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Mixed-membership models of scientific publications
Mixed-membership models of scientific publications
Pages 38-45
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From page 38... ...
Department of Statistics, School of Social Work, and Center for Statistics and the Social Sciences, University of Washington, Seattle, WA 98195, and "Department of Statistics, Computer Science Department, and §Center for Automated Learning and Discovery, Carnegie Mellon University, Pittsburgh, PA 15213 PNAS is one of world's most cited multidisciplinary scientific journals. The PNAS official classification structure of subjects is reflected in topic labels submitted by the authors of articles, largely related to traditionally established disciplines.
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From page 39... ...
The probability distribution of observed responses Xj for each subject is defined fully by the conditional probability Pr~xj~A)
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From page 40... ...
The topic labels provide a classification structure for published materials, and most of the articles are members of only a single topic. For our mixed-membership model, we assume that there is a fixed number of extreme internal categories or aspects, each of which is characterized by multinomial distributions over words (in abstracts)
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From page 41... ...
The first aspect includes words such as ~: Ca2+, kinase, phosphorylation, receptor, and G (protein) chan- ~ v ~ Q ~ ° ~= O ~ ~ a' a; ~ a nel, which pertain to cell signaling and intracellular signal Q Q ~ ~ Q ~ :: ~s ~ a transduction.
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From page 42... ...
1992 BRADFORD MM ANAL BIOCHEM, 1976 MERRITT EA METHOD ENZYMOL, 1997 WUTHRICH K NMR PROTEINS NUCL AC, 1986 KABSCH W BIOPOLYMERS, 1983 202 174 140 118 96 85 81 764 322 66 48 209 41 40 39 Aspect 3 Aspect 4 Author Journal, Year C Author Journal, Year C SAMBROOK J MOL CLON'ING LAB MAN'U, 1989 764 HOGAN B MANIPULATING MOUSE E, i994 68 LAEMMLI UK NATURE, 1970 322 CHOMCZYNSKI P ANALBIOCHE'~, 1987 206 ALTSCHUL SF J MOL BIOL, 1990 253 TALAIRACH J COPLANAR STEREOTAXIC, 1988 60 BRADFORD MM ANAL BIOCHEM, 1976 209 PAXINOS G RAT BRAIN STEREOTAXI, 1986 38 SANGER F P NATL ACAD SCI USA, 1977 140 SAMBROOK J MOL CLONING LAB MANU' 1989 764 MILLER JH EXPTMOLGENETICS, 1972 102 NAGYA PNATLACADSCIUSA, 1993 39 ALTSCHUL SF NUCLEIC ACIDS RES, 1997 160 MANSOUR SL NATURE' 1988 37 THOMPSON JD NUCLEIC ACIDS RES, 1994 147 BRAND AH DEVELOPMENT, 1993 46 CHOMCZYNSKI P ANAL BIOCHEM, 1987 206 HOGAN B MANIPULATING MOUSE E, 1986 32 HARLOW E ANTIBODIES LAB MANUA, 1988 129 TYBULEWICZ VLJ CELL, 1991 46 BLATTNER FR SCIENCE, 1997 56 KWONG KK P NATL ACAD SCI USA, 1992 24 SCHENA M SCIENCE, 1995 40 DUNLAP JC CELL, 1999 19 KYTE ~ J MOL BIOL, 1982 51 Ll E CELL, 1992 35 MU'RASHIGE T PHYSL PLANTARUM, 1962 33 ALTSCHUL SF J MOL BIOL, 1990 253 TOWBIN H P NATL ACAD SCI USA, 1979 86 EISEN MB P NATL ACAD SCI USA, 1998 60 Aspect 5 Aspect 6 Author Journal, Year C Author Journal, Year C SAMBROOK J MOL CLONING LAB MANU, 1989 SIKORS}C:I RS DIGNAM JD LEVINE AJ ELDEIRY WS HARLOW E HARPER ~W FRIEDBERG EC ALTSCHUL SF OGRYZKO W WEINBERG RA KAMEI Y HOLLSTEIN M FIELDS S YANG XJ GENETICS, 1989 NUCLEIC ACIDS RES, 1983 CELL, 1997 CELL, 1993 ANTIBODIES LAB MANUA, 1988 CELL, 1993 DNA REPAIR