The SPECIALIST Lexicon

The MEDLINE.2021 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. 2021 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.
  • PmidTiAbS21n: 0001-1062
    
unigramsn=1< 1.0 hr.
(from ./bin/02.NGramGenAll/logData/${YEAR}/N-gram/*.log)		 
  • param: 10,1, (150000000)
  • 40 min.


    from log.heap.1.50:

  • Documents: 31,850,051
  • Sentences: 209,685,517
  • Tokens: 4,365,354,060

  • split: 1, no split
  • 1-grams (not unique, from log.heap.1.50): 36,150,616
    (it is unique beacuse no split, use wc -l)

  • Files:
    • nGram.out.1.heap.50.s01.0001-1062 (590 MB, use ls -alh)
  • param:
    • 11,1,01,NO,NO
  • 2 min.

  • Group Alphabetically
  • 1-gram (unique): 36,150,616

  • Files:
    • ${NGram}.g01.NO-NO (590 MB|36MB, from 1, from ./logData/${YEAR}/11-1.log1-1.log)
  • param: 12, 1, 30
  • 1 min

  • 1-gram (WC >= 30): 1,185,627

  • File:
    • 1-gram.${YEAR}.30 (20 MB)
  • param: 13, 1, 30
  • 1 min.

  • 1-gram (sorted): 1,185,627

  • File:
    • 1-gram.${YEAR}.30.dwt (20 MB)
bigramsn=23.2 hr. 
  • param: 10,2, (150000000)
  • 2.3 hr.

  • split: 3
  • 2-gram (not unique from log.heap.2.50): 412,168,042

  • Files:
    • s01.0001-0583 (3.1 GB)
    • s02.0584-0890 (3.0 GB)
    • s03.0891-1062 (2.3 GB)
  • param: see file names below
    • 11,2,01,NO,c
    • 11,2,02,c,NO
  • 21 min.

  • Group Alphabetically
  • 2-gram (unique, use wc -l): 325,314,728

  • Files:
    • ${NGram}.g01.NO-c (3.1GB|158MB)
    • ${NGram}.g02.c-NO (3.6GB|167MB)
  • param: 12, 2, 30
  • 22 min.

  • 2-gram (WC >= 30): 7,093,113

  • File:
    • 2-gram.${YEAR}.30 (152 MB)
  • param: 13, 2, 30
  • 8 min.

  • 2-gram (sorted): 7,093,113

  • File:
    • 2-gram.${YEAR}.30.dwt (152 MB)
trigramsn=316 hr. 
  • param: 10,3, (150000000)
  • 5.8 hr.

  • split: 11
  • 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)
    • s11.1006-1062 (3.4 GB)
  • param: see file names below
  • 10.0 hr.

  • Group Alphabetically
  • 3-gram (unique): 1,117,801,654

  • Files:
    • g01.NO-M (4.7GB|197MB)
    • g02.M-b (4.7GB|187MB)
    • g03.b-fn (4.6GB|173MB)
    • g04.fn-n (4.6GB|177MB)
    • g05.n-sh (5.0GB|190MB)
    • g06.sh-NO (4.9B|191MB)
  • param: 12, 3, 30
  • 20 min.

  • 3-gram (WC >= 30): 10,327,977

  • File:
    • 3-gram.${YEAR}.30 (265 MB)
  • param: 13, 3, 30
  • 2 min.

  • 3-gram (sorted): 10,327,977

  • File:
    • 3-gram.${YEAR}.30.dwt (265 MB)
fourgramsn=425 hr. 
  • param: 10,4, (130000000)
  • 5.4 hr.

  • split: 21
  • 4-gram (not unique - from log.heap.4.50): 2,752,252,637

  • 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)
    • s21.1031-1062 (3.7 GB)
  • param: see file names below
  • 18.7 hr.

  • Group Alphabetically
  • 4-gram (unique): 2,093,669,210

  • Files:
    • g01.NO-C (4.9GB|171MB)
    • g02.C-S (5.1GB|165MB)
    • g03.S-and (4.9GB|160MB)
    • g04.and-bcm (3.9GB|128MB)
    • g05.bcm-cs (5.2GB|164MB)
    • g06.cs-f (4.6GB|140MB)
    • g07.f-i (4.3GB|138MB)
    • g08.i-j (3.6GB|115MB)
    • g09.j-o (4.9GB|154MB)
    • g10.o-pe (4.6GB|157MB)
    • g11.pe-ri (5.0GB|153MB)
    • g12.ri-th (4.5GB|141MB)
    • g13.th-tr (4.5GB|153MB)
    • g14.tr-NO (4.5GB|148MB)
  • param: 12, 4, 30
  • 52 min.

  • 4-gram (WC >= 30): 6,620,884

  • File:
    • 4-gram.${YEAR}.30 (201 MB)
  • param: 13, 4, 30
  • 2 min.

  • 4-gram (sorted): 6,620,884

  • File:
    • 4-gram.${YEAR}.30.dwt (201 MB)
fivegramsn=536.7 hr. 
  • param: 10,5, (120000000)
  • 6.0 hr.

  • split: 25
  • 5-gram (not unique): 3,158,816,663

    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)
    • s23.0951-0980 (4.5 GB)
    • s24.0981-1008 (4.4 GB)
    • s25.1009-1036 (4.4 GB)
    • s26.1037-1062 (4.1 GB)
  • param: see file names below
  • 29.4 hr.

  • Group Alphabetically
  • 5-gram (unique): 2,729,911,636

  • Files:
    • g01.NO-A (4.9GB|148MB)
    • g02.A-I (4.7GB|128MB)
    • g03.I-T (4.7GB|128MB)
    • g04.T-a (2.6GB|69MB)
    • g05.a-am (3.8GB|104)
    • g06.am-ao (4.6GB|128MB)
    • g07.ao-c (5.1GB|142MB)
    • g08.c-ct (5.4GB|140)
    • g09.ct-em (4.7GB|123MB)
    • g10.em-ft (5.2GB|140MB)
    • g11.ft-in (4.3GB|112MB)
    • g12.in-io (4.4GB|119MB)
    • g13.io-mj (5.2GB|143MB)
    • g14.mj-of (3.2GB|85MB)
    • g15.of-og (4.2GB|124MB)
    • g16.og-pm (4.3GB|115MB)
    • g17.pm-rem (4.9GB|127MB)
    • g18.rem-sp (4.6GB|121MB)
    • g19.sp-the (4.4GB|118MB)
    • g20.the-thf (4.5GB|128MB)
    • g21.thf-v (4.8GB|133MB)
    • g22.v-NO (5.1GB|144MB)
  • param: 12, 5, 30
  • 1.2 hr.

  • 5-gram (WC >= 30): 2,875,651

  • File:
    • 5-gram.${YEAR}.30 (102 MB)
  • param: 13, 5, 30
  • 2 min.

  • 5-gram (sorted): 2,875,651

  • File:
    • 5-gram.${YEAR}.30.dwt (102 MB)