------------------------------------------------------------- index.script Sat 19 Mar 2022 01:31:28 PM EDT SETTINGS -------- ---------------- General settings ---------------- Compile: yes SQL: no zipf: no kwic: no discrim: no proximity: no doc doc matrix: yes document cluster: yes tt_correlations: Database name not given - default osu database used -------------------------- DocumentTermMarix settings -------------------------- Max Number of Docs: 5000 Words must be longer than: 4 Kill docs with fewer than 20 words A word must appear at least: 5 times in the collection A word must appear in at least 5 separate docs A word may appear in no more than: 1250 docs ----------------------------------- Inverse Document Frequency settings ----------------------------------- Delete words with IDF value less than: 4. Delete docs after IDF with fewer than 5 words ---------------------- Document weights ---------------------- delete words with weight less than 10 delete documents with fewer than 5 ------------------------- Term-Term matrix settings ------------------------- Related terms must have this correlation: 0.250 Min co-occurances for term-term matrix: 3 ------------------------- Proximity matrix settings ------------------------- Proximity matrix min count: 20 --------------------------------- Document-document matrix settings --------------------------------- Doc Words in common for inclusion: 5 Min doc-doc matrix cosine: 0.25 -------------------------- Jaccard term-term settings -------------------------- Jaccard minimum:$ jaccard_min ------------------ Clusterdd settings ------------------ Minimu doc-doc cosine: 0.25 --------------------- Hypercluster settings --------------------- Hyper cluser min cosine: .3 ------------------------- Term-term cluster settings ------------------------- Min term-term cluster correlation: .1 ----------------------------------------------------------------------- ---> make modules to be compiled: make: Nothing to be done for 'isr'. ------------------------------------------------------------------------- map osu.medline ------------------------------------------------------------------------- titles.list (5000) ------------------------------------------------------------------------- reformat min_word_length=4 osu.medline osu.converted ------------------------------------------------------------------------- osu.converted (4999) stem-words.tmp (303748) wordlist.tmp (34960) elapsed time 6 ------------------------------------------------------------------------- Stemmed Vocabulary ------------------------------------------------------------------------- stemmed-vocabulary.tmp (20601) ------------------------------------------------------------------------- FrequencyFilter min_collection_word_count=5 max_collection_word_count=1250 ------------------------------------------------------------------------- deleted-words-for-frequency.txt (13847) stop.words (13847) elapsed time 6 ------------------------------------------------------------------------- loadTitles ------------------------------------------------------------------------- titles.list (5000) elapsed time 6 ------------------------------------------------------------------------- DocumentTermMatrix min_doc_vector_word_count=20 min_doc_word_count=5 ------------------------------------------------------------------------- document-term-matrix.txt (37928) dict.tmp (266211) doc.tmp (266211) dict.sorted.tmp (6754) doc.sorted.tmp (172101) df.tmp (162142) df.sorted.tmp (6747) DocCount (1) term-frequencies.unsorted.tmp (4748) term-frequencies.txt (4748) Document count after deletion of documents with fewer than 20 words: 3180 elapsed time 40 ------------------------------------------------------------------------- idf min_idf=4 ------------------------------------------------------------------------- elapsed time 40 ------------------------------------------------------------------------- idf-cutoff min_idf_vector_count=5 ------------------------------------------------------------------------- Delete words whose IDF value is less than 4. Delete documents with fewer than 5 words IDF total docs deleted: 0 IDF remaining documents: 3180 IDF number of words remaining: 4618 idf-deleted-documents.txt (0) idf-deleted-words.txt (130) Document count after removal of low IDF words: 3180 idf-weights.sorted.txt (4618) High IDF: 9.313 xlink Low IDF: 4.005 examination elapsed time 45 ------------------------------------------------------------------------- weight.mps ------------------------------------------------------------------------- 88194 document word instances with weight < 10 deleted 590 docs with less than 5 words deleted document-term-matrix-weighted.txt (9540) term-document-matrix-weighted.txt (3952) elapsed time 154 ------------------------------------------------------------------------- soundex ------------------------------------------------------------------------- soundex.txt (3412) elapsed time 155 ------------------------------------------------------------------------- docdoc1 min_doc_doc_cooccur=5 min_dd_cosine=0.25 ------------------------------------------------------------------------- docdoc.txt (372) elapsed time 159 ------------------------------------------------------------------------- clusterdd min_cluster_cosine=0.25 ------------------------------------------------------------------------- document-clusters.txt (1457) document-clusters-by-title.txt (480) elapsed time 164 ------------------------------------------------------------------------- hypercluster hyper_min=.3 hyper_wgt=.3 ------------------------------------------------------------------------- hyperclusters.txt (441) elapsed time 397 ------------------------------------------------------------------------- medlineRetrieve ------------------------------------------------------------------------- query term: bile Words in this stem group are: bile adding related phrase words: none words that may sound similar to bile: none 20 documents found. Doc Rel Title 560 0.723 Effect of bile acids on hepatic protoporphyrin metabolism in perfused ... matched keys: bile 561 0.700 Modulation of bile secretion by hepatic low-density lipoprotein uptake ... matched keys: bile 3673 0.681 Effects of partial ileocolectomy and Crohn's disease on biliary lipid ... matched keys: bile 3779 0.601 75Se HCAT test in the detection of bile acid malabsorption in function ... matched keys: bile 2132 0.593 Bile acids in radiation-induced diarrhea. ... matched keys: bile 3627 0.564 Serum bile acid profile in thyroid dysfunction and effect of medical t ... matched keys: bile 557 0.493 Antroduodenal resistance to flow in the control of duodenogastric bile ... matched keys: bile 110 0.483 Loss of substance in bile ducts treated by a new surgical endoprosthes ... matched keys: bile 3620 0.476 Bile acid binding to dietary casein: a study in vitro and in vivo. ... matched keys: bile 1018 0.468 Absorption of biliary calcium from the canine gallbladder: protection ... matched keys: bile *Time used: 0 seconds elapsed time 397