mantak / distances.jl

A Julia package for evaluating distances (metrics) between vectors.

Distances.jl

A Julia package for evaluating distances(metrics) between vectors.

This package also provides optimized functions to compute column-wise and pairwise distances, which are often substantially faster than a straightforward loop implementation. (See the benchmark section below for details).

Supported distances

• Euclidean distance
• Squared Euclidean distance
• Cityblock distance
• Total variation distance
• Jaccard distance
• Rogers-Tanimoto distance
• Chebyshev distance
• Minkowski distance
• Hamming distance
• Cosine distance
• Correlation distance
• Chi-square distance
• Kullback-Leibler divergence
• Generalized Kullback-Leibler divergence
• Rényi divergence
• Jensen-Shannon divergence
• Mahalanobis distance
• Squared Mahalanobis distance
• Bhattacharyya distance
• Hellinger distance
• Haversine distance
• Mean absolute deviation
• Mean squared deviation
• Root mean squared deviation
• Normalized root mean squared deviation
• Bray-Curtis dissimilarity
• Bregman divergence

For Euclidean distance, Squared Euclidean distance, Cityblock distance, Minkowski distance, and Hamming distance, a weighted version is also provided.

Basic Use

The library supports three ways of computation: computing the distance between two vectors, column-wise computation, and pairwise computation.

Computing the distance between two vectors

Each distance corresponds to a distance type. You can always compute a certain distance between two vectors using the following syntax

r = evaluate(dist, x, y)

Here, dist is an instance of a distance type. For example, the type for Euclidean distance is Euclidean (more distance types will be introduced in the next section), then you can compute the Euclidean distance between x and y as

r = evaluate(Euclidean(), x, y)

Common distances also come with convenient functions for distance evaluation. For example, you may also compute Euclidean distance between two vectors as below

r = euclidean(x, y)

Computing distances between corresponding columns

Suppose you have two m-by-n matrix X and Y, then you can compute all distances between corresponding columns of X and Y in one batch, using the colwise function, as

r = colwise(dist, X, Y)

The output r is a vector of length n. In particular, r[i] is the distance between X[:,i] and Y[:,i]. The batch computation typically runs considerably faster than calling evaluate column-by-column.

Note that either of X and Y can be just a single vector -- then the colwise function will compute the distance between this vector and each column of the other parameter.

Computing pairwise distances

Let X and Y respectively have m and n columns. Then the pairwise function with the dims=2 argument computes distances between each pair of columns in X and Y:

R = pairwise(dist, X, Y, dims=2)

In the output, R is a matrix of size (m, n), such that R[i,j] is the distance between X[:,i] and Y[:,j]. Computing distances for all pairs using pairwise function is often remarkably faster than evaluting for each pair individually.

If you just want to just compute distances between columns of a matrix X, you can write

R = pairwise(dist, X, dims=2)

This statement will result in an m-by-m matrix, where R[i,j] is the distance between X[:,i] and X[:,j]. pairwise(dist, X) is typically more efficient than pairwise(dist, X, X), as the former will take advantage of the symmetry when dist is a semi-metric (including metric).

For performance reasons, it is recommended to use matrices with observations in columns (as shown above). Indeed, the Array type in Julia is column-major, making it more efficient to access memory column by column. However, matrices with observations stored in rows are also supported via the argument dims=1.

Computing column-wise and pairwise distances inplace

If the vector/matrix to store the results are pre-allocated, you may use the storage (without creating a new array) using the following syntax (i being either 1 or 2):

colwise!(r, dist, X, Y)
pairwise!(R, dist, X, Y, dims=i)
pairwise!(R, dist, X, dims=i)

Please pay attention to the difference, the functions for inplace computation are colwise! and pairwise! (instead of colwise and pairwise).

Distance type hierarchy

The distances are organized into a type hierarchy.

At the top of this hierarchy is an abstract class PreMetric, which is defined to be a function d that satisfies

d(x, x) == 0  for all x
d(x, y) >= 0  for all x, y

SemiMetric is a abstract type that refines PreMetric. Formally, a semi-metric is a pre-metric that is also symmetric, as

d(x, y) == d(y, x)  for all x, y

Metric is a abstract type that further refines SemiMetric. Formally, a metric is a semi-metric that also satisfies triangle inequality, as

d(x, z) <= d(x, y) + d(y, z)  for all x, y, z

This type system has practical significance. For example, when computing pairwise distances between a set of vectors, you may only perform computation for half of the pairs, and derive the values immediately for the remaining halve by leveraging the symmetry of semi-metrics.

