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Link to original content: https://unpaywall.org/10.1089/CMB.2018.0093
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[(events.)-371(For)-362(examp)-10.9(le,)-365(the)-359.7(BP)-369.7(term)-365.9(GO:0)-8(006874)-363.1(has)-369.5(the)-365.3(denition)-369()48.5(Any)-367.5(process)-371.8(involved)-366.2(in)-362.8(the)-365.3(maint)-9(e-)]TJ 0 -1.2007 TD [(nance)-282.3(of)-276.6(an)-282.2(intern)-8.2(al)-273.5(ste)-8(ady)-277.2(state)-281.6(of)-282.3(calcium)-281.5(ions)-280.1(at)-279.2(the)-280(leve)-9.4(l)-276.7(o)0(f)-276.6(a)-275.7(cel)-8.6(l.)50.3()-275.9(I)0(n)-282.3(each)-281.6(categor)-9.7(y,)-274.3(the)-280(GO)-282.5(terms)-282.5(are)]TJ T* [(organ)-7.6(ized)-293.9(into)-298.8(a)-292.8(tree)-295.9(whe)-8(re)-295.5(there)-296.7(is)-295.7(only)-296(one)]TJ /F6 1 Tf 18.4943 0 TD (root)Tj /F1 1 Tf 1.9632 0 TD [(node)-295.1(\(Gene)-303.5(Ontology)-300.1(Consorti)-8.1(um,)-295.7(2017\).)-296.4(In)-293.7(this)-294.3(tre)-8.8(e)-292.8(o)0(f)]TJ -20.4575 -1.2007 TD [(GO)-396.3(terms)-402(\(or)-398.9(GO)-396.3(tree\),)-401.4(a)-395.2(mor)-7.8(e)-395.2(generic)-402.4(term)-400.1(\(i.e.,)-402.6(lyase)-398.3(activit)-8.6(y\))-396.2(is)-398.1(closer)-401(to)-396.9(the)-393.8(root)-7.8(,)-393(wherea)-10.2(s)-394.6(a)-395.2(mor)-7.8(e)]TJ T* [(specic)-343.9(term)-337.5(\(i.e.,)-334.3(carb)-8.6(oxy-lyas)-8.1(e)-332.6(act)-8.6(ivity\))-333.5(is)-335.5(clos)-8.8(er)-335.3(to)-334.3(a)-332.6(leaf)-341.4(node.)]TJ 1.0015 -1.2007 TD [(Because)-314.3(there)-313.7(are)-315.1(three)-308(GO)-311(cat)-8.6(egories)-310.7(in)-311.6(the)-308.4(data)-9.4(base,)-309.8(there)-313.7(are)-309.4(thr)-7(ee)-306.7(GO)-311(trees.)-315.3(Intere)-9.2(stingly,)-311.1(there)-313.7(are)]TJ -1.0015 -1.2007 TD [(edges)-463.8(connec)-9.9(ting)-463.8(terms)-470.3(in)-459.5(differ)-9.4(ent)-462.1(GO)-464.6(trees)-468.6(\(Fig.)-462.6(1\).)-464.8(The)-464.8(GO)-464.6(database)-472.4(can)-466.8(be)-458.6(repr)-8.8(esented)-469.9(as)-459.7(thr)-7(ee)]TJ T* [(connec)-9.9(ted)-336.9(GO)-333.8(trees.)]TJ 1.0015 -1.195 TD [(One)-303.9(application)-309.3(of)-299.4(the)-302.7(GO)-305.3(database)-313.1(is)-301.4(the)-302.7(comparison)-310.9(of)-299.4(two)-304.9(genes)-304.5(by)-297.4(rst)-304.1(com)-7.6(paring)-307(the)-302.7(similarity)-308.8(of)]TJ -1.0015 -1.2007 TD [(the)-308.4(GO)-305.3(terms)-311(that)-312(annotate)-312.9(them)-307(\(Gene)-314.9(Ontology)-311.5(Consorti)-8.1(um,)-307(2017\).)-307.8(To)-308.6(this)-305.7(end,)-311.7(we)-303.2(need)-313.9(a)-304.2(good)-304.7(metri)-10.9(c)]TJ T* [(for)-239.6(comparing)-246.3(GO)-242.7(terms.)-243.1(To)-240.3(solve)-237.2(thi)-7.8(s)-235.3(problem)-9.7(,)-233.7(w)0(e)-240.6(need)-245.6(to)-237.6(focus)-242.1(on)-234.8(the)-240.2(GO)-242.7(trees)-240.9(and)-243.1(the)-240.2(deni)-7.6(tions)-238.2(of)-236.8(GO)]TJ T* [(terms.)-260.1(Because)-257.4(of)-253.9(the)-257.2(GO)-254.1(trees,)-258.4(GO)-254.1(terms)-259.7(with)-257.2(a)-252.9(direct)-254.7(ances)-10.4(tor)-251.7(\(i.e.,)-254.7(sibli)-7.6(ng)-251.9(nodes\))-259.9(are)-252.5(deem)-10.2(ed)-253.7(to)-249(be)-253.7(mor)-7.8(e)]TJ T* [(related)-245.8(than)-240.9(GO)-237(terms)-242.7(with)-240.1(a)-235.9(distal)-243.5(ancestor)-11.7(.)-233.7(More)-8.8(over,)-240.5(because)-241.3(of)-242.5(this)-237.4(design,)-244(existing)-239.3(method)-12.6(s)-235.3(t)0(o)-237.6(measur)-9.1(e)]TJ T* [(the)-285.7(similarity)-286(of)-282.3(two)-287.8(GO)-282.5(terms)-288.2(mostly)-288(rely)-282.7(on)-280.4(the)-285.7(GO)-282.5(trees)-286.5(\()-88.1(Mazandu)-291.5(et)-279.2(al.,)-285.7(2017\).)-285(Very)-283.9(few)-288.8(studies)-288.2(have)]TJ T* [(yet)-336.9(to)-334.3(directly)-338.6(com)-7.6(pare)-338.7(the)-336.9(deniti)-8.9(ons)-333.5(of)-333.6(GO)-339.4(terms)-339.4(\(Pesaran)-10.1(ghader)-340.2(et)-336.1(al.,)-336.9(2015\).)]TJ 1.0015 -1.2007 TD [(In)-327.9(this)-328.4(artic)-9.2(le,)-325.1(we)-331.6(introdu)-7.2(ce)-329.5(two)-333.3(new)-332.4(solutions)-336.2(to)-328.7(measure)-336.1(the)-331.2(semantic)-334.7(simi)-7.6(larity)-329.6(of)-327.9(two)-333.3(GO)-328.1(terms)-333.7(by)]TJ -1.0015 -1.195 TD [(focusing)-321.1(on)-314.5(the)-319.8(denitions)-319.7(of)-316.5(the)-314.1(GO)-322.4(terms.)-317(Our)-321.2(approach)-320.7(is)-312.8(mos)-7(t)-310.8(simi)-7.6(lar)-316.1(to)-317.3(Pesarangha)-11.5(der)-319(et)-313.4(al.)-313.7(\(2015\))-8.5(;)]TJ 0 -1.2007 TD [(however)-9.1(,)-302(w)0(e)-308.8(appl)-7.6(y)-302.4(neural)-308.8(networ)-9.3(k-bas)-8.8(ed)-304.9(techniq)-8.7(ues)-306.9(from)-306.4(the)-308.4(natural)-312.3(language)-310.1(p)-6.5(rocessing)-313.5(\(NLP\))-306.6(doma)-8.4(in.)]TJ 1.0015 -1.2007 TD [(First,)-245.4(we)-246.2(com)-7.6(pare)-247.6(words)-249.9(by)-246.2(converting)-252(them)-250.1(into)-241.9(wor)-8.2(d)-245.5(embeddings.)-252.4(We)-250.6(train)-246.4(the)-245.8(Word)-7.6(2vec)-245.6(mode)-8.4(l)-242.5(using)]TJ -1.0015 -1.2007 TD [(open)-369(acce)-10.2(ss)-368.1(artic)-9.2(les)-366.5(on)-371.4(PubMed)-7.5(,)-370.3(s)0(o)-366.9(that)-374.6(we)-371.4(can)-370.1(represe)-10.2(nt)-368.5(a)-366.7(wor)-8.2(d)-365(a)0(s)-368.7(a)0(n)]TJ /F6 1 Tf 30.1599 0 TD (N)Tj /F1 1 Tf .6658 0 TD [(-di)-7(mensional)-373.5(vect)-9.4(or)-367.7(\()-82.4(Mik)-7(olov)]TJ -30.8257 -1.2007 TD [(et)-347.5(al.,)-348.3(2013)-8.7(\).)-344.6(Cosine)-356.5(similarity)-354.3(is)-346.9(used)-353.2(to)-345.7(com)-7.6(pare)-350(two)-350.4(words.)-352.7(To)-348.5(com)-7.6(pare)-350(two)-350.4(GO)-350.8(terms,)-351.2(we)-348.7(tre)-8.8(at)-347.5(their)]TJ T* [(deni)-7.6(tions)-334.9(as)-340.2(two)-339(unorde)-8.3(red)-336.1(set)-8(s)-337.7(o)0(f)-333.6(word)-9(s,)-332.4(and)-339.8(use)-341(the)-336.9(weight)-10.1(ed)-339.1(modied)-342.7(Hausdor)-8.5(ff)-335.5(distanc)-9.9(e)-338.3(\()-82.4(MH)-7.4(D\))-337.5(to)]TJ T* [(measur)-9.1(e)-281.4(the)-285.7(distanc)-9.9(e)-287.1(between)-290.5(two)-287.8(sets)-288.8(\(Dubuisson)-291.8(and)-282.9(Jai)-8(n,)-280(199)-8(4\).)-282.7(We)-284.7(nam)-7.6(e)-281.4(this)-288.6(metric)-292.3(w2vGO)]TJ /F7 1 Tf 39.481 0 TD (:)Tj /F1 1 Tf .5577 0 TD (w2vGO)Tj -40.0387 -1.2007 TD [(is)-335.5(entirely)-338.6(inde)-7.6(penden)-8.1(t)-333.6(o)0(f)-333.6(the)-336.9(GO)-333.8(tre)-8.8(es.)]TJ 1.0015 -1.195 TD [(Second,)-417.5(we)-417(consi)-9.6(der)-415.8(the)-416.6(word-order)-9.9(ing)-414.8(within)-420.8(the)-416.6(GO)-419.1(denitions.)-422.5(We)-415.6(note)-417.3(that)]TJ /F6 1 Tf 34.1262 0 TD [(entailme)-10.5(nt)]TJ /F1 1 Tf 4.6606 0 TD (relation-)Tj -39.7883 -1.2007 TD [(ships)-458.5(exis)-8.8(t)-453.1(i)0(n)-459.5(the)-462.1(GO)-458.9(tree)-460.9(\(i.e.,)-459.5(two)-464.2(GO)-458.9(terms)-458.9(are)-463.1(linked)-461.4(by)-456.8(a)-457.8(dir)-7(ected)-461.5(edge\))-464.6(\(Fig.)-456.9(1\).)-459.1(We)-461.1(train)-462.7(the)]TJ T* [(sentence)-364.3(encoder)-359.8(InferSen)-9.1(t)-356.3(using)-354.9(the)-354(d)-6.5(enitions)-358.8(of)-356.3(childpa)-9.5(rent)-356.7(and)-356.9(randomly)-357.6(matche)-10.5(d)-353.6(G)0(O)-356.5(terms)-362.2(\(Con-)]TJ T* [(neau)-461.9(et)-455.6(al.,)-462.1(2017\).)-461.4(InferSen)-9.1(t)-453.1(emb)-7.6(eds)-460.5(sentences)-463(into)-463.8(an)]TJ /F6 1 Tf 23.7239 0 TD (N)Tj /F1 1 Tf .6658 0 TD [(-dime)-8.2(nsional)-463.4(vector)-462.4(space)-459.9(and)-459.3(com)-7.6(putes)-459.1(the)]TJ -24.3897 -1.2007 TD [(proba)-7.6(bility)-408.3(that)-408.7(one)-408.1(sentence)-415.5(entails)-411(anot)-7.6(her.)-404.8(We)-409.9(nam)-7.6(e)-406.6(this)-408.1(approach)-411.8(InferSen)-9.1(tGO.)-411.6(InferSen)-9.1(tGO)-411.2(needs)]TJ T* [(the)-445(GO)-447.6(trees)-451.5(for)-444.4(the)-450.7(training)-450.6(phase)-8.6(.)-444.2(Once)-448.7(the)-445(mode)-8.4(l)-441.7(i)0(s)-449.3(trained,)-449.3(only)-449.7(the)-445(deni)-7.6(tions)-448.7(of)-441.7(GO)-453.3(terms)-447.5(are)]TJ T* [(require)-9.9(d)-376.3(for)-381.8(calculat)-10.1(ing)-380.6(their)-383(semantic)-385.9(similarit)-12.1(ies.)-378.3(The)-385.2(original)-382.3(autho)-8.4(rs)-374.6(of)-379.1(Infe)-8.8(rSent)-379.4(did)-380.6(not)-380.6(nam)-7.6(e)-378.1(their)]TJ ET q 178.532 0 0 231.08 107.603 70.639 cm /Im1 Do Q BT /F2 1 Tf 8.9663 0 0 8.9663 298.8849 210.3307 Tm [(FIG.)-435.9(1.)]TJ /F1 1 Tf 4.2174 0 TD [(Terms)-443.4(shown)-438.3(are)-435.9(ancestors)-441.8(of)-437.9(GO:0009055)-442(\(yellow\).)]TJ -4.2174 -1.2203 TD [(GO:0003674)-309.2(and)-310.8(GO:0008150)-315.6(are)-309.5(root)-314.5(nodes)-311(for)-313.6(the)-308.5(MF)-314.5(and)-310.8(BP)]TJ 0 -1.2266 TD [(trees,)-386.2(respectively.)-395.6(Colors)-389(denote)-391.6(part)-386.5(of)-387.3(\(blue\))-388.1(and)-393(is)-389.9(a)-387.6(\(black\))]TJ 0 -1.2203 TD [(relationship.)