Notes on algorithms(2) -- Principles of Dynamic Programming

Dynamic Programming is to convert a problem into a polynomial time algorithm by storing some of the middle results first. This is to avoid searching some redundant spaces in the problem.

In the book (J.K. and E.T.), the following 3 are the rules of dynamic programming:

1) There are only a polynomial number of subproblems.

2) The solution to the original problem can be easily computed from the solutions to the subproblems.

3) There is a natural ordering on subproblems from "seallest" to "largest".

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A simple implementation of DTW(Dynamic Time Warping) in C#/python

DTW(Dynamic Time Warping) is a very useful tools for time series analysis. This is a very simple (but not very efficient) c# implementation of DTW, the source code is available at https://gist.github.com/1966342 . Use the program as below: double[] x = {9,3,1,5,1,2,0,1,0,2,2,8,1,7,0,6,4,4,5}; double[] y = {1,0,5,5,0,1,0,1,0,3,3,2,8,1,0,6,4,4,5}; SimpleDTW dtw = new SimpleDTW(x,y); dtw.calculateDTW(); The python implementation is available at https://gist.github.com/3265694 . from python-dtw import Dtw import math dtw = Dtw([1, 2, 3, 4, 6], [1, 2, 3, 5], distance_func=lambda x, y: math.fabs(x - y)) print dtw.calculate() #calculate the distance print dtw.get_path() #calculate the mapping path

Change the default user when start a docker container

When run(start) a docker container from an image, we can specify the default user by passing -u option in command line(In https://docs.docker.com/engine/reference/run/#user ). For example docker run -i -t -u ubuntu ubuntu:latest /bin/bash We can also use the USER instruction in DOCKERFILE to do the same thing(In https://docs.docker.com/engine/reference/builder/#user), note that the option in command line will override the one in the DOCKERFILE. And there is actually another way to start a container with neither DOCKERFILE nor -u option, just by a command like: docker run -i -t ubuntu:latest /bin/bash # with ubuntu as the default user This happens when your start the container from an image committed by a container with ubuntu as the default user. Or in detail: Run a container from some basic images, create ubuntu user inside it, commit the container to CUSTOM_IMAGE:1 . Run a container from CUSTOM_IMAGE:1 with "-u ubuntu" option, and commit the container to CUSTOM...

Notes on Sequential Pattern Mining (2) -- Partial Order Pattern Mining and Contrast Mining

1. In , the authors induce TEIRESIAS algorithms to mining combinatorial patterns with gap constraints in biological sequences. The patterns TEIRESIAS mined is similiar with the common sequential patterns, but it could contain "." the wild card which is also in the alphbel of the sequences database standing for any other item available, for example pattern "A..B" is a length-4 pattern, with two arbitrary items between the first A and the last B. Patterns "AC.B", "AADB" are all said to be more specific than pattern "A..B". TEIRESIAS mining all the maximal patterns () with a support over a min threshold K. There some key points of TEIRESIAS algorithms: 1)The growth of the patterns The growth of the patterns is accomplished by convolute current pattern by a short length pattern. Pattern A and pattern B are convolutable if the last L(very small) characters of pattern A is the same as the first L characters of pattern B, then ...

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