weka 0.2.0-java → 0.3.0-java
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/README.md +3 -669
- data/lib/weka/core/attribute.rb +7 -7
- data/lib/weka/core/dense_instance.rb +29 -10
- data/lib/weka/core/instances.rb +6 -0
- data/lib/weka/version.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 949c1294da4acebd35a534c14a8ddd7ebc7ac126
|
4
|
+
data.tar.gz: de345d42f452a2846dbbbaded9bb0fbfd6fdd7b7
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 359199eb33e50e51f673468271386d7668f661e495a75efc3b1afeeae9f7c52be5d19d5457106412f5131b2f237c41867c7c08c152553af18a7dbe017187edca
|
7
|
+
data.tar.gz: 7a0e3b343960027d9156b03c885f733f9e50aaf1cbbf9905dedd55ff51113add5e5212ba9dfb1f5b15907951316b5d61546fbe92e9cde37d7da708736e424ad8
|
data/README.md
CHANGED
@@ -23,14 +23,7 @@ Or install it yourself as:
|
|
23
23
|
|
24
24
|
## Usage
|
25
25
|
|
26
|
-
|
27
|
-
* [Filters](#filters)
|
28
|
-
* [Attribute selection](#attribute-selection)
|
29
|
-
* [Classifiers](#classifiers)
|
30
|
-
* [Clusterers](#clusterers)
|
31
|
-
* [Serializing objects](#serializing-objects)
|
32
|
-
|
33
|
-
Start using Weka's Machine Learning and Data Mining algorithms by requiring the gem:
|
26
|
+
Use Weka's Machine Learning and Data Mining algorithms by requiring the gem:
|
34
27
|
|
35
28
|
```ruby
|
36
29
|
require 'weka'
|
@@ -40,667 +33,8 @@ The weka gem tries to carry over the namespaces defined in Weka and enhances som
|
|
40
33
|
|
41
34
|
The idea behind keeping the namespaces is, that you can also use the [Weka documentation](http://weka.sourceforge.net/doc.dev/) for looking up functionality and classes.
|
42
35
|
|
43
|
-
|
44
|
-
|
45
|
-
| Namespace | Description |
|
46
|
-
|----------------------------|------------------------------------------------------------------|
|
47
|
-
| `Weka::Core` | defines base classes for loading, saving, creating, and editing a dataset |
|
48
|
-
| `Weka::Classifiers` | defines classifier classes in different sub-modules (`Bayes`, `Functions`, `Lazy`, `Meta`, `Rules`, and `Trees` ) |
|
49
|
-
| `Weka::Filters` | defines filter classes for processing datasets in the `Supervised` or `Unsupervised`, and `Attribute` or `Instance` sub-modules |
|
50
|
-
| `Weka::Clusterers` | defines clusterer classes |
|
51
|
-
| `Weka::AttributeSelection` | defines classes for selecting attributes from a dataset |
|
52
|
-
|
53
|
-
### Instances
|
54
|
-
|
55
|
-
Instances objects hold the dataset that is used to train a classifier or that
|
56
|
-
should be classified based on training data.
|
57
|
-
|
58
|
-
Instances can be loaded from files and saved to files.
|
59
|
-
Supported formats are *ARFF*, *CSV*, and *JSON*.
|
60
|
-
|
61
|
-
#### Loading Instances from a file
|
62
|
-
|
63
|
-
Instances can be loaded from ARFF, CSV, and JSON files:
|
64
|
-
|
65
|
-
```ruby
|
66
|
-
instances = Weka::Core::Instances.from_arff('weather.arff')
|
67
|
-
instances = Weka::Core::Instances.from_csv('weather.csv')
|
68
|
-
instances = Weka::Core::Instances.from_json('weather.json')
|
69
|
-
```
|
70
|
-
|
71
|
-
#### Creating Instances
|
72
|
-
|
73
|
-
Attributes of an Instances object can be defined in a block using the `with_attributes` method. The class attribute can be set by the `class_attribute: true` option on the fly with defining an attribute.
|
74
|
-
|
75
|
-
```ruby
|
76
|
-
# create instances with relation name 'weather' and attributes
|
77
|
-
instances = Weka::Core::Instances.new(relation_name: 'weather').with_attributes do
|
78
|
-
nominal :outlook, values: ['sunny', 'overcast', 'rainy']
|
79
|
-
numeric :temperature
|
80
|
-
numeric :humidity
|
81
|
-
nominal :windy, values: [true, false]
|
82
|
-
date :last_storm, 'yyyy-MM-dd'
|
83
|
-
nominal :play, values: [:yes, :no], class_attribute: true
|
84
|
-
end
|
85
|
-
```
|
86
|
-
|
87
|
-
You can also pass an array of Attributes on instantiating new Instances:
|
88
|
-
This is useful, if you want to create a new empty Instances object with the same
|
89
|
-
attributes as an already existing one:
|
90
|
-
|
91
|
-
```ruby
|
92
|
-
# Take attributes from existing instances
|
93
|
-
attributes = instances.attributes
|
94
|
-
|
95
|
-
# create an empty Instances object with the given attributes
|
96
|
-
test_instances = Weka::Core::Instances.new(attributes: attributes)
|
97
|
-
```
|
98
|
-
|
99
|
-
#### Saving Instances as files
|
100
|
-
|
101
|
-
You can save Instances as ARFF, CSV, or JSON file.
