move word features in python code

pubmed-word-features.txt

@@ -1,501 +0,0 @@
-w-rat
-w-common
-w-use
-w-examin
-w-pathogenesi
-w-retinopathi
-w-mous
-w-studi
-w-anim
-w-model
-w-metabol
-w-abnorm
-w-contribut
-w-develop
-w-investig
-w-mice
-w-2
-w-month
-w-compar
-w-obtain
-w-method
-w-induc
-w-6
-w-inject
-w-experiment
-w-normal
-w-diet
-w-30
-w-hyperglycemia
-w-level
-w-lipid
-w-oxid
-w-activ
-w-protein
-w-kinas
-w-c
-w-measur
-w-result
-w-increas
-w-retin
-w-stress
-w-3
-w-similar
-w-observ
-w-conclus
-w-play
-w-import
-w-role
-w-present
-w-p
-w-m
-w-r
-w-muscl
-w-control
-w-chang
-w-dure
-w-lower
-w-higher
-w-mass
-w-correl
-w-decreas
-w-determin
-w-concentr
-w-stimul
-w-period
-w-caus
-w-mark
-w-group
-w-evid
-w-fast
-w-type
-w-signific
-w-differ
-w-ratio
-w-suggest
-w-degre
-w-occur
-w-vivo
-w-respect
-w-dysfunct
-w-region
-w-high
-w-appear
-w-sever
-w-affect
-w-cardiovascular
-w-complic
-w-primari
-w-death
-w-patient
-w-clinic
-w-suscept
-w-cardiac
-w-tissu
-w-specif
-w-function
-w-defect
-w-possibl
-w-indic
-w-state
-w-onli
-w-bodi
-w-weight
-w-loss
-w-valu
-w-howev
-w-4
-w-condit
-w-durat
-w-8
-w-week
-w-onset
-w-data
-w-direct
-w-report
-w-provid
-w-addit
-w-evalu
-w-sensit
-w-heart
-w-object
-w-mean
-w-blood
-w-glucos
-w-strong
-w-hba
-w-1c
-w-a1c
-w-variabl
-w-independ
-w-assess
-w-relat
-w-trial
-w-research
-w-design
-w-profil
-w-sampl
-w-particip
-w-n
-w-1
-w-consist
-w-befor
-w-min
-w-predict
-w-adjust
-w-sex
-w-treatment
-w-7
-w-gt
-w-0
-w-larg
-w-influenc
-w-base
-w-standard
-w-14
-w-10
-w-wherea
-w-enhanc
-w-manag
-w-day
-w-secret
-w-cholesterol
-w-insulin
-w-24
-w-h
-w-low
-w-rate
-w-fatti
-w-acid
-w-effect
-w-hormon
-w-hepat
-w-contrast
-w-product
-w-major
-w-plasma
-w-current
-w-flow
-w-chronic
-w-mechan
-w-test
-w-therefor
-w-analys
-w-mrna
-w-streptozotocin
-w-did
-w-15
-w-g
-w-25
-w-mmol
-w-l
-w-5
-w-reduc
-w-number
-w-densiti
-w-posit
-w-cell
-w-17
-w-mm
-w-18
-w-induct
-w-associ
-w-express
-w-glycem
-w-respons
-w-therapi
-w-random
-w-initi
-w-ani
-w-singl
-w-new
-w-agent
-w-metformin
-w-medic
-w-glycosyl
-w-hemoglobin
-w-analysi
-w-baselin
-w-health
-w-factor
-w-process
-w-care
-w-9
-w-01
-w-95
-w-interv
-w-ci
-w-12
-w-reduct
-w-achiev
-w-target
-w-lt
-w-diseas
-w-class
-w-age
-w-obes
-w-renal
-w-improv
-w-progress
-w-noninsulindepend
-w-mellitus
-w-becaus
-w-s
-w-index
-w-hypertens
-w-need
-w-followup
-w-year
-w-mg
-w-dl
-w-remain
-w-subject
-w-treat
-w-oral
-w-requir
-w-0001
-w-mortal
-w-includ
-w-vs
-w-background
-w-poor
-w-drug
-w-13
-w-rang
-w-combin
-w-intervent
-w-daili
-w-dose
-w-100
-w-toler
-w-receiv
-w-11
-w-postprandi
-w-kg
-w-hypoglycemia
-w-frequent
-w-event
-w-versus
-w-symptom
-w-incid
-w-parent
-w-complex
-w-longterm
-w-inhibitor
-w-peripher
-w-nerv
-w-stz
-w-conduct
-w-demonstr
-w-frequenc
-w-inhibit
-w-neuropathi
-w-pathway
-w-shown
-w-time
-w-ii
-w-individu
-w-adult
-w-50
-w-60
-w-diagnosi
-w-healthi
-w-follow
-w-young
-w-seen
-w-alter
-w-gene
-w-e
-w-identifi
-w-previous
-w-mediat
-w-vascular
-w-lipoprotein
-w-involv
-w-phenotyp
-w-confirm
-w-variant
-w-endotheli
-w-potenti
-w-disord
-w-popul
-w-nonobes
-w-aim
-w-serum
-w-hba1c
-w-hypoglycaemia
-w-continu
-w-case
-w-impair
-w-risk
-w-known
-w-men
-w-women
-w-40
-w-complet
-w-estim
-w-like
-w-particular
-w-human
-w-character
-w-elev
-w-synthesi
-w-greater
-w-small
-w-reveal
-w-liver
-w-niddm
-w-genet
-w-receptor
-w-growth
-w-pancreat
-w-betacel
-w-molecul
-w-enzym
-w-regul
-w-polymorph
-w-total
-w-allel
-w-02
-w-resist
-w-cpeptid
-w-hypothesi
-w-perform
-w-score
-w-001
-w-05
-w-histori
-w-action
-w-approxim
-w-suppress
-w-glucagon
-w-ml
-w-x
-w-free
-w-peopl
-w-uptak
-w-intens
-w-relationship
-w-prevent
-w-autoimmun
-w-recent
-w-preval
-w-nondiabet
-w-genotyp
-w-conclud
-w-linkag
-w-islet
-w-peptid
-w-form
-w-membran
-w-transgen
-w-failur
-w-isol
-w-negat
-w-earli
-w-famili
-w-chromosom
-w-immun
-w-support
-w-16
-w-cohort
-w-insulindepend
-w-outcom
-w-screen
-w-approach
-w-infus
-w-multipl
-w-depend
-w-physic
-w-transport
-w-acut
-w-releas
-w-presenc
-w-glycaem
-w-male
-w-antibodi
-w-femal
-w-pattern
-w-t2dm
-w-promot
-w-fat
-w-d
-w-bmi
-w-haplotyp
-w-triglycerid
-w-interact
-w-marker
-w-describ
-w-area
-w-20
-w-cytokin
-w-bind
-w-bb
-w-alpha
-w-beta
-w-cd4
-w-spontan
-w-given
-w-vitro
-w-basal
-w-protect
-w-pressur
-w-detect
-w-exercis
-w-children
-w-adolesc
-w-life
-w-b
-w-antigen
-w-iddm
-w-american
-w-hla
-w-arteri
-w-nephropathi
-w-review
-w-destruct
-w-content
-w-autoantibodi
-w-dm
-w-select
-w-infect
-w-recipi
-w-intak
-w-placebo
-w-db
-w-pancrea
-w-diagnos
-w-glomerular
-w-albumin
-w-excret
-w-syndrom
-w-t
-w-lymphocyt
-w-produc
-w-coronari
-w-status
-w-microalbuminuria
-w-nod
-w-mhc
-w-insul
-w-administr
-w-revers
-w-transplant
-w-graft
-w-t1d
-w-lead
-w-v
-w-dietari
-w-general
-w-macrophag
-w-kidney
-w-urinari
-w-myocardi
-w-meal
-w-ica
-w-locus
-w-tcell
-w-depress
-w-bone
-w-mutat
-summary

