Is there a general way to convert between a measure of similarity and a measure of distance?
Consider a similarity measure like the number of 2-grams that two strings have in common.
2-grams('beta', 'delta') = 1
2-grams('apple', 'dappled') = 4
What if I need to feed this to an optimization algorithm that expects a measure of difference, like Levenshtein distance?
This is just an example...I'm looking for a general solution, if one exists. Like how to go from Levenshtein distance to a measure of similarity?
I appreciate any guidance you may offer.
Let d denotes distance, s denotes similarity. To convert distance measure to similarity measure, we need to first normalize d to [0 1], by using d_norm = d/max(d). Then the similarity measure is given by:
s = 1 - d_norm.
where s is in the range [0 1], with 1 denotes highest similarity (the items in comparison are identical), and 0 denotes lowest similarity (largest distance).
If your similarity measure (s) is between 0 and 1, you can use one of these:
1-s
sqrt(1-s)
-log(s)
(1/s)-1
Doing 1/similarity is not going to keep the properties of the distribution.
the best way is
distance (a->b) = highest similarity - similarity (a->b).
with highest similarity being the similarity with the biggest value. You hence flip your distribution.
the highest similarity becomes 0 etc
Yes, there is a most general way to change between similarity and distance: a strictly monotone decreasing function f(x).
That is, with f(x) you can make similarity = f(distance) or distance = f(similarity). It works in both directions. Such function works, because the relation between similarity and distance is that one decreases when the other increases.
Examples:
These are some well-known strictly monotone decreasing candidates that work for non-negative similarities or distances:
f(x) = 1 / (a + x)
f(x) = exp(- x^a)
f(x) = arccot(ax)
You can choose parameter a>0 (e.g., a=1)
Edit 2021-08
A very practical approach is to use the function sim2diss belonging to the statistical software R. This functions provides a up to 13 methods to compute dissimilarity from similarities. Sadly the methods are not at all explained: you have to look into the code :-\
similarity = 1/difference
and watch out for difference = 0
According to scikit learn:
Kernels are measures of similarity, i.e. s(a, b) > s(a, c) if objects a and b are considered “more similar” than objects a and c. A kernel must also be positive semi-definite.
There are a number of ways to convert between a distance metric and a similarity measure, such as a kernel. Let D be the distance, and S be the kernel:
S = np.exp(-D * gamma), where one heuristic for choosing gamma is 1 /
num_features
S = 1. / (D / np.max(D))
In the case of Levenshtein distance, you could increase the sim score by 1 for every time the sequences match; that is, 1 for every time you didn't need a deletion, insertion or substitution. That way the metric would be a linear measure of how many characters the two strings have in common.
In one of my projects (based on Collaborative Filtering) I had to convert between correlation (cosine between vectors) which was from -1 to 1 (closer 1 is more similar, closer to -1 is more diverse) to normalized distance (close to 0 the distance is smaller and if it's close to 1 the distance is bigger)
In this case: distance ~ diversity
My formula was: dist = 1 - (cor + 1)/2
If you have similarity to diversity and the domain is [0,1] in both cases the simlest way is:
dist = 1 - sim
sim = 1 - dist
Cosine similarity is widely used for n-gram count or TFIDF vectors.
from math import pi, acos
def similarity(x, y):
return sum(x[k] * y[k] for k in x if k in y) / sum(v**2 for v in x.values())**.5 / sum(v**2 for v in y.values())**.5
Cosine similarity can be used to compute a formal distance metric according to wikipedia. It obeys all the properties of a distance that you would expect (symmetry, nonnegativity, etc):
def distance_metric(x, y):
return 1 - 2 * acos(similarity(x, y)) / pi
Both of these metrics range between 0 and 1.
If you have a tokenizer that produces N-grams from a string you could use these metrics like this:
>>> import Tokenizer
>>> tokenizer = Tokenizer(ngrams=2, lower=True, nonwords_set=set(['hello', 'and']))
>>> from Collections import Counter
>>> list(tokenizer('Hello World again and again?'))
['world', 'again', 'again', 'world again', 'again again']
>>> Counter(tokenizer('Hello World again and again?'))
Counter({'again': 2, 'world': 1, 'again again': 1, 'world again': 1})
>>> x = _
>>> Counter(tokenizer('Hi world once again.'))
