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.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
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+# Installer logs
+pip-log.txt
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+htmlcov/
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+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
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+.media/
+local_settings.py
+
+# Flask stuff:
+instance/
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+# Scrapy stuff:
+.scrapy
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+# PyBuilder
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+
+requirements-dev.txt
+.idea

LICENSE

+BSD 2-Clause License
+
+Copyright (c) 2019, DBIS
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pyproject.toml

+[tool.poetry]
+name = "tuhlbox"
+version = "0.1.0"
+description = ""
+authors = ["Benjamin Murauer <b.murauer@gmail.com>"]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+sklearn = "^0.0"
+treegrams = "^0.1.0"
+gensim = "^3.8.3"
+dstoolbox = "^0.10.1"
+
+[tool.poetry.dev-dependencies]
+pytest = "^5.2"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

tests/test_doc2vec.py

+from nltk import word_tokenize
+
+from tuhlbox.doc2vec import Doc2VecTransformer
+
+
+def test_transformation():
+    documents = [
+        word_tokenize("This is an example sentence."),
+        word_tokenize("This is a second piece of text."),
+    ]
+
+    transformer = Doc2VecTransformer(vector_size=123)
+    actual = transformer.fit_transform(documents)
+    assert len(actual) == len(documents)
+    assert len(actual[0]) == 123
+    assert len(actual[1]) == 123

tests/test_life.py

+import itertools
+import unittest
+
+import numpy as np
+
+from tuhlbox.life import LifeVectorizer
+
+
+class TestLife(unittest.TestCase):
+    def test_short_fragment(self):
+        fragment_sizes = [1000]  # larger than text
+        text = [str(x) for x in range(100)]
+
+        transformer = LifeVectorizer(fragment_sizes, 1, "fragment", force=True)
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [100.0, 100.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        self.assertEqual(actual, predicted)
+
+    def test_short_bow(self):
+        fragment_sizes = [1000]  # larger than text
+        text = [str(x) for x in range(100)]
+
+        transformer = LifeVectorizer(fragment_sizes, 1, "bow", force=True)
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [100.0, 100.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        self.assertEqual(actual, predicted)
+
+    def test_short_both(self):
+        fragment_sizes = [1000]  # larger than text
+        text = [str(x) for x in range(100)]
+
+        transformer = LifeVectorizer(fragment_sizes, 1, "both", force=True)
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [
+            100.0,
+            100.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            100.0,
+            100.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+        ]
+        self.assertEqual(actual, predicted)
+
+    def test_short_document_exceptions(self):
+        text = [str(x) for x in range(100)]
+        for m in ["fragment", "bow", "both"]:
+            transformer = LifeVectorizer([1000], 1, m, force=False)
+            self.assertRaises(ValueError, transformer.transform, text)
+
+    def test_random_shape_sizes(self):
+        n_sizes = np.random.randint(1, 10)
+        fragment_sizes = np.random.randint(2, 50, size=n_sizes)
+        text = [str(x) for x in range(100)]
+
+        vec1 = LifeVectorizer(fragment_sizes, 1, "fragment")
+        vec2 = LifeVectorizer(fragment_sizes, 1, "bow")
+        vec3 = LifeVectorizer(fragment_sizes, 1, "both")
+
+        self.assertEqual(vec1.transform(text)[0].shape, (n_sizes * 8,))
+        self.assertEqual(vec2.transform(text)[0].shape, (n_sizes * 8,))
+        self.assertEqual(vec3.transform(text)[0].shape, (n_sizes * 16,))
+
+    def test_life_single_fragment(self):
+        transformer = LifeVectorizer([42], 50, "fragment")
+        text = [str(x) for x in range(100)]
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [42.0, 42.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        self.assertEqual(actual, predicted)
+
+    def test_life_single_bow(self):
+        transformer = LifeVectorizer([42], 100, "bow")
+        text = [str(x) for x in range(100)]
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [42.0, 42.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        self.assertEqual(actual, predicted)
+
+    def test_life_single_bfs(self):
+        transformer = LifeVectorizer([42], 100, "both")
+        text = [str(x) for x in range(100)]
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [
+            42.0,
+            42.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            42.0,
+            42.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+        ]
+        self.assertEqual(actual, predicted)
+
+    def test_life_double_fragment(self):
+        transformer = LifeVectorizer([42, 41], 50, "fragment")
+        text = [str(x) for x in range(100)]
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [
+            42.0,
+            42.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            41.0,
+            41.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+        ]
+        self.assertEqual(actual, predicted)
+
+    def test_life_double_bow(self):
+        transformer = LifeVectorizer([42, 41], 100, "bow")
+        text = [str(x) for x in range(100)]
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [
+            42.0,
+            42.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            41.0,
+            41.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+        ]
+        self.assertEqual(actual, predicted)
+
+    def test_life_double_bfs(self):
+        rand_1 = np.random.randint(2, 100)
+        rand_2 = np.random.randint(2, 100)
+        transformer = LifeVectorizer([rand_1, rand_2], 100, "both")
+        text = [str(x) for x in range(100)]
+        actual = transformer.transform([text])[0].tolist()
+        predicted = [
+            float(rand_1),
+            float(rand_1),
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            float(rand_1),
+            float(rand_1),
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            float(rand_2),
+            float(rand_2),
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            float(rand_2),
+            float(rand_2),
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+            0.0,
+        ]
+        self.assertEqual(actual, predicted)
+
+    def test_life_half_fragment(self):
+        frag_size = np.random.randint(2, 100)
+        transformer = LifeVectorizer([frag_size], 100, "fragment")
+        # this text consists of pairs of two identical words
+        pairs = [(y, y) for y in range(100)]
+        text = list(itertools.chain.from_iterable(pairs))
+        actual = transformer.transform([text])[0].tolist()
+
+        vocabulary_size = actual[0]
+        freq_1_count = actual[1]
+        freq_4_count = actual[2]
+        freq_10_count = actual[3]
+
+        self.assertTrue(vocabulary_size <= frag_size / 2 + 1)
+        self.assertTrue(vocabulary_size >= frag_size / 2)
+        #  in the most extreme case, no samples have a hapax legomena
+        self.assertTrue(freq_1_count >= 0)
+        #  in the most extreme case, all samples have 2 hapax legomena
+        self.assertTrue(freq_1_count <= 2)
+        #  in the most extreme case, all samples have 2 hapax legomena and
+        #  (frag_size-2)/2 dis legomena
+        self.assertTrue(freq_4_count >= frag_size / 2 - 1)
+        #  in the most extreme case, no samples have hapax legomena and
+        #  frag_size/2 dis legomena
+        self.assertTrue(freq_4_count <= frag_size / 2)
+        #  no sample should have word occurring more often than twice
+        self.assertAlmostEqual(freq_10_count, 0.0)

