The SPECIALIST Lexicon

The MEDLINE.2023 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. 2023 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 (~400 files/hr).
  • PmidTiAbS22n: 0001-1166
    
unigramsn=1< 1.0 hr.
(from ./bin/02.NGramGenAll/logData/${YEAR}/N-gram/*.log)		 
  • param: 10,1, (150000000)
  • 45 min.


    from ./bin/Log.${YER}/02-NGramGen/log.heap.1.50:

  • Documents: 34,960,700
  • Sentences: 238,939,832
  • Tokens: 5,001,000,732

  • split: 1, no split
  • 1-grams (not unique, from log.heap.1.50): 41,049,611
    (it is unique beacuse no split, use wc -l)

  • Files:
    • nGram.out.1.heap.50.s01.0001-1166 (673 MB, use ls -alh)
  • param:
    • 11,1,01,NO,NO
  • 2 min.

  • Group Alphabetically
  • 1-gram (unique): 41,049,611

  • Files:
    • ${NGram}.g01.NO-NO (673 MB|41MB, from ./logData/${YEAR}/1-gram/11-1.log)
  • param: 12, 1, 30
  • 1 min

  • 1-gram (WC >= 30): 1,311,936

  • File:
    • 1-gram.${YEAR}.30 (22 MB)
  • param: 13, 1, 30
  • 1 min.

  • 1-gram (sorted): 1,311,936

  • File:
    • 1-gram.${YEAR}.30.dwt (22 MB)
bigramsn=23.5 hr. 
  • param: 10,2, (150000000)
  • 2.5 hr.

  • split: 4
  • 2-gram (not unique from log.heap.2.50): 477,925,459

  • Files:
    • s01.0001-0583 (3.1 GB)
    • s02.0584-0890 (3.0 GB)
    • s03.0891-1140 (3.1 GB)
    • s02.1141-1166 (537M)
  • 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): 365,653,326

  • Files:
    • ${NGram}.g01.NO-M (2.0GB|106MB)
    • ${NGram}.g02.M-k (3.0GB|142MB)
    • ${NGram}.g03.k-NO (2.5GB|116MB)
  • param: 12, 2, 30
  • 7 min.

  • 2-gram (WC >= 30): 7,943,407

  • File:
    • 2-gram.${YEAR}.30 (170 MB)
  • param: 13, 2, 30
  • 2 min.

  • 2-gram (sorted): 7,943,407

  • File:
    • 2-gram.${YEAR}.30.dwt (170 MB)
trigramsn=313 hr. 
  • param: 10,3, (150000000)
  • 4.2 hr.

  • split: 14
  • 3-gram (not unique - from log.heap.3.50): 1,922,187,885

  • Files:
    • s01.0001-0151 (3.5 GB)
    • s02.0152-0309 (3.5 GB)
    • s03.0310-0400 (3.5 GB)
    • s04.0401-0532 (3.5 GB)
    • s05.0533-0614 (3.5 GB)
    • s06.0615-0692 (3.5 GB)
    • s07.0693-0760 (3.5 GB)
    • s08.0761-0826 (3.5 GB)
    • s09.0827-0890 (3.5 GB)
    • s10.0891-0954 (3.6 GB)
    • s11.0955-1014 (3.5 GB)
    • s12.1015-1073 (3.5 GB)
    • s13.1074-1131 (3.5 GB)
    • s14.1132-1166 (2.3 GB)
  • param: see file names below
  • 8.0 hr.

  • Group Alphabetically
  • 3-gram (unique wc -l): 1,260,314,546

  • Files:
    • g01.NO-E (4.1GB|175MB)
    • g02.E-Z (3.6GB|145MB)
    • g03.Z-c (3.9GB|151MB)
    • g04.c-f (4.0GB|146MB)
    • g05.f-j (3.7GB|140MB)
    • g06.j-o (2.5GB|93MB)
    • g07.o-r (3.5GB|133MB)
    • g08.r-th (3.2GB|120MB)
    • g09.th-NO (3.8GB|153MB)
  • param: 12, 3, 30
  • 30 min.

  • 3-gram (WC >= 30): 11,773,385

  • File:
    • 3-gram.${YEAR}.30 (303 MB)
  • param: 13, 3, 30
  • 2 min.