Counter({'again': 1, 'world once': 1, 'hi': 1, 'once again': 1, 'world': 1, 'hi world': 1, 'once': 1})
>>> y = _
>>> sum(x[k]*y[k] for k in x if k in y) / sum(v**2 for v in x.values())**.5 / sum(v**2 for v in y.values())**.5
0.42857142857142855
>>> distance_metric(x, y)
0.28196592805724774
I found the elegant inner product of Counter in this SO answer
Related
I have a problem and I feel like there should be a well-known algorithm for solving it that's better than just brute force, but I can't think of one, so I'm asking here.
The problem is as follows: given n sorted (from low to high) lists containing m probabilities, choose one index for each list such that the sum of the chosen indexes is less than m. Then, for each list, we flip a coin, where the chance of it landing heads is equal to the probability at the chosen index for that list. Maximize the chance of the coin landing heads at least once.
Are there any algorithms for solving this problem that are better than just brute force?
This problem seems most similar to the knapsack problem, except the value of the items in the knapsack isn't merely a sum of the items in the knapsack. (Written in Python, instead of sum(p for p in chosen_probabilities) it's 1 - math.prod([1 - p for p in chosen_probabilities])) And, there's restrictions on what items you can add given what items are already in the knapsack. For example, if the index = 3 item for a particular list is already in the knapsack, then adding in the item with index = 2 for that same list isn't allowed (since you can only pick one index for each list). So there are certain items that can and can't be added to the knapsack based on what items are already in it.
Linear optimization won't work because the values in the lists don't increase linearly, the final coin probability isn't linear with respect to the chosen probabilities, and our constraint is on the sum of the indexes, rather than the values in the lists themselves. As David has pointed out, linear optimization will work if you use binary variables to pick out the indexes and a logarithm to deal with the non-linearity.
EDIT:
I've found that explaining the motivation behind this problem can be helpful for understanding it. Imagine you have 10 seconds to solve a problem, and three different ways to solve it. You have models of how likely it is that each method will solve the problem, given how many seconds you try that method for, but if you switch methods, you lose all progress on the one you were previously trying. What methods should you try and for how long?
Maximizing 1 - math.prod([1 - p for p in chosen_probabilities]) is equivalent to minimizing math.prod([1 - p for p in chosen_probabilities]), which is equivalent to minimizing the log of this objective, which is a linear function of 0-1 indicator variables, so you could do an integer programming formulation this way.
I can't promise that this will be much better than brute force. The problem is that math.log(1 - p) is well approximated by -p when p is close to zero. My intuition is that for nontrivial instances it will be qualitatively similar to using integer programming to solve subset sum, which doesn't go particularly well.
If you're willing to settle for a bicriteria approximation scheme (get an answer such that the sum of the chosen indexes is less than m, that is at least as good as the best answer summing to less than (1 − ε) m) then you can round up the probability to multiples of ε and use dynamic programming to get an algorithm that runs in time polynomial in n, m, 1/ε.
Here is working code for David Eisenstat's solution.
To understand the implementation, I think it helps to go through the math first.
As a reminder, there are n lists, each with m options. (In the motivating example at the bottom of the question, each list represents a method for solving the problem, and you are given m-1 seconds to solve the problem. Each list is such that list[index] gives the chance of solving the problem with that method if the method is run for index seconds.)
We let the lists be stored in a matrix called d (named data in the code), where each row in the matrix is a list. (And thus each column represents an index, or, if following the motivating example, an amount of time.)
The probability of the coin landing heads, given that we chose index j* for list i, is computed as
We would like to maximize this.
(To explain the stats behind this equation, we're computing 1 minus the probability that the coin doesn't land on heads. The probability that the coin doesn't land on heads is the probability that each flip doesn't land on heads. The probability that a single flip doesn't land on heads is just 1 minus the probability that does land on heads. And the probability it does land on heads is the number we've chosen, d[i][j*]. Thus, the total probability that all the flips land on tails is just the product of the probability that each one lands on tails. And then the probability that the coin lands on heads is just 1 minus the probability that all the flips land on tails.)
Which, as David pointed out, is the same as minimizing:
Which is the same as minimizing:
Which is equivalent to:
Then, since this is linear sum, we can turn it into an integer program.
We'll be minimizing:
This lets the computer choose the indexes by allowing it to create an n by m matrix of 1s and 0s called x where the 1s pick out particular indexes. We'll then define rules so that it doesn't pick out invalid sets of indexes.
The first rule is that you have to pick out an index for each list:
The second rule is that you have to respect the constraint that the indexes chosen must sum to m or less:
And that's it! Then we can just tell the computer to minimize that sum according to those rules. It will spit out an x matrix with a single 1 on each row to tell us which index it has picked for the list on that row.
