I have a problem with the second derivation of an image function I(x,y).
The first derivations are:
I_x(x,y) = I(x+1,y) - I(x,y) and
I_y(x,y) = I(x,y+1) - I(x,y).
But when I try to derive I_x in x-direction again, I get this:
I_xx(x,y) = I(x+2,y) - 2*I(x+1,y) + I(x,y), but the right answer seems to be this: I_xx(x,y) = I(x+1,y) + I(x-1,y) -2*I(x,y). Where is my mistake? Can anybody please explain it?
The answer to your question can be seen in the following example. In the "right" answer the second derivative at x is centered around the point x. In your answer, the second derivative is centered around the point x+1. It is good to have derivatives line up as much as possible in many applications. In some sense you have the right answer just as well as the "right" answer. It is a matter of defining your alignment and being consistent. Given an array (let's use 1 based arrays for the moment)
x(1), x(2), x(3), x(4), x(5), x(6)
x = [3, 2, 1, 8, 9, 4]
The first derivative is
x'(1), x'(2), x'(3), x'(4), x'(5)
f'(x) = [3-2, 2-1, 1-8, 8-9, 9-4]
Notice that the x' has one element less than x. We can get around this if we make assumptions on the boundary conditions, which we will not do at present.
The second derivative is
x'(1)-x'(2), x'(2)-x'(3), x'(3)-x'(4), x'(4)-x'(5)
We only have 4 points that have a valid second derivative. In the way you computed the 2nd derivative you simple take the first second derivative to be x''(1). In this way we get the labeling as follows:
x''(1), x''(2), x''(3), x''(4),
x''=[(3-2)-(2-1), (2-1)-(1-8), (1-8)-(8-9), (8-9)-(9-4)]
In general your second derivative which is what you came up with can be written as:
x''(p) = x(p+2)-2*x(p+1)+x(p)
In your second derivative valid indices take the values 1..4 You do not have defined x''(5) as that would require x(5+2)-2*x(5+1)+x(5) and the original array has only 6 elements so x(7) is undefined.
Another way to label the points with the 2nd derivatives centered and aligned such that the nth second derivative is centered around the nth point in the original array is as follows:
x''(2), x''(3), x''(4), x''(5),
x''=[(3-2)-(2-1), (2-1)-(1-8), (1-8)-(8-9), (8-9)-(9-4)]
In general this can be written as:
x''(p) = x(p+1)-2*x(p)+x(p-1)
Notice that this second derivative valid indices are in the range 2..5 In this case x''(1) is not defined as that would require x(1+1)-2*x(1)+x(1-1) and the original array since we have 1 based arrays does not have a value at x(0).
In both cases the form is the same. It's just you are labeling the points differently.
Odd numbered derivatives we cannot center around points in a finite difference, whereas even numbered derivatives we can center to have more intuitive alignment for downstream calculations.
Related
I have a question that can we normalize the levenshtein edit distance by dividing the e.d value by the length of the two strings?
I am asking this because, if we compare two strings of unequal length, the difference between the lengths of the two will be counted as well.
for eg:
ed('has a', 'has a ball') = 4 and ed('has a', 'has a ball the is round') = 15.
if we increase the length of the string, the edit distance will increase even though they are similar.
Therefore, I can not set a value, what a good edit distance value should be.
Yes, normalizing the edit distance is one way to put the differences between strings on a single scale from "identical" to "nothing in common".
A few things to consider:
Whether or not the normalized distance is a better measure of similarity between strings depends on the application. If the question is "how likely is this word to be a misspelling of that word?", normalization is a way to go. If it's "how much has this document changed since the last version?", the raw edit distance may be a better option.
If you want the result to be in the range [0, 1], you need to divide the distance by the maximum possible distance between two strings of given lengths. That is, length(str1)+length(str2) for the LCS distance and max(length(str1), length(str2)) for the Levenshtein distance.
The normalized distance is not a metric, as it violates the triangle inequality.
