Jaccard index – Wikipedia
Measure of similarity and variety between units
The Jaccard index, also called the Jaccard similarity coefficient, is a statistic used for gauging the similarity and diversity of sample units. It was developed by Grove Karl Gilbert in 1884 as his ratio of verification (v)^{[1]} and now could be incessantly known as the Vital Success Index in meteorology.^{[2]} It was later developed independently by Paul Jaccard, initially giving the French title coefficient de communauté,^{[3]} and independently formulated once more by T. Tanimoto.^{[4]} Thus, the Tanimoto index or Tanimoto coefficient are additionally utilized in some fields. Nevertheless, they’re similar in usually taking the ratio of Intersection over Union. The Jaccard coefficient measures similarity between finite pattern units, and is outlined as the scale of the intersection divided by the scale of the union of the pattern units:
- ${displaystyle J(A,B)={Acap B over Acup B}={Acap B over A}.}$
Observe that by design, ${displaystyle 0leq J(A,B)leq 1.}$ If A intersection B is empty, then J(A,B) = 0. The Jaccard coefficient is broadly utilized in pc science, ecology, genomics, and different sciences, the place binary or binarized data are used. Each the precise resolution and approximation strategies can be found for speculation testing with the Jaccard coefficient.^{[5]}
Jaccard similarity additionally applies to luggage, i.e., Multisets. This has an identical system,^{[6]} however the symbols imply
bag intersection and bag sum (not union). The utmost worth is 1/2.
- ${displaystyle J(A,B)={Acap B over Auplus B}={Acap B over B}.}$
The Jaccard distance, which measures dissimilarity between pattern units, is complementary to the Jaccard coefficient and is obtained by subtracting the Jaccard coefficient from 1, or, equivalently, by dividing the distinction of the sizes of the union and the intersection of two units by the scale of the union:
- ${displaystyle d_{J}(A,B)=1-J(A,B)=Acup B.}$
An alternate interpretation of the Jaccard distance is because the ratio of the scale of the symmetric difference ${displaystyle Atriangle B=(Acup B)-(Acap B)}$ to the union.
Jaccard distance is often used to calculate an n × n matrix for clustering and multidimensional scaling of n pattern units.
This distance is a metric on the gathering of all finite units.^{[7]}^{[8]}^{[9]}
There’s additionally a model of the Jaccard distance for measures, together with probability measures. If ${displaystyle mu }$ is a measure on a measurable space ${displaystyle X}$, then we outline the Jaccard coefficient by
- ${displaystyle J_{mu }(A,B)={{mu (Acap B)} over {mu (Acup B)}},}$
and the Jaccard distance by
- ${displaystyle d_{mu }(A,B)=1-J_{mu }(A,B)={{mu (Atriangle B)} over {mu (Acup B)}}.}$
Care should be taken if ${displaystyle mu (Acup B)=0}$ or ${displaystyle infty }$, since these formulation aren’t nicely outlined in these circumstances.
The MinHash min-wise unbiased permutations locality sensitive hashing scheme could also be used to effectively compute an correct estimate of the Jaccard similarity coefficient of pairs of units, the place every set is represented by a constant-sized signature derived from the minimal values of a hash function.
Similarity of uneven binary attributes[edit]
Given two objects, A and B, every with n binary attributes, the Jaccard coefficient is a helpful measure of the overlap that A and B share with their attributes. Every attribute of A and B can both be 0 or 1. The overall variety of every mixture of attributes for each A and B are specified as follows:
- ${displaystyle M_{11}}$ represents the whole variety of attributes the place A and B each have a worth of 1.
- ${displaystyle M_{01}}$ represents the whole variety of attributes the place the attribute of A is 0 and the attribute of B is 1.
- ${displaystyle M_{10}}$ represents the whole variety of attributes the place the attribute of A is 1 and the attribute of B is 0.
- ${displaystyle M_{00}}$ represents the whole variety of attributes the place A and B each have a worth of 0.