|
102
|
-
|
103
|
-
```ruby
|
104
|
-
instances.to_arff('weather.arff')
|
105
|
-
instances.to_csv('weather.csv')
|
106
|
-
instances.to_json('weather.json')
|
107
|
-
```
|
108
|
-
|
109
|
-
#### Adding additional attributes
|
110
|
-
|
111
|
-
You can add additional attributes to the Instances after its initialization.
|
112
|
-
All records that are already in the dataset will get an unknown value (`?`) for
|
113
|
-
the new attribute.
|
114
|
-
|
115
|
-
```ruby
|
116
|
-
instances.add_numeric_attribute(:pressure)
|
117
|
-
instances.add_nominal_attribute(:grandma_says, values: [:hm, :bad, :terrible])
|
118
|
-
instances.add_date_attribute(:last_rain, 'yyyy-MM-dd HH:mm')
|
119
|
-
```
|
120
|
-
|
121
|
-
#### Adding a data instance
|
122
|
-
|
123
|
-
You can add a data instance to the Instances by using the `add_instance` method:
|
124
|
-
|
125
|
-
```ruby
|
126
|
-
data = [:sunny, 70, 80, true, '2015-12-06', :yes, 1.1, :hm, '2015-12-24 20:00']
|
127
|
-
instances.add_instance(data)
|
128
|
-
|
129
|
-
# with custom weight:
|
130
|
-
instances.add_instance(data, weight: 2.0)
|
131
|
-
```
|
132
|
-
|
133
|
-
Multiple instances can be added with the `add_instances` method:
|
134
|
-
|
135
|
-
```ruby
|
136
|
-
data = [
|
137
|
-
[:sunny, 70, 80, true, '2015-12-06', :yes, 1.1, :hm, '2015-12-24 20:00'],
|
138
|
-
[:overcast, 80, 85, false, '2015-11-11', :no, 0.9, :bad, '2015-12-25 18:13']
|
139
|
-
]
|
140
|
-
|
141
|
-
instances.add_instances(data, weight: 2.0)
|
142
|
-
```
|
143
|
-
|
144
|
-
If the `weight` argument is not given, then a default weight of 1.0 is used.
|
145
|
-
The weight in `add_instances` is used for all the added instances.
|
146
|
-
|
147
|
-
#### Setting a class attribute
|
148
|
-
|
149
|
-
You can set an earlier defined attribute as the class attribute of the dataset.
|
150
|
-
This allows classifiers to use the class for building a classification model while training.
|
151
|
-
|
152
|
-
```ruby
|
153
|
-
instances.add_nominal_attribute(:size, values: ['L', 'XL'])
|
154
|
-
instances.class_attribute = :size
|
155
|
-
```
|
156
|
-
|
157
|
-
The added attribute can also be directly set as the class attribute:
|
158
|
-
|
159
|
-
```ruby
|
160
|
-
instances.add_nominal_attribute(:size, values: ['L', 'XL'], class_attribute: true)
|
161
|
-
```
|
162
|
-
|
163
|
-
Keep in mind that you can only assign existing attributes to be the class attribute.
|
164
|
-
The class attribute will not appear in the `instances.attributes` anymore and can be accessed with the `class_attribute` method.
|
165
|
-
|
166
|
-
|
167
|
-
#### Alias methods
|
168
|
-
|
169
|
-
`Weka::Core::Instances` has following alias methods:
|
170
|
-
|
171
|
-
| method | alias |
|
172
|
-
|-----------------------|-------------------------|
|
173
|
-
| `numeric` | `add_numeric_attribute` |
|
174
|
-
| `nominal` | `add_nominal_attribute` |
|
175
|
-
| `date` | `add_date_attribute` |
|
176
|
-
| `string` | `add_string_attribute` |
|
177
|
-
| `set_class_attribute` | `class_attribute=` |
|
178
|
-
| `with_attributes` | `add_attributes` |
|
179
|
-
|
180
|
-
The methods on the left side are meant to be used when defining
|
181
|
-
attributes in a block when using `#with_attributes` (or `#add_attributes`).
|
182
|
-
|
183
|
-
The alias methods are meant to be used for explicitly adding
|
184
|
-
attributes to an Instances object or defining its class attribute later on.
|
185
|
-
|
186
|
-
## Filters
|
187
|
-
|
188
|
-
Filters are used to preprocess datasets.
