Similarity distance measures

Question

Vectors like this

v1 = {0 0 0 1 1 0 0 1 0 1 1}
v2 = {0 1 1 1 1 1 0 1 0 1 0}
v3 = {0 0 0 0 0 0 0 0 0 0 1}

Need to calculate similarity between them. Hamming distance between v1 and v2 is 4 and between v1 and v3 is also 4. But because I am interested in the groups of '1' which are together for me v2 is far more similar to v1 then v3 is.

Is there any distance metrics that can capture this in the data?

The data represent occupancy of house in time, that's why it is important to me. '1' means occupied, '0' means non occupied.

Guinna

so what is the question ? – Crinum

sorry, already edited, if there is any distance metrics that can capture this – Guinna

I am interested in the groups of '1' which are together. Could you explain what you mean by that? 1 and 2 are more simliar because of the same amount of groups? – Sesqui

well basically yes, 1 and 2 are more similar there is same amount of groups. Because v2 is basically vector v1 only with the first group of '1' being "wider". V3 is almost empty vector – Guinna

Answer 1

It sounds like you need cosine similarity measure:

similarity = cos(v1, v2) = v1 * v2 / (|v1| |v2|)

where v1 * v2 is dot product between v1 and v2:

v1 * v2 = v1[1]*v2[1] + v1[2]*v2[2] + ... + v1[n]*v2[n]

Essentially, dot product shows how many elements in both vectors have 1 at the same position: if v1[k] == 1 and v2[k] == 1, then final sum (and thus similarity) is increased, otherwise it isn't changed.

You can use dot product itself, but sometimes you would want final similarity to be normalized, e.g. be between 0 and 1. In this case you can divide dot product of v1 and v2 by their lengths - |v1| and |v2|. Essentially, vector length is square root of dot product of the vector with itself:

|v| = sqrt(v[1]*v[1] + v[2]*v[2] + ... + v[n]*v[n])

Having all of these, it's easy to implement cosine distance as follows (example in Python):

from math import sqrt

def dot(v1, v2):
    return sum(x*y for x, y in zip(v1, v2))

def length(v):
    return sqrt(dot(v, v))

def sim(v1, v2): 
    return dot(v1, v2) / (length(v1) * length(v2))

Note, that I described similarity (how much two vectors are close to each other), not distance (how far they are). If you need exactly distance, you can calculate it as dist = 1 / sim.

Lutenist

I believe it should be dist = 1 - sim and not 1 / sim – Magdaleno

@ThalisK.: both will work. The idea is that distance is in some sense inverse of similarity, so any inverse (and strictly monotone) function should work, and you can select concrete function based on your concrete interpretation of "distance". – Lutenist

Thanks. That makes sense. I would appreciate it if you would then take a look at this question: #25181604 – Magdaleno

if i have more than three vectors, like if i want to check v4 is different from v1, v2, and v3, can i apply your answer? – Jeddy

Cosine similarity is a pairwise distance measure, so you can use it to any number of vectors as long as you consider their pairs (e.g. v4 vs v1, v4 vs v2, etc.). If you want a measure that works with 3 or more vectors at the same time, you should be more specific about desirable properties of this measure. E.g. you may want an average distance of v4 from v1, v2 and v3 and that is as easy as (dist(v4, v1) + dist(v4, v2) + dist(v4, v3)) / 3. So it all depends on what exactly you want to achieve. – Lutenist

Any reason why your length function does not account for the sqrt? |v| = sqrt(v_1^2 + v_2^2 + ...) =/= v_1^2 + v_2^2 + ... – Regimen

You've just got a badge for watchfulness :) I've edited the code, thanks. – Lutenist

Answer 2

There are literally hundreds of distance functions, including distance measures for sets, such as Dice and Jaccard.

You may want to get the book "Dictionary of Distance Functions", it's pretty good.

Immunotherapy

Looked up the title and didn't find it. Could your provide author, isbn, exact title please? – Magdaleno

First result on Google Books. ISBN: 9780080465548 – Immunotherapy

The book is a great reference. It has been updated and renamed as Encyclopedia of distances: link.springer.com/book/10.1007/978-3-662-52844-0 – Dispirited

Answer 3

Case 1: IF the position of the ones in the series is relevant, THEN:

I recommend Dynamic Time Warping Distance (DTW). In application of time-series data it has proven incredibly useful.

To check whether it can be applied to your problem, I used the code presented here: https://jeremykun.com/2012/07/25/dynamic-time-warping/

d13 = dynamicTimeWarp(v1,v3)
d12 = dynamicTimeWarp(v1,v2)
d23 = dynamicTimeWarp(v2,v3)

d23,d12,d13
(3, 1, 3)

As you see, d12 is lowest, therefore v1 and v2 are most similiar. Further information of DTW can be found anywhere in this forum and for research papers, I recommend anything by Eamonn Keogh.

Case 2: Position of ones is not relevant:

I simply agree Deepu for taking the average as a feature.

Discalced

Answer 4

I think you can simply take the average of the values in each set. For example v1 here will have an average 0.4545, average of v2 is 0.6363 and average of v3 is 0.0909. If the only possible values in the set are 0 and 1, then the sets with equal or nearly equal values will serve your purpose.

Newel

That's actually good idea, the problem I have though is that I have to mix the two metrics somehow together. Because vectors 0 0 1 1 and 1 1 0 0 would with average return both 0,5 and with my metrics 4 that all of them are displaced. Is it possible to somehow combine these two metrics that each yields half of the final value? Or is that too unpredictable? – Guinna

What about Standard Deviation? Will it help? – Newel

In a way I guess if the distribution below it was gaussian. But if I again take the the 0 0 1 1 and 1 1 0 0 example the std will have same results. I know how you mean it but then I would have to first cluster it make means of the clusters and then compare means and std of each cluster. But if such a complicated solution makes significant different. – Guinna

Answer 5

There is a web site introducing the various type of vector similarity methods

http://dataaspirant.com/2015/04/11/five-most-popular-similarity-measures-implementation-in-python/

I think it will help you to decide what similarity you should use

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Briefly explaining the above link, there are five popular similarity measurement between vectors

1. Euclidean Distance - Simply the absolute distance between the vectors

2. Cosine - Cosine degree(theta) difference between the vectors

3. Manhattan -the sum of the absolute differences of their Cartesian coordinates, for example,

In a plane with p1 at (x1, y1) and p2 at (x2, y2). Manhattan distance = |x1 – x2| + |y1 – y2|

4. Minkowski - generalized metric form of Euclidean distance and Manhattan distance

5. Jaccard - Similarity between the objects. So each feature in one set will be compared to another set and finds out its difference

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With the keyword above you can google for further explanation. Hope it would help you

Appendage