I used the following successfully:
len = std::max(s1.length(), s2.length());
// normalize by length, high score wins
fDist = float(len - levenshteinDistance(s1, s2)) / float(len);
Then chose the highest score. 1.0 means an exact match.
I had used a normalized edit distance or similarity (NES) which I think is very useful, defined by Daniel Lopresti and Jiangyin Zhou, in Equation (6) of their work: http://www.cse.lehigh.edu/~lopresti/Publications/1996/sdair96.pdf.
The NES in python is:
import math
def normalized_edit_similarity(m, d):
# d : edit distance between the two strings
# m : length of the shorter string
return ( 1.0 / math.exp( d / (m - d) ) )
print(normalized_edit_similarity(3, 0))
print(normalized_edit_similarity(3, 1))
print(normalized_edit_similarity(4, 1))
print(normalized_edit_similarity(5, 1))
print(normalized_edit_similarity(5, 2))
1.0
0.6065306597126334
0.7165313105737893
0.7788007830714049
0.513417119032592
More examples can be found in Table 2 in the above paper.
The variable m in the above function can be replaced with the length of the longer string, depending on your application.
I have a set of points (x,y).
i need to return two points with minimal distance.
I use this:
http://www.cs.ucsb.edu/~suri/cs235/ClosestPair.pdf
but , i dont really understand how the algo is working.
Can explain in more simple how the algo working?
or suggest another idea?
Thank!
If the number of points is small, you can use the brute force approach i.e:
for each point find the closest point among other points and save the minimum distance with the current two indices till now.
If the number of points is large, I think you may find the answer in this thread:
Shortest distance between points algorithm
Solution for Closest Pair Problem with minimum time complexity O(nlogn) is divide-and-conquer methodology as it mentioned in the document that you have read.
Divide-and-conquer Approach for Closest-Pair Problem
Easiest way to understand this algorithm is reading an implementation of it in a high-level language (because sometimes understanding the algorithms or pseudo-codes can be harder than understanding the real codes) like Python:
# closest pairs by divide and conquer
# David Eppstein, UC Irvine, 7 Mar 2002
from __future__ import generators
def closestpair(L):
def square(x): return x*x
def sqdist(p,q): return square(p[0]-q[0])+square(p[1]-q[1])
# Work around ridiculous Python inability to change variables in outer scopes
# by storing a list "best", where best[0] = smallest sqdist found so far and
# best[1] = pair of points giving that value of sqdist. Then best itself is never
# changed, but its elements best[0] and best[1] can be.
#
# We use the pair L[0],L[1] as our initial guess at a small distance.
best = [sqdist(L[0],L[1]), (L[0],L[1])]
# check whether pair (p,q) forms a closer pair than one seen already
def testpair(p,q):
d = sqdist(p,q)
if d < best[0]:
best[0] = d
best[1] = p,q
# merge two sorted lists by y-coordinate
def merge(A,B):
i = 0
j = 0
while i < len(A) or j < len(B):
if j >= len(B) or (i < len(A) and A[i][1] <= B[j][1]):
yield A[i]
i += 1
else:
yield B[j]
j += 1
# Find closest pair recursively; returns all points sorted by y coordinate
def recur(L):
if len(L) < 2:
return L
split = len(L)/2
L = list(merge(recur(L[:split]), recur(L[split:])))
# Find possible closest pair across split line
# Note: this is not quite the same as the algorithm described in class, because
# we use the global minimum distance found so far (best[0]), instead of
# the best distance found within the recursive calls made by this call to recur().
for i in range(len(E)):
for j in range(1,8):
if i+j < len(E):
testpair(E[i],E[i+j])
return L
L.sort()
recur(L)
return best[1]
closestpair([(0,0),(7,6),(2,20),(12,5),(16,16),(5,8),\
(19,7),(14,22),(8,19),(7,29),(10,11),(1,13)])
# returns: (7,6),(5,8)
Taken from: https://www.ics.uci.edu/~eppstein/161/python/closestpair.py
Detailed explanation:
First we define an Euclidean distance aka Square distance function to prevent code repetition.