|
189
|
-
|
190
|
-
There are two categories of filters which are also reflected by the namespaces:
|
191
|
-
|
192
|
-
* *supervised* – The filter requires a class atribute to be set
|
193
|
-
* *unsupervised* – A class attribute is not required to be present
|
194
|
-
|
195
|
-
In each category there are two sub-categories:
|
196
|
-
|
197
|
-
* *attribute-based* – Attributes (columns) are processed
|
198
|
-
* *instance-based* – Instances (rows) are processed
|
199
|
-
|
200
|
-
Thus, Filter classes are organized in the following four namespaces:
|
201
|
-
|
202
|
-
```ruby
|
203
|
-
Weka::Filters::Supervised::Attribute
|
204
|
-
Weka::Filters::Supervised::Instance
|
205
|
-
|
206
|
-
Weka::Filters::Unsupervised::Attribute
|
207
|
-
Weka::Filters::Unsupervised::Instance
|
208
|
-
```
|
209
|
-
|
210
|
-
#### Filtering Instances
|
211
|
-
|
212
|
-
Filters can be used directly to filter Instances:
|
213
|
-
|
214
|
-
```ruby
|
215
|
-
# create filter
|
216
|
-
filter = Weka::Filters::Unsupervised::Attribute::Normalize.new
|
217
|
-
|
218
|
-
# filter instances
|
219
|
-
filtered_data = filter.filter(instances)
|
220
|
-
```
|
221
|
-
|
222
|
-
You can also apply a Filter on an Instances object:
|
223
|
-
|
224
|
-
```ruby
|
225
|
-
# create filter
|
226
|
-
filter = Weka::Filters::Unsupervised::Attribute::Normalize.new
|
227
|
-
|
228
|
-
# apply filter on instances
|
229
|
-
filtered_data = instances.apply_filter(filter)
|
230
|
-
```
|
231
|
-
|
232
|
-
With this approach, it is possible to chain multiple filters on a dataset:
|
233
|
-
|
234
|
-
```ruby
|
235
|
-
# create filters
|
236
|
-
include Weka::Filters::Unsupervised::Attribute
|
237
|
-
|
238
|
-
normalize = Normalize.new
|
239
|
-
discretize = Discretize.new
|
240
|
-
|
241
|
-
# apply a filter chain on instances
|
242
|
-
filtered_data = instances.apply_filter(normalize).apply_filter(discretize)
|
243
|
-
|
244
|
-
# or even shorter
|
245
|
-
filtered_data = instances.apply_filters(normalize, discretize)
|
246
|
-
```
|
247
|
-
|
248
|
-
#### Setting Filter options
|
249
|
-
|
250
|
-
Any Filter has several options. You can list a description of all options of a filter:
|
251
|
-
|
252
|
-
```ruby
|
253
|
-
puts Weka::Filters::Unsupervised::Attribute::Normalize.options
|
254
|
-
# -S <num> The scaling factor for the output range.
|
255
|
-
# (default: 1.0)
|
256
|
-
# -T <num> The translation of the output range.
|
257
|
-
# (default: 0.0)
|
258
|
-
# -unset-class-temporarily Unsets the class index temporarily before the filter is
|
259
|
-
# applied to the data.
|
260
|
-
# (default: no)
|
261
|
-
```
|
262
|
-
|
263
|
-
To get the default option set of a Filter you can run `.default_options`:
|
264
|
-
|
265
|
-
```ruby
|
266
|
-
Weka::Filters::Unsupervised::Attribute::Normalize.default_options
|
267
|
-
# => '-S 1.0 -T 0.0'
|
268
|
-
```
|
269
|
-
|
270
|
-
Options can be set while building a Filter:
|
271
|
-
|
272
|
-
```ruby
|
273
|
-
filter = Weka::Filters::Unsupervised::Attribute::Normalize.build do
|
274
|
-
use_options '-S 0.5'
|
275
|
-
end
|
276
|
-
```
|
277
|
-
|
278
|
-
Or they can be set or changed after you created the Filter:
|
279
|
-
|
280
|
-
```ruby
|
281
|
-
filter = Weka::Filters::Unsupervised::Attribute::Normalize.new
|
282
|
-
filter.use_options('-S 0.5')
|
283
|
-
```
|
284
|
-
|
285
|
-
## Attribute selection
|
286
|
-
|
287
|
-
Selecting attributes (features) from a set of instances is important
|
288
|
-
for getting the best result out of a classification or clustering.
|
289
|
-
Attribute selection reduces the number of attributes and thereby can speed up
|
290
|
-
the runtime of the algorithms.
|
291
|
-
It also avoids processing too many attributes when only a certain subset is essential
|
292
|
-
for building a good model.
|
293
|
-
|
294
|
-
For attribute selection you need to apply a search and an evaluation method on a dataset.
|
295
|
-
|
296
|
-
Search methods are defined in the `Weka::AttributeSelection::Search` module.
|
297
|
-
There are search methods for subset search and individual attribute search.
|
298
|
-
|
299
|
-
Evaluators are defined in the `Weka::AttributeSelection::Evaluator` module.