In code (using the motivating example), this is implemented as:
'''
Requirements:
cvxopt==1.2.6
cvxpy==1.1.10
ecos==2.0.7.post1
numpy==1.20.1
osqp==0.6.2.post0
qdldl==0.1.5.post0
scipy==1.6.1
scs==2.1.2
'''
import math
import cvxpy as cp
import numpy as np
# number of methods
n = 3
# if you have 10 seconds, there are 11 options for each method (0 seconds, 1 second, ..., 10 seconds)
m = 11
# method A has 30% chance of working if run for at least 3 seconds
# equivalent to [0, 0, 0, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]
A_list = [0, 0, 0] + [0.3] * (m - 3)
# method B has 30% chance of working if run for at least 3 seconds
# equivalent to [0, 0, 0, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]
B_list = [0, 0, 0] + [0.3] * (m - 3)
# method C has 40% chance of working if run for 4 seconds, 30% otherwise
# equivalent to [0.3, 0.3, 0.3, 0.3, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4]
C_list = [0.3, 0.3, 0.3, 0.3] + [0.4] * (m - 4)
data = [A_list, B_list, C_list]
# do the logarithm
log_data = []
for row in data:
log_row = []
for col in row:
# deal with domain exception
if col == 1:
new_col = float('-inf')
else:
new_col = math.log(1 - col)
log_row.append(new_col)
log_data.append(log_row)
log_data = np.array(log_data)
x = cp.Variable((n, m), boolean=True)
objective = cp.Minimize(cp.sum(cp.multiply(log_data, x)))
# the current solver doesn't work with equalities, so each equality must be split into two inequalities.
# see https://github.com/cvxgrp/cvxpy/issues/1112
one_choice_per_method_constraint = [cp.sum(x[i]) <= 1 for i in range(n)] + [cp.sum(x[i]) >= 1 for i in range(n)]
# constrain the solution to not use more time than is allowed
# note that the time allowed is (m - 1), not m, because time is 1-indexed and the lists are 0-indexed
js = np.tile(np.array(list(range(m))), (n, 1))
time_constraint = [cp.sum(cp.multiply(js, x)) <= m - 1, cp.sum(cp.multiply(js, x)) >= m - 1]
constraints = one_choice_per_method_constraint + time_constraint
prob = cp.Problem(objective, constraints)
result = prob.solve()
def compute_probability(data, choices):
# compute 1 - ((1 - p1) * (1 - p2) * ...)
return 1 - np.prod(np.add(1, -np.multiply(data, choices)))
print("Choices:")
print(x.value)
'''
Choices:
[[0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0.]
[0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0.]
[0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0.]]
'''
print("Chance of success:")
print(compute_probability(data, x.value))
'''
Chance of success:
0.7060000000000001
'''
And there we have it! The computer has correctly determined that running method A for 3 seconds, method B for 3 seconds, and method C for 4 seconds is optimal. (Remember that the x matrix is 0-indexed, while the times are 1-indexed.)
Thank you, David, for the suggestion!
I'm trying to find a name for my problem, so I don't have to re-invent wheel when coding an algorithm which solves it...
I have say 2,000 binary (row) vectors and I need to pick 500 from them. In the picked sample I do column sums and I want my sample to be as close as possible to a pre-defined distribution of the column sums. I'll be working with 20 to 60 columns.
A tiny example:
Out of the vectors:
110
010
011
110
100
I need to pick 2 to get column sums 2, 1, 0. The solution (exact in this case) would be
110
100
My ideas so far
one could maybe call this a binary multidimensional knapsack, but I did not find any algos for that
Linear Programming could help, but I'd need some step by step explanation as I got no experience with it
as exact solution is not always feasible, something like simulated annealing brute force could work well
a hacky way using constraint solvers comes to mind - first set the constraints tight and gradually loosen them until some solution is found - given that CSP should be much faster than ILP...?
My concrete, practical (if the approximation guarantee works out for you) suggestion would be to apply the maximum entropy method (in Chapter 7 of Boyd and Vandenberghe's book Convex Optimization; you can probably find several implementations with your favorite search engine) to find the maximum entropy probability distribution on row indexes such that (1) no row index is more likely than 1/500 (2) the expected value of the row vector chosen is 1/500th of the predefined distribution. Given this distribution, choose each row independently with probability 500 times its distribution likelihood, which will give you 500 rows on average. If you need exactly 500, repeat until you get exactly 500 (shouldn't take too many tries due to concentration bounds).
Firstly I will make some assumptions regarding this problem:
Regardless whether the column sum of the selected solution is over or under the target, it weighs the same.