pubmed.py

@@ -52,6 +52,9 @@ _CLASS_LABELS = [
     "Diabetes Mellitus Type 2"
 ]
 
+_WORD_FEATURES = ["w-rat", "w-common", "w-use", "w-examin", "w-pathogenesi", "w-retinopathi", "w-mous", "w-studi", "w-anim", "w-model", "w-metabol", "w-abnorm", "w-contribut", "w-develop", "w-investig", "w-mice", "w-2", "w-month", "w-compar", "w-obtain", "w-method", "w-induc", "w-6", "w-inject", "w-experiment", "w-normal", "w-diet", "w-30", "w-hyperglycemia", "w-level", "w-lipid", "w-oxid", "w-activ", "w-protein", "w-kinas", "w-c", "w-measur", "w-result", "w-increas", "w-retin", "w-stress", "w-3", "w-similar", "w-observ", "w-conclus", "w-play", "w-import", "w-role", "w-present", "w-p", "w-m", "w-r", "w-muscl", "w-control", "w-chang", "w-dure", "w-lower", "w-higher", "w-mass", "w-correl", "w-decreas", "w-determin", "w-concentr", "w-stimul", "w-period", "w-caus", "w-mark", "w-group", "w-evid", "w-fast", "w-type", "w-signific", "w-differ", "w-ratio", "w-suggest", "w-degre", "w-occur", "w-vivo", "w-respect", "w-dysfunct", "w-region", "w-high", "w-appear", "w-sever", "w-affect", "w-cardiovascular", "w-complic", "w-primari", "w-death", "w-patient", "w-clinic", "w-suscept", "w-cardiac", "w-tissu", "w-specif", "w-function", "w-defect", "w-possibl", "w-indic", "w-state", "w-onli", "w-bodi", "w-weight", "w-loss", "w-valu", "w-howev", "w-4", "w-condit", "w-durat", "w-8", "w-week", "w-onset", "w-data", "w-direct", "w-report", "w-provid", "w-addit", "w-evalu", "w-sensit", "w-heart", "w-object", "w-mean", "w-blood", "w-glucos", "w-strong", "w-hba", "w-1c", "w-a1c", "w-variabl", "w-independ", "w-assess", "w-relat", "w-trial", "w-research", "w-design", "w-profil", "w-sampl", "w-particip", "w-n", "w-1", "w-consist", "w-befor", "w-min", "w-predict", "w-adjust", "w-sex", "w-treatment", "w-7", "w-gt", "w-0", "w-larg", "w-influenc", "w-base", "w-standard", "w-14", "w-10", "w-wherea", "w-enhanc", "w-manag", "w-day", "w-secret", "w-cholesterol", "w-insulin", "w-24", "w-h", "w-low", "w-rate", "w-fatti", "w-acid", "w-effect", "w-hormon", "w-hepat", "w-contrast", "w-product", "w-major", "w-plasma", "w-current", "w-flow", "w-chronic", "w-mechan", "w-test", "w-therefor", "w-analys", "w-mrna", "w-streptozotocin", "w-did", "w-15", "w-g", "w-25", "w-mmol", "w-l", "w-5", "w-reduc", "w-number", "w-densiti", "w-posit", "w-cell", "w-17", "w-mm", "w-18", "w-induct", "w-associ", "w-express", "w-glycem", "w-respons", "w-therapi", "w-random", "w-initi", "w-ani", "w-singl", "w-new", "w-agent", "w-metformin", "w-medic", "w-glycosyl", "w-hemoglobin", "w-analysi", "w-baselin", "w-health", "w-factor", "w-process", "w-care", "w-9", "w-01", "w-95", "w-interv", "w-ci", "w-12", "w-reduct", "w-achiev", "w-target", "w-lt", "w-diseas", "w-class", "w-age", "w-obes", "w-renal", "w-improv", "w-progress", "w-noninsulindepend", "w-mellitus", "w-becaus", "w-s", "w-index", "w-hypertens", "w-need", "w-followup", "w-year", "w-mg", "w-dl", "w-remain", "w-subject", "w-treat", "w-oral", "w