Each distance corresponds to a distance type. The type name and the corresponding mathematical definitions of the distances are listed in the following table.

type name	convenient syntax	math definition
Euclidean	euclidean(x, y)	sqrt(sum((x - y) .^ 2))
SqEuclidean	sqeuclidean(x, y)	sum((x - y).^2)
Cityblock	cityblock(x, y)	sum(abs(x - y))
TotalVariation	totalvariation(x, y)	sum(abs(x - y)) / 2
Chebyshev	chebyshev(x, y)	max(abs(x - y))
Minkowski	minkowski(x, y, p)	sum(abs(x - y).^p) ^ (1/p)
Hamming	hamming(k, l)	sum(k .!= l)
RogersTanimoto	rogerstanimoto(a, b)	2(sum(a&!b) + sum(!a&b)) / (2(sum(a&!b) + sum(!a&b)) + sum(a&b) + sum(!a&!b))
Jaccard	jaccard(x, y)	1 - sum(min(x, y)) / sum(max(x, y))
BrayCurtis	braycurtis(x, y)	sum(abs(x - y)) / sum(abs(x + y))
CosineDist	cosine_dist(x, y)	1 - dot(x, y) / (norm(x) * norm(y))
CorrDist	corr_dist(x, y)	cosine_dist(x - mean(x), y - mean(y))
ChiSqDist	chisq_dist(x, y)	sum((x - y).^2 / (x + y))
KLDivergence	kl_divergence(p, q)	sum(p .* log(p ./ q))
GenKLDivergence	gkl_divergence(x, y)	sum(p .* log(p ./ q) - p + q)
RenyiDivergence	renyi_divergence(p, q, k)	log(sum( p .* (p ./ q) .^ (k - 1))) / (k - 1)
JSDivergence	js_divergence(p, q)	KL(p, m) / 2 + KL(p, m) / 2 with m = (p + q) / 2
SpanNormDist	spannorm_dist(x, y)	max(x - y) - min(x - y)
BhattacharyyaDist	bhattacharyya(x, y)	-log(sum(sqrt(x .* y) / sqrt(sum(x) * sum(y)))
HellingerDist	hellinger(x, y)	sqrt(1 - sum(sqrt(x .* y) / sqrt(sum(x) * sum(y))))
Haversine	haversine(x, y, r)	Haversine formula
Mahalanobis	mahalanobis(x, y, Q)	sqrt((x - y)' * Q * (x - y))
SqMahalanobis	sqmahalanobis(x, y, Q)	(x - y)' * Q * (x - y)
MeanAbsDeviation	meanad(x, y)	mean(abs.(x - y))
MeanSqDeviation	msd(x, y)	mean(abs2.(x - y))
RMSDeviation	rmsd(x, y)	sqrt(msd(x, y))
NormRMSDeviation	nrmsd(x, y)	rmsd(x, y) / (maximum(x) - minimum(x))
WeightedEuclidean	weuclidean(x, y, w)	sqrt(sum((x - y).^2 .* w))
WeightedSqEuclidean	wsqeuclidean(x, y, w)	sum((x - y).^2 .* w)
WeightedCityblock	wcityblock(x, y, w)	sum(abs(x - y) .* w)
WeightedMinkowski	wminkowski(x, y, w, p)	sum(abs(x - y).^p .* w) ^ (1/p)
WeightedHamming	whamming(x, y, w)	sum((x .!= y) .* w)
Bregman	bregman(F, ∇, x, y; inner = LinearAlgebra.dot)	F(x) - F(y) - inner(∇(y), x - y)

Note: The formulas above are using Julia's functions. These formulas are mainly for conveying the math concepts in a concise way. The actual implementation may use a faster way. The arguments x and y are arrays of real numbers; k and l are arrays of distinct elements of any kind; a and b are arrays of Bools; and finally, p and q are arrays forming a discrete probability distribution and are therefore both expected to sum to one.

Precision for Euclidean and SqEuclidean

For efficiency (see the benchmarks below), Euclidean and SqEuclidean make use of BLAS3 matrix-matrix multiplication to calculate distances. This corresponds to the following expansion:

(x-y)^2 == x^2 - 2xy + y^2

However, equality is not precise in the presence of roundoff error, and particularly when x and y are nearby points this may not be accurate. Consequently, Euclidean and SqEuclidean allow you to supply a relative tolerance to force recalculation:

julia> x = reshape([0.1, 0.3, -0.1], 3, 1);

julia> pairwise(Euclidean(), x, x)
1×1 Array{Float64,2}:
 7.45058e-9

julia> pairwise(Euclidean(1e-12), x, x)
1×1 Array{Float64,2}:
 0.0

Benchmarks

The implementation has been carefully optimized based on benchmarks. The script in benchmark/benchmarks.jl defines a benchmark suite for a variety of distances, under column-wise and pairwise settings.

