Tools for reviewers

If you review research articles, or aspiring researcher, following links may be useful to you.

PubPeer
Publons
COPE
Retraction Watch

Machine Learning

Question: Which of them is a supervised classification problem?

Answer: Using labeled financial data to predict whether the value of a stock will go up or go down next week.

"Exactly! In this example, there are two discrete, qualitative outcomes: the stock market going up, and the stock market going down. This can be represented using a binary variable, and is an application perfectly suited for classification."

So this supervised learning can be used to predict whether something will go up or down (stock prices, temperature, number of sales, etc. To do this you need labelled data because, this is a supervised learning. This can be used whether spin is up or down kind of problem.

Where this type of model can be used in physics, chemistry, mathematics, etc? Is there such studies?

A common data sets used is Iris dataset.

This data set contain

1. petal length 
2. petal width
3. Setal length
4. Setal width

Here, in this blog, you can see how these four quantities are measured. 

Target variable?

In machine learning, a target variable is one that should be the output (after the analysis)

Three different flower species. 

          0. Setosa
          1. Versicolor
          2. Virginica
Here, we are going to give the four data of an unknown flower (to the trained model), and we are going to find out which flower it is (the model will give 0 or 1 or 2 based on the input).

iris.data.shape gives (150, 4) which means that there are 154 rows (data) with four different information (here petal length, petal width, Setal length, Setal width).  

iris.data.shape   

(150,4)

iris.target_names

(names of the target in an array)

(to be continued)

RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility in jupyter notebook python

/usr/lib/python3.5/importlib/_bootstrap.py:222:

RuntimeWarning: numpy.dtype size changed, 

may indicate binary incompatibility.

Expected 96, got 88 return f(*args, **kwds)

This warning is harmless. 

This is due to the Numpy version 1.15.0 or 1.15.1

You can ignore this. 

Or you can go back to Numpy version 1.14.5 

You can do this by

conda install numpy1.14.5

Or, you can wait until Numpy1.15.2 is released.

What you need to know about job talk (MIT OCW)?

I recently watched "How To Speak by Patrick Winston" from MIT OCW.  Thanks to Patrick Wilson who summarized everything you need to know when you are giving a talk which otherwise would take a complete course or at least 10 hours of lectures.

This 60 minutes talk provide you

1. Rules of Engagement @03:17
2. How to Start @04:20
3. Four Sample Heuristics @05:44
4. The Tools: Time and Place @10:23
5. The Tools: Boards, Props, and Slides @13:30
6. Informing: Promise, Inspiration, How to Think @36:35
7. Persuading: Oral Exams, Job Talks, Getting Famous @41:45
8. How to Stop: Final Slide, Final Words @53:15
9. Final Words: Joke, Thank You, Examples @56:40

In a job talk, Patrick Winston says (based on discussion with his colleagues) , the candidate should show

1. vision
2. done something
..
...
......
Conclusions by enumerating what you have done.


How to show that you have a vision?
You have to define the big problem and your approach to solve that big problem. He uses his field of interest "AI" to show the vision. How to understand human intelligence? What are the differences between Chimpanzee, Neanderthals  and Humans? Well. Human has the ability to grasp symbols and tell story based on a number of symbols by connecting them. How can I do to machines so that I could achieve the intelligence that human have in machines? That is an example for vision.

How to show that you have done something important?
List the number of steps you need to solve in order to solve the big problem (which you defined in your vision).
You can say "Here is what needs to be done". Specify some behavior, etc.

How to conclude your job talk?
You highlight what you have done so far and emphasize on where you are in achieving the big goal which you defined in your vision.

The transcript of the full talk (a 22 page pdf document) and the video can be accessed here.

English phrases for writing papers

Following list may be useful for writing papers, articles, etc.

"In recent years” vs “in the recent years”

Native speakers would generally prefer the second. The article is unnecessary and awkward. Both are correct. Personally, I find them all awkward and am much more likely to say things like "over the last few years" or just "recently".

Ref: https://english.stackexchange.com/a/59603/161843

Why you should learn Physics?

Why you should study Physics? Here is the answer from eminent people.

Elon Musk (SpaceX, Tesla, Boring Founder).

Physics gives you the way to think. There is something called "First principles" thinking where you don't assume anything and deconstruct very big problem (no matter how big it is) in to a smallest and simplest one. Elon Musk says in an interview that he use this first principles thinking to design rocket. He goes on, "What a rocket is made of?" A bunch of metals. What is the cost of those metals? About 2% of the total cost of the rocket. So, I can design a rocket at a much lower cost". 

Paul Graham (Y-Combinator)

Dr. Graham, a computer scientist (did PhD in computer science) gave a talk to aspiring entrepreneurs. What would you study in college (if a chance is given)? His answer is  

Best resources for Researchers

Lindau Nobel Laureate Meetings
Contain precious lectures given by prominent scientists

Web of Stories (YouTube Channel)
Contains memories of famous scientists told by themselves

What is your biggest lesson after publishing in Nature Journal?

"What is your biggest lesson?" This is the question that Nature asked researchers published in Nature recently.

Christina Hicks:
"I need to focus on myself for me. It’s easy to become really busy. I run up and down the mountains in the UK Lake District for fun. My brain gets cluttered and overworked if I don’t take a break. Running helps me to slow down."

Johan van den Hoogen:
"Working on that nematode paper helped me to appreciate the value of outsourcing — I didn’t develop the models in it. You should let other people do the things that they’re good at. I understand the models in the paper, but it would have taken me a year and half to create them on my own."

"My biggest realization is that you don’t need to move up the academic career ladder to have a satisfying career in science. The moment I stopped worrying about advancing in academia marked a change for me."

Stephanie Ellis:
"You have to have people around you who can point out the weaknesses in anything you do."

Oscar Serrano:
"Some relationships are more mutually beneficial than others. You can collaborate for years with someone and then realize it’s been a one-way street. You’re sharing ideas and resources with them but getting little in return. But other people really do give back as much as they get and really help you grow your career. I want to be the person that people want to collaborate with because it’s reciprocal."

Here is the full article from Nature.com

This is how a researcher actually develop a new method and what others think of it.

When a new method is developed, how different persons involved perceive the path of the research flow? Here it is.

How much is this true? Comment on this.

Credit: Facebook page Interesting Science.

configure, make, make install

Most of the linux/unix packages can be installed just by following three simple steps:

"configure, make and make install"

Try:

./configure
make
make install


If you are working in a cluster or workstation where you don't have sudo previleges, you just need to change the configure as follow. Remaining same.

Try:

./configure --prefix=/the/location/where/you/want/to/install/the/package
make
make install


Some codes use make -j . What is that?

Here is the explanation from "man" page of make.

-j [jobs], --jobs[=jobs]
"Specifies  the number of jobs (commands) to run simultaneously.  If there is more than one -j option, the last one is effective.  If the -j option is given without an argument, make will not limit the number of jobs that can run simultaneously."

Some other questions about make.

What is the difference between make and make all?

To List of things you need to work on HPC (for researchers)

For learning more, see
Make install but not to default directories
How to build: Configure and make