|
300
|
-
Corresponding to search method types there are two evalutor types for subset search and individual search.
|
301
|
-
|
302
|
-
The search methods and evaluators from each category can be combined to perform an attribute selection.
|
303
|
-
|
304
|
-
**Classes for attribute *subset* selection:**
|
305
|
-
|
306
|
-
| Search | Evaluators |
|
307
|
-
|-------------------------------|------------------------------|
|
308
|
-
| `BestFirst`, `GreedyStepwise` | `CfsSubset`, `WrapperSubset` |
|
309
|
-
|
310
|
-
**Classes for *individual* attribute selection:**
|
311
|
-
|
312
|
-
| Search | Evaluators |
|
313
|
-
|----------|------------|
|
314
|
-
| `Ranker` | `CorrelationAttribute`, `GainRatioAttribute`, `InfoGainAttribute`, `OneRAttribute`, `ReliefFAttribute`, `SymmetricalUncertAttribute` |
|
315
|
-
|
316
|
-
An attribute selection can either be performed with the `Weka::AttributeSelection::AttributeSelection` class:
|
317
|
-
|
318
|
-
```ruby
|
319
|
-
instances = Weka::Core::Instances.from_arff('weather.arff')
|
320
|
-
|
321
|
-
selection = Weka::AttributeSelection::AttributeSelection.new
|
322
|
-
selection.search = Weka::AttributeSelection::Search::Ranker.new
|
323
|
-
selection.evaluator = Weka::AttributeSelection::Evaluator::PricipalComponents.new
|
324
|
-
|
325
|
-
selection.select_attribute(instances)
|
326
|
-
puts selection.summary
|
327
|
-
```
|
328
|
-
|
329
|
-
Or you can use the supervised `AttributeSelection` filter to directly filter instances:
|
330
|
-
|
331
|
-
```ruby
|
332
|
-
instances = Weka::Core::Instances.from_arff('weather.arff')
|
333
|
-
search = Weka::AttributeSelection::Search::Ranker.new
|
334
|
-
evaluator = Weka::AttributeSelection::Evaluator::PricipalComponents.new
|
335
|
-
|
336
|
-
filter = Weka::Filters::Supervised::Attribute::AttributeSelection.build do
|
337
|
-
use_search search
|
338
|
-
use_evaluator evaluator
|
339
|
-
end
|
340
|
-
|
341
|
-
filtered_instances = instances.apply_filter(filter)
|
342
|
-
```
|
343
|
-
|
344
|
-
## Classifiers
|
345
|
-
|
346
|
-
Weka‘s classification and regression algorithms can be found in the `Weka::Classifiers`
|
347
|
-
namespace.
|
348
|
-
|
349
|
-
The classifier classes are organised in the following submodules:
|
350
|
-
|
351
|
-
```ruby
|
352
|
-
Weka::Classifiers::Bayes
|
353
|
-
Weka::Classifiers::Functions
|
354
|
-
Weka::Classifiers::Lazy
|
355
|
-
Weka::Classifiers::Meta
|
356
|
-
Weka::Classifiers::Rules
|
357
|
-
Weka::Classifiers::Trees
|
358
|
-
```
|
359
|
-
|
360
|
-
#### Getting information about a classifier
|
361
|
-
|
362
|
-
To get a description about the classifier class and its available options
|
363
|
-
you can use the class methods `.description` and `.options` on each classifier:
