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Merged
merged 1 commit into from
Mar 2, 2020
Merged

v1.3 compat #8

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188 changes: 188 additions & 0 deletions Manifest.toml
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# This file is machine-generated - editing it directly is not advised

[[Arpack]]
deps = ["Arpack_jll", "Libdl", "LinearAlgebra"]
git-tree-sha1 = "2ff92b71ba1747c5fdd541f8fc87736d82f40ec9"
uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
version = "0.4.0"

[[Arpack_jll]]
deps = ["Libdl", "OpenBLAS_jll", "Pkg"]
git-tree-sha1 = "68a90a692ddc0eb72d69a6993ca26e2a923bf195"
uuid = "68821587-b530-5797-8361-c406ea357684"
version = "3.5.0+2"

[[Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[BinaryProvider]]
deps = ["Libdl", "SHA"]
git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c"
uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
version = "0.5.8"

[[DataAPI]]
git-tree-sha1 = "674b67f344687a88310213ddfa8a2b3c76cc4252"
uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
version = "1.1.0"

[[DataStructures]]
deps = ["InteractiveUtils", "OrderedCollections"]
git-tree-sha1 = "5a431d46abf2ef2a4d5d00bd0ae61f651cf854c8"
uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
version = "0.17.10"

[[Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[Distributed]]
deps = ["Random", "Serialization", "Sockets"]
uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"

[[Distributions]]
deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
git-tree-sha1 = "6b19601c0e98de3a8964ed33ad73e130c7165b1d"
uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
version = "0.22.4"

[[FillArrays]]
deps = ["LinearAlgebra", "Random", "SparseArrays"]
git-tree-sha1 = "85c6b57e2680fa28d5c8adc798967377646fbf66"
uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
version = "0.8.5"

[[InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[LibGit2]]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"

[[Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"

[[LinearAlgebra]]
deps = ["Libdl"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[Missings]]
deps = ["DataAPI"]
git-tree-sha1 = "de0a5ce9e5289f27df672ffabef4d1e5861247d5"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
version = "0.4.3"

[[OpenBLAS_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "e2551d7c25d52f35b76d86a50917a3ba8988f519"
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
version = "0.3.7+5"

[[OpenSpecFun_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "65f672edebf3f4e613ddf37db9dcbd7a407e5e90"
uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.3+1"

[[OrderedCollections]]
deps = ["Random", "Serialization", "Test"]
git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.1.0"

[[PDMats]]
deps = ["Arpack", "LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"]
git-tree-sha1 = "5f303510529486bb02ac4d70da8295da38302194"
uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
version = "0.9.11"

[[Pkg]]
deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

[[Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[[QuadGK]]
deps = ["DataStructures", "LinearAlgebra"]
git-tree-sha1 = "dc84e810393cfc6294248c9032a9cdacc14a3db4"
uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
version = "2.3.1"

[[REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[Random]]
deps = ["Serialization"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[Rmath]]
deps = ["BinaryProvider", "Libdl", "Random", "Statistics"]
git-tree-sha1 = "2bbddcb984a1d08612d0c4abb5b4774883f6fa98"
uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa"
version = "0.6.0"

[[SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"

[[Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"

[[SortingAlgorithms]]
deps = ["DataStructures", "Random", "Test"]
git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd"
uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
version = "0.3.1"

[[SparseArrays]]
deps = ["LinearAlgebra", "Random"]
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[SpecialFunctions]]
deps = ["OpenSpecFun_jll"]
git-tree-sha1 = "e19b98acb182567bcb7b75bb5d9eedf3a3b5ec6c"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "0.10.0"

[[Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[[StatsBase]]
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"]
git-tree-sha1 = "be5c7d45daa449d12868f4466dbf5882242cf2d9"
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.32.1"

[[StatsFuns]]
deps = ["Rmath", "SpecialFunctions"]
git-tree-sha1 = "f290ddd5fdedeadd10e961eb3f4d3340f09d030a"
uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
version = "0.9.4"

[[SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"

[[Test]]
deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
18 changes: 18 additions & 0 deletions Project.toml
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name = "TopicModels"
uuid = "e9825ca3-3499-4c9b-97dc-a93734876e50"
authors = ["Jonathan Chang <slycoder @gmail.com>"]
version = "0.1.0"

