hmm 0.1.0 → 0.2.0
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- data/Rakefile +1 -0
- data/VERSION +1 -1
- data/hmm.gemspec +5 -2
- data/lib/hmm.rb +16 -3
- data/test/test_hmm.rb +8 -0
- metadata +12 -2
data/Rakefile
CHANGED
@@ -12,6 +12,7 @@ begin
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12
12
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gem.authors = ["David Tresner-Kirsch"]
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13
13
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gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
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14
14
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gem.add_development_dependency "narray", ">= 0"
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15
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+
gem.add_dependency "narray", ">= 0"
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15
16
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# gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
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16
17
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end
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17
18
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Jeweler::GemcutterTasks.new
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.
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1
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+
0.2.0
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data/hmm.gemspec
CHANGED
@@ -5,11 +5,11 @@
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5
5
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6
6
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Gem::Specification.new do |s|
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7
7
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s.name = %q{hmm}
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8
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-
s.version = "0.
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8
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+
s.version = "0.2.0"
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9
9
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10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["David Tresner-Kirsch"]
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12
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-
s.date = %q{
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12
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+
s.date = %q{2010-03-08}
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13
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s.description = %q{This project is a Ruby gem ('hmm') for machine learning that natively implements a (somewhat) generalized Hidden Markov Model classifier.}
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14
14
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s.email = %q{dwkirsch@gmail.com}
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15
15
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s.extra_rdoc_files = [
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@@ -45,13 +45,16 @@ Gem::Specification.new do |s|
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45
45
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
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46
46
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s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
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47
47
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s.add_development_dependency(%q<narray>, [">= 0"])
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48
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+
s.add_runtime_dependency(%q<narray>, [">= 0"])
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48
49
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else
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49
50
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s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
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50
51
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s.add_dependency(%q<narray>, [">= 0"])
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52
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+
s.add_dependency(%q<narray>, [">= 0"])
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51
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end
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52
54
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else
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53
55
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s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
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54
56
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s.add_dependency(%q<narray>, [">= 0"])
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57
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+
s.add_dependency(%q<narray>, [">= 0"])
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55
58
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end
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56
59
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end
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57
60
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data/lib/hmm.rb
CHANGED
@@ -309,6 +309,15 @@ class HMM
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309
309
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alpha
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310
310
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end
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311
311
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312
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+
def log_likelihood(sequence)
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313
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+
alpha = forward_probability(sequence)
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314
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+
log_add(alpha[-1, true])
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315
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+
end
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316
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+
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317
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+
def likelihood(sequence)
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318
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+
exp(log_likelihood(sequence))
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319
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+
end
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320
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+
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312
321
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def log_add(values)
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313
322
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x = values.max
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314
323
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if x > -Infinity
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@@ -407,9 +416,13 @@ class HMM
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407
416
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end
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408
417
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end
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409
418
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410
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-
def exp(
|
411
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-
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412
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-
|
419
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+
def exp(subject)
|
420
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+
if subject.is_a?(Array) or subject.is_a?(NArray)
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421
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+
# e to the power of each element
|
422
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+
subject.collect{|n| Math::E ** n}
|
423
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+
else
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424
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+
return Math::E ** subject
|
425
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+
end
|
413
426
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end
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414
427
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415
428
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def argmax(narray)
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data/test/test_hmm.rb
CHANGED
@@ -46,6 +46,14 @@ class TestHmm < Test::Unit::TestCase
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46
46
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assert close_enough(expected_beta, \
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47
47
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@simple_model.backward_probability(["A","B","A"]).collect{|x| Math::E**x})
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48
48
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end
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49
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+
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50
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+
should "compute sequence likelihoods" do
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51
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+
assert @simple_model.likelihood(["A", "A"]) \
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52
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+
+@simple_model.likelihood(["A", "B"]) \
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53
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+
+@simple_model.likelihood(["B", "B"]) \
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54
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+
+@simple_model.likelihood(["B", "A"]) \
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55
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== 1
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56
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+
end
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49
57
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|
50
58
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should "compute xi" do
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51
59
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@simple_model.gamma(@simple_model.xi(["A","B","A"]))
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: hmm
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.
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4
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+
version: 0.2.0
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- David Tresner-Kirsch
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@@ -9,7 +9,7 @@ autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
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11
11
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|
12
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-
date:
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12
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+
date: 2010-03-08 00:00:00 -05:00
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13
13
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default_executable:
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14
14
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dependencies:
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15
15
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- !ruby/object:Gem::Dependency
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@@ -32,6 +32,16 @@ dependencies:
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32
32
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- !ruby/object:Gem::Version
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33
33
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version: "0"
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34
34
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version:
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35
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+
- !ruby/object:Gem::Dependency
|
36
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+
name: narray
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37
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+
type: :runtime
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38
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+
version_requirement:
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39
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+
version_requirements: !ruby/object:Gem::Requirement
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40
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+
requirements:
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41
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+
- - ">="
|
42
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+
- !ruby/object:Gem::Version
|
43
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+
version: "0"
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44
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+
version:
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35
45
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description: This project is a Ruby gem ('hmm') for machine learning that natively implements a (somewhat) generalized Hidden Markov Model classifier.
|
36
46
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email: dwkirsch@gmail.com
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37
47
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executables: []
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