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removed Plots and UMAP, removed Manifest #11

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Merged
merged 1 commit into from
May 31, 2020
Merged

removed Plots and UMAP, removed Manifest #11

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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1 +1,3 @@
.DS_Store
*.jld
Manifest.toml
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Should manifest be ignored or committed? If it's like package management in a few other languages it seems like something that should be kept to ensure that git-shas are maintained.

87 changes: 0 additions & 87 deletions Manifest.toml
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2 changes: 0 additions & 2 deletions Project.toml
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Expand Up @@ -6,10 +6,8 @@ version = "0.1.0"
[deps]
Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
UMAP = "c4f8c510-2410-5be4-91d7-4fbaeb39457e"

[compat]
julia = "1.3"
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16 changes: 6 additions & 10 deletions examples/LDA.jl
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@@ -1,4 +1,4 @@
using TopicModels, Plots, UMAP
using TopicModels

##################################################################################################################################
# Fit and Visualize Real-World Text Data
Expand All @@ -17,9 +17,10 @@ state = State(model,corpus)
topWords = topTopicWords(model, state, 10)

# visualize the fit
@time embedding = umap(state.topics, 2, n_neighbors=10)
maxlabels = vec(map(i->i[1], findmax(state.topics,dims=1)[2]))
scatter(embedding[1,:], embedding[2,:], zcolor=maxlabels, title="UMAP: Max-Likelihood Doc Topics on Learned", marker=(2, 2, :auto, stroke(0)))
# using Plots, UMAP
# @time embedding = umap(state.topics, 2, n_neighbors=10)
# maxlabels = vec(map(i->i[1], findmax(state.topics,dims=1)[2]))
# scatter(embedding[1,:], embedding[2,:], zcolor=maxlabels, title="UMAP: Max-Likelihood Doc Topics on Learned", marker=(2, 2, :auto, stroke(0)))

##################################################################################################################################
# Fit, Validate, and Visualize Synthetic Data Derived from a Fully-Generative Simulation (Poisson-distributed document-length)
Expand All @@ -34,13 +35,8 @@ testCorpus = LdaCorpus(k, lexLength, corpLambda, corpLength, scaleK, scaleL)

testModel = Model(testCorpus.alpha, testCorpus.beta, testCorpus)
testState = State(testModel, testCorpus)
@time trainModel(testModel, testState, 100)
@time trainModel(testModel, testState, 100)

# compute validation metrics on a single fit
CorpusARI(testState,testModel,testCorpus) # ARI for max. likelihood. document topics
DocsARI(testState,testCorpus) # ARI for actual word topics

# visualize the fit
@time embedding = umap(testState.topics, 2;n_neighbors=10)
maxlabels = vec(map(i->i[1], findmax(CorpusTopics(testCorpus),dims=1)[2]))
scatter(embedding[1,:], embedding[2,:], zcolor=maxlabels, title="UMAP: True on Learned", marker=(2, 2, :auto, stroke(0)))
4 changes: 2 additions & 2 deletions src/TopicModels.jl
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Expand Up @@ -3,7 +3,7 @@ module TopicModels
#Imports
import Base.length

using Random, Distributions, Plots, UMAP
using Random, Distributions
using SpecialFunctions: loggamma
using Clustering: randindex

Expand All @@ -29,4 +29,4 @@ include("Computation.jl")

#Stuff like perplexity and ARI:
include("Validation.jl")
end #module
end #module
5 changes: 5 additions & 0 deletions test/runtests.jl
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@@ -0,0 +1,5 @@
using Test

@testset "Inference" begin
include("Gibbs_unit_tests.jl")
end