The sum of the first, second, and third column are equally weighted in the solution (i.e. If there's a solution whereas the first column sum is off by 1, and another where the third column sum is off by 1, the solution are equally good).
The closest problem I can think of this problem is the Subset sum problem, which itself can be thought of a special case of Knapsack problem.
However both of these problem are NP-Complete. This means there are no polynomial time algorithm that can solve them, even though it is easy to verify the solution.
If I were you the two most arguably efficient solution of this problem are linear programming and machine learning.
Depending on how many columns you are optimising in this problem, with linear programming you can control how much finely tuned you want the solution, in exchange of time. You should read up on this, because this is fairly simple and efficient.
With Machine learning, you need a lot of data sets (the set of vectors and the set of solutions). You don't even need to specify what you want, a lot of machine learning algorithms can generally deduce what you want them to optimise based on your data set.
Both solution has pros and cons, you should decide which one to use yourself based on the circumstances and problem set.
This definitely can be modeled as (integer!) linear program (many problems can). Once you have it, you can use a program such as lpsolve to solve it.
We model vector i is selected as x_i which can be 0 or 1.
Then for each column c, we have a constraint:
sum of all (x_i * value of i in column c) = target for column c
Taking your example, in lp_solve this could look like:
min: ;
+x1 +x4 +x5 >= 2;
+x1 +x4 +x5 <= 2;
+x1 +x2 +x3 +x4 <= 1;
+x1 +x2 +x3 +x4 >= 1;
+x3 <= 0;
+x3 >= 0;
bin x1, x2, x3, x4, x5;
If you are fine with a heuristic based search approach, here is one.
Go over the list and find the minimum squared sum of the digit wise difference between each bit string and the goal. For example, if we are looking for 2, 1, 0, and we are scoring 0, 1, 0, we would do it in the following way:
Take the digit wise difference:
2, 0, 1
Square the digit wise difference:
4, 0, 1
Sum:
5
As a side note, squaring the difference when scoring is a common method when doing heuristic search. In your case, it makes sense because bit strings that have a 1 in as the first digit are a lot more interesting to us. In your case this simple algorithm would pick first 110, then 100, which would is the best solution.
In any case, there are some optimizations that could be made to this, I will post them here if this kind of approach is what you are looking for, but this is the core of the algorithm.
You have a given target binary vector. You want to select M vectors out of N that have the closest sum to the target. Let's say you use the eucilidean distance to measure if a selection is better than another.
If you want an exact sum, have a look at the k-sum problem which is a generalization of the 3SUM problem. The problem is harder than the subset sum problem, because you want an exact number of elements to add to a target value. There is a solution in O(N^(M/2)). lg N), but that means more than 2000^250 * 7.6 > 10^826 operations in your case (in the favorable case where vectors operations have a cost of 1).
First conclusion: do not try to get an exact result unless your vectors have some characteristics that may reduce the complexity.
Here's a hill climbing approach:
sort the vectors by number of 1's: 111... first, 000... last;
use the polynomial time approximate algorithm for the subset sum;
you have an approximate solution with K elements. Because of the order of elements (the big ones come first), K should be a little as possible:
if K >= M, you take the M first vectors of the solution and that's probably near the best you can do.
if K < M, you can remove the first vector and try to replace it with 2 or more vectors from the rest of the N vectors, using the same technique, until you have M vectors. To sumarize: split the big vectors into smaller ones until you reach the correct number of vectors.
Here's a proof of concept with numbers, in Python:
import random
def distance(x, y):
return abs(x-y)
def show(ls):
if len(ls) < 10:
return str(ls)
else:
return ", ".join(map(str, ls[:5]+("...",)+ls[-5:]))
def find(is_xs, target):
# see https://en.wikipedia.org/wiki/Subset_sum_problem#Pseudo-polynomial_time_dynamic_programming_solution
S = [(0, ())] # we store indices along with values to get the path
for i, x in is_xs:
T = [(x + t, js + (i,)) for t, js in S]
U = sorted(S + T)
y, ks = U[0]
S = [(y, ks)]
for z, ls in U:
if z == target: # use the euclidean distance here if you want an approximation
return ls
if z != y and z < target:
y, ks = z, ls
S.append((z, ls))
ls = S[-1][1] # take the closest element to target
return ls
N = 2000
M = 500
target = 1000
xs = [random.randint(0, 10) for _ in range(N)]
print ("Take {} numbers out of {} to make a sum of {}", M, xs, target)
xs = sorted(xs, reverse = True)
is_xs = list(enumerate(xs))
print ("Sorted numbers: {}".format(show(tuple(is_xs))))
ls = find(is_xs, target)
print("FIRST TRY: {} elements ({}) -> {}".format(len(ls), show(ls), sum(x for i, x in is_xs if i in ls)))
splits = 0
while len(ls) < M:
first_x = xs[ls[0]]
js_ys = [(i, x) for i, x in is_xs if i not in ls and x != first_x]
replace = find(js_ys, first_x)
splits += 1
if len(replace) < 2 or len(replace) + len(ls) - 1 > M or sum(xs[i] for i in replace) != first_x:
print("Give up: can't replace {}.\nAdd the lowest elements.")