MUTAGENES, 1995 J MOL BIOL 1990 CELL, 1996 CELL, 1995 CELL 1996 SCIENCE, 1991 NATURE, 1989 NATURE, 1996 764 102 68 57 54 129 50 58 253 41 40 39 41 67 37 Aspect 7 Aspect 8 Author Jou~nal7 Year C Author Journal,Year C DENG HK NATURE, 1996 46 CHOMCZYNSKI P ANAL BIOCHEM, 1987 206 DRAGIC T NATURE, 1996 45 BRADFORD MM ANAL BIOCHEM, 1976 209 DORANZ BJ CELL, 1996 45 LAEMMLI UK NATURE, 1970 322 FENGY SCIENCE, 1996 43 LOWRY OH JBIOLCHEM, 1951 73 ALKHATIB G SCIENCE, 1996 43 ZHANG Y NATURE, 1994 31 COCCHI F SCIENCE, 1995 41 KUIPER GGJM P NATL ACAD SCI USA, 1996 27 CHOE H CELL, 1996 41 SAMBROOKJ MOL CLON LAB MANU, 1989 764 THOMPSON CB SCIENCE, 1995 38 MONCADA S PHARMACOLREV, 1991 25 ZOU H CELL, 1997 40 PELLEYMOUNTERMA SCIENCE, 1995 23 'DARNELL JE SCIENCE. 1994 40 CAMPFIELD LA SCIENCE, 1995 23 MUZIOM CELL, 1996 35 KUIPERGGJM ENDOCRINOLOGY, 1997 22 Ll P CELL, 1997 36 HALAAS JL SCIENCE, 1995 21 XIAZG SCIENCE, 1995 38 BLIGH EG CAN J BIOCH PHYSL, 1959 45 BOLDIN MP CELL, 1996 34 BROWN MS CELL, 1997 28 PEAR WS PNATL ACAD SCI USA 1993 57 ZHANG SH SCIENCE 1992 18 For each aspect, the top references are shown in order of decreasing probability, according to the model.
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Table 3 provides attributes of 15 high-probability references for each aspect that were available in the database together with PNAS citation counts (number of times cited by PNAS articles in the database)
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From page 44... ...
, together with a graphical representation of this table (Upper) Biochemistry Medical Sciences Neurobiology Cell Biology Genetics Immunology Biophysics Evolution Microbiology Plant Biology Developmental Biology Physiology Pharmacology Topic 1 , _ r _ 2 3 4 5 6 7 8 Biochemistry 0.0469 0.0347 0.1810 0.0178 0.3838 0.2057 0.0477 0.0823 Medical sciences 0.0244 0.0502 0.0938 0.1274 0.0181 0.1075 0.3286 0.2500 Neurobiology 0.2875 0.0398 0.0722 0.3768 0.0196 0.0296 0.0441 0.1304 Cell biology 0.1691 0.0165 0.1420 0.0684 0.1097 0.2423 0.1637 0.0884 Genetics 0.0141 0.3056 0.1422 0.1532 0.0487 0.2621 0.0395 0.0347 Immunology 0.0127 0.0593 0.1003 0.0413 0.0422 0.0915 0.6244 0.0283 Biophysics 0.0507 0.0295 0.2398 0.0162 0.5496 0.0542 0.0176 0.0423 Evolution 0.0042 0.7679 0.0465 0.0913 0.0289 0.0378 0.0101 0.0133 Microbiology 0.0158 0.1725 0.3431 0.0335 0.0647 0.1174 0.1870 0.0661 Plant biology 0.1333 0.0983 0.4400 0.0360 0.0462 0.0954 0.0166 0.1344 Developmental biology 0.0475 0.0288 0.1071 0.3729 0.0274 0.2558 0.0974 0.0631 Physiology 0.3179 0.0275 0.0712 0.1123 0.0258 0.0116 0.0595 0.3743 Pharmacology 0.2883 0.0161 0.0772 0.1965 0.0299 0.0349 0.0537 0.3033 For clarity, the six lowest-frequency topics, which make up 3.4% of the biological sciences articles, are not shown.
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From page 45... ...
For example, three biophysics dual-classified articles with loadings 0.9 for the second and 0.1 for the third aspect turned out to be similar to 86 singly classified articles from biophysics, biochemistry, cell biology, developmental biology, evolution, genetics, immunology, medical sciences, and microbiology. Concluding Remarks We have presented results from fitting a m~xed-membership model to PNAS biological sciences publications, from 1997 to 2001, providing an implicit semantic decomposition of words and references in the articles.
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