-requir", "w-0001", "w-mortal", "w-includ", "w-vs", "w-background", "w-poor", "w-drug", "w-13", "w-rang", "w-combin", "w-intervent", "w-daili", "w-dose", "w-100", "w-toler", "w-receiv", "w-11", "w-postprandi", "w-kg", "w-hypoglycemia", "w-frequent", "w-event", "w-versus", "w-symptom", "w-incid", "w-parent", "w-complex", "w-longterm", "w-inhibitor", "w-peripher", "w-nerv", "w-stz", "w-conduct", "w-demonstr", "w-frequenc", "w-inhibit", "w-neuropathi", "w-pathway", "w-shown", "w-time", "w-ii", "w-individu", "w-adult", "w-50", "w-60", "w-diagnosi", "w-healthi", "w-follow", "w-young", "w-seen", "w-alter", "w-gene", "w-e", "w-identifi", "w-previous", "w-mediat", "w-vascular", "w-lipoprotein", "w-involv", "w-phenotyp", "w-confirm", "w-variant", "w-endotheli", "w-potenti", "w-disord", "w-popul", "w-nonobes", "w-aim", "w-serum", "w-hba1c", "w-hypoglycaemia", "w-continu", "w-case", "w-impair", "w-risk", "w-known", "w-men", "w-women", "w-40", "w-complet", "w-estim", "w-like", "w-particular", "w-human", "w-character", "w-elev", "w-synthesi", "w-greater", "w-small", "w-reveal", "w-liver", "w-niddm", "w-genet", "w-receptor", "w-growth", "w-pancreat", "w-betacel", "w-molecul", "w-enzym", "w-regul", "w-polymorph", "w-total", "w-allel", "w-02", "w-resist", "w-cpeptid", "w-hypothesi", "w-perform", "w-score", "w-001", "w-05", "w-histori", "w-action", "w-approxim", "w-suppress", "w-glucagon", "w-ml", "w-x", "w-free", "w-peopl", "w-uptak", "w-intens", "w-relationship", "w-prevent", "w-autoimmun", "w-recent", "w-preval", "w-nondiabet", "w-genotyp", "w-conclud", "w-linkag", "w-islet", "w-peptid", "w-form", "w-membran", "w-transgen", "w-failur", "w-isol", "w-negat", "w-earli", "w-famili", "w-chromosom", "w-immun", "w-support", "w-16", "w-cohort", "w-insulindepend", "w-outcom", "w-screen", "w-approach", "w-infus", "w-multipl", "w-depend", "w-physic", "w-transport", "w-acut", "w-releas", "w-presenc", "w-glycaem", "w-male", "w-antibodi", "w-femal", "w-pattern", "w-t2dm", "w-promot", "w-fat", "w-d", "w-bmi", "w-haplotyp", "w-triglycerid", "w-interact", "w-marker", "w-describ", "w-area", "w-20", "w-cytokin", "w-bind", "w-bb", "w-alpha", "w-beta", "w-cd4", "w-spontan", "w-given", "w-vitro", "w-basal", "w-protect", "w-pressur", "w-detect", "w-exercis", "w-children", "w-adolesc", "w-life", "w-b", "w-antigen", "w-iddm", "w-american", "w-hla", "w-arteri", "w-nephropathi", "w-review", "w-destruct", "w-content", "w-autoantibodi", "w-dm", "w-select", "w-infect", "w-recipi", "w-intak", "w-placebo", "w-db", "w-pancrea", "w-diagnos", "w-glomerular", "w-albumin", "w-excret", "w-syndrom", "w-t", "w-lymphocyt", "w-produc", "w-coronari", "w-status", "w-microalbuminuria", "w-nod", "w-mhc", "w-insul", "w-administr", "w-revers", "w-transplant", "w-graft", "w-t1d", "w-lead", "w-v", "w-dietari", "w-general", "w-macrophag", "w-kidney", "w-urinari", "w-myocardi", "w-meal", "w-ica", "w-locus", "w-tcell", "w-depress", "w-bone", "w-mutat"
+                  ]
+
 