-496(Snapshot)-489.2(is)-497.4(downloaded)-494.1(from)-493.6(ebi.ac.uk/QuickGO.)]TJ T* [(BPs,)-448.6(biological)-458.6(processes;)-455.2(GO,)-451.1(gene)-451.8(ontology;)-450.3(MFs,)-457.2(molecular)]TJ 0 -1.2266 TD (functions.)Tj /F2 1 Tf 9.9626 0 0 9.9626 107.6031 737.4045 Tm [(SEMANT)-12.2(IC)-336.7(SIMILA)-11.7(RITY)-335.5(OF)-340.6(GO)-338.6(DEFINITIO)-14(NS)-19750.9(39)]TJ ET endstream endobj 5 0 obj <>stream Adobed       t  s!1AQa"q2B#R3b$r%C4Scs5D'6Tdt& EFVU(eufv7GWgw8HXhx)9IYiy*:JZjzm!1AQa"q2#BRbr3$4CS%cs5DT &6E'dtU7()󄔤euFVfvGWgw8HXhx9IYiy*:JZjz ??~j򾳧[h+7$ѣՃXٳ顒$:>0 y?̒@vЏfw~.U?ֶ]CiC*+MI Xy{-meƘN5ށ:/?<2I'kWw͛O}_mQyU#g>Ǟ8?6"kN+ 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[(simDEF)-247.6(builds)-243.9(a)-250.2(second-order)-250.4(matrix)-242.7(from)-252(t)4.9(he)-244.5(rst)4.9(-)]TJ -21.5217 -1.2007 TD .0189 Tc [(order)-473.2(m)-2.5(atrix)-476.9(\(Islam)-480.5(a)-.7(nd)-476.9(Inkpen,)-476.6(2006\).)-470.9(L)-4.4(oosely)-476.9(s)]TJ 22.085 0 TD [(peaking,)-476.7(each)-477(row)-475.3(i)-1.8(n)-477(s)-.2(econd-order)-479(m)-2.6(atrix)-477(i)3.9(s)-478.2(a)-.8(n)]TJ -22.085 -1.2007 TD .0186 Tc [(ex)-4.9(ten)-4.9(d).8(ed)-335(GO)-338.9(denitio)-4.9(n).8(.)-334.6(E).9(ach)-335(column)-329.3(is)-336.2(the)-336.8(w)-3.2(ord)-335(c)-1(ount)-332.1(fo)-4.9(r)-331.3(a)-336.8(word)-335(in)-335(the)-336.8(d).8(enition.)-334.6(Fo)-4.9(urth,)-334.6(s)-.4(imDE)-4.7(F)]TJ 0 -1.195 TD .0188 Tc [(ap)-4.7(plies)-375.8(t)-1.8(he)-376.4(Poin)-4.7(twise)-376.4(M)-1(utual)-377.4(I)-1(nformation)-374.6(\()-1(PMI\))-376.6(function)-374.6(o)1(n)-380.3(t)3.9(h)-4.7(e)-376.4(second-order)-376.6(m)-2.6(atrix)-380.3(\()4.7(Islam)-378.1(a)-.8(nd)-374.6(In-)]TJ 0 -1.2007 TD [(k)-4.7(p)1(en,)-328.7(200)-4.7(6\).)-328.7(I)-1(n)-329.1(t)3.9(heir)-331.1(article,)-328.7(Pesarang)-4.7(hader)-331.1(e)-.8(t)-326.2(a)-.8(l.)-328.7(\(2015)-4.7(\))-325.4(r)-1(efer)-331.1(to)-329.1(this)-330.3(outcome)-330.9(as)-330.3(the)-330.9(P)-3.9(MI-o)-4.7(n)1(-second-)]TJ T* .0193 Tc [(or)5.2(der)-336.3(m)3.6(atrix.)-333.9(Here,)-333.9(each)-340(row)-338.2(r)5.2(epresents)-341.2(a)-.3(n)-334.3(e)-.3(xtended)-340(G)-2.5(O)-332.5(d)-4.2(enition,)-333.9(a)-.3(nd)-340(the)-341.8(e)-.3(ntr)5.2(y)-340(for)-336.3(each)-334.3(row)-338.2(i)-1.3(s)-335.5(t)-1.3(he)]TJ T* .0197 Tc [(transformed)-430.6(w)3.6(or)5.6(d)-430.6(c).1(ount)-427.7(for)-432.6(a)-432.4(wor)5.6(d)-430.6(in)-430.6(the)-426.7(d)-3.8(eniti)4.8(on.)-430.2(F)2.6(if)5.6(th,)-430.2(c).1(osine)-432.4(d)1.9(istance)-432.4(i)4.8(s)-431.8(u)1.9(sed)-430.6(t)-.9(o)-430.6(m)4(easur)5.6(e)-432.4(t)-.9(he)]TJ T* .02 Tc [(simil)5.1(a).4(rit)5.1(y)-345(between)-339.3(two)-339.3(G)-1.8(O)-343.2(t)-.6(erms)-346.2(\(i)5.1(.e.,)-338.9(two)-339.3(r).2(ows)-340.5(i)-.6(n)-339.3(t)]TJ 22.5801 0 TD .0194 Tc [(he)-347.3(PMI-on-second-order)-341.8(matr)5.3(ix\).)-345.2(We)-341.7(now)-343.8(i)4.5(ntro-)]TJ -22.5801 -1.2007 TD .0184 Tc [(d)-5.1(u).6(ce)-331.3(o)-5.1(u).6(r)-331.5(m)-3(ethods)-336.4(and)-335.2(outline)-337(th)-5.1(eir)-337.2(d).6(ifferences)-336.4(from)-333(s)-.6(imDE)-4.9(F.)]TJ /F2 1 Tf 0 67.0005 TD 0 Tc (40)Tj 35.8334 0 TD [(DUO)-8(NG)-339(ET)-335.3(AL.)]TJ ET endstream endobj 11 0 obj <> endobj 12 0 obj <>/ProcSet[/PDF/Text]/ExtGState<>>> endobj 13 0 obj <>stream /GS1 gs BT /F6 1 Tf 10.959 0 0 10.959 107.6031 714.7841 Tm 0 0 0 rg 0 Tc 0 Tw [(2.2.)-496.9(Word2vec)-333.1(model)]TJ /F1 1 Tf 9.9626 0 0 9.9626 117.5811 696.8691 Tm [(Here,)-360(we)-365.7(describe)-364.5(our)-357.1(rst)-361(metri)-10.9(c)-355.4(W2vG)-9.5(O.)-357.9(We)-364.4(use)-358.1(W2vG)-9.5(O)-357.5(a)0(s)-357.3(pure)-365.3(NLP)-358.1(tec)-8.6(hnique;)-359.8(that)-363.2(is,)-358.7(W2vG)-9.5(O)]TJ -1.0015 -1.2007 TD [(focuses)-246.6(stric)-8.6(tly)-241.1(on)-246.2(the)-240.2(GO)-248.4(denitio)-9.7(ns)-241.7(and)-243.1(is)-244.5(comple)-8.7(tely)-243.7(independe)-9.3(nt)-243.3(of)-242.5(the)-245.8(GO)-242.7(trees.)-247(Fo)-6.4(r)-241.7(this)-243.1(reason,)-245(u)-6.5(nlike)]TJ T* [(simDE)-9.3(F,)-432.8(we)-434(d)-6.5(o)-433.3(not)-431.8(conca)-9.2(tenate)-442.3(a)-435(G)0(O)-436.2(deni)-7.6(tion)-435.4(with)-439.3(the)-433.6(deni)-7.6(tions)-437.3(of)-436(its)-435.8(parents)-441.6(and)-436.6(childr)-8.2(en.)-436.2(This)]TJ 0 -1.195 TD [(extensi)-9.9(on)-331.6(of)-333.6(a)-338.3(G)0(O)-333.7(de)-9(nition)-337.2(requires)-341.9(informat)-9.5(ion)-335.1(from)-334.9(the)-336.9(GO)-339.4(tree.)]TJ 1.0015 -1.2007 TD [(To)-496.4(com)-7.6(pare)-503.7(two)-504.1(GO)-498.8(terms)-9.4(,)-495.5(W2vG)-9.5(O)-499.8(compare)-10.5(s)-497(their)-502.5(de)-9(nitions)-504.2(by)-496.6(treat)-9.2(ing)-500.1(the)-501.9(denitio)-9.7(ns)-497.8(as)-499.6(two)]TJ -1.0015 -1.2007 TD [(unorde)-8.3(red)-250.7(sets)-254.7(of)-253.9(words.)-256(To)-257.4(solve)-254.2(this)-254.5(problem)-9.7(,)-250.8(w)0(e)-251.9(wan)-8(t)-248.2(t)0(o)-254.7(rst)-252.9(be)-253.7(able)-254.1(to)-254.7(compare)-260.9(two)-253.7(words.)-256(To)-257.4(this)-248.8(end,)]TJ T* [(we)-388.5(use)-386.5(the)-388.1(word)-384.5(emb)-7.6(edding)-390.4(model)-387.5(Word)-7.6(2vec)-387.9(\()-82.4(Mik)-7(olov)-387.1(et)-387.3(al.,)-382.4(2013)-8.7(\).)-384.4(Word2vec)-389.8(is)-386.8(a)-389.5(distributio)-8.3(nal)-388.1(lin-)]TJ T* [(guistic)-363.7(model.)-359.4(Lo)-7(osely)-356.7(speak)-8.6(ing,)-358.2(Word)-7.6(2vec)-359.4(anal)-9.4(yzes)-360.6(how)-359(often)-363.2(words)-358(co-oc)-9.4(cur.)-359.2(Howeve)-10.3(r,)-355.9(Word)-7.6(2vec)-359.4(is)]TJ T* [(very)-336.9(differ)-9.4(ent)-331.2(from)-340.6(simDE)-9.3(F)-330(co-oc)-9.4(currence)-11.5(s)-332(matrice)-10.3(s.)]TJ 1.0015 -1.2007 TD [(The)-333.9(Word)-7.6(2vec)-331(mode)-8.4(l)-333.6(converts)-340(a)-332.6(word)-333.3(into)-332.9(an)]TJ /F6 1 Tf 19.3308 0 TD (N)Tj /F1 1 Tf .6715 0 TD [(-dimensi)-8.7(onal)-332(vect)-9.4(or.)-328.2(Th)-7(e)-332.6(user)-332.4(speci)-11.3(es)]TJ /F6 1 Tf 16.3546 0 TD (N)Tj /F1 1 Tf .6715 0 TD [(;)-333.6(i)0(n)-328.7(prac)-8.6(tice,)]TJ -38.0299 -1.2007 TD [(people)-380.8(often)-380.2(set)]TJ /F6 1 Tf 6.988 0 TD (N)Tj /F8 1 Tf 1.1723 0 TD (=)Tj /F1 1 Tf .9958 0 TD (300)Tj /F7 1 Tf 1.508 0 TD (:)Tj /F1 1 Tf .643 0 TD [(These)-384(vectors)-379(are)-377.7(kno)-8(wn)-375.4(as)-374.4(wor)-8.2(d)-370.7(emb)-7.6(eddings.)-381.3(Word)-7.6(2vec)-376.5(transf)-8.6(orms)-379.6(similar)]TJ -11.3071 -1.195 TD [(words)-267(into)-264.7(similar)-266.8(vectors)-9.1(,)-262.1(thus)-263.1(enablin)-8.7(g)-262.5(u)0(s)-258.8(t)0(o)-260.4(q)-6.5(uantify)-265(the)-262.9(simi)-7.6(larity)-267(between)-267.8(two)-265.1(words)-267(by)-263.3(computing)-268.1(the)]TJ 0 -1.2007 TD [(Euclidea)-11.1(n)-302.4(d)-6.5(istance)-313.3(or)-305.1(cosine)-313.7(similarity.)-314.8(At)-309.8(the)-308.4(heart)-313.7(of)-305.1(the)-308.4(Word)-7.6(2vec)-308.2(is)-307.1(a)-309.8(neural)-308.8(networ)-9.3(k)-308.1(model)-307.8(with)-314.1(one)]TJ T* [(input)-339.4(layer,)-336.9(one)-339.8(hidden)-339.2(layer,)-336.9(and)-339.8(one)-334.1(outpu)-6.6(t)-333.6(layer)-336.5(\()-88.1(Mikolov)-337.2(et)-336.1(al.,)-336.9(2013\).)]TJ 1.0015 -1.2007 TD [(Loosely)-238.5(speak)-8.6(ing,)-238.7(one)-237.4(can)-239.2(view)-244.8(the)-234.5(Word)-7.6(2vec)-239.9(mode)-8.4(l)-231.2(a)0(s)-243.5(a)-235.9(predictio)-9.3(n)-234.1(problem)-243(\(Rong,)-244.2(2014\).)-239.5(First,)-239.7(a)-235.9(word)]TJ /F6 1 Tf -1.0015 -1.2007 TD (w)Tj /F1 1 Tf 1.0015 0 TD [(from)-340.6(the)-336.9(input)-339.4(layer)-342.2(is)-335.5(map)-7.6(ped)-334.1(into)-338.6(an)]TJ /F6 1 Tf 16.3091 0 TD (N)Tj /F1 1 Tf .6658 0 TD [(-di)-7(mensional)-345(vector)-337.2(at)-341.8(the)-336.9(hidden)-339.2(laye)-9.4(r.)-333.2(Word)-7.6(2vec)-336.7(lea)-8.6(rns)-335.5(the)]TJ -17.9764 -1.2007 TD [(values)-245.4(for)-239.6(the)-245.8(hidden)-242.4(layer)-245.4(based)-241.9(on)-240.5(the)-245.8(coconcurr)-10.5(ences)-243.7(betwee)-10.9(n)]TJ /F6 1 Tf 26.2221 0 TD (w)Tj /F1 1 Tf .9048 0 TD [(and)-243.1(its)-242.3(neighboring)-245.3(wor)-8.2(ds.)-236.4(Th)-7(e)-235.9(key)-243.1(idea)]TJ -27.1269 -1.2007 TD [(is)-335.5(to)-334.3(predict)-340.8(the)-336.9(vectors)-339.2(for)-336.3(the)-336.9(surroundi)-9.1(ng)-337.3(context)-338.8(words)-341(based)-338.6(on)-331.6(the)-336.9(vect)-9.4(or)-333.6(for)]TJ /F6 1 Tf 34.2287 0 TD (w)Tj /F1 1 Tf .6658 0 TD (.)Tj -33.8929 -1.2007 TD [(The)-248.6(purpose)-249.3(of)-248.2(this)-243.1(artic)-9.2(le)-245.1(is)-244.5(not)-249.7(to)-243.3(dissect)-250.1(the)-251.5(Word2vec)-253.2(model;)-248.7(we)-251.9(are)-246.8(interest)-9.7(ed)-242.3(in)-249(adopting)-252.4(this)-243.1(mode)-8.4(l)]TJ -1.0015 -1.195 TD [(to)-237.6(measure)-245(the)-234.5(simi)-7.6(larity)-238.6(of)-236.8(GO)-237(terms)-242.7(and)-237.4(compare)-243.8(it)-234.7(with)-240.1(other)-238(methods)-8.9(.)