tests/test_stringkernels.py

+import numpy as np
+from numpy.testing import assert_array_equal
+
+from tuhlbox.stringkernels import (
+    intersection_kernel,
+    presence_kernel,
+    spectrum_kernel,
+)
+
+docs = [
+    "I like this old movie. The movie is very nice.",
+    "In my opinion the book tells a very nice story. I really like it.",
+    "I wonder if you could drink this juice. It tastes so bad. Isn’t it bad?",
+    "Your dish is too spicy. You must be a such bad cook. "
+    "Don’t worry, I am as bad as you.",
+]
+
+ngram_min, ngram_max = 1, 4
+
+
+def test_intersection_kernel():
+    # obtained from java ComputeStringKernel intersection 1 4 sentences.txt <outfile> # noqa E501
+    expected = np.array(
+        [[178, 95, 66, 49], [95, 254, 72, 72], [66, 72, 278, 112],
+         [49, 72, 112, 334]],
+        dtype=int,
+    )
+    assert_array_equal(expected,
+                       intersection_kernel(docs, docs, ngram_min, ngram_max))
+
+
+def test_presence_kernel():
+    # obtained from java ComputeStringKernel presence 1 4 sentences.txt <outfile> # noqa E501
+
+    expected = np.array(
+        [[128, 67, 42, 29], [67, 197, 38, 42], [42, 38, 209, 64],
+         [29, 42, 64, 235]],
+        dtype=int,
+    )
+    assert_array_equal(expected,
+                       presence_kernel(docs, docs, ngram_min, ngram_max))
+
+
+def test_spectrum_kernel():
+    # obtained from java ComputeStringKernel spectrum 1 4 sentences.txt <outfile> # noqa E501
+    expected = np.array(
+        [
+            [390, 335, 300, 313],
+            [335, 598, 393, 458],
+            [300, 393, 680, 585],
+            [313, 458, 585, 1006],
+        ],
+        dtype=int,
+    )
+    assert_array_equal(expected,
+                       spectrum_kernel(docs, docs, ngram_min, ngram_max))

tests/test_subset.py

+from tuhlbox.subfreq import SubFrequencyVectorizer
+
+
+def test_subset_vectorizer():
+    transformer = SubFrequencyVectorizer()
+
+    texts = [
+        'male boy man girly ',
+        'female girly woman boy boy woman',
+        'super duper super man ',
+        'man manly boy man',
+    ]
+    targets = [0, 1, 2]
+
+    actual = transformer.fit_transform(texts, targets)
+    assert actual.shape == (4, 3)  # 4 samples, 3 classes