A B |
0 | 1 |
---|---|---|
0 | ${displaystyle M_{00}}$ | ${displaystyle M_{10}}$ |
1 | ${displaystyle M_{01}}$ | ${displaystyle M_{11}}$ |
Every attribute should fall into one in all these 4 classes, that means that
- ${displaystyle M_{11}+M_{01}+M_{10}+M_{00}=n.}$
The Jaccard similarity coefficient, J, is given as
- ${displaystyle J={M_{11} over M_{01}+M_{10}+M_{11}}.}$
The Jaccard distance, d_{J}, is given as
- ${displaystyle d_{J}={M_{01}+M_{10} over M_{01}+M_{10}+M_{11}}=1-J.}$
Statistical inference might be made primarily based on the Jaccard similarity coefficients, and consequently associated metrics.^{[5]} Given two pattern units A and B with n attributes, a statistical take a look at might be performed to see if an overlap is statistically significant. The precise resolution is out there, though computation might be pricey as n will increase.^{[5]} Estimation strategies can be found both by approximating a multinomial distribution or by bootstrapping.^{[5]}
Distinction with the straightforward matching coefficient (SMC)[edit]
When used for binary attributes, the Jaccard index is similar to the simple matching coefficient. The principle distinction is that the SMC has the time period ${displaystyle M_{00}}$ in its numerator and denominator, whereas the Jaccard index doesn’t. Thus, the SMC counts each mutual presences (when an attribute is current in each units) and mutual absence (when an attribute is absent in each units) as matches and compares it to the whole variety of attributes within the universe, whereas the Jaccard index solely counts mutual presence as matches and compares it to the variety of attributes which were chosen by a minimum of one of many two units.
In market basket analysis, for instance, the basket of two customers who we want to evaluate may solely comprise a small fraction of all of the accessible merchandise within the retailer, so the SMC will normally return very excessive values of similarities even when the hampers bear little or no resemblance, thus making the Jaccard index a extra acceptable measure of similarity in that context. For instance, think about a grocery store with 1000 merchandise and two prospects. The basket of the primary buyer accommodates salt and pepper and the basket of the second accommodates salt and sugar. On this situation, the similarity between the 2 baskets as measured by the Jaccard index could be 1/3, however the similarity turns into 0.998 utilizing the SMC.
In different contexts, the place 0 and 1 carry equal info (symmetry), the SMC is a greater measure of similarity. For instance, vectors of demographic variables saved in dummy variables, equivalent to gender, could be higher in contrast with the SMC than with the Jaccard index because the influence of gender on similarity needs to be equal, independently of whether or not male is outlined as a 0 and feminine as a 1 or the opposite means round. Nevertheless, when now we have symmetric dummy variables, one might replicate the behaviour of the SMC by splitting the dummies into two binary attributes (on this case, female and male), thus reworking them into uneven attributes, permitting the usage of the Jaccard index with out introducing any bias. The SMC stays, nonetheless, extra computationally environment friendly within the case of symmetric dummy variables because it doesn’t require including further dimensions.
Weighted Jaccard similarity and distance[edit]
If ${displaystyle mathbf {x} =(x_{1},x_{2},ldots ,x_{n})}$ and ${displaystyle mathbf {y} =(y_{1},y_{2},ldots ,y_{n})}$ are two vectors with all actual ${displaystyle x_{i},y_{i}geq 0}$, then their Jaccard similarity coefficient (additionally identified then as Ruzicka similarity) is outlined as
- ${displaystyle J_{mathcal {W}}(mathbf {x} ,mathbf {y} )={frac {sum _{i}min(x_{i},y_{i})}{sum _{i}max(x_{i},y_{i})}},}$
and Jaccard distance (additionally identified then as Soergel distance)
- ${displaystyle d_{J{mathcal {W}}}(mathbf {x} ,mathbf {y} )=1-J_{mathcal {W}}(mathbf {x} ,mathbf {y} ).}$
With much more generality, if ${displaystyle f}$ and ${displaystyle g}$ are two non-negative measurable capabilities on a measurable area ${displaystyle X}$ with measure ${displaystyle mu }$, then we will outline
- ${displaystyle J_{mathcal {W}}(f,g)={frac {int min(f,g)dmu }{int max(f,g)dmu }},}$
the place ${displaystyle max }$ and ${displaystyle min }$ are pointwise operators. Then Jaccard distance is
- ${displaystyle d_{J{mathcal {W}}}(f,g)=1-J_{mathcal {W}}(f,g).}$
Then, for instance, for 2 measurable units ${displaystyle A,Bsubseteq X}$, now we have ${displaystyle J_{mu }(A,B)=J(chi _{A},chi _{B}),}$ the place ${displaystyle chi _{A}}$ and ${displaystyle chi _{B}}$ are the attribute capabilities of the corresponding set.
Likelihood Jaccard similarity and distance[edit]
The weighted Jaccard similarity described above generalizes the Jaccard Index to optimistic vectors, the place a set corresponds to a binary vector given by the indicator function, i.e. ${displaystyle x_{i}in {0,1}}$. Nevertheless, it doesn’t generalize the Jaccard Index to chance distributions, the place a set corresponds to a uniform chance distribution, i.e.