-233.7(Int)-7(erested)-238.6(read)-8.6(ers)-240.6(are)-235.5(encour)-10.1(aged)]TJ 0 -1.2007 TD [(to)-334.3(read)-338.7(the)-336.9(origina)-8.9(l)-333.6(article)-339.6(by)-337.3(Mikolov)-337.2(et)-336.1(al.)-336.5(\(2013\),)-339(and)-334.1(the)-336.9(introdu)-7.1(ction)-341.2(by)-331.6(Ron)-7(g)-330.8(\(2014\))-8.5(.)]TJ /F6 1 Tf 10.959 0 0 10.959 117.5811 431.3763 Tm [(2.2.1.)-497(Measure)-357.1(similarity)-365.8(of)-362.3(two)-358.4(words)-362.7(using)-363.7(Word2vec.)]TJ /F1 1 Tf 9.9626 0 0 9.9626 383.8676 431.3763 Tm [(The)-368.1(training)-376.7(data)-367.9(inue)-7.6(nce)-370.1(the)-371(appli-)]TJ -27.73 -1.2007 TD [(cation)-360.8(of)-356.3(wor)-8.2(d)-353.6(emb)-7.6(edding)-361.9(model.)-359.4(Ex)-7(isting)-361.2(pretraine)-10.3(d)-353.6(Word)-7.6(2vec)-359.4(mode)-8.4(ls)-358.3(are)-355(o)-6.5(ften)-356.7(mad)-7.6(e)-355.4(b)0(y)-360(corpora)-360(col-)]TJ T* [(lecte)-9(d)-450.3(from)-454.4(new)-8(s,)-451.9(books,)-460.6(or)-453.1(the)-456.4(Internet.)-457.7(To)-456.6(obtain)-455.7(suitabl)-10.9(e)-452.1(word)-458.5(vectors)-9.2(,)-449.9(i)0(n)-453.8(this)-453.6(wor)-8.2(k,)-450.7(we)-456.8(train)-457(the)]TJ T* [(Word)-7.6(2vec)-279.8(to)-271.7(reco)-8.6(gnize)-283.3(biological)-284(words.)-278.7(We)-279(set)-281.2(the)-274.3(d)-6.5(imension)]TJ /F6 1 Tf 26.0058 0 TD (N)Tj /F8 1 Tf 1.1723 0 TD (=)Tj /F1 1 Tf 1.0015 0 TD [(300)-275.4(and)-277.2(use)-278.4(20GB)-284.8(of)-276.7(data)-276.8(from)-278(op)-7.2(en)]TJ -28.1796 -1.2007 TD [(access)-361.2(artic)-9.2(les)-355.2(on)-354.3(Pub)-7.2(Med.)-353.5(Th)-7(e)-355.4(raw)-357.1(count)-361.2(of)-350.6(un)-7.2(ique)-354.7(and)-356.9(repe)-8.6(ated)-356.5(words)-358(is)-358.3(14,526,52)-6.1(7,855.)-356.6(We)-358.7(remo)-10.3(ve)]TJ 0 -1.195 TD [(words)-295.4(that)-294.9(appea)-9.2(r)]TJ /F8 1 Tf 7.5115 0 TD (<)Tj /F1 1 Tf .552 0 TD [(25)-291.7(times)-294.7(in)-294.5(the)-291.4(whol)-9.7(e)-287.1(tra)-8.8(ining)-293.9(data,)-294.3(thus)-297.2(reducing)-298.9(the)-291.4(n)-6.4(al)-290.6(numb)-6.6(er)-289.8(of)-293.7(uniqu)-6.6(e)-292.8(words)-295.4(to)]TJ -8.0635 -1.2007 TD [(986,615.)-289.9(We)-296.1(keep)-291.2(stop)-285.8(wor)-8.2(ds)-287.2(and)-288.6(sym)-7(bols)-285.8(such)-296.2(as)]TJ /F8 1 Tf 21.1233 0 TD (+)Tj /F1 1 Tf 1.0072 0 TD (and)Tj /F8 1 Tf 1.9006 0 TD (-)Tj /F1 1 Tf 1.0072 0 TD [(in)-288.8(the)-291.4(data)-288.2(becau)-9.2(se)-289(they)-292.1(may)-292.1(have)-291.2(important)]TJ -25.0384 -1.2007 TD [(biologi)-7.9(cal)-293.1(mea)-9.4(nings.)-298.4(We)-296.1(use)-295.5(the)-297.1(Python)-296.8(lib)-7.8(rary)-293.3(gensi)-9.6(m)-294.5(t)0(o)-294.5(train)-297.6(the)-297.1(Word2vec)-304.4(model)-296.4(\(Rehur)-9.3(ek)-293.5(and)-300(Sojka,)]TJ T* [(2011\).)-336.2(A)-334.8(simpl)-8.4(e)-332.6(Python)-342.3(user)-338.1(interface)-342.2(is)-335.5(availa)-9.8(ble)-331.2(at)-336.1(our)-340(GitHub.)]TJ 1.0015 -1.2007 TD [(There)-248.2(are)-246.8(two)-248(important)-250.1(detail)-10.7(s)-241(here.)-248(First,)-251.1(the)-245.8(training)-251.5(data)-248.4(do)-240.5(not)-249.7(contain)-247.7(deni)-7.6(tions)-243.8(of)-248.2(GO)-242.7(ter)-8.8(ms)-245.3(found)]TJ -1.0015 -1.2007 TD [(in)-243.3(the)-240.2(GO)-248.4(database.)-250.9(This)-245.8(helps)-242.9(us)-241.7(avoi)-7.6(d)-239.8(data)-242.7(reus)-8(e.)-241.9(Second,)-246.7(theo)-7.6(retically)-247.2(speak)-8.6(ing,)-244.4(Word2vec)-247.5(mode)-8.4(l)-242.5(can)-244.9(be)]TJ T* [(trained)-448.9(on)-439.7(the)-445(GO)-447.6(terms)-447.5(in)-442.5(the)-445(PubMed)-451.4(data,)-442.2(so)-446.6(that)-442.8(one)-447.9(can)-444(convert)-446.1(a)-446.4(G)0(O)-441.9(ter)-8.8(m)-442.5(into)-441.1(a)-446.4(vector.)-445.7(Un-)]TJ T* [(fortuna)-8.1(tely,)-244.1(the)-245.8(IDs)-248.4(of)-242.5(the)-245.8(GO)-248.4(terms)-248.4(are)-241.2(n)-6.5(o)0(t)-243.3(used)-245(too)-244.1(often)-249.3(in)-243.3(publishe)-8.9(d)-239.8(artic)-9.2(les,)-241.7(and)-248.8(detecting)-253.8(denitions)-251.4(of)]TJ 0 -1.195 TD [(GO)-311(terms)-311(in)-305.9(artic)-9.2(les)-309.6(is)-307.1(a)-309.8(different)-312.1(type)-314.9(of)-305.1(researc)-11.9(h)-308.1(problem)-311.3(\(Tuan)-314.7(et)-307.7(al.,)-308.4(2013\).)-313.5(For)-310.8(these)-307.3(reas)-9.8(ons,)-305.5(we)-314.5(use)]TJ 0 -1.2007 TD [(the)-336.9(Word2)-8.3(vec)-335.9(model)-336.2(as)-340.2(a)-332.6(metric)-337.8(to)-340(compare)-340.6(two)-339(biological)-340.9(words.)]TJ 1.0015 -1.2007 TD .0196 Tc [(To)-413.6(compare)-415.4(t)-1(wo)-413.6(vector)-415.6(representations)-414.8(o)1.8(f)-415.6(t)4.7(wo)-413.7(wo)]TJ 21.8688 0 TD .0192 Tc [(rds,)-413.7(we)-415.8(use)-415.8(t)-1.4(he)-415.8(cosine)-421.5(similarity,)-413.7(b)1.4(ecause)-415.8(it)-416.8(is)]TJ -22.8703 -1.2007 TD .0186 Tc [(boun)-4.9(ded,)-277.7(whereas)-273.6(E)-4.7(u).8(clide)-6.7(a)-1(n)-272.4(d)-4.9(istance)-279.9(i)3.7(s)-279.3(not.)-277.7(W)-1.8(e)-279.9(d).8(ene)-279.9(the)-279.9(f)4.5(u)-4.9(n).8(ction)-278.1(w)18.6(2)18.6(v)]TJ /F6 1 Tf 30.8371 0 TD 0 Tc (z)Tj /F1 1 Tf .387 0 TD ()Tj /F6 1 Tf .5008 0 TD (v)Tj /F9 1 Tf -1.2747 0 TD 1.3335 Tc ()Tj /F1 1 Tf 2.3843 0 TD .0196 Tc [(as)-278.3(t)4.7(h)1.8(e)-278.9(s).6(imilari)4.7(ty)-277.1(score)-278.9(o)1.8(f)]TJ -32.8345 -1.2007 TD .0183 Tc [(two)-335.3(w)-3.5(ords)]TJ /F6 1 Tf 4.7516 0 TD 0 Tc (z)Tj /F1 1 Tf .387 0 TD ()Tj /F6 1 Tf .5008 0 TD (v)Tj /F7 1 Tf .4496 0 TD (:)Tj /F6 1 Tf 10.959 0 0 10.959 117.5811 201.4299 Tm [(2.2.2.)-497(Measuring)-355.9(similarity)-360.7(of)-362.3(two)-358.4(GO)-359.1(terms)-360.3(using)-363.7(Word2vec.)]TJ /F1 1 Tf 9.9626 0 0 9.9626 410.1731 201.4299 Tm [(A)-363.2(G)0(O)-367.9(ter)-8.8(m)-362.8(com)-7.6(es)-363(with)-371(a)-366.8(de-)]TJ -30.3705 -1.2007 TD [(nition)-325.8(that)-323.3(is)-318.5(usually)-326.8(one)-322.7(or)-322.2(two)-322(sentence)-11.5(s)-320.6(describ)-9.1(ing)-323.7(some)-322.5(biologi)-7.9(cal)-321.6(featur)-9.2(e.)-321.6(For)-322.2(exampl)-8.7(e,)-321.6(GO:0003700)]TJ T* [(has)-329.6(the)-325.5(fol)-7(lowing)-327(de)-9(nition:)-329.4()48.5(Interactin)-10.9(g)-325.1(select)-11(ively)-329.8(and)-328.4(noncova)-8.9(lently)-327.6(with)-331.2(a)-326.9(speci)-11.3(c)-326.9(DNA)-327.1(seque)-8.6(nce)-330.2(in)]TJ T* [(order)-368.1(to)-362.8(modu)-6.6(late)-370.6(transcrip)-9.7(tion.)-367.5(The)-368.1(transcrip)-9.7(tion)-367.1(factor)-367.7(may)-371.8(or)-362(may)-366.1(no)-7.2(t)-362(also)-367.3(intera)-10(ct)-364.6(selective)-12.1(ly)-362.8(with)-371(a)]TJ 0 -1.195 TD [(protei)-8.2(n)-330.8(o)0(r)-333.6(mac)-9.4(romolecul)-10.1(ar)-335.3(comple)-8.7(x.)47.3()]TJ 1.0015 -1.2007 TD [(When)-331.7(a)-326.9(G)0(O)-328.1(term)-331.8(denition)-329.1(h)-6.5(a)0(s)-323.2(mor)-7.8(e)-326.9(than)-326.3(one)-328.4(sent)-8.8(ence,)-327.5(we)-331.6(conca)-9.2(tenate)-328.4(thes)-8.8(e)-326.9(sentence)-11.5(s)-326.3(into)-327.2(the)-325.5(sam)-8.8(e)]TJ -1.0015 -1.2007 TD [(sentence)-267.6(by)-263.3(ignorin)-7.2(g)-256.8(the)-262.9(period)-261.5(sym)-7(bol.)-261.5(For)-259.6(exampl)-8.7(e,)-259(the)-262.9(two)-259.4(sent)-8.8(ences)-266.4(for)-256.6(GO)-9.4(:0003700)-264.9(are)-263.9(considered)-269.3(as)]TJ T* [(one)-334.1(long)-335.9(sent)-8.8(ence.)]TJ 1.0015 -1.2007 TD [(Thus,)-311.7(the)-314.1(task)-316.1(to)-311.6(com)-7.6(pare)-315.9(two)-310.6(GO)-316.7(terms)-316.7(reduces)-321.2(to)-311.6(the)-314.1(problem)-317(of)-310.8(com)-7.6(paring)-312.7(their)-314.7(de)-9(nitions)-316.4(that)-312(are)]TJ -1.0015 -1.2007 TD [(two)-333.3(sent)-8.8(ences.)-340.8(Suppose)-337.6(that)-334.7(GO)-339.4(terms)]TJ /F6 1 Tf 16.1782 0 TD (a)Tj /F1 1 Tf .8308 0 TD (and)Tj /F6 1 Tf 1.7868 0 TD (b)Tj /F1 1 Tf .8308 0 TD [(have)-336.7(sent)-8.8(ences)]TJ /F6 1 Tf 6.4132 0 TD (Z)Tj /F1 1 Tf .6146 0 TD ()Tj /F6 1 Tf .5008 0 TD (V)Tj /F1 1 Tf 1.03 0 TD [(as)-340.3(their)-337.5(denitions,)-342.8(respective)-12.1(ly.)