|
364
|
-
|
365
|
-
```ruby
|
366
|
-
puts Weka::Classifiers::Trees::RandomForest.description
|
367
|
-
# Class for constructing a forest of random trees.
|
368
|
-
# For more information see:
|
369
|
-
# Leo Breiman (2001). Random Forests. Machine Learning. 45(1):5-32.
|
370
|
-
|
371
|
-
puts Weka::Classifiers::Trees::RandomForest.options
|
372
|
-
# -I <number of trees> Number of trees to build.
|
373
|
-
# (default 100)
|
374
|
-
# -K <number of features> Number of features to consider (<1=int(log_2(#predictors)+1)).
|
375
|
-
# (default 0)
|
376
|
-
# ...
|
377
|
-
|
378
|
-
```
|
379
|
-
|
380
|
-
The default options that are used for a classifier can be displayed with:
|
381
|
-
|
382
|
-
```ruby
|
383
|
-
Weka::Classifiers::Trees::RandomForest.default_options
|
384
|
-
# => "-I 100 -K 0 -S 1 -num-slots 1"
|
385
|
-
```
|
386
|
-
|
387
|
-
#### Creating a new classifier
|
388
|
-
|
389
|
-
To build a new classifiers model based on training instances you can use
|
390
|
-
the following syntax:
|
391
|
-
|
392
|
-
```ruby
|
393
|
-
instances = Weka::Core::Instances.from_arff('weather.arff')
|
394
|
-
instances.class_attribute = :play
|
395
|
-
|
396
|
-
classifier = Weka::Classifiers::Trees::RandomForest.new
|
397
|
-
classifier.use_options('-I 200 -K 5')
|
398
|
-
classifier.train_with_instances(instances)
|
399
|
-
```
|
400
|
-
You can also build a classifier by using the block syntax:
|
401
|
-
|
402
|
-
```ruby
|
403
|
-
classifier = Weka::Classifiers::Trees::RandomForest.build do
|
404
|
-
use_options '-I 200 -K 5'
|
405
|
-
train_with_instances instances
|
406
|
-
end
|
407
|
-
|
408
|
-
```
|
409
|
-
|
410
|
-
#### Evaluating a classifier model
|
411
|
-
|
412
|
-
You can evaluate the trained classifier using [cross-validation](https://en.wikipedia.org/wiki/Cross-validation_(statistics)):
|
413
|
-
|
414
|
-
```ruby
|
415
|
-
# default number of folds is 3
|
416
|
-
evaluation = classifier.cross_validate
|
417
|
-
|
418
|
-
# with a custom number of folds
|
419
|
-
evaluation = classifier.cross_validate(folds: 10)
|
420
|
-
```
|
421
|
-
|
422
|
-
The cross-validation returns a `Weka::Classifiers::Evaluation` object which can be used to get details about the accuracy of the trained classification model:
|
423
|
-
|
424
|
-
```ruby
|
425
|
-
puts evaluation.summary
|
426
|
-
#
|
427
|
-
# Correctly Classified Instances 10 71.4286 %
|
428
|
-
# Incorrectly Classified Instances 4 28.5714 %
|
429
|
-
# Kappa statistic 0.3778
|
430
|
-
# Mean absolute error 0.4098
|
431
|
-
# Root mean squared error 0.4657
|
432
|
-
# Relative absolute error 87.4588 %
|
433
|
-
# Root relative squared error 96.2945 %
|
434
|
-
# Coverage of cases (0.95 level) 100 %
|
435
|
-
# Mean rel. region size (0.95 level) 96.4286 %
|
436
|
-
# Total Number of Instances 14
|
437
|
-
```
|
438
|
-
|
439
|
-
The evaluation holds detailed information about a number of different meassures of interest,
|
440
|
-
like the [precision and recall](https://en.wikipedia.org/wiki/Precision_and_recall), the FP/FN/TP/TN-rates, [F-Measure](https://en.wikipedia.org/wiki/F1_score) and the areas under PRC and [ROC](https://en.wikipedia.org/wiki/Receiver_operating_characteristic) curve.
|
441
|
-
|
442
|
-
If your trained classifier should be evaluated against a set of *test instances*,
|
443
|
-
you can use `evaluate`:
|
444
|
-
|
445
|
-
```ruby
|
446
|
-
test_instances = Weka::Core::Instances.from_arff('test_data.arff')
|
447
|
-
test_instances.class_attribute = :play
|
448
|
-
|
449
|
-
evaluation = classifier.evaluate(test_instances)
|
450
|
-
```
|
451
|
-
|
452
|
-
#### Classifying new data
|
453
|
-
|
454
|
-
Each classifier implements either a `classify` method or a `distibution_for` method, or both.
|
455
|
-
|
456
|
-
The `classify` method takes a Weka::Core::DenseInstance or an Array of values as argument and returns the predicted class value:
|
457
|
-
|
458
|
-
```ruby
|
459
|
-
instances = Weka::Core::Instances.from_arff('unclassified_data.arff')
|
460
|
-
|
461
|
-
# with an instance as argument
|
462
|
-
instances.map do |instance|
|
463
|
-
classifier.classify(instance)
|
464
|
-
end
|
465
|
-
# => ['no', 'yes', 'yes', ...]
|
466
|
-
|
467
|
-
# with an Array of values as argument
|
468
|
-
classifier.classify [:sunny, 80, 80, :FALSE, '?']
|
469
|
-
# => 'yes'
|
470
|
-
```
|
471
|
-
|
472
|
-
The `distribution_for` method takes a Weka::Core::DenseInstance or an Array of values as argument as well and returns a hash with the distributions per class value:
|
473
|
-
|
474
|
-
```ruby
|
475
|
-
instances = Weka::Core::Instances.from_arff('unclassified_data.arff')
|
476
|
-
|
477
|
-
# with an instance as argument
|
478
|
-
classifier.distribution_for(instances.first)
|
479
|
-
# => { "yes" => 0.26, "no" => 0.74 }
|
480
|
-
|
481
|
-
# with an Array of values as argument
|
482
|
-
classifier.distribution_for [:sunny, 80, 80, :FALSE, '?']
|
483
|
-
# => { "yes" => 0.62, "no" => 0.38 }
|
484
|
-
```
|
485
|
-
|
486
|
-
### Clusterers
|
487
|
-
|
488
|
-
Clustering is an unsupervised machine learning technique which tries to find patterns in data and group sets of data. Clustering algorithms work without class attributes.
