Why is "machine_learning" lemmatized both as "machine_learning" and "machine_learne"? - machine-learning
I am running LDA on a number of texts. When I generated some visualizations of the produced topics, I found that the bigram "machine_learning" had been lemmatized both as "machine_learning" and "machine_learne". Here is as minimal a reproducible example as I can provide:
import en_core_web_sm
tokenized = [
[
'artificially_intelligent', 'funds', 'generating', 'excess', 'returns',
'artificial_intelligence', 'deep_learning', 'compelling', 'reasons',
'join_us', 'artificially_intelligent', 'fund', 'develop', 'ai',
'machine_learning', 'capabilities', 'real', 'cases', 'big', 'players',
'industry', 'discover', 'emerging', 'trends', 'latest_developments',
'ai', 'machine_learning', 'industry', 'players', 'trading',
'investing', 'live', 'investment', 'models', 'learn', 'develop',
'compelling', 'business', 'case', 'clients', 'ceos', 'adopt', 'ai',
'machine_learning', 'investment', 'approaches', 'rare', 'gathering',
'talents', 'including', 'quants', 'data_scientists', 'researchers',
'ai', 'machine_learning', 'experts', 'investment_officers', 'explore',
'solutions', 'challenges', 'potential', 'risks', 'pitfalls',
'adopting', 'ai', 'machine_learning'
],
[
'recent_years', 'topics', 'data_science', 'artificial_intelligence',
'machine_learning', 'big_data', 'become_increasingly', 'popular',
'growth', 'fueled', 'collection', 'availability', 'data',
'continually', 'increasing', 'processing', 'power', 'storage', 'open',
'source', 'movement', 'making', 'tools', 'widely', 'available',
'result', 'already', 'witnessed', 'profound', 'changes', 'work',
'rest', 'play', 'trend', 'increase', 'world', 'finance', 'impacted',
'investment', 'managers', 'particular', 'join_us', 'explore',
'data_science', 'means', 'finance_professionals'
]
]
nlp = en_core_web_sm.load(disable=['parser', 'ner'])
def lemmatization(descrips, allowed_postags=None):
if allowed_postags is None:
allowed_postags = ['NOUN', 'ADJ', 'VERB',
'ADV']
lemmatized_descrips = []
for descrip in descrips:
doc = nlp(" ".join(descrip))
lemmatized_descrips.append([
token.lemma_ for token in doc if token.pos_ in allowed_postags
])
return lemmatized_descrips
lemmatized = lemmatization(tokenized)
print(lemmatized)
As you will notice, "machine_learne" is found nowhere in the input tokenized, but both "machine_learning" and "machine_learne" are found in the output lemmatized.
What is the cause of this and can I expect it to cause issues with other bigrams/trigrams?
I think you misunderstood the process of POS Tagging and Lemmatization.
POS Tagging is based on several other informations than the word alone (I don't know which is your mother language, but that is common to many languages), but also on the surrounding words (for example, one common learned rule is that in many statements verb is usually preceded by a noun, which represents the verb's agent).
When you pass all these 'tokens' to your lemmatizer, spacy's lemmatizer will try to "guess" which is the Part of Speech of your solitary word.
In many cases it'll go for a default noun and, if it is not in a lookup table for common and irregular nouns, it'll attempt to use generic rules (such as stripping plural 's').
In other cases it'll go for a default verb based on some patterns (the "-ing" in the end), which is probably your case. Since no verb "machine_learning" exists in any dictionary (there's no instance in its model), it'll go for a "else" route and apply generic rules.
Therefore, machine_learning is probably being lemmatized by a generic '"ing" to "e"' rule (such as in the case of making -> make, baking -> bake), common to many regular verbs.
