Univariate density estimation via Bernstein polynomials; able to model explicit combinatorial shape constraints.
Author visuddhi
3 Stars
Updated Last
2 Years Ago
Started In
June 2019


Julia Package for univariate density estimation with combinatorial constraints, based on Bernstein polynomials.

Installing the package

Run the following code to install the package.

import Pkg

Or install directly through

import Pkg

from Julia registries.

You need to also have Julia v1.1 installed (the package does not support the syntax for older Julia versions before v1.0) to be able to use this package.

The mirror-descent (MD) algorithm

It is recommended to use BernsteinEstimate_MD(Y,m,a,b,k,e,T,MaxIter,obj,flag,Reg) when combinatorial constraints are not imposed.

  • Y: data
  • m: number of Bernstein basis
  • [a,b]: domain of the estimator
  • k: number of modes (only k=0,1 is supported for 'BernsteinEstimate_MD' now; k=0 means vanilla density estimation, k=1 means unimodal density estimation)
  • e: tolerance of error, 1e-4 by default
  • T: maximum computational time (in sceonds), 10e10 by default
  • MaxIter: maximum number of iterations
  • obj: "Log" or "Quad", "Log" -> maximum log likelihood estimator; "Quad" -> Anderson-Darling estimator
  • flag: "Acc" or "NonAcc", only applicable for k=0, "Acc" -> accelerated mirror descent, "NonAcc" -> nonaccelerated mirror descent
  • Reg: coefficient of the L2 regularizer

The mixed-integer-qudratic-optimization (MIQO) algorithm

It is recommended to use BernsteinEstimate_MIQO(Y,m,a,b,k,e,T) when there are combinatorial constraints.

  • Y: data
  • m: number of Bernstein basis
  • [a,b]: domain of the estimator
  • k: number of modes, k can be arbitrary positive integer
  • e: MIP gap
  • T: maximum computational time (in sceonds)

Caution: you need to install Gurobi and maintain a valid license in order for the MIQO algorithm to work.

An example

The provided notebook (https://github.com/visuddhi/UnivariateDensityEstimate.jl/blob/master/Example.ipynb) contains a basic example of how to use the package to do density estimation, based on a tweet timing real dataset.
import Pkg
using UnivariateDensityEstimate, Statistics, Plots

After importing the package, we read the dataset:

using DelimitedFiles
Y1 = readdlm("data/tweet_data.txt",',');
Y1 = log.(Y1[:,2])
Y1 = Y1[Y1.>6]
Y1 = sort(vec(Y1));
a = Float64(minimum(Y1)-Statistics.std(Y1)/length(Y1)^0.5)
b = Float64(maximum(Y1)+Statistics.std(Y1)/length(Y1)^0.5)

We first plot the histogram of the dataset: it can be seen the empirical distribution has several modes.

histogram(Y1, label = "tweet data")


Then we compute the solution from both the MD algorithm and MIQO algorithm for different number of modes:

m = 250  
sol_MD_0, obj_MD_0 = BernsteinEstimate_MD(Y1,m,a,b,0,-1,10e10,15000,"Log","Acc",0);
sol_MIQO_0 = BernsteinEstimate_MIQO(Y1,m,a,b,0,0,500);
sol_MIQO_1 = BernsteinEstimate_MIQO(Y1,m,a,b,1,0,500);
sol_MIQO_2 = BernsteinEstimate_MIQO(Y1,m,a,b,2,0,500);
sol_MIQO_3 = BernsteinEstimate_MIQO(Y1,m,a,b,3,0,500);

D = 1000

val_MD_0 = vec(zeros(D,1))
val_MIQO_0 = vec(zeros(D,1))
val_MIQO_1 = vec(zeros(D,1))
val_MIQO_2 = vec(zeros(D,1))
val_MIQO_3 = vec(zeros(D,1))
x = range(a,stop = b, length = D)
for i = 1:D
    for j = 1:m
        val_MD_0[i] = val_MD_0[i]+sol_MD_0[j]*betapdf(j, m-j+1, (x[i]-a)/(b-a))/(b-a);
        val_MIQO_0[i] = val_MIQO_0[i]+sol_MIQO_0[j]*betapdf(j, m-j+1, (x[i]-a)/(b-a))/(b-a);
        val_MIQO_1[i] = val_MIQO_1[i]+sol_MIQO_1[j]*betapdf(j, m-j+1, (x[i]-a)/(b-a))/(b-a);
        val_MIQO_2[i] = val_MIQO_2[i]+sol_MIQO_2[j]*betapdf(j, m-j+1, (x[i]-a)/(b-a))/(b-a);
        val_MIQO_3[i] = val_MIQO_3[i]+sol_MIQO_3[j]*betapdf(j, m-j+1, (x[i]-a)/(b-a))/(b-a);

We plot the estimated density functions and we see when no combinatorial constraints are imposed, the estimated density is close to the empirical denstiy; and when we constrain the number of modes, the estimated density become more regular (less significant modes are eliminated).

plot(x,val_MD_0,label="MD pdf (k=0)")
plot!(x,val_MIQO_0,label="QO pdf (k=0)")
plot!(x,val_MIQO_1,label="MIQO pdf (k=1)")
plot!(x,val_MIQO_2,label="MIQO pdf (k=2)")
plot!(x,val_MIQO_3,label="MIQO pdf (k=3)")


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