[deps]
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"

[compat]
julia = "1.3"

[extras]
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Test"]
Empty file removed REQUIRE
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34 changes: 17 additions & 17 deletions src/TopicModels.jl
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Expand Up @@ -2,9 +2,9 @@ module TopicModels

import Base.length

typealias RaggedMatrix{T} Array{Array{T,1},1}
RaggedMatrix{T} = Array{Array{T,1},1}

type Corpus
struct Corpus
documents::RaggedMatrix{Int64}
weights::RaggedMatrix{Float64}

Expand All @@ -15,7 +15,7 @@ type Corpus
weights
)
end

Corpus(documents::RaggedMatrix{Int64}) = begin
weights = map(documents) do doc
ones(Float64, length(doc))
Expand All @@ -27,7 +27,7 @@ type Corpus
end
end

type Model
struct Model
alphaPrior::Vector{Float64}
betaPrior::Float64
topics::Array{Float64,2}
Expand All @@ -37,9 +37,9 @@ type Model
frozen::Bool
corpus::Corpus

Model(alphaPrior::Vector{Float64},
betaPrior::Float64,
V::Int64,
Model(alphaPrior::Vector{Float64},
betaPrior::Float64,
V::Int64,
corpus::Corpus) = begin
K = length(alphaPrior)
m = new(
Expand All @@ -48,7 +48,7 @@ type Model
zeros(Float64, K, V), # topics
zeros(Float64, K), # topicSums
zeros(Float64, K, length(corpus.documents)), #documentSums
fill(Array(Int64, 0), length(corpus.documents)), # assignments
Array{Array{Int64,1},1}(undef,length(corpus.documents)), # assignments
false,
corpus
)
Expand Down Expand Up @@ -111,8 +111,8 @@ function wordDistribution(word::Int,
out::Vector{Float64})
V = size(model.topics, 2)
for ii in 1:length(out)
u = (model.documentSums[ii, document] + model.alphaPrior[ii]) *
(model.topics[ii, word] + model.betaPrior) /
u = (model.documentSums[ii, document] + model.alphaPrior[ii]) *
(model.topics[ii, word] + model.betaPrior) /
(model.topicSums[ii] + V * model.betaPrior)
@inbounds out[ii] = u
end
Expand All @@ -128,10 +128,10 @@ function sampleWord(word::Int,
end


function updateSufficientStatistics(word::Int64,
function updateSufficientStatistics(word::Int64,
topic::Int64,
document::Int64,
scale::Float64,
scale::Float64,
model::Model)
fr = Float64(!model.frozen)
@inbounds model.documentSums[topic, document] += scale
Expand All @@ -146,7 +146,7 @@ function sampleDocument(document::Int,
Nw = length(words)
@inbounds weights = model.corpus.weights[document]
K = length(model.alphaPrior)
p = Array(Float64, K)
p = Array{Float64,1}(undef,K)
@inbounds assignments = model.assignments[document]
for ii in 1:Nw
@inbounds word = words[ii]
Expand All @@ -170,10 +170,10 @@ end
function termToWordSequence(term::AbstractString)
parts = split(term, ":")
fill(parse(Int64, parts[1]) + 1, parse(Int64, parts[2]))
end
end

# The functions below are designed for public consumption
function trainModel(model::Model,
function trainModel(model::Model,
numIterations::Int64)
for ii in 1:numIterations
println(string("Iteration ", ii, "..."))
Expand All @@ -183,7 +183,7 @@ function trainModel(model::Model,
end

function topTopicWords(model::Model,
lexicon::Array{ASCIIString,1},
lexicon::Array{String,1},
numWords::Int64)
[lexicon[reverse(sortperm(model.topics'[1:end, row]))[1:numWords]]
for row in 1:size(model.topics,1)]
Expand All @@ -198,7 +198,7 @@ end

function readLexicon(stream)
lines = readlines(stream)
map(chomp, convert(Array{AbstractString,1}, lines))
convert(Array{String,1},map(chomp, convert(Array{AbstractString,1}, lines)))
end

export Corpus,
Expand Down