> function myjaccard2(a::Array{Float64,1}, b::Array{Float64,1}) > num = 0. > den = 0. > for I in 1:length(a) > @inbounds ai = a[I] > @inbounds bi = b[I] > num = num + min(ai,bi) > den = den + max(ai,bi) > end > 1. - num/den > end > > > > function testDistances2(v1::Array{Float64,1}, v2::Array{Float64,1}) > for i in 1:50000 > myjaccard2(v1,v2) > end > end
I recommend using the values returned for something, otherwise the compiler sometimes eliminates the loop (but not here): julia> function testDistances2(v1::Array{Float64,1}, v2::Array{Float64,1}) out = 0.0 for i in 1:50000 out += myjaccard2(v1,v2) end out end > @time testDistances2(v1,v2) > machine 3.217329 seconds (200.01 M allocations: 2.981 GB, 19.91% gc time) I cannot reproduce this, when I run it I get no allocations: julia> v2 = rand(10^4); # warm-up julia> @time testDistances2(v1,v2) 3.604478 seconds (8.15 k allocations: 401.797 KB, 0.42% gc time) 24999.00112162811 julia> @time testDistances2(v1,v2) 3.647563 seconds (5 allocations: 176 bytes) 24999.00112162811 What version of Julia are you running. Me 0.4.5. > function myjaccard5(a::Array{Float64,1}, b::Array{Float64,1}) > num = 0. > den = 0. > for I in 1:length(a) > @inbounds ai = a[I] > @inbounds bi = b[I] > abs_m = abs(ai-bi) > abs_p = abs(ai+bi) > num += abs_p - abs_m > den += abs_p + abs_m > end > 1. - num/den > end > > > function testDistances5(a::Array{Float64,1}, b::Array{Float64,1}) > for i in 1:5000 > myjaccard5(a,b) > end > end > > end > > > julia> @time testDistances5(v1,v2) > 0.166979 seconds (4 allocations: 160 bytes) > > > > We see that using abs is faster. > > I do not do a pull request beccause > > I would expect a good implementation to be 2 or 3 times slower than > Euclidean, and I have not > that yet. > > Le lundi 13 juin 2016 13:43:00 UTC+2, Kristoffer Carlsson a écrit : >> >> It seems weird to me that you guys want to call Jaccard distance with >> float arrays. AFAIK Jaccard distance measures the distance between two >> distinct samples from a pair of sets so basically between two Vector{Bool}, >> see: >> http://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.jaccard.html >> >> "Computes the Jaccard-Needham dissimilarity between two boolean 1-D >> arrays." >> >> Is there some more general formulation of it that extends to vectors in a >> continuous vector space? >> >> And, to note, Jaccard is type stable for inputs of Vector{Bool} in >> Distances.jl. >> >> On Monday, June 13, 2016 at 3:53:14 AM UTC+2, jean-pierre both wrote: >>> >>> >>> >>> I encountered in my application with Distances.Jaccard compared with >>> Distances.Euclidean >>> It was very slow. >>> >>> For example with 2 vecteurs Float64 of size 11520 >>> >>> I get the following >>> julia> D=Euclidean() >>> Distances.Euclidean() >>> julia> @time for i in 1:500 >>> evaluate(D,v1,v2) >>> end >>> 0.002553 seconds (500 allocations: 7.813 KB) >>> >>> and with Jaccard >>> >>> julia> D=Jaccard() >>> Distances.Jaccard() >>> @time for i in 1:500 >>> evaluate(D,v1,v2) >>> end >>> 1.995046 seconds (40.32 M allocations: 703.156 MB, 9.68% gc time) >>> >>> With a simple loop for computing jaccard : >>> >>> >>> function myjaccard2(a::Array{Float64,1}, b::Array{Float64,1}) >>> num = 0 >>> den = 0 >>> for i in 1:length(a) >>> num = num + min(a[i],b[i]) >>> den = den + max(a[i],b[i]) >>> end >>> 1. - num/den >>> end >>> myjaccard2 (generic function with 1 method) >>> >>> julia> @time for i in 1:500 >>> myjaccard2(v1,v2) >>> end >>> 0.451582 seconds (23.04 M allocations: 351.592 MB, 20.04% gc time) >>> >>> I do not see the problem in jaccard distance implementation in the >>> Distances packages >>> >>