been tested it in the real cows, however one should not be surprised to see such studies to be verified in near future.

In a recent work, published in arxiv,  Sun et. al. study the collective behavior of animals such as cows.  Animals are coupled oscillators. They simply model the cow as coupled oscillator. By considering the discrete states of such animals and by considering such couplings, they study the collective decision bearing of such system.
Specifically, they consider three states of cows: standing, sitting and grazing; say "1", "2" and "3" just for sake of easy symbolization. By coupling the states, they assume that behavior of one is going affect the behavior of nearby ones. So, there is more tendency of uniform state such as 1,1,1,1,1 than 1,2,3,2,1 or 1,2,1,2,3. However, for larger cow population there can be some nice oscillatory behavior between the stable states.
The paper is interesting! Have a look.

Acknowledgements are due to the first author for suggests in the draft version of the post and allowing to use the figures.

Fig: Coupled cows.

On the lighter side:
One can see the influence of "spherical cow" on the coupling diagrams. See Jackson, J.D. Third Edition Ch3 problem#15.

Friday, July 2, 2010

Heading for MaxEnt 2010, Chamonix France

I will be visiting France for a week to attend the MaxEnt 2010 Conference.

There, I will be presenting my work on "Entropy Based Search Algorithm for Experimental Design".

Friday, June 18, 2010

Diffusive Nested Sampling: Brewer et. al.

Brendon et. al. has a newer version of nested sampling algorithm, they call it Diffusive Nested Sampling (DNS). As the name indicates, it principally differs from the "classic" nested sampling in presenting the hard constraint. It relaxes the hard evolving constraint and lets the samples to explore the mixture distribution of nested probability distributions, each successive distribution occupying e^-1 times the enclosed prior mass of the previously seen distributions. The mixture distribution is weighted at will (a hack :P) which is a clever trick of exploration. This reinforces the idea of "no peaks left behind" for multimodal problems.

On a test problem they claim that DNS "can achieve four times the accuracy of classic Nested Sampling, for the same computational effort; equivalent to a factor of 16 speedup".

I have not played with it yet. However, it seems worth trying. Just a note to myself.

What can grow out of side talks in a conference?
If you know the power of scrapping in the napkin paper, you would not be surprised.

The paper is available in arxiv:
The code is available at:; comes with handy instructions.

Thanks are due to Dr. Brewer for indicating typos in the draft and suggestions + allowing to use the figures.
 The original nested sampling code is available in the book by sivia and skilling: Data Analysis: A Bayesian Tutorial
Data Analysis: A Bayesian Tutorial 
Edit: Sep 5, 2013 An illustrative animation of Diffusive Nested Sampling ( sampling a multimodal posterior distribution. The size of the yellow circle indicates the importance weight. The method can travel between the modes because the target distribution includes the (uniform) prior as a mixture component.

Saturday, June 5, 2010

Human Body as an Ecosystem and advent of Green Medicine

This sounds fascinating concept; equally impressive to grasp!

In an article published in scientific american, Humans Carry More Bacterial Cells than Human Ones, scientists claim human body to contain more bacterial cell than the human cell itself. So if you have 100 trillion cells in your body,  about the same number of bacteria are are paying you homage. Nice host. Moreover, it has also been reported that they have also contributed to human genes ( Strangely, other species seem to have less  connections with bacteria; or may be it is yet to be discovered.

By definition, Ecosystem is a functional unit consisting of living things in a given area, non-living chemical and physical factors of their environment, linked together through nutrient cycle and energy flow. Since they help to maintain various body processes, this makes human as a host and the body as an ecosystem.

We had already learnt that some bacteria were friendly and some were not. Identification of pathogenic bacteria and use of  antibiotic treatment has been hailed as one of the great success in medical history. The side effects of antibiotics are not so unfamiliar and reasoned as  killing off pathogenic as well as friendly bacteria. However, once we are able to understand the ecosystem of human body, curing "infectious" diseases should be just a treat load of another identified bacteria! Shall we call it Green Medicine?

Monday, May 10, 2010

Nested Sampling Algorithm (John Skilling)

Nested Sampling was developed by John Skilling ( //

Nested Sampling is a modified Markov Chain Monte Carlo algorithm which can be used to explore the posterior probability for the given model. The power of Nested Sampling algorithm lies in the fact that it is designed to compute both the mean posterior probability as well as the Evidence. The algorithm is initialized by randomly taking samples from the prior. The algorithm contracts the distribution of samples around high likelihood regions by discarding the sample with the least likelihood, Lworst.
To keep the number of samples constant, another sample is chosen at random and duplicated. This sample is then randomized by taking Markov chain Monte Carlo steps subject to a hard constraint so that its move is accepted only if the new likelihood is greater than the new threshold, L > Lworst. This ensures that the distribution of samples remains uniformly distributed and that new samples have likelihoods greater than the current likelihood threshold. This process is iterated until the convergence. The logarithm of the evidence is given by the area of the sorted log likelihood as a function of prior mass. When the algorithm has converged one can compute the mean parameter values as well as the log evidence.
Data Analysis: A Bayesian Tutorial
For a nice description of Nested Sampling, the book by Sivia and Skilling is highly recommended: Data Analysis: A Bayesian Tutorial.
The  codes in C/python/R with an example of light house problem is available at:
The paper is available at:

Tuesday, May 4, 2010

Teaching and Learning: On the Board

How do you learn?
As a student, I have always been inspired by the class environment for teaching and learning.
One of the best way that I could point out is the fact that students learn by the looking at what the teacher is doing to solve the problem. For example, when my teacher was teaching the anatomy of an earthworm, just by looking at the picture, the way he drew it, I mastered it as soon as he finished drawing. Segment by segment, organ by organ. That was one of the amazing experience of biology class with me. By drawing the figure along with hearing the description worked at that time. Similarly, I had a full body size human skeleton system drawn on my wall.  It just worked straight out of board into brain.
So, when people talk about the interactive display of pictures in the biology classes, I feel what if I was in that class. What if my teacher had decided to bring a poster of earthworm instead of drawing it in the borad? could I learn it the same way?
Different students have different ways of learning. That was just one of the several case with me. Some people better learn by looking at the picture while being described. We all learn differently.
There are basic three kinds pointed in literatues:
  • kinesthetic
  • visual
  • auditory
 In the classroom environments with bunch of students with different learning tendencies mixed together, is just like a puzzle spread around the room. An effective teacher is the one who has an art of touching everyone's style. Putting a video from MIT opencourse ware can be fun, but putting a video on the screen might not always be the best way to go.
Being innovative is rewarding because here is the tricky part: they are going to teach your kids some day.

Sunday, April 25, 2010

Great! you are selected for grad school, now what?

This is one of the post I am writing for the graduate students coming aboard.
First, my congratulations for being selected. Pursuing your dream in higher studies is going to be very important. It is important not only because you get into graduate school but also because it will define your career path for rest of your life.
Graduate Schools in the U.S. 2010 (Peterson's Graduate Schools in the Us)Your question is regarding whether you wanna go the the university that offered you. If you had carefully selected and applied to the universities, you will have no problem in deciding once you get the offer letter But what if two very competent universities are calling you?
I have the following recommendations (and they apply equally to cases when one is preparing to apply for grad school):

  • Visit the University website. Especially, the departmental website. 
  • Visit Each faculty website, see the trends in the department research. Are the faculty actively involved in research?
  • See if the research field particularly interests you.
  • See if you can figure out the number of graduate student to faculty ratio. 
  • If your support comes from doing the TA duties, see if you can figure out the number of undergraduate student to graduate student ratio.
  • How about the weather? Location? Socialization?
These are the basic questions that you need before you start out your venture. They are important as it will guide your next five years (plus/minus 1) and ultimately your academic life.
Once you figure out such basic academic facts, you can then go for planning the (local) life style there. The best case scenario would be if you have any close friend living nearby. If you can contact the department secretary to learn about the housing, it will also make your life much better. Craiglist listing on apartments can also be equally illuminating.

Thursday, April 1, 2010

Survival of the Fittest: Tricks allowed

Surviving in the wild is not easy, especially if you are born to survive in the wild. So, you come up with tricks to survive. You do whatever it takes to survive.
I found few videos, surprisingly awesome!

Cordyceps, a killer fungi, that invades the body of an insect to grow and diminish the insect population. This is one of the Fascinating animal and wildlife video from the BBC epic natural world masterpiece 'Planet Earth'. This video was brought to you by Sir David Attenborough and the Planet Earth team.

The next on is about the Zombie Snails. As written in its description:
... this parasite is called Leucochloridium paradoxum. There are many other "mind-controlling" parasites such as the Spinochordodes Tellinii which infect grasshoppers and forces them to drown themselves... (Where the worm reproduces). Oh and one of my favs is the Toxoplasma Gondii found in cats intestines. But I'll let yall look it up. Savor the knowledge my children.

Who is inside you?

Wednesday, March 10, 2010

Ask questions to Physics Nobel Laureate in YouTube

Have you ever wanted to ask a Nobel Laureate a question?
Now, here's your chance! Ask a Nobel Laureate is offering you a unique opportunity to communicate with some of the world´s most brilliant minds.
The current participating Nobel Laureate is Albert Fert, Nobel Prize in Physics 2007 "for the discovery of Giant Magnetoresistance", which forms the basis of the memory storage system found in your computer.
Albert Fert will answer a selection of your uploaded video questions.
Upload your video question no later than March, 19, 2010.
Vote for your favourite questions, and a selection of the most popular questions will be answered by Albert Fert. Video responses will be posted in early April.

From wikipedia:
Albert Fert (born 7 March 1938 in Carcassonne, Aude) is a French physicist and one of the discoverers of giant magnetoresistance which brought about a breakthrough in gigabyte hard disks. He is currently professor at Université Paris-Sud in Orsay and scientific director of a joint laboratory ('Unité mixte de recherche') between the Centre national de la recherche scientifique (National Scientific Research Centre) and Thales Group. Also, he is an Adjunct professor of physics at Michigan State University. He was awarded the 2007 Nobel Prize in Physics together with Peter Grünberg.
Head on to:
Ask a Nobel Laureate with Albert Fert page:
Ask questions!!!

"The important thing is not to stop questioning. Curiosity has its own reason for existing."
-Albert Einstein

Monday, March 1, 2010

Hubble in IMAX 3D

AVATAR was my first and second(!) IMAX 3D movie.
IMAX is bringing another fantastic movie... it is about the hubble space telescope

Some Screenshots:


Hubble: Imaging Space and TimeHubble: The Mirror on the Universe