|
489
|
-
|
490
|
-
Weka‘s clustering algorithms can be found in the `Weka::Clusterers` namespace.
|
491
|
-
|
492
|
-
The following clusterer classes are available:
|
493
|
-
|
494
|
-
```ruby
|
495
|
-
Weka::Clusterers::Canopy
|
496
|
-
Weka::Clusterers::Cobweb
|
497
|
-
Weka::Clusterers::EM
|
498
|
-
Weka::Clusterers::FarthestFirst
|
499
|
-
Weka::Clusterers::HierarchicalClusterer
|
500
|
-
Weka::Clusterers::SimpleKMeans
|
501
|
-
```
|
502
|
-
|
503
|
-
#### Getting information about a clusterer
|
504
|
-
|
505
|
-
To get a description about the clusterer class and its available options
|
506
|
-
you can use the class methods `.description` and `.options` on each clusterer:
|
507
|
-
|
508
|
-
```ruby
|
509
|
-
puts Weka::Clusterers::SimpleKMeans.description
|
510
|
-
# Cluster data using the k means algorithm.
|
511
|
-
# ...
|
512
|
-
|
513
|
-
puts Weka::Clusterers::SimpleKMeans.options
|
514
|
-
# -N <num> Number of clusters.
|
515
|
-
# (default 2).
|
516
|
-
# -init Initialization method to use.
|
517
|
-
# 0 = random, 1 = k-means++, 2 = canopy, 3 = farthest first.
|
518
|
-
# (default = 0)
|
519
|
-
# ...
|
520
|
-
```
|
521
|
-
|
522
|
-
The default options that are used for a clusterer can be displayed with:
|
523
|
-
|
524
|
-
```ruby
|
525
|
-
Weka::Clusterers::SimpleKMeans.default_options
|
526
|
-
# => "-init 0 -max-candidates 100 -periodic-pruning 10000 -min-density 2.0 -t1 -1.25
|
527
|
-
# -t2 -1.0 -N 2 -A weka.core.EuclideanDistance -R first-last -I 500 -num-slots 1 -S 10"
|
528
|
-
```
|
529
|
-
|
530
|
-
#### Creating a new Clusterer
|
531
|
-
|
532
|
-
To build a new clusterer model based on training instances you can use the following syntax:
|
533
|
-
|
534
|
-
```ruby
|
535
|
-
instances = Weka::Core::Instances.from_arff('weather.arff')
|
536
|
-
|
537
|
-
clusterer = Weka::Clusterers::SimpleKMeans.new
|
538
|
-
clusterer.use_options('-N 3 -I 600')
|
539
|
-
clusterer.train_with_instances(instances)
|
540
|
-
```
|
541
|
-
|
542
|
-
You can also build a clusterer by using the block syntax:
|
543
|
-
|
544
|
-
```ruby
|
545
|
-
classifier = Weka::Clusterers::SimpleKMeans.build do
|
546
|
-
use_options '-N 5 -I 600'
|
547
|
-
train_with_instances instances
|
548
|
-
end
|
549
|
-
```
|
550
|
-
|
551
|
-
#### Evaluating a clusterer model
|
552
|
-
|
553
|
-
You can evaluate trained density-based clusterer using [cross-validation](https://en.wikipedia.org/wiki/Cross-validation_(statistics)) (The only density-based clusterer in the Weka lib is `EM` at the moment).
|
554
|
-
|
555
|
-
The cross-validation returns the cross-validated log-likelihood:
|
556
|
-
|
557
|
-
```ruby
|
558
|
-
# default number of folds is 3
|
559
|
-
log_likelihood = clusterer.cross_validate
|
560
|
-
# => -10.556166997137497
|
561
|
-
|
562
|
-
# with a custom number of folds
|
563
|
-
log_likelihood = clusterer.cross_validate(folds: 10)
|
564
|
-
# => -10.262696653333032
|
565
|
-
```
|
566
|
-
|
567
|
-
If your trained classifier should be evaluated against a set of *test instances*,
|
568
|
-
you can use `evaluate`.
|
569
|
-
The evaluation returns a `Weka::Clusterer::ClusterEvaluation` object which can be used to get details about the accuracy of the trained clusterer model:
|
570
|
-
|
571
|
-
```ruby
|
572
|
-
test_instances = Weka::Core::Instances.from_arff('test_data.arff')
|
573
|
-
evaluation = clusterer.evaluate(test_instances)
|
574
|
-
|
575
|
-
puts evaluation.summary
|
576
|
-
# EM
|
577
|
-
# ==
|
578
|
-
#
|
579
|
-
# Number of clusters: 2
|
580
|
-
# Number of iterations performed: 7
|
581
|
-
#
|
582
|
-
# Cluster
|
583
|
-
# Attribute 0 1
|
584
|
-
# (0.35) (0.65)
|
585
|
-
# ==============================
|
586
|
-
# outlook
|
587
|
-
# sunny 3.8732 3.1268
|
588
|
-
# overcast 1.7746 4.2254
|
589
|
-
# rainy 2.1889 4.8111
|
590
|
-
# [total] 7.8368 12.1632
|
591
|
-
# ...
|
592
|
-
```
|
593
|
-
|
594
|
-
#### Clustering new data
|
595
|
-
|
596
|
-
Similar to classifiers, clusterers come with a either a `cluster` method or a `distribution_for` method which both take a Weka::Core::DenseInstance or an Array of values as argument.
