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Implementations of various Relief-based algorithms in Julia

License: MIT License

Julia 100.00%

machine-learning feature-selection feature-ranking relief relief-f data-science julia

relief.jl's Introduction

Relief.jl

Relief.jl provides implementations of various Relief-based feature selection algorithms in Julia. These include:

Relief
ReliefF
ReliefSeq
ReliefMSS
SURF
SURFstar
MultiSURF
MultiSURF*
SWRF*
BoostedSURF
Iterative Relief
IRelief
Evaporative Cooling ReliefF
VLSRelief
TuRF

The documentation and references can be viewed in help mode:

julia> using Relief

help?> swrfstar
search: swrfstar

  swrfstar(data::Array{<:Real,2}, target::Array{<:Integer, 1}, m::Signed=-1, 
                dist_func::Any=(e1, e2) -> sum(abs.(e1 .- e2), dims=2); 
                f_type::String="continuous")::Array{Float64,1}

  Compute feature weights using SWRF* algorithm. The f_type argument specifies whether the features are continuous or discrete and can either have the value of "continuous" or "discrete".

  ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

  Reference:
  ≡≡≡≡≡≡≡≡≡≡≡≡

    •    Matthew E. Stokes and Shyam Visweswaran. 

  Application of a spatially-weighted Relief algorithm for ranking genetic predictors of disease. BioData mining, 5(1):20–20, Dec 2012. 23198930[pmid].

Online documentation will be provided soon.

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relief.jl's Issues

cannot install due to missing dependency

got the "1 dependency errored". After running Precompile():

ERROR: The following 1 direct dependency failed to precompile:

Relief [e59a39ae-ffc4-11ea-35a5-2b2996f35250]

Error: Missing source file for Relief [e59a39ae-ffc4-11ea-35a5-2b2996f35250
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types C:\Users\miche\AppData\Local\Programs\Julia-1.7.2\share\julia\stdlib\v1.7\Pkg\src\Types.jl:68
[2] precompile(ctx::Pkg.Types.Context; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API C:\Users\miche\AppData\Local\Programs\Julia-1.7.2\share\julia\stdlib\v1.7\Pkg\src\API.jl:1362
[3] precompile
@ C:\Users\miche\AppData\Local\Programs\Julia-1.7.2\share\julia\stdlib\v1.7\Pkg\src\API.jl:1013 [inlined]
[4] #precompile#220
@ C:\Users\miche\AppData\Local\Programs\Julia-1.7.2\share\julia\stdlib\v1.7\Pkg\src\API.jl:1011 [inlined]
[5] precompile()
@ Pkg.API C:\Users\miche\AppData\Local\Programs\Julia-1.7.2\share\julia\stdlib\v1.7\Pkg\src\API.jl:1011
[6] top-level scope
@ REPL[21]:1`

Error when doing "using Relief"

Here is what I am getting:

julia> using Relief
[ Info: Precompiling Relief [e59a39ae-ffc4-11ea-35a5-2b2996f35250]
ERROR: LoadError: LoadError: cannot replace module Relief during compilation
Stacktrace:
 [1] include(::Function, ::Module, ::String) at ./Base.jl:380
 [2] include at ./Base.jl:368 [inlined]
 [3] include(::String) at /Users/logankilpatrick/.julia/packages/Relief/Fl8EM/src/Relief.jl:1
 [4] top-level scope at /Users/logankilpatrick/.julia/packages/Relief/Fl8EM/src/Relief.jl:29
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:467
 [10] top-level scope at ./none:3
in expression starting at /Users/logankilpatrick/.julia/packages/Relief/Fl8EM/src/relief.jl:1
in expression starting at /Users/logankilpatrick/.julia/packages/Relief/Fl8EM/src/Relief.jl:29

VLSRelief Default Argument Computation

The default arguments computed from the data argument cause a sampling error (too many partitions).

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