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The SPECIALIST Lexicon

The MEDLINE.2022 N-gram Set

This page describes the details of generating n-grams (n = 1-5) from MEDLINE. Please make sure all n-grams are generated correctly in the step-11 (group) with correct setup. 2022 MEDLINE n-gram set release using split, combine, and filter algorithm.
The data of these tables are from:

I. Log and data files

DescrptionLocationNotes
Input options for runGen${N}GramAll${MULTIWORDS}/bin/02.NGramGenAll/inData/${YEAR}/${N}-gram
  • Parameters for options 10-13
runGen${N}GramAll log${MULTIWORDS}/bin/02.NGramGenAll/log.${N}
  • run time
log file for options 10~13${MULTIWORDS}/bin/02.NGramGenAll/logData/${YEAR}/${N}-gram
  • Detail log for option 10-13
  • Not used in the table below
1.Split log${MULTIWORDS}/bin/Log.${YEAR}/02.NGramGen/log.heap.${N}.50
  • Total documents, Sentences, Tokens counts
  • Unique unigram count
  • not unique split gram count
N-gram out files${MULTIWORDS}/data/${YEAR}/outData/02.NGram/${N}-gram/*
  • Result files from Split, Group, and FilterCombine

II. Detail logs

ProgramNAppro. Time (Hr.) Option 1.1
  • GenPmidTiAbSentenceFromXmls
  • pubmed{YY}n{DDDD}.xml
  • PmidTiAbSentences{YY}n{DDDD}.txt
Option 10
  • Gen split n-gram
  • GetNGramFromSentenceFiles
  • MAX_CL = 50

  • 1.Split:
Option 11
  • Group split n-grams by alphabetic characters
  • GroupSpliteNGrams

  • 2.Group:
Option 12
  • Filter by WC and combine alphabetic n-grams
  • FilterWcCombineNGrams
  • WC = 30

  • 3.FilterCombine:
Option 13
  • Sort n-grams by dwt, tdw
  • NGramFilter

  • 3.FilterCombine:
Preprocess 4.0
  • ~4.0 hr.
  • PmidTiAbS22n: 0001-1114
    
unigramsn=1< 1.0 hr.
(from ./bin/02.NGramGenAll/logData/${YEAR}/N-gram/*.log)		 
  • param: 10,1, (150000000)
  • 45 min.


    from log.heap.1.50:

  • Documents: 33,405,863
  • Sentences: 224,228,682
  • Tokens: 4,680,725,429

  • split: 1, no split
  • 1-grams (not unique, from log.heap.1.50): 38,591,469
    (it is unique beacuse no split, use wc -l)

  • Files:
    • nGram.out.1.heap.50.s01.0001-1114 (631 MB, use ls -alh)
  • param:
    • 11,1,01,NO,NO
  • 2 min.

  • Group Alphabetically
  • 1-gram (unique): 38,591,469

  • Files:
    • ${NGram}.g01.NO-NO (631 MB|39MB, from ./logData/${YEAR}/1-gram/11-1.log)
  • param: 12, 1, 30
  • 1 min

  • 1-gram (WC >= 30): 1,248,727

  • File:
    • 1-gram.${YEAR}.30 (21 MB)
  • param: 13, 1, 30
  • 1 min.

  • 1-gram (sorted): 1,248,727

  • File:
    • 1-gram.${YEAR}.30.dwt (21 MB)
bigramsn=23.2 hr. 
  • param: 10,2, (150000000)
  • 2.3 hr.

  • split: 3
  • 2-gram (not unique from log.heap.2.50): 438,120,386

  • Files:
    • s01.0001-0583 (3.1 GB)
    • s02.0584-0890 (3.0 GB)
    • s03.0891-1114 (2.8 GB)
  • param: see file names below
    • 11,2,01,NO,M
    • 11,2,02,M,k
    • 11,2,02,k,NO
  • 50 min.

  • Group Alphabetically
  • 2-gram (unique, use wc -l): 345,555,538

  • Files:
    • ${NGram}.g01.NO-M (1.9GB|100MB)
    • ${NGram}.g02.M-k (2.8GB|135MB)
    • ${NGram}.g03.k-NO (2.4GB|111MB)
  • param: 12, 2, 30
  • 7 min.