ls += tuple([i for i, x in is_xs if i not in ls][len(ls)-M:])
break
print ("Replace {} (={}) by {} (={})".format(ls[:1], first_x, replace, sum(xs[i] for i in replace)))
ls = tuple(sorted(ls[1:] + replace)) # use a heap?
print("{} elements ({}) -> {}".format(len(ls), show(ls), sum(x for i, x in is_xs if i in ls)))
print("AFTER {} splits, {} -> {}".format(splits, ls, sum(x for i, x in is_xs if i in ls)))
The result is obviously not guaranteed to be optimal.
Remarks:
Complexity: find has a polynomial time complexity (see the Wikipedia page) and is called at most M^2 times, hence the complexity remains polynomial. In practice, the process is reasonably fast (split calls have a small target).
Vectors: to ensure that you reach the target with the minimum of elements, you can improve the order of element. Your target is (t_1, ..., t_c): if you sort the t_js from max to min, you get the more importants columns first. You can sort the vectors: by number of 1s and then by the presence of a 1 in the most important columns. E.g. target = 4 8 6 => 1 1 1 > 0 1 1 > 1 1 0 > 1 0 1 > 0 1 0 > 0 0 1 > 1 0 0 > 0 0 0.
find (Vectors) if the current sum exceed the target in all the columns, then you're not connecting to the target (any vector you add to the current sum will bring you farther from the target): don't add the sum to S (z >= target case for numbers).
I propose a simple ad hoc algorithm, which, broadly speaking, is a kind of gradient descent algorithm. It seems to work relatively well for input vectors which have a distribution of 1s “similar” to the target sum vector, and probably also for all “nice” input vectors, as defined in a comment of yours. The solution is not exact, but the approximation seems good.
The distance between the sum vector of the output vectors and the target vector is taken to be Euclidean. To minimize it means minimizing the sum of the square differences off sum vector and target vector (the square root is not needed because it is monotonic). The algorithm does not guarantee to yield the sample that minimizes the distance from the target, but anyway makes a serious attempt at doing so, by always moving in some locally optimal direction.
The algorithm can be split into 3 parts.
First of all the first M candidate output vectors out of the N input vectors (e.g., N=2000, M=500) are put in a list, and the remaining vectors are put in another.
Then "approximately optimal" swaps between vectors in the two lists are done, until either the distance would not decrease any more, or a predefined maximum number of iterations is reached. An approximately optimal swap is one where removing the first vector from the list of output vectors causes a maximal decrease or minimal increase of the distance, and then, after the removal of the first vector, adding the second vector to the same list causes a maximal decrease of the distance. The whole swap is avoided if the net result is not a decrease of the distance.
Then, as a last phase, "optimal" swaps are done, again stopping on no decrease in distance or maximum number of iterations reached. Optimal swaps cause a maximal decrease of the distance, without requiring the removal of the first vector to be optimal in itself. To find an optimal swap all vector pairs have to be checked. This phase is much more expensive, being O(M(N-M)), while the previous "approximate" phase is O(M+(N-M))=O(N). Luckily, when entering this phase, most of the work has already been done by the previous phase.
from typing import List, Tuple
def get_sample(vects: List[Tuple[int]], target: Tuple[int], n_out: int,
max_approx_swaps: int = None, max_optimal_swaps: int = None,
verbose: bool = False) -> List[Tuple[int]]:
"""
Get a sample of the input vectors having a sum close to the target vector.
Closeness is measured in Euclidean metrics. The output is not guaranteed to be
optimal (minimum square distance from target), but a serious attempt is made.
The max_* parameters can be used to avoid too long execution times,
tune them to your needs by setting verbose to True, or leave them None (∞).