  • 3-gram (sorted): 11,773,385

  • File:
    • 3-gram.${YEAR}.30.dwt (303 MB)
fourgramsn=431 hr. 
  • param: 10,4, (130000000)
  • 5.5 hr.

  • split: 25
  • 4-gram (not unique - from log.heap.4.50): 3,156,725,405

  • 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)
    • s23.1100-1132 (4.0 GB)
    • S24.1132-1166 (4.0 GB)
    • S25.1132-1166 (0.0)
  • param: see file names below
  • 25 hr.

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

  • Files:
    • g01.NO-9 (4.1GB|148MB)
    • g02.9-I (4.2GB|136MB)
    • g03.I-T (3.9GB|126MB)
    • g04.T-am (4.4GB|143MB)
    • g05.am-at (4.3GB|141MB)
    • g06.at-c (2.5GB|81MB)
    • g07.c-d (4.3GB|132MB)
    • g08.d-es (3.9GB|119MB)
    • g09.es-h (4.5GB|142MB)
    • g10.h-ini (4.2GB|132MB)
    • g11.ini-m (2.9GB|92MB)
    • g12.m-o (4.0GB|124MB)
    • g13.o-p (4.4GB|150MB)
    • g14.p-r (4.2GB|126MB)
    • g15.r-sh (3.6GB|113MB)
    • g16.sh-th (3.8GB|119MB)
    • g17.th-to (3.9GB|130MB)
    • g17.to-v (2.9GB|94MB)
    • g19.v-NO (3.5GB|115MB)
  • param: 12, 4, 30
  • 30 min.

  • 4-gram (WC >= 30): 7,677,188

  • File:
    • 4-gram.${YEAR}.30 (234 MB)
  • param: 13, 4, 30
  • 2 min.

  • 4-gram (sorted): 7,677,188

  • File:
    • 4-gram.${YEAR}.30.dwt (234 MB)
fivegramsn=537.5 hr. 
  • param: 10,5, (120000000)
  • 4.0 hr.

  • split: 30
  • 5-gram (not unique): 3,620,801,104

    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)
    • s26.1037-1064 (4.5 GB)
    • s27.1065-1092 (4.5 GB)
    • s28.1093-1119 (4.4 GB)
    • s29.1120-1146 (4.4 GB)
    • s30.1147-1166 (3.2 GB)
  • param: see file names below
  • 40.5 hr.

  • Group Alphabetically
  • 5-gram (unique): 3,108,592,548

  • Files:
    • g01.NO-4 (5.0GB|133MB)
    • g02.4-D (4.3GB|121MB)
    • g03.D-M (3.9GB|105MB)
    • g04.M-T (4.1GB|109MB)
    • g05.T-a (2.9GB|79MB)
    • g06.a-am (4.3GB|118MB)
    • g07.am-ann (4.9GB|136MB)
    • g08.ann-bo (4.8GB|131MB)
    • g09.bo-ch (3.1GB|84MB)
    • g10.ch-ct (4.5GB|114MB)
    • g11.ct-ef (4.7GB|122MB)
    • g12.ef-for (4.7GB|121MB)
    • g13.for-h (3.7GB|102MB)
    • g14.h-in (3.2GB|82MB)
    • g15.in-io (4.9GB|134MB)
    • g16.io-me (4.3GB|118MB)
    • g17.me-mm (1.7GB|44MB)
    • g18.mm-of (3.6GB|96MB)
    • g19.of-og (4.7GB|139MB)
    • g20.og-pl (4.6GB|124MB)
    • g21.pl-re (4.4GB|114MB)
    • g22.re-s (3.4GB|89MB)
    • g23.s-st (3.8GB|99MB)
    • g24.st-the (4.5GB|122MB)
    • g25.the-then (4.7GB|132MB)
    • g26.then-un (4.9GB|135MB)
    • g27.un-w (2.3GB|60MB)
    • g28.w-NO (4.7GB|133MB)
  • param: 12, 5, 30
  • 1.2 hr.

  • 5-gram (WC >= 30): 3,401,145

  • File:
    • 5-gram.${YEAR}.30 (121 MB)
  • param: 13, 5, 30
  • 2 min.

  • 5-gram (sorted): 3,401,145

  • File:
    • 5-gram.${YEAR}.30.dwt (121 MB)