Look at this test example:
for descrip in tokenized:
doc = nlp(" ".join(descrip))
print([
(token.pos_, token.text) for token in doc
])
Output:
[('NOUN', 'artificially_intelligent'), ('NOUN', 'funds'), ('VERB',
'generating'), ('ADJ', 'excess'), ('NOUN', 'returns'), ('NOUN',
'artificial_intelligence'), ('NOUN', 'deep_learning'), ('ADJ',
'compelling'), ('NOUN', 'reasons'), ('PROPN', 'join_us'), ('NOUN',
'artificially_intelligent'), ('NOUN', 'fund'), ('NOUN', 'develop'),
('VERB', 'ai'), ('VERB', 'machine_learning'), ('NOUN',
'capabilities'), ('ADJ', 'real'), ('NOUN', 'cases'), ('ADJ', 'big'),
('NOUN', 'players'), ('NOUN', 'industry'), ('VERB', 'discover'),
('VERB', 'emerging'), ('NOUN', 'trends'), ('NOUN',
'latest_developments'), ('VERB', 'ai'), ('VERB', 'machine_learning'),
('NOUN', 'industry'), ('NOUN', 'players'), ('NOUN', 'trading'),
('VERB', 'investing'), ('ADJ', 'live'), ('NOUN', 'investment'),
('NOUN', 'models'), ('VERB', 'learn'), ('VERB', 'develop'), ('ADJ',
'compelling'), ('NOUN', 'business'), ('NOUN', 'case'), ('NOUN',
'clients'), ('NOUN', 'ceos'), ('VERB', 'adopt'), ('VERB', 'ai'),
('ADJ', 'machine_learning'), ('NOUN', 'investment'), ('NOUN',
'approaches'), ('ADJ', 'rare'), ('VERB', 'gathering'), ('NOUN',
'talents'), ('VERB', 'including'), ('NOUN', 'quants'), ('NOUN',
'data_scientists'), ('NOUN', 'researchers'), ('VERB', 'ai'), ('ADJ',
'machine_learning'), ('NOUN', 'experts'), ('NOUN',
'investment_officers'), ('VERB', 'explore'), ('NOUN', 'solutions'),
('VERB', 'challenges'), ('ADJ', 'potential'), ('NOUN', 'risks'),
('NOUN', 'pitfalls'), ('VERB', 'adopting'), ('VERB', 'ai'), ('NOUN',
'machine_learning')]
You are getting both machine_learning as verb and noun based on context. But see that just concatenating the words gets you messy because they are not ordered in Natural language as expected.
Not even a human can understand and correctly POS Tag this text:
artificially_intelligent funds generating excess returns
artificial_intelligence deep_learning compelling reasons join_us
artificially_intelligent fund develop ai machine_learning capabilities
real cases big players industry discover emerging trends
latest_developments ai machine_learning industry players trading
investing live investment models learn develop compelling business
case clients ceos adopt ai machine_learning investment approaches rare
gathering talents including quants data_scientists researchers ai
machine_learning experts investment_officers explore solutions
challenges potential risks pitfalls adopting ai machine_learning
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Europe,'Austria',3,260,79,32.7,99.1 Asia,'Azerbaijan',144,163.33,66.9,4.8,80.2 Americas,'Bahamas',5,256.67,69.7,20.2,? Asia,'Bahrain',33,240,74.3,23,102 Asia,'Bangladesh',104,190,62.8,2.1,53.7 Americas,'Barbados',27,243.33,75,17,101.1 Europe,'Belarus',170,133.33,68.1,6.9,94.2 Europe,'Belgium',28,243.33,78.9,31.4,145.4 Americas,'Belize',48,230,71.9,6.8,71.6 Africa,'Benin',122,180,54,1.1,21.8 Asia,'Bhutan',8,253.33,62.9,1.4,? Americas,'Bolivia',117,183.33,64.1,2.9,? Europe, 'Bosnia & Herzegovina',137,170,74.2,6.8,? Africa,'Botswana',123,180,36.3,10.5,81.8 Americas,'Brazil',81,210,70.5,8.4,103.2 Asia, 'Brunei Darussalam',9,253.33,76.4,23.6,? Europe,'Bulgaria',164,143.33,72.2,9.6,92 Africa, 'Burkina Faso',152,156.67,47.5,1.3,10 Asia,'Burma',130,176.67,60.2,1.7,? Africa,'Burundi',178,100,43.6,0.7,? Asia,'Cambodia',110,186.67,56.2,2.2,17.3 