|
597
|
-
|
598
|
-
The `classify` method returns the index of the predicted cluster:
|
599
|
-
|
600
|
-
```ruby
|
601
|
-
instances = Weka::Core::Instances.from_arff('unlabeled_data.arff')
|
602
|
-
|
603
|
-
clusterer = Weka::Clusterers::Canopy.build
|
604
|
-
train_with_instances instances
|
605
|
-
end
|
606
|
-
|
607
|
-
# with an instance as argument
|
608
|
-
instances.map do |instance|
|
609
|
-
clusterer.cluster(instance)
|
610
|
-
end
|
611
|
-
# => [3, 3, 4, 0, 0, 1, 2, 3, 0, 0, 2, 2, 4, 1]
|
612
|
-
|
613
|
-
# with an Array of values as argument
|
614
|
-
clusterer.cluster [:sunny, 80, 80, :FALSE]
|
615
|
-
# => 4
|
616
|
-
```
|
617
|
-
|
618
|
-
The `distribution_for` method returns an Array with the distributions at the cluster‘s index:
|
619
|
-
|
620
|
-
```ruby
|
621
|
-
# with an instance as argument
|
622
|
-
clusterer.distribution_for(instances.first)
|
623
|
-
# => [0.17229465277140552, 0.1675583309853506, 0.15089102301329346, 0.3274056122786787, 0.18185038095127165]
|
624
|
-
|
625
|
-
# with an Array of values as argument
|
626
|
-
classifier.distribution_for [:sunny, 80, 80, :FALSE]
|
627
|
-
# => [0.21517055355632506, 0.16012256401406233, 0.17890840384466453, 0.2202344150907843, 0.2255640634941639]
|
628
|
-
```
|
629
|
-
|
630
|
-
#### Adding a cluster attribute to a dataset
|
631
|
-
|
632
|
-
After building and training a clusterer with training instances you can use the clusterer
|
633
|
-
in the unsupervised attribute filter `AddCluster` to assign a cluster to each instance of a dataset:
|
634
|
-
|
635
|
-
```ruby
|
636
|
-
filter = Weka::Filter::Unsupervised::Attribute::AddCluster.new
|
637
|
-
filter.clusterer = clusterer
|
638
|
-
|
639
|
-
instances = Weka::Core::Instances.from_arff('unlabeled_data.arff')
|
640
|
-
clustered_instances = instances.apply_filter(filter)
|
641
|
-
|
642
|
-
puts clustered_instances.to_s
|
643
|
-
```
|
644
|
-
|
645
|
-
`clustered_instance` now has a nominal `cluster` attribute as the last attribute.
|
646
|
-
The values of the cluster attribute are the *N* cluster names, e.g. with *N = 2* clusters, the ARFF representation looks like:
|
647
|
-
|
648
|
-
```
|
649
|
-
...
|
650
|
-
@attribute outlook {sunny,overcast,rainy}
|
651
|
-
@attribute temperature numeric
|
652
|
-
@attribute humidity numeric
|
653
|
-
@attribute windy {TRUE,FALSE}
|
654
|
-
@attribute cluster {cluster1,cluster2}
|
655
|
-
...
|
656
|
-
```
|
657
|
-
|
658
|
-
Each instance is now assigned to a cluster, e.g.:
|
659
|
-
|
660
|
-
```
|
661
|
-
...
|
662
|
-
@data
|
663
|
-
sunny,85,85,FALSE,cluster1
|
664
|
-
sunny,80,90,TRUE,cluster1
|
665
|
-
...
|
666
|
-
```
|
667
|
-
|
668
|
-
### Serializing Objects
|
669
|
-
|
670
|
-
You can serialize objects with the `Weka::Core::SerializationHelper` class:
|
671
|
-
|
672
|
-
```ruby
|
673
|
-
# writing an Object to a file:
|
674
|
-
Weka::Core::SerializationHelper.write('path/to/file.model', classifier)
|
675
|
-
|
676
|
-
# load an Object from a serialized file:
|
677
|
-
object = Weka::Core::SerializationHelper.read('path/to/file.model')
|
678
|
-
```
|
679
|
-
|
680
|
-
Instead of `.write` and `.read` you can also call the aliases `.serialize` and `.deserialize`.
|
681
|
-
|
682
|
-
Serialization can be helpful if the training of e.g. a classifier model takes
|
683
|
-
some minutes. Instead of running the whole training on instantiating a classifier you
|
684
|
-
can speed up this process tremendously by serializing a classifier once it was trained and later load it from the file again.