:param vects: the list of vectors (tuples) with the same number of "columns"
:param target: the target vector, with the same number of "columns"
:param n_out: the requested sample size
:param max_approx_swaps: the max number of approximately optimal vector swaps,
None means unlimited (default: None)
:param max_optimal_swaps: the max number of optimal vector swaps,
None means unlimited (default: None)
:param verbose: print some info if True (default: False)
:return: the sample of n_out vectors having a sum close to the target vector
"""
def square_distance(v1, v2):
return sum((e1 - e2) ** 2 for e1, e2 in zip(v1, v2))
n_vec = len(vects)
assert n_vec > 0
assert n_out > 0
n_rem = n_vec - n_out
assert n_rem > 0
output = vects[:n_out]
remain = vects[n_out:]
n_col = len(vects[0])
assert n_col == len(target) > 0
sumvect = (0,) * n_col
for outvect in output:
sumvect = tuple(map(int.__add__, sumvect, outvect))
sqdist = square_distance(sumvect, target)
if verbose:
print(f"sqdist = {sqdist:4} after"
f" picking the first {n_out} vectors out of {n_vec}")
if max_approx_swaps is None:
max_approx_swaps = sqdist
n_approx_swaps = 0
while sqdist and n_approx_swaps < max_approx_swaps:
# find the best vect to subtract (the square distance MAY increase)
sqdist_0 = None
index_0 = None
sumvect_0 = None
for index in range(n_out):
tmp_sumvect = tuple(map(int.__sub__, sumvect, output[index]))
tmp_sqdist = square_distance(tmp_sumvect, target)
if sqdist_0 is None or sqdist_0 > tmp_sqdist:
sqdist_0 = tmp_sqdist
index_0 = index
sumvect_0 = tmp_sumvect
# find the best vect to add,
# but only if there is a net decrease of the square distance
sqdist_1 = sqdist
index_1 = None
sumvect_1 = None
for index in range(n_rem):
tmp_sumvect = tuple(map(int.__add__, sumvect_0, remain[index]))
tmp_sqdist = square_distance(tmp_sumvect, target)
if sqdist_1 > tmp_sqdist:
sqdist_1 = tmp_sqdist
index_1 = index
sumvect_1 = tmp_sumvect
if sumvect_1:
tmp = output[index_0]
output[index_0] = remain[index_1]
remain[index_1] = tmp
sqdist = sqdist_1
sumvect = sumvect_1
n_approx_swaps += 1
else:
break
if verbose:
print(f"sqdist = {sqdist:4} after {n_approx_swaps}"
f" approximately optimal swap{'s'[n_approx_swaps == 1:]}")
diffvect = tuple(map(int.__sub__, sumvect, target))
if max_optimal_swaps is None:
max_optimal_swaps = sqdist
n_optimal_swaps = 0
while sqdist and n_optimal_swaps < max_optimal_swaps:
# find the best pair to swap,
# but only if the square distance decreases
best_sqdist = sqdist
best_diffvect = diffvect
best_pair = None
for i0 in range(M):
tmp_diffvect = tuple(map(int.__sub__, diffvect, output[i0]))
for i1 in range(n_rem):
new_diffvect = tuple(map(int.__add__, tmp_diffvect, remain[i1]))
new_sqdist = sum(d * d for d in new_diffvect)
if best_sqdist > new_sqdist:
best_sqdist = new_sqdist
best_diffvect = new_diffvect
best_pair = (i0, i1)
if best_pair:
tmp = output[best_pair[0]]
output[best_pair[0]] = remain[best_pair[1]]
remain[best_pair[1]] = tmp
sqdist = best_sqdist
diffvect = best_diffvect
n_optimal_swaps += 1
else:
break
if verbose:
print(f"sqdist = {sqdist:4} after {n_optimal_swaps}"
f" optimal swap{'s'[n_optimal_swaps == 1:]}")
return output
from random import randrange
C = 30 # number of columns
N = 2000 # total number of vectors
M = 500 # number of output vectors
F = 0.9 # fill factor of the target sum vector
T = int(M * F) # maximum value + 1 that can be appear in the target sum vector
A = 10000 # maximum number of approximately optimal swaps, may be None (∞)
B = 10 # maximum number of optimal swaps, may be None (unlimited)
target = tuple(randrange(T) for _ in range(C))
vects = [tuple(int(randrange(M) < t) for t in target) for _ in range(N)]
sample = get_sample(vects, target, M, A, B, True)
Typical output:
sqdist = 2639 after picking the first 500 vectors out of 2000
sqdist = 9 after 27 approximately optimal swaps
sqdist = 1 after 4 optimal swaps
P.S.: As it stands, this algorithm is not limited to binary input vectors, integer vectors would work too. Intuitively I suspect that the quality of the optimization could suffer, though. I suspect that this algorithm is more appropriate for binary vectors.