Africa,'Cameroon',138,170,45.8,2.4,? Americas,'Canada',10,253.33,80,34,102.6 Africa, 'Cape Verdi',100,193.33,70.4,6.2,? Africa, 'Central African Republic',145,163.33,39.3,1.1,? Africa,'Chad',159,150,43.6,1.5,11.5 Americas,'Chile',71,216.67,77.9,11.3,87.5 Asia,'China',82,210,71.6,6.8,62.8 Americas,'Colombia',34,240,72.4,7.9,70.9 Africa,'Comoros',97,196.67,63.2,0.6,? Africa, 'Congo Democratic Republic',176,110,43.1,0.7,18.4 Africa, 'Congo Republic',105,190,52,1.3,? Americas, 'Costa Rica',13,250,78.2,11.1,50.9 Europe,'Croatia',98,196.67,75,11.6,? Americas,'Cuba',83,210,77.3,3.5,? Europe,'Cyprus',49,230,78.6,7.14,? Europe, 'Czech Republic',77,213.33,75.6,19.5,87.9 Europe,'Denmark',1,273.33,77.2,34.6,? Africa,'Dijbouti',150,160,52.8,1.3,14.7 Americas,'Dominica',29,243.33,75.6,5.5,? Americas, 'Dominican Republic',42,233.33,67.2,7,? Americas,'Ecuador',111,186.67,74.3,4.3,56.7 Africa,'Egypt',151,160,69.8,3.9,? Americas, 'El Salvador',61,220,70.9,4.7,49.8 Africa, 'Equatorial Guinea',135,173.33,43.3,50.2,? Africa,'Eritrea',162,146.67,53.8,1,28.2 Europe,'Estonia',139,170,71.3,16.7,107 Africa,'Ethiopia',153,156.67,47.6,0.9,5.2 Australia, 'Fiji',57,223.33,67.8,6,? Europe,'Finland',6,256.67,78.5,30.9,124.5 Europe,'France',62,220,79.5,29.9,108.7 Africa,'Gabon',88,206.67,54.5,6.8,54.4 Africa,'Gambia',106,190,55.7,1.9,27 Europe,'Georgia',169,136.67,70.5,3.3,77.7 Europe,'Germany',35,240,78.7,30.4,99 Africa,'Ghana',89,206.67,56.8,2.5,37.3 Europe,'Greece',84,210,78.3,22.2,94.6 Americas,'Grenada',72,216.67,65.3,5,? Americas,'Guatemala',43,233.33,67.3,4.7,32.7 Africa,'Guinea',140,170,53.7,2,? Africa,'Guinea-Bissau',124,180,44.7,0.8,20.4 Americas,'Guyana',36,240,63.1,4.6,81 Americas,'Haiti',118,183.33,51.6,1.7,? Americas,'Honduras',37,240,67.8,2.9,? Asia, 'Hong Kong',63,220,81.6,32.9,? Europe,'Hungary',107,190,72.7,16.3,98.6 Europe,'Iceland',4,260,80.7,35.6,108.8 Asia,'India',125,180,63.3,3.3,49.9 Asia,'Indonesia',64,220,66.8,3.6,? Asia,'Iran',96,200,70.4,8.3,80 Europe,'Ireland',11,253.33,77.7,41,123.1 Asia,'Israel',58,223.33,79.7,24.6,93 Europe,'Italy',50,230,80.1,29.2,92.8 Africa, 'Ivory Coast',160,150,45.9,1.6,21.7 Americas,'Jamaica',44,233.33,70.8,4.4,83.6 Asia,'Japan',90,206.67,82,31.5,102.1 Asia,'Jordan',141,170,71.3,4.7,87.7 Asia,'Kazakhstan',101,193.33,63.2,8.2,87 Africa,'Kenya',112,186.67,47.2,1.1,? Asia,'Kuwait',38,240,76.9,19.2,55.6 Asia,'Kyrgyzstan',65,220,66.8,2.1,83 Asia,'Laos',126,180,54.7,1.9,35.6 Europe,'Latvia',154,156.67,71.6,13.2,88.9 Asia,'Lebanon',113,186.67,72,6.2,78.2 Africa,'Lesotho',165,143.33,36.3,2.5,28 Africa,'Libya',108,190,73.6,11.4,? Europe,'Lithuania',155,156.67,72.3,13.7,93.4 Europe,'Luxembourg',12,253.33,78.5,55.6,95.3 Europe,'Macedonia',146,163.33,73.8,7.8,? Africa,'Madagascar',103,193.33,55.4,0.9,? Africa,'Malawi',158,153.33,39.7,0.6,? Asia,'Malaysia',17,246.67,73.2,12.1,98.8 Asia,'Maldives',66,220,66.6,3.9,42.7 Africa,'Mali',131,176.67,47.9,1.2,15 Europe,'Malta',14,250,78.4,19.9,90.4 Africa,'Mauritania',132,176.67,52.7,2.2,? Africa,'Mauritius',73,216.67,72.2,13.1,107.3 Americas,'Mexico',51,230,75.1,10,73.4 Europe,'Moldova',175,116.67,67.7,1.8,? Asia,'Mongolia',59,223.33,64,1.9,64.4 Africa,'Morocco',114,186.67,69.7,4.2,39.3 Africa,'Mozambique',127,180,41.9,1.3,13.9 Africa,'Namibia',74,216.67,48.3,7,59.8 Asia,'Nepal',119,183.33,61.6,1.4,53.9 Europe,'Netherlands',15,250,78.4,30.5,124.1 Australia,' New Zealand',18,246.67,79.1,25.2,112.9 Americas,'Nicaragua',85,210,69.7,2.9,? Africa,'Niger',161,150,44.4,0.9,? Africa,'Nigeria',120,183.33,43.4,1.4,? Europe,'Norway',19,246.67,79.4,42.3,117 