jiahao

# Compute the nth elementary symmetric function (elementary symmetric polynomial) of a a 1D iterable x
# This is the THIRD esf
function esf(n, x)
  summand = zero(eltype(x))
  for j1 = 1:n, j2 = 1:j1-1, j3 = 1:j2-1
    summand += x[j1]*x[j2]*x[j3]
  end
  return summand
end

jiahao

#Problem-specific thing
dualitygap(x...) = nothing
solveeq(x...) = rand()

############################

#Simple backtracking line search
function linesearch(v, dv, α₀= 1.0, δ = 0.6)
    α = α₀
    while v + α*dv ≤ 0

jiahao

using CSV
using Nettle
using ZipFile 

zfilename = download("http://files.grouplens.org/datasets/movielens/ml-20m.zip")

#TODO check hashes
#md5 = readchomp(open(download("http://files.grouplens.org/datasets/movielens/ml-20m.zip.md5")))
#md5dl = open(zfilename) do f hexdigest(readall(f)) end

jiahao

import Base: convert, rand, size, getindex, A_mul_B!

immutable PLINK1Matrix <: AbstractMatrix{UInt8}
    m :: Int
    n :: Int
    data :: Array{UInt8}
end

size(M::PLINK1Matrix, i::Int) = i==1 ? M.m : i==2 ? M.n : error()
size(M::PLINK1Matrix) = (M.m, M.n)

jiahao

jiahao

jiahao

function randsubset(iterable, n::Int, T::Int=22)
    state = start(iterable)
    sample = eltype(iterable)[]
    sizehint!(sample, n)
    for j=1:n #Make first n record candidates for the sample
        x, state = next(iterable, state)
        done(iterable, state) && j<n && error("Requested sample of size $n but only $j items available")
        push!(sample, x)
    end
    t = n #Number of records processed so far

jiahao

include("rankstability.jl")

info("Julia semantics")

axiomsused = Dict()
@axiom matmul Mat * Mat --> Mat
@axiom mattrans transpose(Mat) --> Mat
@axiom matdiv Mat / Mat --> Mat
@axiom matvec Mat * Vec --> Vec

jiahao

"""
Savitzky-Golay filter of window half-width M and degree N

M is the number of points before and after to interpolate, i.e. the full width
of the window is 2M+1
"""
immutable SavitzkyGolayFilter{M,N} end

@generated function Base.call{M,N,T}(::Type{SavitzkyGolayFilter{M,N}},
     data::AbstractVector{T})

jiahao

"""
estimate_coeffs

August, 2015
Anna C. Gilbert

input: xs = samples of signal
  	 Λ = list of (freq,coeff) pairs in current approx
  	 Ω = list of (freq,coeff) pairs found in this iteration
       k = length of short filter