P.P.S.: Execution times with your kind of data are probably acceptable with standard CPython, but get better (like a couple of seconds, almost a factor of 10) with PyPy. To handle bigger sets of data, the algorithm would have to be translated to C or some other language, which should not be difficult at all.
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 like:
(x , y , z , t)
(1 , 3 , 6 , 0.5)
(1.5 , 4 , 6.5 , 1)
(3.5 , 7 , 8 , 1.5)
(4 , 7.25 , 9 , 2)
I am looking to find the best linear fit on these points, let say a function like:
f(t) = a * x +b * y +c * z
This is Linear Regression problem. The "best fit" depends on the metric you define for being better.
One simple example is the Least Squares Metric, which aims to minimize the sum of squares: (f((x_i,y_i,z_i)) - w_i)^2 - where w_i is the measured value for the sample.
So, in least squares you are trying to minimize SUM{(a*x_i+b*y_i+c*z^i - w_i)^2 | per each i }. This function has a single global minimum at:
(a,b,c) = (X^T * X)^-1 * X^T * w
Where:
X is a 3xm matrix (m is the number of samples you have)
X^T - is the transposed of this matrix
w - is the measured results: `(w_1,w_2,...,w_m)`
The * operator represents matrix multiplication
There are more complex other methods, that use other distance metric, one example is the famous SVR with a linear kernel.
It seems that you are looking for the major axis of a point cloud.
You can work this out by finding the Eigenvector associated to the largest Eigenvalue of the covariance matrix. Could be an opportunity to use the power method (starting the iterations with the point farthest from the centroid, for example).
Can also be addressed by Singular Value Decomposition, preferably using methods that compute the largest values only.
If your data set contains outliers, then RANSAC could be a better choice: take two points at random and compute the sum of distances to the line they define. Repeat a number of times and keep the best fit.
Using the squared distances will answer your request for least-squares, but non-squared distances will be more robust.
You have a linear problem.
For example, my equation will be Y=ax1+bx2+c*x3.
In MATLAB do it:
B = [x1(:) x2(:) x3(:)] \ Y;
Y_fit = [x1(:) x2(:) x3(:)] * B;
In PYTHON do it:
import numpy as np
B, _, _, _ = np.linalg.lstsq([x1[:], x2[:], x3[:]], Y)
Y_fit = np.matmul([x1[:] x2[:] x3[:]], B)
Closed. This question does not meet Stack Overflow guidelines. It is not currently accepting answers.
This question does not appear to be about programming within the scope defined in the help center.
Closed 9 years ago.
Improve this question
I'm trying to find a way to find similarities in two arrays of different points. I drew circles around points that have similar patterns and I would like to do some kind of auto comparison in intervals of let's say 100 points and tell what coefficient of similarity is for that interval. As you can see it might not be perfectly aligned also so point-to-point comparison would not be a good solution also (I suppose). Patterns that are slightly misaligned could also mean that they are matching the pattern (but obviously with a smaller coefficient)
What similarity could mean (1 coefficient is a perfect match, 0 or less - is not a match at all):
Points 640 to 660 - Very similar (coefficient is ~0.8)
Points 670 to 690 - Quite similar (coefficient is ~0.5-~0.6)
Points 720 to 780 - Let's say quite similar (coefficient is ~0.5-~0.6)
Points 790 to 810 - Perfectly similar (coefficient is 1)
Coefficient is just my thoughts of how a final calculated result of comparing function could look like with given data.
I read many posts on SO but it didn't seem to solve my problem. I would appreciate your help a lot. Thank you
P.S. Perfect answer would be the one that provides pseudo code for function which could accept two data arrays as arguments (intervals of data) and return coefficient of similarity.
Click here to see original size of image
I also think High Performance Mark has basically given you the answer (cross-correlation). In my opinion, most of the other answers are only giving you half of what you need (i.e., dot product plus compare against some threshold). However, this won't consider a signal to be similar to a shifted version of itself. You'll want to compute this dot product N + M - 1 times, where N, M are the sizes of the arrays. For each iteration, compute the dot product between array 1 and a shifted version of array 2. The amount you shift array 2 increases by one each iteration. You can think of array 2 as a window you are passing over array 1. You'll want to start the loop with the last element of array 2 only overlapping the first element in array 1.