Asia,'Oman',30,243.33,74.1,13.2,67.8 Asia,'Pakistan',166,143.33,63,2.4,39 Asia,'Palestine',128,180,72.5,5.8,80.7 Americas,'Panama',39,240,74.8,7.2,68.7 Australia, 'Papua New Guinea',86,210,55.3,2.6,21.2 Americas,'Paraguay',75,216.67,71,4.9,56.9 Americas,'Peru',115,186.67,70,5.9,80.8 Asia,'Philippines',78,213.33,70.4,5.1,75.9 Europe,'Poland',99,196.67,74.3,13.3,? Europe,'Portugal',92,203.33,77.2,19.3,112 Asia,'Qatar',45,233.33,72.8,27.4,92.4 Europe,'Romania',136,173.33,71.3,8.2,80.2 Europe,'Russia',167,143.33,65.3,11.1,81.9 Africa,'Rwanda',163,146.67,43.9,1.5,12.1 Australia, 'Samoa Western',52,230,70.2,5.8,76 Africa, 'Sao Tome And Principe',60,223.33,63,1.2,? Asia, 'Saudi Arabia',31,243.33,71.8,12.8,68.5 Africa,'Senegal',116,186.67,55.7,1.8,19.5 Africa,'Seychelles',20,246.67,72.7,7.8,? Africa, 'Sierra Leone',143,166.67,40.8,0.8,23.9 Asia,'Singapore',53,230,78.7,28.1,? Europe,'Slovakia',129,180,74,16.1,86.6 Europe,'Slovenia',67,220,76.4,21.6,98.8 Australia, 'Solomon Islands',54,230,62.3,1.7,? Africa, 'South Africa',109,190,48.4,12,90.2 Asia, 'South Korea',102,193.33,77,20.4,97.4 Europe,'Spain',46,233.33,79.5,25.5,112.8 Asia, 'Sri Lanka',93,203.33,74,4.3,? Americas, 'St Kitts And Nevis',21,246.67,70,8.8,? Americas, 'St Lucia',47,233.33,72.4,5.4,94.3 Americas, 'St Vincent And The Grenadines',40,240,71.1,2.9,? Africa,'Sudan',173,120,56.4,2.1,28.8 Americas,'Suriname',32,243.33,69.1,4.1,50.7 Africa,'Swaziland',168,140,32.5,5,? Europe,'Sweden',7,256.67,80.2,29.8,152.8 Europe,'Switzerland',2,273.33,80.5,32.3,99.9 Asia,'Syria',142,170,73.3,3.9,42 Asia,'Taiwan',68,220,76.1,27.6,? Asia,'Tajikistan',94,203.33,63.6,1.2,76 Africa,'Tanzania',121,183.33,46,0.7,5.31 Asia,'Thailand',76,216.67,70,8.3,79 Asia,'Timor-Leste',69,220,65.5,0.4,? Africa,'Togo',147,163.33,54.3,1.7,? Australia,' Tonga',70,220,72.2,2.3,? Americas, 'Trinidad And Tobago',55,230,69.9,16.7,78.4 Africa,'Tunisia',79,213.33,73.3,8.3,74.6 Europe,'Turkey',133,176.67,68.7,8.2,? Asia,'Turkmenistan',171,133.33,62.4,8,? Asia,'Uae',22,246.67,78,43.4,74.4 Africa,'Uganda',156,156.67,47.3,1.8,? Europe,'Ukraine',174,120,66.1,7.2,92.8 Europe, 'United Kingdom',41,236.67,78.4,30.3,157.2 Americas,'Uruguay',87,210,75.4,9.6,91.6 Americas,'Usa',23,246.67,77.4,41.8,94.6 Asia,'Uzbekistan',80,213.33,66.5,1.8,? Australia,' Vanuatu',24,246.67,68.6,2.9,28.5 Americas,'Venezuela',25,246.67,72.9,6.1,? Asia,'Vietnam',95,203.33,70.5,2.8,64.6 Asia,'Yemen',91,206.67,60.6,0.9,? Africa,'Zambia',148,163.33,37.5,0.9,25.5 Africa,'Zimbabwe',177,110,36.9,2.3,45.3
You don't need the M5P line. That's not an attribute. Just omit line 2. Country has some problem: I get the message "Attribute is neither numeric or nominal". (I see you have it as string, so that's right). But when I remove the country attribute, then I can run M5P. (3 rules, correlation = .85). Now, you may be thinking "but I want to keep track of what country my predictions are for". Here's how to do that: First, set up the filtered classifier to remove attribute 2 (country) and run M5P: Second, under more options, choose to Output predictions, choosing a format. Here I chose CSV (comma separated values), and then right clicked to select all attributes (first-last) to output. Now Start the model. This gives you actual, predicted, and all the data, including the country name:
What should be given as an input to linkage function - tfidf matrix or similarity between different elements of tfidf matrixes?