- ${displaystyle x_{i}={start{circumstances}{frac {1}}&iin X�&{textual content{in any other case}}finish{circumstances}}}$
It’s at all times much less if the units differ in measurement. If $X$, and ${displaystyle x_{i}=mathbf {1} _{X}(i)/|X|,y_{i}=mathbf {1} _{Y}(i)/|Y|}$ then
- ${displaystyle J_{mathcal {W}}(x,y)={frac Xcap Y+}<J(X,Y).}$
As a substitute, a generalization that’s steady between chance distributions and their corresponding help units is
- ${displaystyle J_{mathcal {P}}(x,y)=sum _{x_{i}neq 0,y_{i}neq 0}{frac {1}{sum _{j}max left({frac {x_{j}}{x_{i}}},{frac {y_{j}}{y_{i}}}proper)}}}$
which is known as the “Likelihood” Jaccard.^{[10]} It has the next bounds in opposition to the Weighted Jaccard on chance vectors.
- ${displaystyle J_{mathcal {W}}(x,y)leq J_{mathcal {P}}(x,y)leq {frac {2J_{mathcal {W}}(x,y)}{1+J_{mathcal {W}}(x,y)}}}$
Right here the higher sure is the (weighted) Sørensen–Dice coefficient.
The corresponding distance, ${displaystyle 1-J_{mathcal {P}}(x,y)}$, is a metric over chance distributions, and a pseudo-metric over non-negative vectors.
The Likelihood Jaccard Index has a geometrical interpretation as the realm of an intersection of simplices. Each level on a unit ${displaystyle ok}$-simplex corresponds to a chance distribution on ${displaystyle ok+1}$ parts, as a result of the unit ${displaystyle ok}$-simplex is the set of factors in ${displaystyle ok+1}$ dimensions that sum to 1. To derive the Likelihood Jaccard Index geometrically, signify a chance distribution because the unit simplex divided into sub simplices in keeping with the mass of every merchandise. When you overlay two distributions represented on this means on high of one another, and intersect the simplices corresponding to every merchandise, the realm that is still is the same as the Likelihood Jaccard Index of the distributions.
Optimality of the Likelihood Jaccard Index[edit]
Contemplate the issue of setting up random variables such that they collide with one another as a lot as attainable. That’s, if ${displaystyle Xsim x}$ and ${displaystyle Ysim y}$, we wish to assemble ${displaystyle X}$ and ${displaystyle Y}$ to maximise ${displaystyle Pr[X=Y]}$. If we have a look at simply two distributions ${displaystyle x,y}$ in isolation, the very best ${displaystyle Pr[X=Y]}$ we will obtain is given by ${displaystyle 1-{textual content{TV}}(x,y)}$ the place ${displaystyle {textual content{TV}}}$ is the Total Variation distance. Nevertheless, suppose we weren’t simply involved with maximizing that specific pair, suppose we wish to maximize the collision chance of any arbitrary pair. One might assemble an infinite variety of random variables one for every distribution ${displaystyle x}$, and search to maximise ${displaystyle Pr[X=Y]}$ for all pairs ${displaystyle x,y}$. In a reasonably robust sense described under, the Likelihood Jaccard Index is an optimum technique to align these random variables.
For any sampling technique ${displaystyle G}$ and discrete distributions ${displaystyle x,y}$, if ${displaystyle Pr[G(x)=G(y)]>J_{mathcal {P}}(x,y)}$ then for some ${displaystyle z}$ the place ${displaystyle J_{mathcal {P}}(x,z)>J_{mathcal {P}}(x,y)}$ and ${displaystyle J_{mathcal {P}}(y,z)>J_{mathcal {P}}(x,y)}$, both ${displaystyle Pr[G(x)=G(z)]<J_{mathcal {P}}(x,z)}$ or ${displaystyle Pr[G(y)=G(z)]<J_{mathcal {P}}(y,z)}$.^{[10]}
That’s, no sampling technique can obtain extra collisions than ${displaystyle J_{mathcal {P}}}$ on one pair with out reaching fewer collisions than ${displaystyle J_{mathcal {P}}}$ on one other pair, the place the lowered pair is extra comparable beneath ${displaystyle J_{mathcal {P}}}$ than the elevated pair. This theorem is true for the Jaccard Index of units (if interpreted as uniform distributions) and the chance Jaccard, however not of the weighted Jaccard. (The concept makes use of the phrase “sampling technique” to explain a joint distribution over all distributions on an area, as a result of it derives from the usage of weighted minhashing algorithms that obtain this as their collision chance.)
