Matrix Pattern Recognition Algorithm

Question

I am designing a logic analyzer and I would like to implement some Matrix Algorithm. I have several channels each one represented by a row in the matrix and every element in the column would be the state, for example:

Channel 1   1 0 0 1 0 1 1 0 1
Channel 2   1 1 0 1 1 0 0 1 1
Channel 3   0 1 0 1 1 0 1 0 0

I would like to detect a pattern inside my matrix for example, detect ALL the matches of the bitmap inside the matrix:

1 0
1 1

I think it can be accomplished testing element by element but I think there should be a better way of doing it. Is there any Java API or any way to do it ? If there is a API ARM optimized for NEON instructions would be great also but not mandatory.

They will be about 8 matrix of 3 or 2 rows by 20000 columns approximately, the matrix is not fixed, it change every time I scan it because I am constantly receiving data. I need to process them in 500mS or less. I am working on an ARM platform, dual core, 1.2GHz, 1Gb RAM, Android 4.1.2

Thank you very much in advance.