This loop will generate numbers for different amounts of shift, and what you do with that number is up to you. Maybe you compare it (or the absolute value of it) against a threshold that you define to consider two signals "similar".
Lastly, in many contexts, a signal is considered similar to a scaled (in the amplitude sense, not time-scaling) version of itself, so there must be a normalization step prior to computing the cross-correlation. This is usually done by scaling the elements of the array so that the dot product with itself equals 1. Just be careful to ensure this makes sense for your application numerically, i.e., integers don't scale very well to values between 0 and 1 :-)
i think HighPerformanceMarks's suggestion is the standard way of doing the job.
a computationally lightweight alternative measure might be a dot product.
split both arrays into the same predefined index intervals.
consider the array elements in each intervals as vector coordinates in high-dimensional space.
compute the dot product of both vectors.
the dot product will not be negative. if the two vectors are perpendicular in their vector space, the dot product will be 0 (in fact that's how 'perpendicular' is usually defined in higher dimensions), and it will attain its maximum for identical vectors.
if you accept the geometric notion of perpendicularity as a (dis)similarity measure, here you go.
caveat:
this is an ad hoc heuristic chosen for computational efficiency. i cannot tell you about mathematical/statistical properties of the process and separation properties - if you need rigorous analysis, however, you'll probably fare better with correlation theory anyway and should perhaps forward your question to math.stackexchange.com.
My Attempt:
Total_sum=0
1. For each index i in the range (m,n)
2. sum=0
3. k=Array1[i]*Array2[i]; t1=magnitude(Array1[i]); t2=magnitude(Array2[i]);
4. k=k/(t1*t2)
5. sum=sum+k
6. Total_sum=Total_sum+sum
Coefficient=Total_sum/(m-n)
If all values are equal, then sum would return 1 in each case and total_sum would return (m-n)*(1). Hence, when the same is divided by (m-n) we get the value as 1. If the graphs are exact opposites, we get -1 and for other variations a value between -1 and 1 is returned.
This is not so efficient when the y range or the x range is huge. But, I just wanted to give you an idea.
Another option would be to perform an extensive xnor.
1. For each index i in the range (m,n)
2. sum=1
3. k=Array1[i] xnor Array2[i];
4. k=k/((pow(2,number_of_bits))-1) //This will scale k down to a value between 0 and 1
5. sum=(sum+k)/2
Coefficient=sum
Is this helpful ?
You can define a distance metric for two vectors A and B of length N containing numbers in the interval [-1, 1] e.g. as
sum = 0
for i in 0 to 99:
d = (A[i] - B[i])^2 // this is in range 0 .. 4
sum = (sum / 4) / N // now in range 0 .. 1
This now returns distance 1 for vectors that are completely opposite (one is all 1, another all -1), and 0 for identical vectors.
You can translate this into your coefficient by
coeff = 1 - sum
However, this is a crude approach because it does not take into account the fact that there could be horizontal distortion or shift between the signals you want to compare, so let's look at some approaches for coping with that.
You can sort both your arrays (e.g. in ascending order) and then calculate the distance / coefficient. This returns more similarity than the original metric, and is agnostic towards permutations / shifts of the signal.
You can also calculate the differentials and calculate distance / coefficient for those, and then you can do that sorted also. Using differentials has the benefit that it eliminates vertical shifts. Sorted differentials eliminate horizontal shift but still recognize different shapes better than sorted original data points.
You can then e.g. average the different coefficients. Here more complete code. The routine below calculates coefficient for arrays A and B of given size, and takes d many differentials (recursively) first. If sorted is true, the final (differentiated) array is sorted.
procedure calc(A, B, size, d, sorted):
if (d > 0):
A' = new array[size - 1]
B' = new array[size - 1]
for i in 0 to size - 2:
A'[i] = (A[i + 1] - A[i]) / 2 // keep in range -1..1 by dividing by 2
B'[i] = (B[i + 1] - B[i]) / 2
return calc(A', B', size - 1, d - 1, sorted)
else:
if (sorted):
A = sort(A)
B = sort(B)
sum = 0
for i in 0 to size - 1:
sum = sum + (A[i] - B[i]) * (A[i] - B[i])
sum = (sum / 4) / size
return 1 - sum // return the coefficient
procedure similarity(A, B, size):
sum a = 0
a = a + calc(A, B, size, 0, false)
a = a + calc(A, B, size, 0, true)
a = a + calc(A, B, size, 1, false)
a = a + calc(A, B, size, 1, true)
return a / 4 // take average
For something completely different, you could also run Fourier transform using FFT and then take a distance metric on the returning spectra.