-334.7(We)]TJ -28.1853 -1.2007 TD [(treat)-498.6(two)-498.4(sentence)-11.5(s)]TJ /F6 1 Tf 8.6269 0 TD (Z)Tj /F8 1 Tf .7853 0 TD (=)Tj /F1 1 Tf .717 0 TD -.0485 Tc ()Tj /F6 1 Tf .6203 0 TD 0 Tc (z)Tj /F1 1 Tf 6.9738 0 0 6.9738 218.5511 80.3905 Tm (1)Tj /F6 1 Tf 9.9626 0 0 9.9626 225.2976 81.8646 Tm (z)Tj /F1 1 Tf 6.9738 0 0 6.9738 229.1527 80.3905 Tm (2)Tj /F6 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-1.2007 TD (Z)Tj /F8 1 Tf 1.0584 0 TD (=)Tj /F6 1 Tf 1.4966 0 TD (z)Tj /F1 1 Tf 6.9738 0 0 6.9738 136.9133 68.4283 Tm (1)Tj 9.9626 0 0 9.9626 140.9385 69.9023 Tm ()Tj /F6 1 Tf .7739 0 TD (z)Tj /F1 1 Tf 6.9738 0 0 6.9738 152.5039 68.4283 Tm (2)Tj /F10 1 Tf 9.9626 0 0 9.9626 160.9511 69.9023 Tm .1682 Tc (...)Tj /F6 1 Tf 1.5877 0 TD 0 Tc (z)Tj 6.9738 0 0 6.9738 180.6236 68.4283 Tm (N)Tj /F9 1 Tf 9.9626 0 0 9.9626 128.0692 69.9023 Tm 5.3385 Tc (fg)Tj /F1 1 Tf 6.6693 0 TD 0 Tc (and)Tj /F6 1 Tf 1.7868 0 TD (V)Tj /F8 1 Tf 1.1381 0 TD (=)Tj /F6 1 Tf 1.5023 0 TD (v)Tj /F1 1 Tf 6.9738 0 0 6.9738 243.0991 68.4283 Tm (1)Tj 9.9626 0 0 9.9626 247.0676 69.9023 Tm ()Tj /F6 1 Tf .7796 0 TD (v)Tj /F1 1 Tf 6.9738 0 0 6.9738 259.3133 68.4283 Tm (2)Tj /F10 1 Tf 9.9626 0 0 9.9626 267.7039 69.9023 Tm .1682 Tc (...)Tj /F6 1 Tf 1.5934 0 TD 0 Tc (v)Tj 6.9738 0 0 6.9738 288.0566 68.4283 Tm (M)Tj /F9 1 Tf 9.9626 0 0 9.9626 233.6314 69.9023 Tm 5.623 Tc (fg)Tj /F7 1 Tf 6.6238 0 TD 0 Tc (:)Tj /F2 1 Tf -19.2739 67.0005 TD [(SEMANT)-12.2(IC)-336.7(SIMILA)-11.7(RITY)-335.5(OF)-340.6(GO)-338.6(DEFINITIO)-14(NS)-19750.9(41)]TJ ET endstream endobj 14 0 obj <> endobj 15 0 obj <>/ProcSet[/PDF/Text]/ExtGState<>>> endobj 16 0 obj <>stream /GS1 gs BT /F1 1 Tf 9.9626 0 0 9.9626 84.0755 715.4644 Tm 0 0 0 rg 0 Tc 0 Tw [(To)-337.1(measur)-9.1(e)-332.6(the)-336.9(simi)-7.6(larity)-335.3(of)-333.6(sent)-8.8(ences)]TJ /F6 1 Tf 16.2465 0 TD (Z)Tj /F1 1 Tf .882 0 TD (and)Tj /F6 1 Tf 1.7868 0 TD (V)Tj /F1 1 Tf .9503 0 TD [(\(or)-336.3(in)-334.3(other)-334.7(wor)-8.2(ds,)-333.1(terms)]TJ /F6 1 Tf 10.6072 0 TD (a)Tj /F1 1 Tf .8365 0 TD (and)Tj /F6 1 Tf 1.7811 0 TD (b)Tj /F1 1 Tf .5008 0 TD [(\),)-333.2(we)-337.3(use)-335.3(the)-336.9(metri)-10.9(c)]TJ -25.9887 -2.9136 TD (w2vGO)Tj /F6 1 Tf 3.5509 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F8 1 Tf 2.9989 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (mean)Tj /F11 1 Tf 3.9435 .9503 TD (X)Tj /F6 1 Tf 6.9738 0 0 6.9738 266.3999 675.666 Tm (i)Tj /F8 1 Tf .4471 0 TD (=)Tj /F1 1 Tf .7235 0 TD (1)Tj /F10 1 Tf .4959 0 TD (...)Tj /F6 1 Tf .8211 0 TD (N)Tj /F1 1 Tf 9.9626 0 0 9.9626 293.2157 686.4376 Tm [(cont)-7.6(ent)]TJ /F11 1 Tf -3.7728 1.7129 TD (\()Tj /F1 1 Tf 7.0164 -1.7129 TD (\()Tj /F6 1 Tf .3357 0 TD (z)Tj 6.9738 0 0 6.9738 332.7306 684.9636 Tm (i)Tj /F1 1 Tf 9.9626 0 0 9.9626 335.1684 686.4376 Tm [(\))-753.9(max)]TJ /F6 1 Tf 6.9738 0 0 6.9738 342.9353 680.1447 Tm (i)Tj /F8 1 Tf .4471 0 TD (=)Tj /F1 1 Tf .7235 0 TD (1)Tj /F10 1 Tf .4959 0 TD (...)Tj /F6 1 Tf .8129 0 TD (M)Tj /F1 1 Tf 9.9626 0 0 9.9626 370.7715 686.4376 Tm [(w2v)-103(\()]TJ /F6 1 Tf 2.1567 0 TD (z)Tj 6.9738 0 0 6.9738 396.1133 684.9636 Tm (i)Tj /F1 1 Tf 9.9626 0 0 9.9626 398.5511 686.4376 Tm ()Tj /F6 1 Tf .5008 0 TD (v)Tj 6.9738 0 0 6.9738 408.0188 684.9636 Tm (j)Tj /F1 1 Tf 9.9626 0 0 9.9626 410.4566 686.4376 Tm (\))Tj /F11 1 Tf -14.8182 -2.4412 TD (X)Tj /F6 1 Tf 6.9738 0 0 6.9738 258.8031 641.9337 Tm (i)Tj /F8 1 Tf .4471 0 TD (=)Tj /F1 1 Tf .7235 0 TD (1)Tj /F10 1 Tf .4959 0 TD (...)Tj /F6 1 Tf .8129 0 TD (N)Tj /F1 1 Tf 9.9626 0 0 9.9626 285.6188 652.7053 Tm [(cont)-7.6(ent)-280(\()]TJ /F6 1 Tf 3.5737 0 TD (v)Tj 6.9738 0 0 6.9738 325.7007 651.1746 Tm (j)Tj /F1 1 Tf 9.9626 0 0 9.9626 328.1952 652.7053 Tm [(\))-702.7(max)]TJ /F6 1 Tf 6.9738 0 0 6.9738 335.9621 646.3557 Tm (i)Tj /F8 1 Tf .4471 0 TD (=)Tj /F1 1 Tf .7154 0 TD (1)Tj /F10 1 Tf .504 0 TD (...)Tj /F6 1 Tf .8129 0 TD (N)Tj /F1 1 Tf 9.9626 0 0 9.9626 362.7778 652.7053 Tm [(w2v)-103(\()]TJ /F6 1 Tf 2.1567 0 TD (z)Tj 6.9738 0 0 6.9738 388.0629 651.1746 Tm (i)Tj /F1 1 Tf 9.9626 0 0 9.9626 390.5574 652.7053 Tm ()Tj /F6 1 Tf .5008 0 TD (v)Tj 6.9738 0 0 6.9738 400.0251 651.1746 Tm (j)Tj /F1 1 Tf 9.9626 0 0 9.9626 402.4629 652.7053 Tm (\))Tj /F11 1 Tf .3357 1.7129 TD (\))Tj /F1 1 Tf .8024 -1.7129 TD ()Tj 7.9383 1.6958 TD (\(1\))Tj -42.0361 -4.5923 TD [(whe)-8(re)-346.7(cont)-7.6(ent)]TJ /F6 1 Tf 6.1515 0 TD (w)Tj /F9 1 Tf -.387 0 TD .6678 Tc ()Tj /F1 1 Tf 1.7868 0 TD 0 Tc [(is)-346.9(the)-354(weight)-351.6(of)-350.6(the)-348.3(word)]TJ /F6 1 Tf 10.8348 0 TD (w)Tj /F1 1 Tf 1.0129 0 TD [(and)-351.2(is)-346.9(often)-351.8(used)-353.2(to)-345.7(disti)-7.6(nguish)-350(common)-354.8(words)-352.3(from)-352(rare)]TJ -19.3991 -1.2007 TD [(wor)-8.2(ds.)-663.2(The)-664(weights)-666.5(of)-657.9(wor)-8.2(ds)-662.8(can)-660.3(help)-667.7(avoid)-662.8(the)-661.3(inue)-7.6(nce)-666(of)-657.9(hub)-662.4(wor)-8.2(ds)-657.1(\(i.)-6.6(e.,)-657.7(wor)-8.2(ds)-662.8(such)-660.4(as)]TJ /F6 1 Tf T* [(cel)-8.6(l)]TJ /F1 1 Tf 1.4625 0 TD ()Tj /F6 1 Tf .7796 0 TD (DNA)Tj /F1 1 Tf 2.0031 0 TD ()Tj /F6 1 Tf .7796 0 TD [(activit)-8.6(y)]TJ /F1 1 Tf 2.9762 0 TD [(\))-623(that)-630.6(are)-628.1(ubiqu)-6.6(itously)-629.4(associa)-10.1(ted)-627.1(with)-627.1(man)-7.6(y)-621(othe)-7.6(r)-623(wor)-8.2(ds)-623(\(Levy)-633.3(et)-626.3(al.,)-627.1(2014\).)]TJ -8.0009 -1.2007 TD [(Con)-7(tent)]TJ /F6 1 Tf 3.7387 0 TD (w)Tj /F9 1 Tf -.387 .0057 TD .6678 Tc ()Tj /F1 1 Tf 1.7754 -.0057 TD 0 Tc [(is)-335.5(very)-336.9(similar)-340.8(to)-334.3(the)-336.9(IC)-332.6(funct)-10.3(ion)-335.1(\(Li)-336.9(et)-330.4(al.,)-336.9(200)-8(6\))]TJ 4.2679 -2.612 TD [(Conten)-8.2(t)]TJ /F6 1 Tf 3.733 0 TD (w)Tj /F9 1 Tf -.3813 0 TD .6677 Tc ()Tj /F8 1 Tf 1.8836 0 TD .6089 Tc (=-)Tj /F1 1 Tf 2.1624 0 TD 0 Tc (log)Tj ET 264.189 564.264 136.743 .39685 re f BT 9.9626 0 0 9.9626 264.1889 568.7432 Tm [(fre)-8(quency)-281.3(wor)-8.2(d)]TJ /F6 1 Tf 6.6352 0 TD (w)Tj /F1 1 Tf .9446 0 TD [(in)-277.4(training)-285.6(data)]TJ -4.1826 -1.3657 TD [(training)-285.6(data)-282.5(siz)-8(e)]TJ /F11 1 Tf -4.1256 2.0941 TD 13.725 Tc ()Tj /F7 1 Tf 15.1881 -1.4113 TD 0 Tc (:)Tj /F1 1 Tf 8.496 0 TD (\(2\))Tj -41.0345 -2.5892 TD [(Becaus)-10.1(e)-309.8(G)0(O)-311(denitions)-314(are)-309.4(often)-311.9(short,)-311.7(we)-308.8(hope)-312.1(that)-312(the)-308.4(accuracy)-318.6(of)-305.1(w2vGO)-317.2(does)-307.6(not)-312.3(suffer)-309.4(too)-312.3(much)]TJ -1.0015 -1.2007 TD [(from)-283.7(the)-274.3(removal)-284.6(of)-276.7(word-or)-9.5(dering.)-278.9(Surpr)-7(isingly,)-282.6(this)-277.2(assumpt)-10.1(ion)-272.5(holds)-280.9(true)-277(in)-277.4(sever)-10.6(al)-273.5(instanc)-9.9(es)-277.6(\(Table)-280.2(2\).)]TJ T* [(Th)-7(ere)-252.5(are)-252.5(more)-255(sophist)-7.5(icated)-254.5(models)-252.8(that)-255.1(consider)-260.3(the)-251.5(word-order)-9.9(ing)-249.7(in)-254.7(the)-251.5(sentence)-11.5(s;)-250.2(we)-251.9(will)-248.6(consi)-9.6(der)-250.7(one)]TJ T* [(of)-339.2(these)-335.7(methods)-344.7(in)-334.3(the)-336.9(next)-337.6(section.)]TJ 1.0015 -1.2007 TD [(In)-248.2(an)19.4(y)-256.8(c)14.5(as)18.3(e,)-247.6(w)12.4(e)-258.6(ha)19.4(ve)-248(de)25.1(n)16.3(e)14.5(d)-256.8(a)-258.6(m)0(e)15.9(t)13.5(ri)22.2(c)-258.6(t)13.5(o)-256.8(m)0(e)15.9(a)14.5(su)20(re)-250(t)13.5(h)0(e)-248(t)13.5(wo)-250.2(G)12.4(O)-260.8(t)13.5(e)0(r)17.5(m)12.8(s)]TJ /F6 1 Tf 27.0073 0 TD (a)Tj /F1 1 Tf .7568 0 TD [(an)19.5(d)]TJ /F6 1 Tf 1.6844 0 TD (b)Tj /F1 1 Tf .7568 0 TD [(wi)20.2(t)13.5(h)-262.5(de)25.1()11.4(n)0(i)18.5(t)13.5(io)24.2(ns)]TJ /F6 1 Tf 6.3905 0 TD (Z)Tj /F1 1 Tf .8137 0 TD -.0145 Tc [(an)-14.5(d)]TJ /F6 1 Tf 1.6787 0 TD 0 Tc (V)Tj /F1 1 Tf .8763 0 TD [(un)21.2(de)25.1(r)]TJ -40.9663 -1.2007 TD [(the)-342.6(Word)-7.6(2v)-7.2(ec)-335.2(pa)-9(radig)-10.3(m.)-334.7(w2vGO)]TJ /F6 1 Tf 14.2036 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 .0057 TD 1.7831 Tc ()Tj /F1 1 Tf 2.8851 -.0057 TD 0 Tc [(ran)-11.7(ges)-335.3(from)]TJ /F8 1 Tf 5.4174 0 TD (-)Tj /F1 1 Tf .717 0 TD [(1)-336.5(t)0(o)-334.3(1)-336.5(becau)-14.9(se)-334.6(w2v)]TJ /F6 1 Tf 8.422 0 TD (z)Tj /F1 1 Tf .3813 0 TD ()Tj /F6 1 Tf .7796 0 TD (v)Tj /F9 1 Tf -1.5478 .0057 TD 1.6124 Tc ()Tj /F1 1 Tf 2.7144 -.0057 TD 0 Tc [(ran)-11.7(ges)-335.3(from)]TJ /F8 1 Tf 5.4174 0 TD (-)Tj /F1 1 Tf .717 0 TD .3354 Tc [(1t)335.4(o1)328.9(.)]TJ /F6 1 Tf 10.959 0 0 10.959 74.0976 449.4613 Tm 0 Tc [(2.3.)-502(InferSent)-330.1(model)]TJ /F1 1 Tf 9.9626 0 0 9.9626 84.0755 431.5464 Tm [(In)-379.1(the)-382.4(previous)-383.7(sectio)-9.2(n,)-376.7(we)-382.8(have)-382.2(ignored)-387.4(the)-376.7(wor)-8.2(d-ordering)-388(in)-374.2(the)-382.4(sentence)-11.5(s,)-377.9(treat)-9.2(ing)-380.6(them)-381(as)-380.1(sets)-379.9(of)]TJ -1.0015 -1.2007 TD [(wor)-8.2(ds.)-276.2(In)-276.7(this)-282.9(section,)-283.5(we)-280.4(briey)-283.5(explain)-281.9(InferSen)-9.1(t,)-277.1(a)-275.7(mode)-8.4(l)-276.7(that)-277.8(focus)-8.8(es)-277.7(not)-278.2(only)-279(on)-280.4(the)-274.3(wor)-8.2(d)-273.9(emb)-7.6(eddings)]TJ T* [(bu)-7.2(t)-401.9(also)-407.1(on)-405.6(the)-410.9(word-order)-9.9(ing)-409.1(in)-402.6(the)-405.2(sent)-8.8(ences)-408.7(\(Connea)-9.9(u)-404.8(e)0(t)-410.1(al.,)-405.2(2017\).)-410.2(InferSen)-9.1(t)-401.9(i)0(s)-409.5(thus)-405.3(differ)-9.4(ent)-405.2(from)]TJ T* [(simD)-8.8(EF)-336.3(that)-334.7(als)-8(o)-330.8(ignores)-343.1(the)-336.9(word-order)-9.9(ing.)]TJ 1.0015 -1.2007 TD [(Loosel)-10.1(y)-342.2(speak)-8.6(ing,)-346.9(InferSen)-9.1(t)-345(i)0(s)-346.9(similar)-352.2(in)-345.7(spirit)-346.1(to)-345.7(Word)-7.6(2vec;)-351.6(instead)-351.4(of)-344.9(words,)-352.7(InferSen)-9.1(t)-345(identies)-354.9(the)]TJ -1.0015 -1.2007 TD [(rel)-8.8(ationship)-376.6(betwee)-10.9(n)-376.3(two)-373.2(sent)-8.8(ences.)