There are several papers on this topic. A quick google search gives you a list of research papers on this topic. Cointegration technique is sometimes used to do Pairs trading. By checking if a pair of stocks are cointegrated, one could go long on one stock and short on the other (multiplied by Hedge Ratio). We are thus trying to be market neutral. Carol Alexander in the book "Market Models" gives a very good explaination of the theory behind it.

A set of I(1) series are termed "cointegrated" if there is a linear combination of these series that is stationary. Stock A and Stock B are cointegrated if A,B are approximately I(1), but there is Hedge Ratio such that

Spread = StockA - Hedge_Ratio * StockB is Approximately I(0). I.e The spread is stationary or mean reverting.

So We perform the following Steps to Check if two stocks are cointegrated:

Step1 : Check if the two stocks are atleast integrated of order 1, I(1)

This is done with Augmented Dickey fuller Test

Step2: After they pass the above test, perform a Cointegration augmented dickey fuller test

Step 3: After it passes the ADF test, we can perform a Ordinary Least Squares Regression to get the Hedge Ratio (The Beta of the regression)

Step 4: So the Spread = StockA - Hedge_Ratio * StockB would now be Cointegrated (mean reverting)

Step 5: Figuring when to exit : Calculate Half Life

Half life basically tells you how much time it takes for the spread to revert back to half the distance of the mean.

Step 6: Calculate the Spread TODAY. Calculate the Standard deviation of the spread upto the day before. Check how far the current spread is from the historical average. If it is greater than 1.5 standard deviations (or any other threshold), then go short the spread otherwise go long the spread. I.e Go Short Stock A and Long Hedge Ratio * Stock B. Be in the trade until the half life calculated for the pair. If the Half Life time period has passed, Get out of the trade.

These are simple steps. One should put on more work and research on it to develop it into a practical trading strategy.

Some interesting papers are here:

Cointegration Paper I

Cointegration Carol Alexander

MATLAB Code Here:

MATLAB COINTEGRATION CODE

CointPairsTrade.m is the main function and calls all other functions

Please let me know if there are any bugs