I have the following python notebook which aims to cluster different groups of abstracts based on the similarity between their text. I have two approaches here: one to use tfidf numpy array of documents as it is in the linkage function and second is to find the similarity between the tfidf array of different documents and then to use that similarity matrix for clustering. I am unable to understand which one is correct. Approach 1: I used cosine_similarity to find out the similarity matrix (cosine) of tfidf matrix. I first converted the redundant matrix (cosine) into the condensed distance matrix (distance_matrix) using squareform function. Then distance_matrix is fed into linkage function and using Dendograms I have plotted the graph. Approach 2: I used the condensed form of tfidf numpy array into the linkage function and plotted the dendograms. My question is what is correct? According to the data as far as i can understand, the approach 2 seems to be correct, but to me approach 1 makes sense. It would be great if someone can explain me what is right here in this scenario. Thanks in advance. Let me know if anything remains unclear in the question. import pandas, numpy from sklearn.feature_extraction.text import TfidfVectorizer from nltk.corpus import stopwords from nltk.tokenize import RegexpTokenizer ###Data Cleaning stop_words = stopwords.words('english') tokenizer = RegexpTokenizer(r'\w+') df=pandas.read_csv('WIPO_CSV.csv') import sys reload(sys) sys.setdefaultencoding('utf8') documents_no_stopwords=[] def preprocessing(word): tokens = tokenizer.tokenize(word) processed_words = [] for w in tokens: if w in stop_words: continue else: processed_words.append(w) ***This step creates a list of text documents with only the nouns in them*** documents_no_stopwords.append(' '.join(processed_words)) for text in df['TEXT'].tolist(): preprocessing(text) ***Converting into tfidf form*** *Latin is used as utf8 decoder was facing some trouble with the text.* vectoriser = TfidfVectorizer(encoding='latin1') ***we have numpy here which is in normalised form*** tfidf_documents = vectoriser.fit_transform(documents_no_stopwords) ##Cosine Similarity as the input to linkage should be a distance vector from sklearn.metrics.pairwise import cosine_similarity from scipy.spatial.distance import squareform cosine = cosine_similarity(tfidf_documents) distance_matrix = squareform(cosine,force='tovector',checks=False) from scipy.cluster.hierarchy import dendrogram, linkage ##Linkage based on tfidf of each document z_num=linkage(tfidf_documents.todense(),'ward') z_num #tfidf array([[11. , 12. , 0. , 2. ], [18. , 19. , 0. , 2. ], [20. , 31. , 0. , 3. ], [21. , 32. , 0. , 4. ], [22. , 33. , 0. , 5. ], [17. , 34. , 0.38208619, 6. ], [15. , 28. , 1.19375843, 2. ], [ 6. , 9. , 1.24241258, 2. ], [ 7. , 8. , 1.27069483, 2. ], [13. , 37. , 1.28868301, 3. ], [ 4. , 24. , 1.30850122, 2. ], [36. , 39. , 1.32090275, 5. ], [10. , 16. , 1.32602346, 2. ], [27. , 38. , 1.32934025, 3. ], [23. , 25. , 1.32987072, 2. ], [ 3. , 29. , 1.35143582, 2. ], [ 5. , 14. , 1.35401753, 2. ], [26. , 42. , 1.35994878, 3. ], [ 2. , 45. , 1.40055438, 3. ], [ 0. , 40. , 1.40811825, 3. ], [ 1. , 46. , 1.41383622, 3. ], [44. , 