Interpretation of the Confusion Matrix

Actual Positive, Predicted Positive = TP Actual Positive, Predicted Negative = FN Actual Negative, Predicted Negative = TN Actual Negative, Predicted Positive = FP We know from the sample, Actual Positive = TP + FN Actual Negative = TN + FP Prevalence: If the sample can present the population, then prevalence is the ratio: Actual …

Basic Linux Syntax

https://www.panix.com/~elflord/unix/bash-tute.html

The Math behind Linear SVC Classifier

This article is reposted from my Kaggle account. Here is the original link: https://www.kaggle.com/xingewang/the-math-behind-linear-svc-classifier In case there are some Latex format altered below. Linear Support Vector Classifier (Binary Case) The reason why I wrote this article: explanation of SVC/SVM on the internet is overwhelming, but I could not find anything to clarify all the doubts I …

Useful functions in “reshape2” package in R —- stack(), melt()

  In many situations, data is presented in a format that is not ready to dive straight to exploratory data analysis or to use a desired statistical method. The reshape2 package for R provides useful functionality to avoid having to hack data around in a spreadsheet prior to import into R. stack() function For example, we have the data frame read …

Bootstrapping

Problem address In real life, we draw samples from our interested population, and use our samples to estimate the features of the targeted population. However, sometimes, getting samples can be expensive and time consuming. How can we know if the estimators we get from our samples are accurate for the population or not? How can …

The logic behind the hypothesis Testing and p value

The logic behind the hypothesis testing There are two ways to prove your research hypothesis. For example, you want to prove the average grade of English class is higher than 60. You can prove it directly if you have all the information about your interested population. For example, if you are interested in the average …

Linux resources

  You will need to be able to execute basic commands in Linux, like ls, cd, and make. You will also need to get comfortable running programs from the command line. A basic overview of Linux commands: https://www.digitalocean.com/community/tutorials/an-introduction-to-linux-basics A longer overview: http://manuals.bioinformatics.ucr.edu/home/linux-basics More details about I/O, file and directory structures, processes, and permissions: http://linuxcommand.org/learning_the_shell.php

How to check director tree in mac terminal

find . -print | sed -e 's;[^/]*/;|____;g;s;____|; |;g'

What is the difference between SNP and INDEL

http://thegenomefactory.blogspot.com/2013/10/understanding-snps-and-indels-in.html  

Online visualized execution

Here are some links I find very interesting if you want to know what happened "behind the stage" of your code. The default coding language is Python, but the link also provide other languages like, Java, C or C++. http://www.pythontutor.com/visualize.html#mode=edit http://pythontutor.com/