 # TODO: Name of the dataset usually match the script name with CamelCase instead of snake_case
 class PubmedDataset(datasets.GeneratorBasedBuilder):
@@ -80,12 +83,9 @@ class PubmedDataset(datasets.GeneratorBasedBuilder):
 
     def _info(self):
         if self.config.name == "nodes":
-            with open("pubmed-word-features.txt", "rt", encoding="UTF-8") as f:
-                word_features = f.read().split("\n")
-
             features_dict = {
                 w: datasets.Value("float32")
-                for w in word_features
+                for w in _WORD_FEATURES
             }
             features_dict["node"] = datasets.Value("string")
             features_dict["label"] = datasets.ClassLabel(names=_CLASS_LABELS)
@@ -165,9 +165,6 @@ class PubmedDataset(datasets.GeneratorBasedBuilder):
                             neighbors[n] = []
                     neighbors[src].append(target)
 
-            with open("pubmed-word-features.txt", "rt", encoding="UTF-8") as f:
-                word_features = f.read().split("\n")
-
             def _word_feature_tuple(x):
                 w, v = x.split("=")
                 return (w, float(v))
@@ -184,7 +181,7 @@ class PubmedDataset(datasets.GeneratorBasedBuilder):
                     w_features = dict(map(_word_feature_tuple, row[2:-1]))
                     features = {"node": node, "label": label,
                                 "neighbors": neighbors[node]}
-                    for x in word_features:
+                    for x in _WORD_FEATURES:
                         features[x] = w_features.get(x, 0.0)
                     yield id, features