|
685
|
-
|
686
|
-
Classifiers, Clusterers, Instances and Filters also have a `#serialize` method
|
687
|
-
which you can use to directly serialize an Instance of these, e.g. for a Classifier:
|
688
|
-
|
689
|
-
```ruby
|
690
|
-
instances = Weka::Core::Instances.from_arff('weather.arff')
|
691
|
-
instances.class_attribute = :play
|
692
|
-
|
693
|
-
classifier = Weka::Core::Trees::RandomForest.build do
|
694
|
-
train_with_instances instances
|
695
|
-
end
|
696
|
-
|
697
|
-
# store trained model as binary file
|
698
|
-
classifier.serialize('randomforest.model')
|
699
|
-
|
700
|
-
# load Classifier from binary file
|
701
|
-
loaded_classifier = Weka::Core::SerializationHelper.deserialize('randomforest.model')
|
702
|
-
# => #<Java::WekaClassifiersTrees::RandomForest:0x197db331>
|
703
|
-
```
|
36
|
+
Please refer to [the gem‘s Wiki](https://github.com/paulgoetze/weka-jruby/wiki) for
|
37
|
+
detailed information about how to use weka with JRuby and some examplary code snippets.
|
704
38
|
|
705
39
|
## Development
|
706
40
|
|
data/lib/weka/core/attribute.rb
CHANGED
@@ -11,14 +11,14 @@ module Weka
|
|
11
11
|
# The order of the if statements is important here, because a date is also
|
12
12
|
# a numeric.
|
13
13
|
def internal_value_of(value)
|
14
|
-
if
|
15
|
-
|
16
|
-
|
17
|
-
|
18
|
-
|
19
|
-
index_of_value(value.to_s)
|
20
|
-
end
|
14
|
+
return value if value === Float::NAN
|
15
|
+
return Float::NAN if [nil, '?'].include?(value)
|
16
|
+
return parse_date(value.to_s) if date?
|
17
|
+
return value.to_f if numeric?
|
18
|
+
return index_of_value(value.to_s) if nominal?
|
21
19
|
end
|
22
20
|
end
|
21
|
+
|
22
|
+
Weka::Core::Attribute.__persistent__ = true
|
23
23
|
end
|
24
24
|
end
|
@@ -7,7 +7,11 @@ module Weka
|
|
7
7
|
java_import "java.text.SimpleDateFormat"
|
8
8
|
|
9
9
|
def initialize(data, weight: 1.0)
|
10
|
-
|
10
|
+
if data.kind_of?(Integer)
|
11
|
+
super(data)
|
12
|
+
else
|
13
|
+
super(weight, to_java_double(data))
|
14
|
+
end
|
11
15
|
end
|
12
16
|
|
13
17
|
def attributes
|
@@ -30,15 +34,7 @@ module Weka
|
|
30
34
|
|
31
35
|
def to_a
|
32
36
|
to_double_array.each_with_index.map do |value, index|
|
33
|
-
|
34
|
-
|
35
|
-
if attribute.date?
|
36
|
-
format_date(value, attribute.date_format)
|
37
|
-
elsif attribute.numeric?
|
38
|
-
value
|
39
|
-
elsif attribute.nominal?
|
40
|
-
attribute.value(value)
|
41
|
-
end
|
37
|
+
value_from(value, index)
|
42
38
|
end
|
43
39
|
end
|
44
40
|
|
@@ -47,6 +43,29 @@ module Weka
|
|
47
43
|
|
48
44
|
private
|
49
45
|
|
46
|
+
def to_java_double(values)
|
47
|
+
data = values.map do |value|
|
48
|
+
['?', nil].include?(value) ? Float::NAN : value
|
49
|
+
end
|
50
|
+
|
51
|
+
data.to_java(:double)
|
52
|
+
end
|
53
|
+
|
54
|
+
def value_from(value, index)
|
55
|
+
return '?' if value.nan?
|
56
|
+
return value if dataset.nil?
|
57
|
+
|
58
|
+
attribute = attribute_at(index)
|
59
|
+
|
60
|
+
if attribute.date?
|
61
|
+
format_date(value, attribute.date_format)
|
62
|
+
elsif attribute.numeric?
|
63
|
+
value
|
64
|
+
elsif attribute.nominal?
|
65
|
+
attribute.value(value)
|
66
|
+
end
|
67
|
+
end
|
68
|
+
|
50
69
|
def attribute_at(index)
|
51
70
|
return attributes[index] unless dataset.class_attribute_defined?
|
52
71
|
|
data/lib/weka/core/instances.rb
CHANGED
data/lib/weka/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: weka
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.3.0
|
5
5
|
platform: java
|
6
6
|
authors:
|
7
7
|
- Paul Götze
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2016-
|
11
|
+
date: 2016-02-10 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: lock_jar
|