def square(x): return x*x # Define square function
def sqdist(p,q): return square(p[0]-q[0])+square(p[1]-q[1]) # Define Euclidean distance function
Then we are taking the first two points as our initial best guess:
best = [sqdist(L[0],L[1]), (L[0],L[1])]
This is a function definition for comparing Euclidean distances of next pair with our current best pair:
def testpair(p,q):
d = sqdist(p,q)
if d < best[0]:
best[0] = d
best[1] = p,q
def merge(A,B): is just a rewind function for the algorithm to merge two sorted lists that previously divided to half.
def recur(L): function definition is the actual body of the algorithm. So I will explain this function definition in more detail:
if len(L) < 2:
return L
with this part, algorithm terminates the recursion if there is only one element/point left in the list of points.
Split the list to half: split = len(L)/2
Create a recursion (by calling function's itself) for each half: L = list(merge(recur(L[:split]), recur(L[split:])))
Then lastly this nested loops will test whole pairs in the current half-list with each other:
for i in range(len(E)):
for j in range(1,8):
if i+j < len(E):
testpair(E[i],E[i+j])
As the result of this, if a better pair is found best pair will be updated.
So they solve for the problem in Many dimensions using a divide-and-conquer approach. Binary search or divide-and-conquer is mega fast. Basically, if you can split a dataset into two halves, and keep doing that until you find some info you want, you are doing it as fast as humanly and computerly possible most of the time.
For this question, it means that we divide the data set of points into two sets, S1 and S2.
All the points are numerical, right? So we have to pick some number where to divide the dataset.
So we pick some number m and say it is the median.
So let's take a look at an example:
(14, 2)
(11, 2)
(5, 2)
(15, 2)
(0, 2)
What's the closest pair?
Well, they all have the same Y coordinate, so we can look at Xs only... X shortest distance is 14 to 15, a distance of 1.
How can we figure that out using divide-and-conquer?
We look at the greatest value of X and the smallest value of X and we choose the median as a dividing line to make our two sets.
Our median is 7.5 in this example.
We then make 2 sets
S1: (0, 2) and (5, 2)
S2: (11, 2) and (14, 2) and (15, 2)
Median: 7.5
We must keep track of the median for every split, because that is actually a vital piece of knowledge in this algorithm. They don't show it very clearly on the slides, but knowing the median value (where you split a set to make two sets) is essential to solving this question quickly.
We keep track of a value they call delta in the algorithm. Ugh I don't know why most computer scientists absolutely suck at naming variables, you need to have descriptive names when you code so you don't forget what the f000 you coded 10 years ago, so instead of delta let's call this value our-shortest-twig-from-the-median-so-far
Since we have the median value of 7.5 let's go and see what our-shortest-twig-from-the-median-so-far is for Set1 and Set2, respectively:
Set1 : shortest-twig-from-the-median-so-far 2.5 (5 to m where m is 7.5)
Set 2: shortest-twig-from-the-median-so-far 3.5 (looking at 11 to m)
So I think the key take-away from the algorithm is that this shortest-twig-from-the-median-so-far is something that you're trying to improve upon every time you divide a set.
Since S1 in our case has 2 elements only, we are done with the left set, and we have 3 in the right set, so we continue dividing:
S2 = { (11,2) (14,2) (15,2) }
What do you do? You make a new median, call it S2-median
S2-median is halfway between 15 and 11... or 13, right? My math may be fuzzy, but I think that's right so far.
So let's look at the shortest-twig-so-far-for-our-right-side-with-median-thirteen ...
15 to 13 is... 2
11 to 13 is .... 2
14 to 13 is ... 1 (!!!)
So our m value or shortest-twig-from-the-median-so-far is improved (where we updated our median from before because we're in a new chunk or Set...)