This theorem has a visible proof on three ingredient distributions utilizing the simplex illustration.
Tanimoto similarity and distance[edit]
Numerous types of capabilities described as Tanimoto similarity and Tanimoto distance happen within the literature and on the Web. Most of those are synonyms for Jaccard similarity and Jaccard distance, however some are mathematically totally different. Many sources^{[11]} cite an IBM Technical Report^{[4]} because the seminal reference. The report is out there from several libraries.
In “A Laptop Program for Classifying Crops”, printed in October 1960,^{[12]} a way of classification primarily based on a similarity ratio, and a derived distance operate, is given. Plainly that is probably the most authoritative supply for the that means of the phrases “Tanimoto similarity” and “Tanimoto Distance”. The similarity ratio is equal to Jaccard similarity, however the distance operate is not the identical as Jaccard distance.
Tanimoto’s definitions of similarity and distance[edit]
In that paper, a “similarity ratio” is given over bitmaps, the place every little bit of a fixed-size array represents the presence or absence of a attribute within the plant being modelled. The definition of the ratio is the variety of widespread bits, divided by the variety of bits set (i.e. nonzero) in both pattern.
Introduced in mathematical phrases, if samples X and Y are bitmaps, ${displaystyle X_{i}}$ is the ith little bit of X, and ${displaystyle land ,lor }$ are bitwise and, or operators respectively, then the similarity ratio ${displaystyle T_{s}}$ is
- ${displaystyle T_{s}(X,Y)={frac {sum _{i}(X_{i}land Y_{i})}{sum _{i}(X_{i}lor Y_{i})}}}$
If every pattern is modelled as an alternative as a set of attributes, this worth is equal to the Jaccard coefficient of the 2 units. Jaccard will not be cited within the paper, and it appears probably that the authors weren’t conscious of it.^{[citation needed]}
Tanimoto goes on to outline a “distance coefficient” primarily based on this ratio, outlined for bitmaps with non-zero similarity:
- ${displaystyle T_{d}(X,Y)=-log _{2}(T_{s}(X,Y))}$
This coefficient is, intentionally, not a distance metric. It’s chosen to permit the opportunity of two specimens, that are fairly totally different from one another, to each be much like a 3rd. It’s straightforward to assemble an instance which disproves the property of triangle inequality.
Different definitions of Tanimoto distance[edit]
Tanimoto distance is usually referred to, erroneously, as a synonym for Jaccard distance ${displaystyle 1-T_{s}}$. This operate is a correct distance metric. “Tanimoto Distance” is usually said as being a correct distance metric, in all probability due to its confusion with Jaccard distance.
If Jaccard or Tanimoto similarity is expressed over a bit vector, then it may be written as
- ${displaystyle f(A,B)={frac {Acdot B}{|A|^{2}+|B|^{2}-Acdot B}}}$
the place the identical calculation is expressed by way of vector scalar product and magnitude. This illustration depends on the truth that, for a bit vector (the place the worth of every dimension is both 0 or 1) then
- ${displaystyle Acdot B=sum _{i}A_{i}B_{i}=sum _{i}(A_{i}land B_{i})}$
and
- ${displaystyle |A|^{2}=sum _{i}A_{i}^{2}=sum _{i}A_{i}.}$
This can be a doubtlessly complicated illustration, as a result of the operate as expressed over vectors is extra common, except its area is explicitly restricted. Properties of ${displaystyle T_{s}}$ don’t essentially prolong to ${displaystyle f}$. Particularly, the distinction operate ${displaystyle 1-f}$ doesn’t protect triangle inequality, and isn’t subsequently a correct distance metric, whereas ${displaystyle 1-T_{s}}$ is.
There’s a actual hazard that the mixture of “Tanimoto Distance” being outlined utilizing this system, together with the assertion “Tanimoto Distance is a correct distance metric” will result in the false conclusion that the operate ${displaystyle 1-f}$ is in truth a distance metric over vectors or multisets generally, whereas its use in similarity search or clustering algorithms could fail to provide appropriate outcomes.
Lipkus^{[8]} makes use of a definition of Tanimoto similarity which is equal to ${displaystyle f}$, and refers to Tanimoto distance because the operate ${displaystyle 1-f}$. It’s, nonetheless, made clear inside the paper that the context is restricted by means of a (optimistic) weighting vector ${displaystyle W}$ such that, for any vector A being thought-about, ${displaystyle A_{i}in {0,W_{i}}.}$ Below these circumstances, the operate is a correct distance metric, and so a set of vectors ruled by such a weighting vector kinds a metric space beneath this operate.