  • 2-gram (WC >= 30): 7,519,422

  • File:
    • 2-gram.${YEAR}.30 (161 MB)
  • param: 13, 2, 30
  • 2 min.

  • 2-gram (sorted): 7,519,422

  • File:
    • 2-gram.${YEAR}.30.dwt (161 MB)
trigramsn=316 hr. 
  • param: 10,3, (150000000)
  • 5.8 hr.

  • split: 12
  • 3-gram (not unique - from log.heap.3.50): 1,643,134,783

  • Files:
    • s01.0001-0209 (3.8 GB)
    • s02.0210-0324 (3.7 GB)
    • s03.0325-0422 (3.8 GB)
    • s04.0423-0559 (3.8 GB)
    • s05.0560-0646 (3.7 GB)
    • s06.0647-0728 (3.8 GB)
    • s07.0729-0800 (3.7 GB)
    • s08.0801-0870 (3.8 GB)
    • s09.0871-0938 (3.8 GB)
    • s10.0939-1005 (3.8 GB)
    • s11.1006-1069 (3.8 GB)
    • s12.1070-1114 (2.8 GB)
  • param: see file names below
  • 10.0 hr.

  • Group Alphabetically
  • 3-gram (unique): 1,189,180,839

  • Files:
    • g01.NO-G (4.2GB|178MB)
    • g02.G-Z (3.0GB|121MB)
    • g03.Z-c (3.7GB|143MB)
    • g04.c-f (3.8GB|138MB)
    • g05.f-j (3.5GB|133MB)
    • g06.j-n (1.8GB|68MB)
    • g07.n-r (3.8GB|146MB)
    • g08.r-th (3.0GB|113MB)
    • g09.th-NO (3.6GB|145MB)
  • param: 12, 3, 30
  • 20 min.

  • 3-gram (WC >= 30): 11,046,633

  • File:
    • 3-gram.${YEAR}.30 (284 MB)
  • param: 13, 3, 30
  • 2 min.

  • 3-gram (sorted): 10,046,633

  • File:
    • 3-gram.${YEAR}.30.dwt (284 MB)
fourgramsn=425 hr. 
  • param: 10,4, (130000000)
  • 5.5 hr.

  • split: 23
  • 4-gram (not unique - from log.heap.4.50): 2,956,113,231

  • Files:
    • s01.0001-0077 (4.0 GB)
    • s02.0078-0204 (3.9 GB)
    • s03.0205-0272 (3.9 GB)
    • s04.0273-0319 (3.9 GB)
    • s05.0320-0372 (4.0 GB)
    • s06.0373-0419 (4.0 GB)
    • s07.0420-0517 (4.0 GB)
    • s08.0518-0559 (3.9 GB)
    • s09.0560-0605 (3.9 GB)
    • s10.0606-0649 (4.0 GB)
    • s11.0650-0696 (4.0 GB)
    • s12.0697-0735 (4.0 GB)
    • s13.0736-0773 (4.0 GB)
    • s14.0774-0811 (4.0 GB)
    • s15.0812-0848 (4.0 GB)
    • s16.0849-0885 (4.0 GB)
    • s17.0886-0921 (4.0 GB)
    • s18.0922-0959 (4.1 GB)
    • s19.0960-0995 (4.1 GB)
    • s20.0996-1030 (4.1 GB)
    • s21.1031-1065 (4.1 GB)
    • s22.1066-1099 (4.0 GB)
    • s23.1100-1114 (1.9 GB)
  • param: see file names below
  • 18.7 hr.

  • Group Alphabetically
  • 4-gram (unique): 2,233,423,690

  • Files:
    • g01.NO-9 (3.9GB|138MB)
    • g02.9-L (4.5GB|149MB)
    • g03.L-Z (4.4GB|143MB)
    • g04.Z-ane (5.3GB|175MB)
    • g05.ane-bs (3.2GB|102MB)
    • g06.bs-d (4.6GB|143MB)
    • g07.d-f (4.6GB|142MB)
    • g08.f-h (3.2GB|104MB)
    • g09.h-ini (3.9GB|125MB)
    • g10.ini-m (2.8GB|87MB)
    • g11.m-o (3.7GB|117MB)
    • g12.o-p (4.1GB|142MB)
    • g13.p-r (3.9GB|119MB)
    • g14.r-sh (3.4GB|106MB)
    • g15.sh-th (3.6GB|112MB)
    • g16.th-to (3.7GB|123MB)
    • g17.to-v (2.7GB|89MB)
    • g18.v-NO (3.3GB|108MB)
  • param: 12, 4, 30
  • 52 min.