-380.6(One)-372.2(tra)-8.8(ining)-373.5(sample)-379.8(for)-376.1(Infe)-8.8(rSent)-373.7(consi)-9.6(sts)-371.6(of)-379.1(two)-373.2(sentence)-11.5(s)-371.8(havi)-7.6(ng)]TJ T* [(som)-7(e)-474.9(relations)-10.5(hip)]TJ /F6 1 Tf 7.8188 0 TD (R.)Tj /F1 1 Tf 1.3373 0 TD [(Con)-7(sider)-478.2(a)-474.9(simpl)-8.4(e)-474.9(classicat)-13.3(ion)-471.7(whe)-8(re)]TJ /F6 1 Tf 16.827 0 TD (R)Tj /F8 1 Tf 1.0584 0 TD (=)Tj /F6 1 Tf .9958 0 TD [(enta)-7.6(ilment)]TJ /F1 1 Tf 4.7459 0 TD (or)Tj /F6 1 Tf 1.3088 0 TD (neutral)Tj /F7 1 Tf 2.8965 0 TD (:)Tj /F1 1 Tf .2731 0 TD [(.)-472.7(I)0(n)-475.8(this)-476.4(case)-9.6(,)]TJ -37.2617 -1.195 TD [(Infe)-8.8(rSent)-356.7(expects)-361.8(two)-356.1(classes)-358.5(of)-356.3(input.)-356.8(The)-356.7(rst)-355.3(class)]TJ /F6 1 Tf 22.4321 0 TD [(enta)-7.6(ilment)]TJ /F1 1 Tf 4.6037 0 TD [(will)-356.7(have)-353.7(two)-356.1(sentence)-11.5(s)-354.8(where)-354.7(the)-359.7(rst)]TJ /F6 1 Tf -27.0358 -1.2007 TD [(enta)-7.6(ils)]TJ /F1 1 Tf 2.9818 0 TD [(the)-302.7(secon)-8.6(d;)-300.2(for)-296.5(exam)-10.2(ple,)-303.1()48.5(cat)-301.6(is)-301.4(napping)-305.8(on)-297.4(the)-302.7(mat)43.8()]TJ /F6 1 Tf 22.1818 0 TD (entails)Tj /F1 1 Tf 2.9818 0 TD [()48.5(cat)-301.6(is)-301.4(not)-301(running)44.1(.)]TJ /F6 1 Tf 8.9285 0 TD [(Entailm)-11.7(ent)]TJ /F1 1 Tf 4.7118 0 TD [(is)-301.4(a)]TJ -41.7857 -1.2007 TD [(on)-7.2(e-directiona)-11.5(l)-259.6(relations)-10.5(hip,)-261.5(becau)-9.2(se)-260.6()48.5(cat)-261.7(is)-261.6(not)-261.1(running)44.1()-258.8(does)-267.8(not)]TJ /F6 1 Tf 27.2179 0 TD (entail)Tj /F1 1 Tf 2.5494 0 TD [()48.5(cat)-267.4(is)-261.6(napping)-266(on)-257.6(the)-262.9(mat)43.8(.)-259.2(The)]TJ -29.7673 -1.2007 TD [(secon)-8.6(d)-336.5(class)]TJ /F6 1 Tf 5.4117 0 TD (neutral)Tj /F1 1 Tf 3.2322 0 TD [(will)-339.6(have)-342.4(two)-333.3(un)-7.2(related)-342.6(sentence)-11.5(s)-332(such)-341.8(as)-334.6()48.5(cat)-341.4(is)-335.5(napping)-339.9(on)-337.3(the)-336.9(mat)43.8()-332.8(and)-339.8()48.5(boy)-340.8(is)]TJ -8.6439 -1.2007 TD [(watchi)-11.9(ng)-331.6(the)-336.9(cat)-8.6(.)53.8()-338.5(Unlike)]TJ /F6 1 Tf 11.034 0 TD [(entailme)-10.5(nt)]TJ /F1 1 Tf 4.2452 0 TD (,)Tj /F6 1 Tf .5861 0 TD (neutral)Tj /F1 1 Tf 3.2322 0 TD [(is)-335.5(a)-332.6(bidire)-8.2(ctional)-341.6(relations)-10.5(hip.)]TJ -18.0959 -1.2007 TD [(InferSen)-9.1(t)-305.1(i)0(s)-301.4(a)-298.5(classi)-10.4(cation)-309.6(model)-302.1(based)-310.2(on)-297.4(the)-308.4(neural)-303.1(networ)-9.3(k)-302.4(architect)-12.9(ure;)-299.8(it)-7(s)-297.9(full)-306.5(descrip)-9.1(tion)-298.8(is)-301.4(g)-6.5(iven)]TJ -1.0015 -1.2007 TD [(by)-303.1(Con)-7(neau)-302.5(et)-302(al.)-302.4(\(2017\).)-304.8(Here,)-308.8(we)-303.2(briey)-306.2(mention)-306.4(the)-302.7(rst)-304.1(layer)-302.3(of)-305.1(this)-300(networ)-9.3(k.)-297.1(Infe)-8.8(rSents)-304.5(rst)-304.1(layer)-308(is)]TJ T* [(the)-257.2(word)-253.7(vect)-9.4(ors)-250.2(for)-256.6(words)-255.6(in)-249(the)-257.2(entire)-254.7(traini)-10.9(ng)-251.9(data)-254.1(set.)-253.1(Con)-7(neau)-257(et)-250.8(al.)-251.1(\(2017\))-258.9(use)-255.7(the)-251.5(GloV)-8(e)-252.9(word)-253.6(vectors)]TJ 0 -1.195 TD [(\(Penni)-10.3(ngton)-422(et)-421.5(al.,)-422.2(2014\).)-421.6(Howeve)-10.3(r,)-418.5(to)-419.7(obta)-7.6(in)-419.7(the)-422.2(best)-418.5(resu)-8(lt,)-417.2(thes)-8.8(e)-418(word)-424.4(vectors)-424.6(shoul)-7.8(d)-416.2(b)0(e)-424.4(specic)-423.6(to)]TJ 0 -1.2007 TD [(biol)-8.6(ogy.)-332.7(In)-333.6(this)-339.8(article)-9.6(,)-330.4(w)0(e)-337.3(use)-335.3(the)-336.9(Word)-7.6(2vec)-336.7(vect)-9.4(ors)-335.5(in)-334.3(section)-340(2.2.1.)]TJ /F6 1 Tf 10.959 0 0 10.959 84.0755 213.4488 Tm [(2.3.1.)-497(Measuring)-340.4(similarity)-345.1(of)-346.8(two)-342.9(GO)-343.6(terms)-344.7(using)-343(InferSent.)]TJ /F1 1 Tf 9.9626 0 0 9.9626 371.2251 213.4488 Tm [(Infe)-8.8(rSent)-351(takes)-352.8(two)-350.4(sentence)-11.5(s)-343.4(a)0(s)]TJ -29.8242 -1.2007 TD [(on)-7.2(e)-287.1(training)-297(sample)-9.9(.)-284.9(I)0(n)-293.7(this)-294.3(article,)-294.5(the)-291.4(two)-293.5(sentence)-11.5(s)-292.2(will)-294.1(be)-287.8(the)-291.4(deni)-7.6(tions)-295.1(of)-288(two)-293.5(GO)-293.9(terms)]TJ /F6 1 Tf 38.2348 0 TD (a)Tj /F1 1 Tf .791 0 TD (and)Tj /F6 1 Tf 1.7356 0 TD (b.)Tj /F1 1 Tf 1.0414 0 TD (We)Tj -41.8028 -1.2007 TD [(wi)-8.2(ll)-314.3(dene)-319.6(two)-322(categor)-9.7(ies)]TJ /F6 1 Tf 10.8689 0 TD (entailment)Tj /F1 1 Tf 4.5581 0 TD (and)Tj /F6 1 Tf 1.7698 0 TD (neutral)Tj /F1 1 Tf 2.9022 0 TD [(,)-313.4(and)-322.8(estimate)-326.1(the)-314.1(proba)-7.6(bility)]TJ /F12 1 Tf 12.2859 0 TD (P)Tj /F6 1 Tf 1.0015 0 TD (a)Tj /F1 1 Tf .7796 0 TD (entails)Tj /F6 1 Tf 2.9079 0 TD (b)Tj /F9 1 Tf -4.0744 0 TD 4.1902 Tc ()Tj /F1 1 Tf 4.9565 0 TD 0 Tc [(.)-319.1(This)-319.8(metric)]TJ -37.956 -1.2007 TD [(allow)-9.4(s)-383.2(u)0(s)-384(t)0(o)-379.9(gauge)-388.7(the)-388.1(semantic)-391.6(similarity)-388.4(for)]TJ /F6 1 Tf 19.5869 0 TD (a)Tj /F1 1 Tf .882 0 TD (and)Tj /F6 1 Tf 1.8324 0 TD (b)Tj /F1 1 Tf .5008 0 TD [(.)-381.7(W)0(e)-387.1(choose)-384.9(this)-385.3(option)-385.7(becau)-9.2(se)]TJ /F6 1 Tf 13.9248 0 TD [(entailme)-10.5(nt)]TJ /F1 1 Tf 4.6264 0 TD (rela-)Tj -41.3532 -1.195 TD [(tio)-7.8(nship)-303.7(exists)-310.2(in)-300.2(the)-308.4(GO)-305.3(tree.)-307.6(Childpar)-9.5(ent)-302.7(GO)-305.3(terms)-311(are)-303.7(linked)-307.8(by)-303.1(a)-304.2(one-d)-7.6(irectional)-310.5(relations)-10.5(hip)-301(such)-307.6(as)]TJ 0 -1.2007 TD [()48.5(is)-281.4(a,)45.5()-281.6()54.2(par)-8.8(t)-276.7(of,)44.6()-275.9()48.5(regula)-9.9(tes,)45.8()-281.6()54.2(nega)-9.4(tively)-282.1(regulat)-10.7(es,)49.3()-281.6(and)-282.9()48.5(positive)-8.7(ly)-277.4(regulat)-10.7(es.)49.3()-281.6(For)-282.3(example,)-284.8(the)-280(term)]TJ T* [(GO)-9.4(:1900237)-521()48.5(positive)-520.9(regulat)-10.7(ion)-517.2(of)-515.7(induction)-523.4(of)-515.7(conj)-7.6(ugation)-519.1(with)-519(cellular)-522.5(fusi)-9(on)52.6()]TJ /F6 1 Tf 36.4138 0 TD (entails)Tj /F1 1 Tf 3.1924 0 TD [(the)-519(term)]TJ -39.6062 -1.2007 TD [(GO)-9.4(:0010514)-338.9()48.5(induction)-344(of)-333.6(conjugat)-9.5(ion)-335.1(with)-336.9(cellular)-340.4(fusion.)-10.9()54.2()]TJ 1.0015 -1.2007 TD [(To)-359.8(prepa)-9.4(re)-358.1(the)]TJ /F6 1 Tf 6.436 0 TD [(enta)-7.6(ilment)]TJ /F1 1 Tf 4.6093 0 TD [(data)-362.2(set,)-361.2(for)-359.1(all)-362.4(three)-364.9(ontology)-364.4(categor)-9.7(ies,)-361.2(we)-360.1(rando)-7.6(mly)-361.4(pair)-362.4(each)-361.2(GO)-362.2(term)]TJ -12.0469 -1.2007 TD [(wi)-8.2(th)-391.3(one)-391(of)-390.5(its)-396(parents)-9.1(.)-387.3(T)0(o)-394(ensure)-398.3(that)-391.6(thes)-8.8(e)-389.5(childpa)-9.5(rent)-390.8(GO)-396.3(terms)-396.3(are)-394.8(indeed)-397.9(similar)-397.7(in)-391.2(meanin)-8.7(g,)-393.8(we)]TJ T* [(com)-7.6(pute)-246.6(the)-240.2(med)-7.6(ian)-245.8(AIC)-246.2(score)-243.9(for)-245.2(each)-247.4(categor)-9.7(y)-239.8(and)-243.1(retai)-9.2(n)-239.8(pairs)-244.8(havi)-7.6(ng)-240.5(scor)-8(es)-243.5(above)-246.4(the)-245.8(median.)-248.1(Our)-241.5(n)-6.4(al)]TJ T* [(data)-316.7(set)-309.6(contain)-8.7(s)-309.2(17,226)-311.5(pairs.)-313.5(We)-307.5(tre)-8.8(at)-307.7(the)-308.4(three)-313.7(ontology)-313.2(cat)-8.6(egories)-310.7(as)-311.8(one)-311.4(sing)-7(le)-307.7(data)-311(set)-309.6(whe)-8(n)-308.1(training)]TJ 0 -1.195 TD [(the)-336.9(Infe)-8.8(rSent)-333.9(mode)-8.4(l.)]TJ /F2 1 Tf 0 66.9892 TD (42)Tj 35.8334 0 TD [(DUO)-8(NG)-339(ET)-335.3(AL.)]TJ ET endstream endobj 17 0 obj <> endobj 18 0 obj <>/ProcSet[/PDF/Text]/ExtGState<>>> endobj 19 0 obj <>stream /GS1 gs BT /F1 1 Tf 9.9626 0 0 9.9626 117.5811 715.4644 Tm 0 0 0 rg 0 Tc 0 Tw [(To)-251.7(crea)-10.4(te)-256.5(the)]TJ /F6 1 Tf 5.5198 0 TD (neutral)Tj /F1 1 Tf 3.1526 0 TD [(data)-259.8(set)-8(,)-250.8(w)0(e)-257.6(mak)-7.6(e)-252.9(two)-259.4(types)-259.9(of)-253.9(unrelat)-10.7(ed)-253.7(pairs.)-262.3(For)-253.9(the)-262.9(rst)-252.9(type)-7.6(,)-256.5(w)0(e)-257.6(randomly)-260.8(pick)]TJ -9.6739 -1.195 TD [(about)-292.9(half)-294.1(the)-291.4(number)-290.7(of)-293.7(GO)-288.2(terms)-293.9(in)-294.5(the)]TJ /F6 1 Tf 17.2139 0 TD [(entailmen)-11.3(t)]TJ /F1 1 Tf 4.5354 0 TD [(data)-288.2(set)-8(.)-284.9(F)0(o)-6.4(r)-287.3(each)-292.9(term)]TJ /F6 1 Tf 9.5658 0 TD (c)Tj /F1 1 Tf .7398 0 TD [(in)-288.8(this)-288.6(set)-8(,)-284.9(w)0(e)-291.8(pair)-294.1(it)-285.9(wi)-8.2(th)-288.8(a)]TJ -32.0549 -1.2007 TD [(rando)-7.6(mly)-298.8(chosen)-305.2(GO)-299.6(term)]TJ /F6 1 Tf 11.1136 0 TD (d)Tj /F1 1 Tf .7967 0 TD [(in)-300.2(the)-297.1(same)-301.6(ontol)-9.3(ogy)-298.2(categor)-9.7(y.)