Jaccard index in binary classification confusion matrices[edit]
In confusion matrices employed for binary classification, the Jaccard index might be framed within the following system:
- ${displaystyle {textual content{Jaccard index}}={frac {TP}{TP+FP+FN}}}$
the place TP are the true positives, FP the false positives and FN the false negatives.^{[13]}
See additionally[edit]
References[edit]
- ^ Murphy, Allan H. (1996). “The Finley Affair: A Signal Event in the History of Forecast Verification”. Climate and Forecasting. 11 (1): 3. Bibcode:1996WtFor..11….3M. doi:10.1175/1520-0434(1996)011<0003:TFAASE>2.0.CO;2. ISSN 1520-0434. S2CID 54532560.
- ^ https://www.swpc.noaa.gov/sites/default/files/images/u30/Forecast%20Verification%20Glossary.pdf^{[bare URL PDF]}
- ^ Jaccard, Paul (February 1912). “The Distribution of the Flora in the Alpine Zone.1”. New Phytologist. 11 (2): 37–50. doi:10.1111/j.1469-8137.1912.tb05611.x. ISSN 0028-646X.
- ^ ^{a} ^{b} Tanimoto TT (17 Nov 1958). “An Elementary Mathematical concept of Classification and Prediction”. Inside IBM Technical Report. 1957 (8?).
- ^ ^{a} ^{b} ^{c} ^{d} Chung NC, Miasojedow B, Startek M, Gambin A (December 2019). “Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data”. BMC Bioinformatics. 20 (Suppl 15): 644. arXiv:1903.11372. doi:10.1186/s12859-019-3118-5. PMC 6929325. PMID 31874610.
- ^ Leskovec J, Rajaraman A, Ullman J (2020). Mining of Large Datasets. Cambridge. ISBN 9781108476348. and p. 76-77 in an earlier model http://infolab.stanford.edu/~ullman/mmds/ch3.pdf
- ^ Kosub S (April 2019). “A observe on the triangle inequality for the Jaccard distance”. Sample Recognition Letters. 120: 36–8. arXiv:1612.02696. Bibcode:2019PaReL.120…36K. doi:10.1016/j.patrec.2018.12.007. S2CID 564831.
- ^ ^{a} ^{b} Lipkus AH (1999). “A proof of the triangle inequality for the Tanimoto distance”. Journal of Mathematical Chemistry. 26 (1–3): 263–265. doi:10.1023/A:1019154432472. S2CID 118263043.
- ^ Levandowsky M, Winter D (1971). “Distance between units”. Nature. 234 (5): 34–35. Bibcode:1971Natur.234…34L. doi:10.1038/234034a0. S2CID 4283015.
- ^ ^{a} ^{b} Moulton R, Jiang Y (2018). “Maximally Constant Sampling and the Jaccard Index of Likelihood Distributions”. Worldwide Convention on Information Mining, Workshop on Excessive Dimensional Information Mining: 347–356. arXiv:1809.04052. doi:10.1109/ICDM.2018.00050. ISBN 978-1-5386-9159-5. S2CID 49746072.
- ^ For instance Huihuan Q, Xinyu W, Yangsheng X (2011). Clever Surveillance Methods. Springer. p. 161. ISBN 978-94-007-1137-2.
- ^ Rogers DJ, Tanimoto TT (October 1960). “A Laptop Program for Classifying Crops”. Science. 132 (3434): 1115–8. Bibcode:1960Sci…132.1115R. doi:10.1126/science.132.3434.1115. PMID 17790723.
- ^ Aziz Taha, Abdel (2015). “Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool”. BMC Medical Imaging. 15 (29): 1–28. doi:10.1186/s12880-015-0068-x. PMC 4533825. PMID 26263899.
Additional studying[edit]
- Tan PN, Steinbach M, Kumar V (2005). Introduction to Information Mining. ISBN 0-321-32136-7.
- Jaccard P (1901). “Étude comparative de la distribution florale dans une portion des Alpes et des Jura”. Bulletin de la Société vaudoise des sciences naturelles. 37: 547–579.
- Jaccard P (1912). “The Distribution of the flora within the alpine zone”. New Phytologist. 11 (2): 37–50. doi:10.1111/j.1469-8137.1912.tb05611.x.
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