Now that we've found it we know that (14, 2) is one of the points that satisfies the shortest pair equation. You can then check exhaustively against the points in this subset (15, 11, 14) to see which one is the closer one.
Clearly, (15,2) and (14,2) are the winning pair in this case.
Does that make sense? You must keep track of the median when you cut the set, and keep a new median for everytime you cut the set until you have only 2 elements remaining on each side (or in our case 3)
The magic is in the median or shortest-twig-from-the-median-so-far
Thanks for asking this question, I went in not knowing how this algorithm worked but found the right highlighted bullet point on the slide and rolled with it. Do you get it now? I don't know how to explain the median magic other than binary search is f000ing awesome.
I'm looking for a way of getting X points in a fixed sized grid of let's say M by N, where the points are not returned multiple times and all points have a similar chance of getting chosen and the amount of points returned is always X.
I had the idea of looping over all the grid points and giving each point a random chance of X/(N*M) yet I felt like that it would give more priority to the first points in the grid. Also this didn't meet the requirement of always returning X amount of points.
Also I could go with a way of using increments with a prime number to get kind of a shuffle without repeat functionality, but I'd rather have it behave more random than that.
Essentially, you need to keep track of the points you already chose, and make use of a random number generator to get a pseudo-uniformly distributed answer. Each "choice" should be independent of the previous one.
With your first idea, you're right, the first ones would have more chance of getting picked. Consider a one-dimensional array with two elements. With the strategy you mention, the chance of getting the first one is:
P[x=0] = 1/2 = 0.5
The chance of getting the second one is the chance of NOT getting the first one 0.5, times 1/2:
P[x=1] = 1/2 * 1/2 = 0.25
You don't mention which programming language you're using, so I'll assume you have at your disposal random number generator rand() which results in a random float in the range [0, 1), a Hashmap (or similar) data structure, and a Point data structure. I'll further assume that a point in the grid can be any floating point x,y, where 0 <= x < M and 0 <= y < N. (If this is a NxM array, then the same applies, but in integers, and up to (M-1,N-1)).
Hashmap points = new Hashmap();
Point p;
while (items.size() < X) {
p = new Point(rand()*M, rand()*N);
if (!points.containsKey(p)) {
items.add(p, 1);
}
}
Note: Two Point objects of equal x and y should be themselves considered equal and generate equal hash codes, etc.
I want to make a linear fit to few data points, as shown on the image. Since I know the intercept (in this case say 0.05), I want to fit only points which are in the linear region with this particular intercept. In this case it will be lets say points 5:22 (but not 22:30).
I'm looking for the simple algorithm to determine this optimal amount of points, based on... hmm, that's the question... R^2? Any Ideas how to do it?
I was thinking about probing R^2 for fits using points 1 to 2:30, 2 to 3:30, and so on, but I don't really know how to enclose it into clear and simple function. For fits with fixed intercept I'm using polyfit0 (http://www.mathworks.com/matlabcentral/fileexchange/272-polyfit0-m) . Thanks for any suggestions!
EDIT:
sample data:
intercept = 0.043;
x = 0.01:0.01:0.3;
y = [0.0530642513911393,0.0600786706929529,0.0673485248329648,0.0794662409166333,0.0895915873196170,0.103837395346484,0.107224784565365,0.120300492775786,0.126318699218730,0.141508831492330,0.147135757370947,0.161734674733680,0.170982455701681,0.191799936622712,0.192312642057298,0.204771365716483,0.222689541632988,0.242582251060963,0.252582727297656,0.267390860166283,0.282890010610515,0.292381165948577,0.307990544720676,0.314264952297699,0.332344368808024,0.355781519885611,0.373277721489254,0.387722683944356,0.413648156978284,0.446500064130389;];
What you have here is a rather difficult problem to find a general solution of.
One approach would be to compute all the slopes/intersects between all consecutive pairs of points, and then do cluster analysis on the intersepts:
slopes = diff(y)./diff(x);
intersepts = y(1:end-1) - slopes.*x(1:end-1);
idx = kmeans(intersepts, 3);
x([idx; 3] == 2) % the points with the intersepts closest to the linear one.