-297.1(For)-299.4(the)-302.7(second)-299.6(type)-7.6(,)-296.3(w)0(e)-303.2(pair)-299.8(the)-297.1(sam)-8.8(e)-298.5(term)]TJ /F6 1 Tf 30.7859 0 TD (d)Tj /F1 1 Tf -42.6962 -1.2007 TD [(with)-308.4(another)-309.6(rando)-7.6(mly)-304.5(chose)-8.6(n)-302.4(term)]TJ /F6 1 Tf 14.8011 0 TD (e)Tj /F1 1 Tf .4496 0 TD [(.)-307.7(This)-308.4(sampling)-308.3(scheme)-316.3(improv)-7.1(es)-306.1(the)-302.7(trainin)-11.7(g)-302.4(b)0(y)-303.1(allow)-9.4(ing)-306.7(some)-305.5(GO)]TJ -15.2507 -1.2007 TD [(terms)-339.4(to)-334.3(be)-333.4(seen)-343.6(more)-334.7(than)-337.7(once)-336.7(un)-7.2(der)-336.1(different)-340.6(circum)-10.7(stances.)]TJ 1.0015 -1.2007 TD [(Two)-324.7(unrelated)-327(GO)-322.4(terms)-328(should)-321.5(have)]TJ /F12 1 Tf 15.7401 0 TD (P)Tj /F1 1 Tf 1.1723 0 TD (term)Tj 6.9738 0 0 6.9738 304.4409 654.2361 Tm (1)Tj 9.9626 0 0 9.9626 311.1873 655.7101 Tm [(enta)-9.4(ils)-276.5(ter)-8.8(m)]TJ 6.9738 0 0 6.9738 358.5826 654.2361 Tm (2)Tj /F9 1 Tf 9.9626 0 0 9.9626 282.2172 655.7101 Tm 7.6842 Tc ()Tj /F1 1 Tf 8.7691 0 TD 0 Tc (and)Tj /F12 1 Tf 1.7698 0 TD (P)Tj /F1 1 Tf 1.0072 0 TD (term)Tj 6.9738 0 0 6.9738 415.6156 654.2361 Tm (2)Tj 9.9626 0 0 9.9626 422.3621 655.7101 Tm [(enta)-9.4(ils)-276.5(term)]TJ 6.9738 0 0 6.9738 469.7574 654.2361 Tm (1)Tj /F9 1 Tf 9.9626 0 0 9.9626 393.392 655.7101 Tm 7.6785 Tc ()Tj /F1 1 Tf 8.7691 0 TD 0 Tc [(near)-327.3(zero.)-327.6(For)]TJ -37.4552 -1.2007 TD (each)Tj /F6 1 Tf 2.0941 0 TD [(neut)-7.6(ral)]TJ /F1 1 Tf 3.1526 0 TD [(pair,)-254.7(we)-251.9(create)-255.5(two)-253.7(different)-260.9(samples)-256.6(for)-250.9(InferSen)-9.1(t.)-248.6(Th)-7(e)-247.2(rst)-252.9(sample)-260.3(will)-248.6(be)-253.7(the)-251.5(pair)-254.3(\(denit)-8.1(ion)]TJ -5.2467 -1.2007 TD [(of)-390.5(term)]TJ 7.4718 0 0 6.641 138.1606 630.1416 Tm (1)Tj 9.9626 0 0 9.9626 141.9023 631.7856 Tm [(,)-387.3(de)-9(nition)-388.4(of)-390.5(term)]TJ 7.4718 0 0 6.641 221.1023 630.1416 Tm (2)Tj 9.9626 0 0 9.9626 224.844 631.7856 Tm [(\),)-390.1(and)-391(the)-388.1(secon)-8.6(d)-387.7(sample)-396.9(will)-390.8(be)-390.3(the)-388.1(p)-6.5(air)-390.1(\(denit)-8.2(ion)-386.3(of)-390.5(term)]TJ 7.4718 0 0 6.641 477.3542 630.1416 Tm (2)Tj 9.9626 0 0 9.9626 481.0959 631.7856 Tm [(,)-387.3(denitio)-9.7(n)-387.7(o)0(f)]TJ -37.4893 -1.2007 TD (term)Tj 7.4718 0 0 6.641 126.0283 618.1794 Tm (1)Tj 9.9626 0 0 9.9626 129.7133 619.8235 Tm [(\).)-355.9(Our)-361(nal)]TJ /F6 1 Tf 4.9906 0 TD (neutral)Tj /F1 1 Tf 3.255 0 TD [(data)-356.5(set)-355.2(cont)-7.6(ains)-355.9(35,0)-8.4(44)-354.3(pairs)-358.7(of)-356.3(sentence)-11.5(s.)-355.2(Since)-356.5(the)]TJ /F6 1 Tf 22.4378 0 TD (neutral)Tj /F1 1 Tf 3.255 0 TD [(data)-356.5(set)-360.8(is)-352.6(near)-8.6(ly)]TJ -36.1577 -1.195 TD [(twice)-312.7(as)-311.8(large)-308(as)-311.8(the)]TJ /F6 1 Tf 8.6269 0 TD [(enta)-7.6(ilment)]TJ /F1 1 Tf 4.5524 0 TD [(data)-316.7(set,)-310(when)-310.4(training)-314.1(InferSen)-9.1(t,)-305.5(we)-314.5(weigh)-308.2(rat)-8.8(io)-305.9(1:2)-306.7(for)-313.5(the)-308.4(class)]TJ /F6 1 Tf 27.1212 0 TD (neutral)Tj /F1 1 Tf -40.3005 -1.2007 TD (and)Tj /F6 1 Tf 1.7811 0 TD [(enta)-7.6(ilment)]TJ /F7 1 Tf 4.2679 0 TD (:)Tj /F1 1 Tf -5.0475 -1.2007 TD [(The)-242.9(code)-245.6(to)-237.6(train)-246.4(InferSen)-9.1(t)-236.8(i)0(s)-244.5(available)-249.9(at)-239.4(our)-243.3(GitHub.)-246(We)-244.9(attained)-247.4(96.93%)-245.9(accuracy)-250.3(in)-243.3(the)-240.2(validat)-11.5(ion)-238.4(set.)]TJ -1.0015 -1.2007 TD [(We)-279(emphasi)-10.7(ze)-278.2(that)-277.8(InferSen)-9.1(t)-276.7(relies)-278.6(on)-280.4(the)-274.3(GO)-282.5(tree)-278.8(only)-279(for)-279.4(its)-276.5(training)-279.9(phase)-8.6(.)-273.5(Onc)-8(e)-275.7(the)-280(model)-279.3(is)-278.6(trained,)-278.6(it)]TJ T* [(require)-9.9(s)-332(only)-335.9(the)-336.9(GO)-339.4(denitions)-342.5(as)-334.6(the)-336.9(input)-339.4(for)-336.3(predictio)-9.3(n.)]TJ 1.0015 -1.2007 TD [(When)-297.6(terms)]TJ /F6 1 Tf 5.2182 0 TD (a)Tj /F1 1 Tf .7967 0 TD (and)Tj /F6 1 Tf 1.747 0 TD (b)Tj /F1 1 Tf .791 0 TD [(are)-298.1(unrelat)-10.7(ed,)-293.9(we)-297.5(expec)-9.2(t)]TJ /F12 1 Tf 10.2032 0 TD (P)Tj /F6 1 Tf 1.0015 0 TD (a)Tj /F1 1 Tf .7796 0 TD [(entail)-10.7(s)]TJ /F6 1 Tf 2.9079 0 TD (b)Tj /F9 1 Tf -4.0744 0 TD 4.1902 Tc [()3909.4()]TJ /F12 1 Tf 6.2881 0 TD 0 Tc (P)Tj /F6 1 Tf 1.0015 0 TD (b)Tj /F1 1 Tf .7796 0 TD [(enta)-9.4(ils)]TJ /F6 1 Tf 2.9079 0 TD (a)Tj /F9 1 Tf -4.0687 0 TD 4.1845 Tc [()3624.9()]TJ /F1 1 Tf 6.84 0 TD 0 Tc [(0.)-297.1(When)-297.6(GO)-299.6(term)]TJ /F6 1 Tf 7.614 0 TD (a)Tj /F1 1 Tf .7967 0 TD (is)Tj -42.5312 -1.2007 TD [(the)-319.8(child)-318.4(of)-322.2(term)]TJ /F6 1 Tf 7.1929 0 TD (b)Tj /F1 1 Tf .5008 0 TD [(,)-313.4(w)0(e)-320.2(expec)-9.2(t)]TJ /F12 1 Tf 4.9963 0 TD (P)Tj /F6 1 Tf 1.0015 0 TD (a)Tj /F1 1 Tf .7796 0 TD (entails)Tj /F6 1 Tf 2.9079 0 TD (b)Tj /F9 1 Tf -4.0744 0 TD 4.1902 Tc ()Tj /F1 1 Tf 5.2751 0 TD 0 Tc [(to)-317.3(b)-6.5(e)-315.5(high,)-319.2(whe)-8(reas)]TJ /F12 1 Tf 8.3196 0 TD (P)Tj /F6 1 Tf 1.0015 0 TD (b)Tj /F1 1 Tf .7796 0 TD [(enta)-9.4(ils)]TJ /F6 1 Tf 2.9079 0 TD (a)Tj /F9 1 Tf -4.0687 0 TD 4.1845 Tc ()Tj /F1 1 Tf 5.2751 0 TD 0 Tc [(may)-320.6(be)-316.3(low.)-322.3(Howeve)-10.3(r,)-316.1(in)]TJ -32.7946 -1.2007 TD [(this)-294.3(case)-9.6(,)-290.6(w)0(e)-297.5(still)-294.9(wan)-8(t)-288.1(the)-297.1(simi)-7.6(larity)-295.5(betwee)-10.9(n)]TJ /F6 1 Tf 18.8471 0 TD (a)Tj /F1 1 Tf .7796 0 TD (and)Tj /F6 1 Tf 1.7299 0 TD (b)Tj /F1 1 Tf .791 0 TD [(to)-294.5(be)-293.5(high.)-296.4(Fo)-6.4(r)-293(this)-294.3(reason,)-301.9(to)-288.8(mea)-9.4(sure)-298.2(the)-291.4(sem)-8.8(antic)]TJ -22.1476 -1.195 TD [(similarity)-342.9(for)-336.3(two)-339(GO)-333.8(terms)-9.4(,)-330.4(w)0(e)-337.3(use)-335.3(the)-336.9(metric)]TJ 9.4065 -1.9234 TD [(InferSen)-9.1(tGO)]TJ /F6 1 Tf 5.5654 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7739 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7831 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (=)Tj /F1 1 Tf 1.0015 0 TD (max)Tj /F12 1 Tf 2.5095 0 TD (P)Tj /F6 1 Tf 1.0015 0 TD (a)Tj /F1 1 Tf .7796 0 TD (entails)Tj /F6 1 Tf 2.9079 0 TD (b)Tj /F9 1 Tf -4.0744 0 TD 4.1902 Tc ()Tj /F1 1 Tf 4.9622 0 TD 0 Tc ()Tj /F12 1 Tf .7796 0 TD (P)Tj /F6 1 Tf 1.0015 0 TD (b)Tj /F1 1 Tf .7796 0 TD (entails)Tj /F6 1 Tf 2.9079 0 TD (a)Tj /F9 1 Tf -4.0744 0 TD 4.1902 Tc ()Tj -7.4717 -.0057 TD 11.9282 Tc (fg)Tj /F7 1 Tf 12.9346 .0057 TD 0 Tc (:)Tj /F1 1 Tf 8.5074 0 TD (\(3\))Tj -41.0289 -1.9006 TD [(InferSen)-9.1(tGO)]TJ /F6 1 Tf 5.5597 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F1 1 Tf 2.8851 0 TD 0 Tc [(range)-9.4(s)-332(from)-340.6(0)-330.8(t)0(o)-334.3(1)0(.)]TJ /F6 1 Tf 10.959 0 0 10.959 107.6031 447.8739 Tm [(2.4.)-496.9(Combining)-328.9(node-based)-328.4(and)-331.3(NLP)-335.6(methods)]TJ /F1 1 Tf 9.9626 0 0 9.9626 117.5811 429.9589 Tm [(In)-344.9(this)-345.5(sect)-10.6(ion,)-346.9(we)-348.7(discuss)-349.2(a)-349.7(few)-345.7(exam)-10.2(ples)-350.2(and)-345.5(motiv)-7.2(ate)-350.1(the)-348.3(need)-348.1(for)-347.7(combining)-353.4(node-)-7.6(based)-350(and)-345.5(NLP)]TJ -1.0015 -1.2007 TD [(methods)-8.9(.)-324.7(Here,)-331.6(we)-331.6(choose)-333.7(the)-325.5(no)-7.2(de-based)-333.3(Resni)-8.6(k)-325.1(and)-328.4(AIC,)-332(becau)-9.2(se)-328.9(GraSM)-331.3(and)-328.4(RWC)-332.9(do)-325.9(not)-329.4(yield)-329.8(good)]TJ T* [(results)-341.4(\(Table)-337.1(2\).)]TJ 1.0015 -1.2007 TD [(In)-271(essence,)-282.7(both)-273.3(Resnik)-276.8(and)-271.5(AI)-7.4(C)-272.9(focus)-276.2(on)-269(the)-274.3(fraction)-280.9(of)-271(shar)-8(ed)-270.8(ances)-10.4(tors)-270.7(and)-277.2(weigh)-274.1(this)-277.2(ratio)-274.9(by)-269(the)-274.3(IC)]TJ -1.0015 -1.2007 TD [(values.)-405.1(So)-6.4(metime)-9.3(s,)-400.7(even)-405(when)-407.1(two)-401.6(terms)-407.7(are)-406.2(very)-405.2(similar)-409.1(in)-402.6(meanin)-8.7(g,)-399.5(they)-405.9(can)-404.2(have)-405(a)-400.9(low)-407.3(score.)-403.6(Fo)-6.4(r)]TJ 0 -1.195 TD [(exampl)-8.7(e,)-287.5(consider)-294.4(the)-285.7(terms)-288.2(GO:0)-8(005887)-289.1(and)-288.6(GO:0)-8(016021)-289.1(in)-283.1(the)-291.4(CC)-289.8(ontology)-290.5(\(Table)-291.5(1)-285.3(Row)-289.8(1\).)-288.4(This)-285.7(is)-290(a)]TJ 0 -1.2007 TD [(childpa)-9.5(rent)-390.8(pair,)-396.9(having)-390.4(almost)-397.9(identi)-9(cal)-389.9(deni)-7.6(tion.)-390.2(Howeve)-10.3(r,)-390.1(the)-393.8(Resnik)-396.3(and)-391(AIC)-394.2(scores)-393.8(are)-394.8(not)-392(high)]TJ T* [(enough.)