50. , 1.4379821 , 5. ], [41. , 43. , 1.44575227, 8. ], [48. , 51. , 1.45876241, 8. ], [49. , 53. , 1.47130328, 11. ], [47. , 52. , 1.49944936, 11. ], [54. , 55. , 1.69814818, 22. ], [30. , 56. , 1.91299937, 24. ], [35. , 57. , 3.1967033 , 30. ]]) from matplotlib import pyplot as plt plt.figure(figsize=(25, 10)) dn = dendrogram(z_num) plt.show() Linkage based on similarity z_sim=linkage(distance_matrix,'ward') z_sim *Cosine Similarity* array([[0.00000000e+00, 1.00000000e+00, 0.00000000e+00, 2.00000000e+00], [2.00000000e+00, 3.00000000e+01, 0.00000000e+00, 3.00000000e+00], [1.70000000e+01, 3.10000000e+01, 0.00000000e+00, 4.00000000e+00], [3.00000000e+00, 4.00000000e+00, 0.00000000e+00, 2.00000000e+00], [1.00000000e+01, 3.30000000e+01, 0.00000000e+00, 3.00000000e+00], [5.00000000e+00, 7.00000000e+00, 0.00000000e+00, 2.00000000e+00], [6.00000000e+00, 1.80000000e+01, 0.00000000e+00, 2.00000000e+00], [1.10000000e+01, 1.90000000e+01, 0.00000000e+00, 2.00000000e+00], [1.20000000e+01, 2.00000000e+01, 0.00000000e+00, 2.00000000e+00], [8.00000000e+00, 2.40000000e+01, 0.00000000e+00, 2.00000000e+00], [1.60000000e+01, 2.10000000e+01, 0.00000000e+00, 2.00000000e+00], [2.20000000e+01, 2.70000000e+01, 0.00000000e+00, 2.00000000e+00], [9.00000000e+00, 2.90000000e+01, 0.00000000e+00, 2.00000000e+00], [2.60000000e+01, 4.20000000e+01, 0.00000000e+00, 3.00000000e+00], [1.40000000e+01, 3.40000000e+01, 3.97089886e-03, 4.00000000e+00], [2.30000000e+01, 4.40000000e+01, 1.81733052e-02, 5.00000000e+00], [3.20000000e+01, 3.50000000e+01, 2.14592323e-02, 6.00000000e+00], [2.50000000e+01, 4.00000000e+01, 2.84944415e-02, 3.00000000e+00], [1.30000000e+01, 4.70000000e+01, 5.02045376e-02, 4.00000000e+00], [4.10000000e+01, 4.30000000e+01, 5.10902795e-02, 5.00000000e+00], [3.70000000e+01, 4.50000000e+01, 5.40176402e-02, 7.00000000e+00], [3.80000000e+01, 3.90000000e+01, 6.15118462e-02, 4.00000000e+00], [1.50000000e+01, 4.60000000e+01, 7.54874869e-02, 7.00000000e+00], [2.80000000e+01, 5.00000000e+01, 9.55487454e-02, 8.00000000e+00], [5.20000000e+01, 5.30000000e+01, 3.86911095e-01, 1.50000000e+01], [4.90000000e+01, 5.40000000e+01, 4.16693529e-01, 2.00000000e+01], [4.80000000e+01, 5.50000000e+01, 4.58764920e-01, 2.40000000e+01], [3.60000000e+01, 5.60000000e+01, 5.23422380e-01, 2.60000000e+01], [5.10000000e+01, 5.70000000e+01, 5.49419077e-01, 3.00000000e+01]]) from matplotlib import pyplot as plt plt.figure(figsize=(25, 10)) dn = dendrogram(z_sim) plt.show() accuracy for clustering of data is compared with this photo: https://drive.google.com/file/d/1EgkPqwh7AKhGqOe1zf9KNjSMxPQ9Xfd9/view?usp=sharing The dendogram that I got are available in the following notebook link: https://drive.google.com/file/d/1TB7aFK4lPDo43GY74FPOqVOx1AxWV-A_/view?usp=sharing open this html using internet browser.
Scipy only supports distances for HAC, not similarities. Then the results should be the same. So there is no "right" or "wrong". At some point you need the distance matrix in linearized form. It is probably most efficient to use a) a method that can process sparse data (avoiding any todense call), and b) directly produces the linearize form, rather than generating the entire matrix and then dropping half of it.