This requires the statistics toolbox (for kmeans). This is the best of all methods I tried, although the range of points found this way might have a few small holes in it; e.g., when the slopes of two points in the start and end range lie close to the slope of the line, these points will be detected as belonging to the line. This (and other factors) will require a bit more post-processing of the solution found this way.
Another approach (which I failed to construct successfully) is to do a linear fit in a loop, each time increasing the range of points from some point in the middle towards both of the endpoints, and see if the sum of the squared error remains small. This I gave up very quickly, because defining what "small" is is very subjective and must be done in some heuristic way.
I tried a more systematic and robust approach of the above:
function test
%% example data
slope = 2;
intercept = 1.5;
x = linspace(0.1, 5, 100).';
y = slope*x + intercept;
y(1:12) = log(x(1:12)) + y(12)-log(x(12));
y(74:100) = y(74:100) + (x(74:100)-x(74)).^8;
y = y + 0.2*randn(size(y));
%% simple algorithm
[X,fn] = fminsearch(#(ii)P(ii, x,y,intercept), [0.5 0.5])
[~,inds] = P(X, y,x,intercept)
end
function [C, inds] = P(ii, x,y,intercept)
% ii represents fraction of range from center to end,
% So ii lies between 0 and 1.
N = numel(x);
n = round(N/2);
ii = round(ii*n);
inds = min(max(1, n+(-ii(1):ii(2))), N);
% Solve linear system with fixed intercept
A = x(inds);
b = y(inds) - intercept;
% and return the sum of squared errors, divided by
% the number of points included in the set. This
% last step is required to prevent fminsearch from
% reducing the set to 1 point (= minimum possible
% squared error).
C = sum(((A\b)*A - b).^2)/numel(inds);
end
which only finds a rough approximation to the desired indices (12 and 74 in this example).
When fminsearch is run a few dozen times with random starting values (really just rand(1,2)), it gets more reliable, but I still wouln't bet my life on it.
If you have the statistics toolbox, use the kmeans option.
Depending on the number of data values, I would split the data into a relative small number of overlapping segments, and for each segment calculate the linear fit, or rather the 1-st order coefficient, (remember you know the intercept, which will be same for all segments).
Then, for each coefficient calculate the MSE between this hypothetical line and entire dataset, choosing the coefficient which yields the smallest MSE.
I have a symmetric matrix like shown in the image attached below.
I've made up the notation A.B which represents the value at grid point (A, B). Furthermore, writing A.B.C gives me the minimum grid point value like so: MIN((A,B), (A,C), (B,C)).
As another example A.B.D gives me MIN((A,B), (A,D), (B,D)).
My goal is to find the minimum values for ALL combinations of letters (not repeating) for one row at a time e.g for this example I need to find min values with respect to row A which are given by the calculations:
A.B = 6
A.C = 8
A.D = 4
A.B.C = MIN(6,8,6) = 6
A.B.D = MIN(6, 4, 4) = 4
A.C.D = MIN(8, 4, 2) = 2
A.B.C.D = MIN(6, 8, 4, 6, 4, 2) = 2
I realize that certain calculations can be reused which becomes increasingly important as the matrix size increases, but the problem is finding the most efficient way to implement this reuse.
Can point me in the right direction to finding an efficient algorithm/data structure I can use for this problem?
You'll want to think about the lattice of subsets of the letters, ordered by inclusion. Essentially, you have a value f(S) given for every subset S of size 2 (that is, every off-diagonal element of the matrix - the diagonal elements don't seem to occur in your problem), and the problem is to find, for each subset T of size greater than two, the minimum f(S) over all S of size 2 contained in T. (And then you're interested only in sets T that contain a certain element "A" - but we'll disregard that for the moment.)