-245.7(In)-242.5(a)-241.6(sample)-248.9(of)-242.5(3244)-242.1(childpa)-9.5(rent)-248.6(pairs)-244.8(in)-237.6(the)-245.8(CC)-244.3(ontology,)-251(we)-240.6(found)-244.8(the)-245.8(median)-247.7(score)-243.9(to)-243.3(be)-242.3(5.5933)]TJ T* [(and)-334.1(0.9278)-339.9(for)-336.3(Resni)-8.6(k)-330.8(and)-339.8(AIC,)-337.7(respective)-12.1(ly.)]TJ 1.0015 -1.2007 TD .0123 Tc [(In)-255.9(the)-252(s)-1(eco)-5.5(nd)-250.2(example)-252(\()-1.8(T)-5.4(a)-1.6(ble)-252(1)-255.9(Row)-254.2(2).1(\),)-249.9(GO:0006)-5.5(814)]TJ 22.3468 0 TD .0128 Tc [(and)-249.7(GO:00)-5(06874)-249.7(are)-251.5(unrelated)-5(,)-249.3(s)-.5(haring)-255.4(only)-249.7(t)3.6(h)-5(e)]TJ -23.3483 -1.2007 TD .0132 Tc [(root)-235(node.)-237.6(I)4.8(nterestingly,)-237.6(one)-239.7(can)-238(ar)4.8(gue)-234(t)-1.7(hat)-235(b)-4.6(oth)-238(t)-1.7(er)]TJ 21.038 0 TD .0129 Tc [(ms)-239.4(are)-234.3(n)-4.9(ot)-235.3(entirely)-238.3(distinct)-235.3(because)-240(they)-238.3(both)-238.2(m)-2.8(ention)]TJ -21.038 -1.2007 TD .0131 Tc [(the)-319.5(r)-1(egulation)-323.4(o)1(f)-319.7(i)3.9(o)-4.7(n)1(s.)-317.3(Similarly)-4.7(,)-317.3(in)-317.7(the)-319.5(t)-1.8(hi)]TJ 17.8456 0 TD [(rd)-317.7(example)-319.5(\()-1(Table)-319.5(1)-323.4(Row)-321.7(3)1(\),)-323(GO:0005829)-323.4(and)-323.4(G)2.7(O:0005615)]TJ -17.8456 -1.2007 TD .0125 Tc [(share)-485.1(o).4(nly)-483.3(t)3.3(he)-485.1(root)-486.1(node,)-483(b)-5.3(ut)-480.4(bo)-5.3(th)-483.3(mention)-483.3()-4.6(uid)-483.3(c)-1.4(ont)]TJ 23.7524 0 TD .0131 Tc [(aining)-482.7(protein)-482.7(c)-.8(o)-4.7(m)3.1(plexes.)-482.4(I)-1(n)-482.7(both)-482.7(e)-.8(xamples,)]TJ -23.7524 -1.195 TD [(W2vGO)-452.5(o)-4.7(n)-454.3(i)3.9(ts)-455.5(own)-454.3(o)1(r)-456.3(a)-.8(n)-454.3(a)-.8(verage)-456.1(of)-456.3(AIC)-459(a)-.8(nd)-454.3(InferSentGO)-458.2(m)3.1(ay)-454.3(g)-4.7(i)3.9(ve)-456.1(a)-456.1(m)-2.6(ore)-456.1(s)-.2(atisfying)-454.3(s)-.2(core.)-453.9(I)-1(n-)]TJ 0 -1.2007 TD .0139 Tc [(fer)5.5(S)-3.2(ent)4.7(G)-2.2(O)-474.5(a)0(nd)-476.3(AI)5.5(C)-475.3(o)-3.9(n)-470.6(t)-1(hei)4.7(r)-478.2(own)-470.6(m)-1.8(ay)-470.6(underes)6.3(timate)-472.4(a)0(nd)-470.6(overesti)4.7(mate)-472.3(the)-472.3(s).6(imilar)5.5(ity,)-470.2(r)-.2(espectivel)4.7(y.)]TJ T* .0131 Tc [(Resnik)-260.8(on)-260.8(its)-267.7(o)1(wn)-266.5(is)-267.7(not)-263.6(the)-262.6(b)1(est)-263.6(b)1(ecause)-262.6(when)-260.8(terms)-267.7(s)-.2(hare)-262.6(only)-260.8(t)-1.8(he)-262.6(root)-263.6(node,)-260.4(t)-1.8(he)-262.6(similarity)-266.5(score)-262.6(i)-1.8(s)-262(t)3.9(he)]TJ T* .0129 Tc [(IC)-334(of)-331.3(the)-331.1(r)-1.2(oot)-337.7(that)-332.1(is)-336.2(0.)]TJ 1.0015 -1.2007 TD -.0163 Tc [(In)-284.5(the)-286.3().8(nal)-287.3(e)3.9(xample)-280.6(\(Table)-280.6(1)-284.5(R)1(ow)-282.8(4\),)-284.1(GO:00)5.7(04620)-284.5(and)-284.5(G)1.8(O:001990)5.7(5)-284.5(s)-1.2(hare)-286.3(on)5.7(ly)-284.5(the)-280.6(r)-2(oot)-281.6(node)-280.6(and)-278.8(t)-2.8(ruly)-278.8(are)]TJ -1.0015 -1.2007 TD -.0154 Tc [(diff)4.6(er)4.6(ent)-331.9(i)3.8(n)-334.8(m)3.1(ea)4.8(ning)6.6(.)-334.5(H)2.7(er)4.6(e,)-328.8(Re)4.8(snik)-334.8(a)4.8(n).9(d)-334.8(I)4.6(nfe)4.8(r)-1.1(Sent)]TJ 19.382 0 TD -.0169 Tc [(GO)-334.6(give)-332.4(more)-338.1(reasonab)5.1(l)-3.4(e)-332.4(s)-1.8(cores)-331.8(t)2.3(han)-330.7(A)-4.5(IC)-335.4(and)-336.3(W)2.5(2vGO)-334.6(d)5.1(o.)]TJ -18.3805 -1.2007 TD 0 Tc [(These)-275.8(exampl)-8.7(es)-272(sugges)-8.7(t)-271(that)-277.8(no)-269(one)-277.2(method)-280.1(is)-272.9(always)-277.8(the)-274.3(best,)-276.6(and)-271.5(that)-277.8(we)-274.7(need)-274.1(to)-277.4(combine)-277(node-)-7.6(based)]TJ -1.0015 -1.2007 TD [(and)-322.8(NLP)-329.6(approache)-10.3(s.)-321(To)-325.7(this)-322.7(end,)-323.1(taking)-330.6(an)-322(aver)-8.6(age)-324.5(of)-322.2(AIC)-325.9(and)-322.7(InferSen)-9.1(tGO)-325.9(is)-324.2(reasonabl)-12.5(e.)-321.6(Empiri)-9.7(cally,)]TJ 0 -1.195 TD [(from)-340.6(the)-342.6(exam)-10.2(ples,)-344.9(we)-343(have)-342.4(seen)-343.6(that)-346.1(this)-339.8(aver)-8.6(age)-341.6(produc)-8.3(es)-340.3(a)-338.3(reas)-9.8(onable)-346.7(value.)-340.6(Th)-7(eoreticall)-10.7(y,)-342.6(only)-341.6(AIC)]TJ 0 -1.2007 TD [(and)-300(InferSen)-9.1(tGO)-297.4(scor)-8(es)-294.7(are)-303.7(in)-294.5(the)-297.1(same)-574.7(0)-447.4(1)]TJ /F9 1 Tf 16.5083 0 TD 1.7843 Tc ()Tj /F1 1 Tf 2.6177 0 TD 0 Tc [(range)-9.4(;)-293.7(whe)-8(reas)-300(Resnik)-299.6(and)-300(W2vG)-9.5(O)-294.9(scores)-302.7(are)-298.1(in)-300.2(the)-297.1(range)]TJ -18.8528 -1.2007 TD (0)Tj /F9 1 Tf 1.2747 0 TD (1)Tj -1.5478 0 TD 2.2794 Tc ()Tj /F1 1 Tf 3.1184 0 TD 0 Tc (and)Tj /F8 1 Tf 2.1795 0 TD (-)Tj /F1 1 Tf .7227 0 TD [(1)-441.7(1)]TJ /F9 1 Tf -1.1609 0 TD 2.6663 Tc ()Tj /F1 1 Tf 3.2095 0 TD 0 Tc [(,)-296.3(respective)-12.1(ly)-294.5(\(see)-300(Appendi)-8.1(x\).)-294.1(We)-296.1(n)-6.5(ote)-291.4(that)-300.6(simDE)-9.3(F)-290.2(scor)-8(e)-292.8(range)-299.6(is)]TJ /F8 1 Tf 27.9406 0 TD (-)Tj /F1 1 Tf .7227 0 TD [(1)-447.4(1)]TJ /F9 1 Tf -1.1609 0 TD 2.672 Tc ()Tj /F1 1 Tf 3.2095 0 TD 0 Tc [(,)-296.3(making)-297.2(it)]TJ -38.7811 -1.2007 TD [(incompa)-9.5(tible)-338.2(with)-336.9(Resni)-8.6(k)-330.8(and)-339.8(AIC.)]TJ 1.0015 -1.2007 TD [(For)-333.5(two)-339(GO)-333.7(terms)]TJ /F6 1 Tf 7.8928 0 TD (a)Tj /F1 1 Tf .8365 0 TD (and)Tj /F6 1 Tf 1.7811 0 TD (b)Tj /F1 1 Tf .5008 0 TD [(,)-336.1(w)0(e)-337.3(introdu)-7.1(ce)-335.2(the)-336.9(metric)]TJ -2.612 -2.6006 TD [(AicIn)-8.6(ferSent)-9.1(GO)]TJ /F6 1 Tf 7.0164 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (=)Tj ET 308.75 107.49 131.187 .39685 re f BT /F1 1 Tf 9.9626 0 0 9.9626 308.7495 111.9684 Tm (AIC)Tj /F6 1 Tf 2.1112 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7739 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7774 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (+)Tj /F1 1 Tf 1.0015 0 TD [(InferSen)-9.1(tGO)]TJ /F6 1 Tf 5.5597 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .5008 0 TD (b)Tj /F9 1 Tf -1.3885 0 TD 1.5043 Tc ()Tj /F1 1 Tf -4.5581 -1.3657 TD 0 Tc (2)Tj /F7 1 Tf 6.9994 .6829 TD (:)Tj /F1 1 Tf 8.5074 0 TD (\(4\))Tj -41.0289 -2.3331 TD [(From)-326.4(AICs)-330.6(perspectiv)-10.3(e,)-327.3(AicInfer)-10.9(SentGO)-329.2(improv)-7.1(es)-323.2(the)-331.2(distinction)-332.5(between)-330.4(childpa)-9.5(rent)-328.2(and)-328.4(randomly)]TJ -1.0015 -1.2007 TD [(matche)-10.5(d)-393.4(G)0(O)-396.3(terms,)-396.7(espec)-10.4(ially)-395.2(in)-396.9(the)-399.5(CC)-392.2(and)-396.7(MF)-395.3(o)-6.5(ntologies)-399.4(\(Fig.)-400(2\).)-390.8(From)-400.4(InferSen)-9.1(tGOs)-398.9(pers)-8(pective,)]TJ /F2 1 Tf 0 66.9948 TD [(SEMANT)-12.2(IC)-336.7(SIMILA)-11.7(RITY)-335.5(OF)-340.6(GO)-338.6(DEFINITIO)-14(NS)-19750.9(43)]TJ ET endstream endobj 20 0 obj <> endobj 21 0 obj <>/ProcSet[/PDF/Text]/ExtGState<>>> endobj 22 0 obj <>stream /GS1 gs BT /F1 1 Tf 9.9626 0 0 9.9626 74.0976 355.4078 Tm 0 0 0 rg 0 Tc 0 Tw [(Ai)-8.2(cInferSentG)-14.2(O)-363.2(give)-7.6(s)-366.2(a)-366.7(mor)-7.8(e)-366.7(continuo)-7.7(us)-366.9(scor)-8(e,)-367.1(allowing)-372.9(for)-370.4(a)-366.7(better)-374.1(reso)-8(lution)-371.4(when)-367.3(com)-7.6(paring)-369.6(terms)-9.4(.)]TJ 0 -1.2007 TD [(Infe)-8.8(rSentG)-8.6(O)-334.8(o)0(n)-331.6(its)-339.1(own)-336.3(tends)-339.6(to)-334.3(give)-337.7(a)-332.6(stiff)-338.8(0/1)-335.1(score.)]TJ /F6 1 Tf 10.959 0 0 10.959 74.0976 313.455 Tm [(2.5.)-502(Measuring)-330.1(similarity)-329.6(of)-331.2(two)-332.6(genes)]TJ /F1 1 Tf 9.9626 0 0 9.9626 84.0755 295.5401 Tm 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[(as)-260.6(a)-258.6(set)-264.1(of)-259.6(GO)-265.5(terms)-9.4(.)-256.5(A)-260.8(GO)-265.5(term)]TJ /F6 1 Tf 13.498 0 TD (a)Tj /F1 1 Tf .7625 0 TD [(is)-255.9(in)-266.1(the)]TJ -40.0046 -1.195 TD (set)Tj /F6 1 Tf 1.4511 0 TD (A)Tj /F1 1 Tf .9503 0 TD (\(i.e.,)Tj /F6 1 Tf 2.151 0 TD (a)Tj /F9 1 Tf .7739 0 TD (2)Tj /F6 1 Tf .9389 0 TD (A)Tj /F1 1 Tf .6146 0 TD .3328 Tc [(\)i)332.8(f)]TJ /F6 1 Tf 1.6161 0 TD 0 Tc (a)Tj /F1 1 Tf .8308 0 TD [(is)-335.5(used)-341.8(to)-334.3(annotat)-8.7(e)]TJ /F6 1 Tf 8.0351 0 TD (A)Tj /F1 1 Tf .6146 0 TD (.)Tj -16.9749 -1.2007 TD -.016 Tc [(To)-238.7(ass)4.8(e)-1.5(ss)-239.9(the)-240.5(s)-.9(imilar)4(ity)-238.7(b).3(etween)-238.7(two)-238.7(g).3(e)4.2(n).3(es)]TJ /F6 1 Tf 16.827 0 TD 0 Tc (A)Tj /F1 1 Tf .8365 0 TD -.0154 Tc (and)Tj /F6 1 Tf 1.6389 0 TD 0 Tc (B)Tj /F1 1 Tf .5975 0 TD -.0156 Tc [(,)-237.9(w)2.5(e)-240.1(m)-2.8(us)5.2(t)-241.1(c)-1.1(o)6.4(m)-2.8(pa)4.6(re)-240.1(two)-238.3(s)5.2(ets)-239.5(o).7(f)-240.3(G)2.5(O)-242.2(t)3.6(erms.)-237.9(T).9(he)4.6(re)-240.1(ar)4.4(e)-240.1(m)2.9(any)]TJ -20.9014 -1.2007 TD -.0162 Tc [(metrics)-262.8(f)3.8(or)-257.9(this)-257.2(task)-261.7(\()-81.5(M)-1.9(azandu)-256(et)-258.7(al)]TJ 13.8394 0 TD -.0166 Tc [(.,)-256(2017\).)