  • 4-gram (WC >= 30): 7,142,084

  • File:
    • 4-gram.${YEAR}.30 (217 MB)
  • param: 13, 4, 30
  • 2 min.

  • 4-gram (sorted): 7,142,084

  • File:
    • 4-gram.${YEAR}.30.dwt (217 MB)
fivegramsn=536.7 hr. 
  • param: 10,5, (120000000)
  • 6.0 hr.

  • split: 28
  • 5-gram (not unique): 3,388,345,780

    Files:

    • s01.0001-0064 (4.3 GB)
    • s02.0065-0112 (4.3 GB)
    • s03.0113-0233 (4.3 GB)
    • s04.0234-0279 (4.3 GB)
    • s05.0280-0316 (4.4 GB)
    • s06.0317-0360 (4.4 GB)
    • s07.0361-0398 (4.4 GB)
    • s08.0399-0482 (4.4 GB)
    • s09.0483-0524 (4.4 GB)
    • s10.0525-0558 (4.4 GB)
    • s11.0559-0597 (4.4 GB)
    • s12.0598-0633 (4.4 GB)
    • s13.0634-0671 (4.4 GB)
    • s14.0672-0705 (4.4 GB)
    • s15.0706-0736 (4.4 GB)
    • s16.0737-0767 (4.4 GB)
    • s17.0768-0798 (4.4 GB)
    • s18.0799-0828 (4.4 GB)
    • s19.0829-0858 (4.4 GB)
    • s20.0859-0889 (4.5 GB)
    • s21.0890-0918 (4.4 GB)
    • s22.0919-0950 (4.5 GB)
    • s23.0951-0979 (4.4 GB)
    • s24.0980-1007 (4.4 GB)
    • s25.1008-1035 (4.4 GB)
    • s26.1036-1063 (4.5 GB)
    • s27.1064-1091 (4.5 GB)
    • s28.1092-1114 (3.7 GB)
  • param: see file names below
  • 29.4 hr.

  • Group Alphabetically
  • 5-gram (unique): 2,918,497,553

  • Files:
    • g01.NO-9 (5.0GB|148MB)
    • g02.9-E (3.7GB|101MB)
    • g03.E-N (3.8GB|104MB)
    • g04.N-T (3.1GB|81MB)
    • g05.T-a (2.7GB|74MB)
    • g06.a-am (4.1GB|111MB)
    • g07.am-ann (4.5GB|127MB)
    • g08.ann-bo (4.6GB|123MB)
    • g09.bo-ch (2.9GB|79MB)
    • g10.ch-ct (4.2GB|107MB)
    • g11.ct-ef (4.4GB|114MB)
    • g12.ef-fr (5.6GB|149MB)
    • g13.fr-i (4.4GB|117MB)
    • g14.i-inc (2.9GB|81MB)
    • g15.inc-io (2.7GB|67MB)
    • g16.io-m (3.7GB|85MB)
    • g17.m-o (5.6GB|148MB)
    • g18.o-off (4.8GB|139MB)
    • g19.off-pl (4.4GB|118MB)
    • g20.pl-re (4.2GB|107MB)
    • g21.re-s (3.2GB|84MB)
    • g22.s-st (3.5GB|93MB)
    • g23.st-the (4.3GB|114MB)
    • g24.the-then (4.4GB|124MB)
    • g25.then-un (4.6GB|127MB)
    • g26.un-w (2.1GB|56MB)
    • g27.w-NO (4.4GB|125MB)
  • param: 12, 5, 30
  • 1.2 hr.

  • 5-gram (WC >= 30): 3,133,905

  • File:
    • 5-gram.${YEAR}.30 (111 MB)
  • param: 13, 5, 30
  • 2 min.

  • 5-gram (sorted): 3,133,905

  • File:
    • 5-gram.${YEAR}.30.dwt (111 MB)