First of all, note that if you have n letters, that this amounts to asking Omega(2^n) questions, roughly one for each subset. (Excluding the zero- and one-element subsets and those that don't include "A" saves you n + 1 sets and a factor of two, respectively, which is allowed for big Omega.) So if you want to store all these answers for even moderately large n, you'll need a lot of memory. If n is large in your applications, it might be best to store some collection of pre-computed data and do some computation whenever you need a particular data point; I haven't thought about what would work best, but for example computing data only for a binary tree contained in the lattice would not necessarily help you anything beyond precomputing nothing at all.
With these things out of the way, let's assume you actually want all the answers computed and stored in memory. You'll want to compute these "layer by layer", that is, starting with the three-element subsets (since the two-element subsets are already given by your matrix), then four-element, then five-element, etc. This way, for a given subset S, when we're computing f(S) we will already have computed all f(T) for T strictly contained in S. There are several ways that you can make use of this, but I think the easiest might be to use two such subset S: let t1 and t2 be two different elements of T that you may select however you like; let S be the subset of T that you get when you remove t1 and t2. Write S1 for S plus t1 and write S2 for S plus t2. Now every pair of letters contained in T is either fully contained in S1, or it is fully contained in S2, or it is {t1, t2}. Look up f(S1) and f(S2) in your previously computed values, then look up f({t1, t2}) directly in the matrix, and store f(T) = the minimum of these 3 numbers.
If you never select "A" for t1 or t2, then indeed you can compute everything you're interested in while not computing f for any sets T that don't contain "A". (This is possible because the steps outlined above are only interesting whenever T contains at least three elements.) Good! This leaves just one question - how to store the computed values f(T). What I would do is use a 2^(n-1)-sized array; represent each subset-of-your-alphabet-that-includes-"A" by the (n-1) bit number where the ith bit is 1 whenever the (i+1)th letter is in that set (so 0010110, which has bits 2, 4, and 5 set, represents the subset {"A", "C", "D", "F"} out of the alphabet "A" .. "H" - note I'm counting bits starting at 0 from the right, and letters starting at "A" = 0). This way, you can actually iterate through the sets in numerical order and don't need to think about how to iterate through all k-element subsets of an n-element set. (You do need to include a special case for when the set under consideration has 0 or 1 element, in which case you'll want to do nothing, or 2 elements, in which case you just copy the value from the matrix.)
Well, it looks simple to me, but perhaps I misunderstand the problem. I would do it like this:
let P be a pattern string in your notation X1.X2. ... .Xn, where Xi is a column in your matrix
first compute the array CS = [ (X1, X2), (X1, X3), ... (X1, Xn) ], which contains all combinations of X1 with every other element in the pattern; CS has n-1 elements, and you can easily build it in O(n)
now you must compute min (CS), i.e. finding the minimum value of the matrix elements corresponding to the combinations in CS; again you can easily find the minimum value in O(n)
done.
Note: since your matrix is symmetric, given P you just need to compute CS by combining the first element of P with all other elements: (X1, Xi) is equal to (Xi, X1)
If your matrix is very large, and you want to do some optimization, you may consider prefixes of P: let me explain with an example
when you have solved the problem for P = X1.X2.X3, store the result in an associative map, where X1.X2.X3 is the key
later on, when you solve a problem P' = X1.X2.X3.X7.X9.X10.X11 you search for the longest prefix of P' in your map: you can do this by starting with P' and removing one component (Xi) at a time from the end until you find a match in your map or you end up with an empty string
if you find a prefix of P' in you map then you already know the solution for that problem, so you just have to find the solution for the problem resulting from combining the first element of the prefix with the suffix, and then compare the two results: in our example the prefix is X1.X2.X3, and so you just have to solve the problem for
X1.X7.X9.X10.X11, and then compare the two values and choose the min (don't forget to update your map with the new pattern P')
if you don't find any prefix, then you must solve the entire problem for P' (and again don't forget to update the map with the result, so that you can reuse it in the future)
This technique is essentially a form of memoization.