tests/test_tree.py

+import unittest
+
+import nltk
+
+from tuhlbox.tree import (
+    StringToTreeTransformer,
+    TreeChainTransformer,
+    WordToPosTransformer,
+)
+
+
+class TestTrees(unittest.TestCase):
+    def test_tree_parsing(self):
+        transformer = StringToTreeTransformer()
+        # one document could contain many sentences, and each sentence is a
+        # tree.
+        documents = [["(S (NP I) (VP (V saw) (NP him)))"]]
+        expected = [[nltk.Tree.fromstring(documents[0][0])]]
+        actual = transformer.transform(documents)
+        self.assertEqual(actual, expected)
+
+    def test_pos_extraction(self):
+        transformer = WordToPosTransformer()
+        documents = [
+            [nltk.Tree.fromstring("(S (NP I) (VP (V saw) (NP him)))")]]
+        expected = [["NP", "V", "NP"]]
+        actual = transformer.transform(documents)
+        self.assertEqual(actual, expected)
+
+    def test_pos_short_chains(self):
+        transformer = TreeChainTransformer(max_length=2,
+                                           combine_chain_elements=" ")
+        documents = [
+            # document 1
+            [
+                #  tree 1
+                nltk.Tree.fromstring(
+                    "(S (DP (D the) (NP dog)) (VP (V chased) (DP (D the) (NP "
+                    "cat))))"
+                )
+            ],
+            # document 2
+            [
+                # tree 2
+                nltk.Tree.fromstring("(S (NP I) (VP (V saw) (NP him)))"),
+                # tree 3
+                nltk.Tree.fromstring("(S (NP I) (VP (V saw) (NP him)))"),
+            ],
+        ]
+        expected = [
+            # document 1
+            [
+                # tree 1
+                ["S DP", "DP D", "DP NP", "S VP", "VP V", "VP DP", "DP D",
+                 "DP NP"]
+            ],
+            # document 2
+            [
+                # tree 2
+                ["S NP", "S VP", "VP V", "VP NP"],
+                # tree 3
+                ["S NP", "S VP", "VP V", "VP NP"],
+            ],
+        ]
+        actual = list(transformer.transform(documents))
+        self.assertEqual(actual, expected)
+
+    def test_pos_short_chains_nocombine(self):
+        transformer = TreeChainTransformer(max_length=2,
+                                           combine_chain_elements=None)
+        documents = [
+            # document 1
+            [
+                #  tree 1
+                nltk.Tree.fromstring(
+                    "(S (DP (D the) (NP dog)) (VP (V chased) (DP (D the) (NP "
+                    "cat))))"
+                )
+            ],
+            # document 2
+            [
+                # tree 2
+                nltk.Tree.fromstring("(S (NP I) (VP (V saw) (NP him)))"),
+                # tree 3
+                nltk.Tree.fromstring("(S (NP I) (VP (V saw) (NP him)))"),
+            ],
+        ]
+        expected = [
+            # document 1
+            [
+                # tree 1
+                [
+                    ["S", "DP"],
+                    ["DP", "D"],
+                    ["DP", "NP"],
+                    ["S", "VP"],
+                    ["VP", "V"],
+                    ["VP", "DP"],
+                    ["DP", "D"],
+                    ["DP", "NP"],
+                ]
+            ],
+            # document 2
+            [
+                # tree 2
+                [["S", "NP"], ["S", "VP"], ["VP", "V"], ["VP", "NP"]],
+                # tree 3
+                [["S", "NP"], ["S", "VP"], ["VP", "V"], ["VP", "NP"]],
+            ],
+        ]
+        actual = list(transformer.transform(documents))
+        self.assertEqual(actual, expected)
+
+    def test_pos_long_chains(self):
+        transformer = TreeChainTransformer(max_length=None,
+                                           combine_chain_elements=" ")
+        documents = [
+            # document 1
+            [
+                #  tree 1
+                nltk.Tree.fromstring(
+                    "(S (DP (D the) (NP dog)) (VP (V chased) (DP (D the) (NP "
+                    "cat))))"
+                )
+            ],
+            # document 2
+            [
+                # tree 2
+                nltk.Tree.fromstring("(S (NP I) (VP (V saw) (NP him)))")
+            ],
+        ]
+        expected = [
+            # document 1
+            [
+                # tree 1
+                ["S DP D", "S DP NP", "S VP V", "S VP DP D", "S VP DP NP"]
+            ],
+            # document 2
+            [
+                # tree 2
+                ["S NP", "S VP V", "S VP NP"]
+            ],
+        ]
+        actual = list(transformer.transform(documents))
+        self.assertEqual(actual, expected)
+