From Encyclopedia of Statistical Sciences I understand that given $p$ dichotomous (binary: 1=present; 0=absent) attributes (variables), we can form a contingency table for any two objects i and j of a sample:

         j
       1   0
      -------
  1  | a | b |
i     -------
  0  | c | d |
      -------
a = number of variables on which both objects i and j are 1
b = number of variables where object i is 1 and j is 0
c = number of variables where object i is 0 and j is 1
d = number of variables where both i and j are 0
a+b+c+d = p, the nubmer of variables.

We can calculate from these values similarity coefficients between any pair of objects, specifically the Jaccard coefficient $$ \frac{a}{a+b+c} $$ and the Russell and Rao coefficient $$ \frac{a}{a+b+c+d} = \frac{a}{p}. $$

When calculated these coefficients will give different values, but I can't find any resources which explain why I should choose one over the other. Is it just because for some datasets, the simultaneous absence of both attributes ($d$) doesn't convey any information?

up vote 14 down vote accepted

There exist many such coefficients (most are expressed here). Just try to meditate on what are the consequences of the differences in formulas, especially when you compute a matrix of coefficients.

Imagine, for example, that objects 1 and 2 similar, as objects 3 and 4 are. But 1 and 2 have many of the attributes on the list while 3 and 4 have only few attributes. In this case, Russell-Rao (proportion of co-attributes to the total number of attributes under consideration) will be high for pair 1-2 and low for pair 3-4. But Jaccard (proportion of co-attributes to the combined number of attributes both objects have = probability that if either object has an attribute then they both have it) will be high for both pairs 1-2 and 3-4.

This adjustment for the base level of "saturation by attributes" makes Jaccard so popular and more useful than Russell-Rao, e.g. in cluster analysis or multidimensional scaling. You might, in a sense, further refine the above adjustment by selecting Kulczynski-2 measure which is the arithmetic mean probability that if one object has an attribute, the other object has it too: $$ (\frac{a}{a+b} + \frac{a}{a+c}) /2 $$ Here the base (or field) of attributes for the two objects is not pooled, as in Jaccard, but is own for each of the two objects. Consequently, if the objects differ greatly on the number of attributes they have, and all its attributes the "poorer" object shares with the "richer" one, Kulczynski will be high whereas Jaccard will be moderate.

Or you could prefer to compute geometric mean probability that if one object has an attribute, the other object has it too, which yields Ochiai measure: $$ \sqrt {\frac{a}{a+b} \frac{a}{a+c}} $$ Because product increases weaker than sum when only one of the terms grows, Ochiai will be really high only if both of the two proportions (probabilities) are high, which implies that to be considered similar by Ochiai the objects must share the great shares of their attributes. In short, Ochiai curbs similarity if $b$ and $c$ are unequal. Ochiai is in fact the cosine similarity measure (and Russell-Rao is the dot product similarity).


P.S.

Is it just because for some datasets, the simultaneous absence of both attributes (d) doesn't convey any information?

Speaking of similarity measures, one shouldn't mix nominal dichotomous attributes (e.g. female, male) with binary attributes (present vs absent). Binary attribute isn't symmetric (in general), - if you and I share a characteristic, it is the basis for calling us similar; if you and I both miss the characteristic, it may or may not be considered the evidence of similarity, depending on the context of the study. Hence the divergent treatment of $d$ is possible.

Note also that if you wish to compute similarity between objects based on 1+ nominal attributes (dichotomous or polytomous), recode each such variable into the set of dummy binary variables. Then the recommended similarity measure to compute will be Dice (which, when computed for 1+ sets of dummy variables, is equivalent to Ochiai and Kulczynski-2).

  • 2
    Various terms have been suggested by supposed analogy with "dichotomous" for classifications with more than two categories. "Polytomous" is preferable linguistically to "polychotomous", which is based on an incorrect guess that "dichotomous" parses into two Greek roots, "di" and "chotomous". "Multichotomous" compounds that error with use of a Latin root. Although words with separate Latin and Greek roots have survived the disdain of linguists (e.g. "television") I advise the use of "polytomous" here. – Nick Cox Jun 17 '13 at 10:44
  • Thank you for reminding it. I actually knew what you are saying about, and try to be puristic myself... when I'm not in a hurry. I'll edit it. – ttnphns Jun 17 '13 at 10:53

The usefulness of the Tanimoto coefficient over the traditional accuracy (i.e. Russell-Rao) is evident in image analysis, when comparing a segmentation to a gold-standard. Consider these two images:

enter image description here

In each of these images which are binary 'masks', we have two objects of the same size but placed at slightly different locations, and we want to evaluate to what extent these objects are identical in shape and position by assessing their overlap. Usually one (e.g. the purple mask) is a segmentation (produced by a computer algorithm), e.g. this could be an attempt to locate the heart from a medical image. The other, (e.g. green) is the gold-standard (i.e. the heart, as identified by an expert clinician). Where there is white colour, the two shapes overlap. Black pixels are background.

The two images are identical (i.e. the outcome of the segmentation algorithm, as well as the gold standard, are the same in both images), except for a lot of background "padding" in the second image (e.g. this could represent two experiments with two different x-ray machines, where the 2nd machine had a wider ray covering more body area, but otherwise the size of the heart is the same in both image sets).

Clearly, since the segmentation and gold standard in both images are identical, if we evaluate the segmentation accuracy against the gold standard, we would like our metric to output the same 'accuracy' result in both experiments.

However, if we attempt to assess the quality of the segmentation using the Russel-Rao approach, we would get a misleadingly high accuracy for the right image (close to 100%), because "background pixels identified correctly as background pixels" contribute towards the overall accuracy of the sets, and background pixels are disproportionately represented in the second set. The objects whose overlap we want to evaluate in medical segmentation are often tiny specks in a massive background, so this is not very useful to us. Furthermore, this would lead to problems if we were trying to compare the accuracy of one segmentation algorithm to another, and the two were evaluated on images of different size! (or, equivalently, at different scales). The scaling / size of the embedding image should not make a difference in the evaluation of a segmentation against a gold-standard!.

By contrast, the tanimoto coefficient does not care about the background pixels, making it invariant to 'scale'. So as far as the tanimoto coefficient is concerned, the similarity of both these sets will be identical, making it a far more useful similarity metric for us to use to evaluate the quality of a segmentation algorithm.

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