Here are benchmarks obtained running Julia 0.6 on a computer with a quad-core Intel Core i5-2500K processor @ 3.3 GHz. The tables below can be replicated using the script in benchmark/print_table.jl.

Column-wise benchmark

The table below compares the performance (measured in terms of average elapsed time of each iteration) of a straightforward loop implementation and an optimized implementation provided in Distances.jl. The task in each iteration is to compute a specific distance between corresponding columns in two 200-by-10000 matrices.

distance	loop	colwise	gain
SqEuclidean	0.005460s	0.001676s	3.2582
Euclidean	0.005513s	0.001681s	3.2792
Cityblock	0.005409s	0.001675s	3.2292
Chebyshev	0.008592s	0.004575s	1.8779
Minkowski	0.056741s	0.048808s	1.1625
Hamming	0.005320s	0.001670s	3.1847
CosineDist	0.005663s	0.001697s	3.3378
CorrDist	0.010000s	0.013904s	0.7192
ChiSqDist	0.009626s	0.004734s	2.0333
KLDivergence	0.046696s	0.035091s	1.3307
RenyiDivergence	0.021123s	0.012006s	1.7594
RenyiDivergence	0.080503s	0.066987s	1.2018
JSDivergence	0.066404s	0.059564s	1.1148
BhattacharyyaDist	0.013065s	0.008807s	1.4836
HellingerDist	0.013013s	0.008679s	1.4993
WeightedSqEuclidean	0.005534s	0.001676s	3.3028
WeightedEuclidean	0.005601s	0.001723s	3.2513
WeightedCityblock	0.005496s	0.001675s	3.2815
WeightedMinkowski	0.057847s	0.051389s	1.1257
WeightedHamming	0.005439s	0.001673s	3.2513
SqMahalanobis	0.134717s	0.019530s	6.8980
Mahalanobis	0.129455s	0.020114s	6.4361
BrayCurtis	0.005666s	0.001680s	3.3736

We can see that using colwise instead of a simple loop yields considerable gain (2x - 4x), especially when the internal computation of each distance is simple. Nonetheless, when the computation of a single distance is heavy enough (e.g. KLDivergence, RenyiDivergence), the gain is not as significant.

Pairwise benchmark

The table below compares the performance (measured in terms of average elapsed time of each iteration) of a straightforward loop implementation and an optimized implementation provided in Distances.jl. The task in each iteration is to compute a specific distance in a pairwise manner between columns in a 100-by-200 and 100-by-250 matrices, which will result in a 200-by-250 distance matrix.

distance	loop	pairwise	gain
SqEuclidean	0.015116s	0.000192s	78.7747
Euclidean	0.015565s	0.000390s	39.8829
Cityblock	0.015048s	0.001400s	10.7469
Chebyshev	0.023325s	0.010921s	2.1358
Minkowski	0.143427s	0.121050s	1.1849
Hamming	0.015191s	0.001334s	11.3856
CosineDist	0.016688s	0.000393s	42.5158
CorrDist	0.029024s	0.000435s	66.7043
ChiSqDist	0.026035s	0.012194s	2.1351
KLDivergence	0.115800s	0.086968s	1.3315
RenyiDivergence	0.055551s	0.029628s	1.8749
RenyiDivergence	0.205270s	0.163031s	1.2591
JSDivergence	0.165078s	0.148902s	1.1086
BhattacharyyaDist	0.035493s	0.022429s	1.5824
HellingerDist	0.035028s	0.021867s	1.6019
WeightedSqEuclidean	0.016330s	0.000276s	59.2117
WeightedEuclidean	0.016600s	0.000508s	32.6478
WeightedCityblock	0.015604s	0.001816s	8.5913
WeightedMinkowski	0.159052s	0.128427s	1.2385
WeightedHamming	0.015212s	0.001634s	9.3110
SqMahalanobis	0.607881s	0.000365s	1665.3228
Mahalanobis	0.623032s	0.000604s	1031.9581
BrayCurtis	0.015843s	0.002273s	6.9695

For distances of which a major part of the computation is a quadratic form (e.g. Euclidean, CosineDist, Mahalanobis), the performance can be drastically improved by restructuring the computation and delegating the core part to GEMM in BLAS. The use of this strategy can easily lead to 100x performance gain over simple loops (see the highlighted part of the table above).