-261.7(H)1.5(ere,)-261.7(we)-258.2(use)-258.2(t)-3.1(he)-258.2(MHD)-260.3(a)-2.1(nd)-256.4(the)-258.2(b)-.3(est)-259.1(m)-3.8(ax)-262.1(av)5.4(erage)-263.9(d)-.3(istance)-263.9(\()3.4(BMA\).)]TJ -13.8394 -1.2007 TD -.016 Tc [(MHD)-299.5(i)3.2(s)-296.8(a)-303.1(trad)6(itional)-298.4(m)2.5(etric)-303.1(f)4(or)-297.6(comparing)-295.6(t)-2.5(wo)-301.3(s)4.8(e)-1.5(ts)4.8(,)-300.9(a)-1.5(n)6(d)]TJ 22.5175 0 TD [(was)-302.5(o)6(ften)-301.3(us)4.8(ed)-301.3(in)-295.6(image)-297.4(p).3(roc)4.2(e)-1.5(ss)4.8(ing)-295.6(\()-1.7(i.e.,)-295.2(t)3.2(o)-301.3(c)-1.5(ompar)4(e)]TJ -22.5175 -1.2007 TD -.0164 Tc [(two)-267.6(s)-1.3(ets)-268.7(o)-.1(f)-269.5(p)-.1(ixels\))-263.8(\(Dubuisso)5.6(n)-273.2(a)3.8(nd)-267.6(Jain,)-267.2(1994\).)-267.2(B).9(MA)-271.5(has)-268.7(b)]TJ 23.0524 0 TD [(een)-267.6(shown)-273.2(t)2.8(o)-267.6(b)-.1(e)-269.3(b)-.1(etter)-269.5(t)2.8(han)-267.6(t)2.8(aking)-267.6(t)2.8(he)-269.3(maximum)-265.4(o)-.1(r)]TJ -23.0524 -1.2007 TD [(minimum)-333.8(o)5.5(f)-337.9(a)3.7(ll)-327.3(pairwise)-337.7(d)5.5(i)-3(stan)5.5(ces)-331.4(for)-332.2(t)2.7(he)-332(elements)-331.4(in)-330.2(the)-337.7(t)2.7(wo)-335.9(sets)-337.1(\(Pesqu)5.5(ita)-332(e)-2(t)-333(a)-2(l.,)-329.9(2008\).)]TJ 7.3124 -2.9136 TD 0 Tc (MHD)Tj /F6 1 Tf 2.7144 0 TD (A)Tj /F1 1 Tf .6146 0 TD ()Tj /F6 1 Tf .7796 0 TD (B)Tj /F9 1 Tf -1.7811 0 TD 2.0107 Tc ()Tj /F8 1 Tf 3.2265 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (min)Tj ET 240.264 161.178 12.019 .39687 re f BT 9.9626 0 0 9.9626 243.7794 165.7133 Tm (1)Tj /F6 1 Tf -.0341 -1.3714 TD (A)Tj /F9 1 Tf -.3187 0 TD .6689 Tc (jj)Tj /F11 1 Tf 1.5421 1.6389 TD 0 Tc (X)Tj /F6 1 Tf 6.9738 0 0 6.9738 256.592 148.1385 Tm (a)Tj /F9 1 Tf .504 0 TD (2)Tj /F6 1 Tf .6585 0 TD (A)Tj /F1 1 Tf 9.9626 0 0 9.9626 273.2598 158.9102 Tm (max)Tj /F6 1 Tf 6.9738 0 0 6.9738 275.6976 152.5039 Tm (b)Tj /F9 1 Tf .504 0 TD (2)Tj /F6 1 Tf .6585 0 TD (B)Tj 9.9626 0 0 9.9626 293.8393 158.9102 Tm .3889 Tc (sa)Tj /F1 1 Tf 1.2747 0 TD 0 Tc ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F1 1 Tf 2.5494 0 TD 0 Tc ()Tj ET 332.561 161.178 11.509 .39687 re f BT 9.9626 0 0 9.9626 335.792 165.7133 Tm (1)Tj /F6 1 Tf -.0569 -1.3714 TD (B)Tj /F9 1 Tf -.2675 0 TD .612 Tc (jj)Tj /F11 1 Tf 1.599 1.6389 TD 0 Tc (X)Tj /F6 1 Tf 6.9738 0 0 6.9738 349.455 148.0818 Tm (b)Tj /F9 1 Tf .504 0 TD (2)Tj /F6 1 Tf .6585 0 TD (B)Tj /F1 1 Tf 9.9626 0 0 9.9626 367.2566 158.9102 Tm (max)Tj /F6 1 Tf 6.9738 0 0 6.9738 369.6944 152.6173 Tm (a)Tj /F9 1 Tf .504 0 TD (2)Tj /F6 1 Tf .6503 0 TD (A)Tj 9.9626 0 0 9.9626 388.9133 158.9102 Tm .3889 Tc (sa)Tj /F1 1 Tf 1.2747 0 TD 0 Tc ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F11 1 Tf -16.3888 1.7129 TD 18.4207 Tc (\(\))Tj /F7 1 Tf 20.025 -1.7129 TD 0 Tc (:)Tj /F1 1 Tf 6.4132 0 TD (\(5\))Tj -35.4863 -3.6363 TD (BMA)Tj /F6 1 Tf 2.942 0 TD (A)Tj /F1 1 Tf .6146 0 TD ()Tj /F6 1 Tf .7796 0 TD (B)Tj /F9 1 Tf -1.7811 0 TD 2.0107 Tc ()Tj /F8 1 Tf 3.2265 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (mean)Tj ET 241.058 124.951 12.019 .39685 re f BT 9.9626 0 0 9.9626 244.5732 129.4299 Tm (1)Tj /F6 1 Tf -.0285 -1.3657 TD (A)Tj /F9 1 Tf -.3244 -.0057 TD .6689 Tc (jj)Tj /F11 1 Tf 1.6559 1.6389 TD 0 Tc (X)Tj /F6 1 Tf 6.9738 0 0 6.9738 258.5196 111.9118 Tm (a)Tj /F9 1 Tf .4959 0 TD (2)Tj /F6 1 Tf .6585 0 TD (A)Tj /F1 1 Tf 9.9626 0 0 9.9626 276.2645 122.6834 Tm (max)Tj /F6 1 Tf 6.9738 0 0 6.9738 278.7023 116.2771 Tm (b)Tj /F9 1 Tf .504 0 TD (2)Tj /F6 1 Tf .6585 0 TD (B)Tj 9.9626 0 0 9.9626 297.9779 122.6834 Tm (s)Tj /F1 1 Tf .387 0 TD (\()Tj /F6 1 Tf .3301 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F1 1 Tf .5008 0 TD (\))Tj ET 335.622 124.951 11.565 .39685 re f BT 9.9626 0 0 9.9626 338.9102 129.4299 Tm (1)Tj /F6 1 Tf -.0569 -1.3657 TD (B)Tj /F9 1 Tf -.2731 -.0057 TD .6177 Tc (jj)Tj /F11 1 Tf 1.6047 1.6389 TD 0 Tc (X)Tj /F6 1 Tf 6.9738 0 0 6.9738 352.5731 111.7984 Tm (b)Tj /F9 1 Tf .4959 0 TD (2)Tj /F6 1 Tf .6585 0 TD (B)Tj /F1 1 Tf 9.9626 0 0 9.9626 370.318 122.6834 Tm (max)Tj /F6 1 Tf 6.9738 0 0 6.9738 372.7558 116.3338 Tm (a)Tj /F9 1 Tf .504 0 TD (2)Tj /F6 1 Tf .6585 0 TD (A)Tj 9.9626 0 0 9.9626 392.0314 122.6834 Tm (s)Tj /F1 1 Tf .387 0 TD (\()Tj /F6 1 Tf .3301 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F1 1 Tf .5008 0 TD (\))Tj /F11 1 Tf -18.7333 1.7129 TD 18.5459 Tc (\(\))Tj /F7 1 Tf 20.7079 -1.7129 TD 0 Tc (:)Tj /F1 1 Tf 5.6507 0 TD (\(6\))Tj -41.0345 -2.8965 TD [(In)-259.6(the)-262.9(above,)-263.8(the)-262.9(functi)-8.2(on)]TJ /F6 1 Tf 10.5901 0 TD (s)Tj /F1 1 Tf .387 0 TD (\()Tj /F6 1 Tf .3357 0 TD (a)Tj /F1 1 Tf .5008 0 TD (,)Tj /F6 1 Tf .5065 0 TD (b)Tj /F1 1 Tf .5008 0 TD [(\))-258.8(i)0(s)-261.6(a)-264.3(generic)-265.8(placehol)-11.3(der)-262.1(for)-256.6(mea)-9.4(suring)-260.9(the)-262.9(simi)-7.6(larity)-261.3(of)-259.6(GO)-265.5(terms)]TJ /F6 1 Tf 27.1724 0 TD (a)Tj /F1 1 Tf .7568 0 TD (and)Tj /F6 1 Tf -41.7516 -1.2007 TD (b)Tj /F1 1 Tf .5008 0 TD [(.)-307.7(For)-305.1(exam)-10.2(ple,)-303.1(if)-307.9(one)-305.7(u)-6.5(ses)-308.1(Resnik,)-311.3(AIC,)-309.2(or)-305.1(W2vGO)-310.1(metri)-10.9(c,)-304.5(then)]TJ /F6 1 Tf 26.5407 0 TD .3832 Tc (sa)Tj /F1 1 Tf 1.269 0 TD 0 Tc ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7774 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (=)Tj /F1 1 Tf 1.0015 0 TD (Resnik)Tj /F6 1 Tf 3.1696 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F1 1 Tf 2.5551 0 TD 0 Tc [()-446.6(AIC)]TJ /F6 1 Tf 2.8851 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F1 1 Tf 2.5551 0 TD .302 Tc [(,o)302(r)]TJ -41.8142 -1.2007 TD 0 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[(First,)-256.8(intuitivel)-8.9(y,)-245.8(whe)-8(n)-245.5(u)-6.5(sing)-251.7(all)-248.6(BP,)-250.5(CC,)-256(and)-248.8(MF)-253.1(terms)-254.1(in)-249(the)-251.5(gene)-257(annotat)-8.7(ion,)-250.1(one)-248.8(can)-256.2(better)-254.6(under)-7.6(stand)]TJ -1.0015 -1.2007 TD [(the)-314.1(genes)-312.9(functi)-8.2(onality.)-311.7(For)-310.8(exampl)-8.7(e,)-304.5(whe)-8(n)-308.1(looking)-312.5(at)-307.7(the)-308.4(CC)-312.6(ontology)-313.2(terms)-311(alone,)-312.1(argua)-9.4(bly)-306.7(protei)-8.2(ns)-304.3(in)]TJ T* [(the)-280(same)-278.8(part)-277(of)-271(the)-274.3(cel)-8.6(l)-271(d)0(o)-274.7(not)-272.5(neces)-10.4(sarily)-276.8(interact)-10.3(.)-273.5(Howeve)-10.3(r,)-270.6(whe)-8(n)-268.2(w)0(e)-280.4(consider)-277.4(not)-278.2(only)-273.3(the)-274.3(loca)-9.4(tions)-272.3(bu)-7.2(t)]TJ T* 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[(bein)-7.6(g)-330.8(sma)-8.8(ll,)-331.8(has)-341(a)-332.6(nontriv)-7.1(ial)-334(repe)-8.6(rcussio)-8.6(n.)]TJ 1.0015 -1.2007 TD [(This)-445(effect)-443.4(is)-438(espec)-10.4(ially)-440.7(true)-442.1(for)-438.7(Resni)-8.6(k)-438.9(and)-442.3(AIC)-439.7(whos)-8.2(e)-435(key)-442.2(ideas)-443.8(rely)-442.1(on)-439.7(the)-439.3(numb)-6.6(er)-437.8(of)-441.7(common)]TJ -1.0015 -1.2007 TD [(ances)-10.4(tors.)-282.5(For)-282.3(example,)-284.8(consid)-10.3(er)-278.4(the)-280(term)-286.3(GO:0009055)-285.7(in)-283.1(the)-280(MF)-281.5(ontology)-284.8(with)-280(its)-282.1(parent)-286(GO:0022)-10.3(900)-275.4(in)]TJ T* [(the)-359.7(BP)-358.3(categor)-9.7(y)-353.6(\(Fig)-7(.)-353.2(1\).)-356.7(When)-360.2(treating)-361.4(the)-359.6(BP)-358.3(and)-356.9(MF)-355.5(trees)-360.4(separ)-10.5(ately,)-360.4(GO:0009)-10.3(055)-355.1(and)-356.9(GO:0)-8(022900)]TJ T* [(have)-274.1(AIC)-269(scor)-8(e)-270(0)-262.5(becau)-9.2(se)-272(they)-269.4(will)-271.3(not)-266.8(have)-274.1(any)-265.8(shar)-8(ed)-270.8(ancestors.)-275.8(When)-274.8(treating)-270.3(the)-274.3(trees)-269.4(jointly,)-272.8(the)-268.6(AI)-7.4(C)]TJ 0 -1.195 TD [(scor)-8(e)-287.1(i)0(s)-290(0.7197.)-289.1(Th)-7(us,)-287.6(we)-291.8(can)-290.4(better)-294.5(estimate)-297.6(the)-285.7(simi)-7.6(larity)-289.8(betwee)-10.9(n)-285.3(genes)-293.1(cont)-7.6(aining)-290.7(not)-289.6(only)-290.3(these)-295.9(terms)]TJ 0 -1.2007 TD [(bu)-7.2(t)-333.6(also)-333.2(their)-337.5(d)-6.5(escendant)-342.3(terms.)]TJ ET 74.098 361.417 430.413 .51022 re f 74.098 130.904 430.413 .51022 re f 74.098 342.992 430.413 .51022 re f 74.098 236.976 430.413 .45352 re f BT /F4 1 Tf 8.9663 0 0 8.9663 109.474 367.5967 Tm (Table)Tj /F1 1 Tf 2.9971 0 TD (2.)Tj /F4 1 Tf 1.2519 0 TD [(Area)-335(Under)-334.4(the)-333.5(Curves)-330.2(for)-334.7(Classifying)-336.5(Human)-338.9(ProteinProtein)-329.8(Interactions)]TJ /F6 1 Tf -8.1945 -2.0233 TD [(Set)-340.1(metric)-5053.8(GO)-334.4(metric)-5875.8(BPs)-5494(CCs)-5390(MFs)-5167.5(Joint)]TJ /F1 1 Tf 6.7246 0 0 5.9768 456.1511 353.4802 Tm (a)Tj /F6 1 Tf 8.9663 0 0 8.9663 462.1605 349.455 Tm (\()Tj /F1 1 Tf .3351 0 TD (p)Tj /F6 1 Tf .8346 0 TD (value)Tj /F1 1 Tf 2.1751 0 TD (*)Tj /F6 1 Tf .4995 0 TD (\))Tj /F1 1 Tf -47.1247 -2.0739 TD [(MHD)-5721.7(Resnik)-7748.7(0.84194)-3907.6(0.77278)-3913.9(0.70436)-3913.9(0.86074)-335.1(\(2.93E-05\))]TJ 8.0427 -1.2266 TD (Resnik)Tj 6.2762 0 0 6.2762 173.5936 318.5574 Tm (RWC)Tj 8.9663 0 0 8.9663 240.6046 319.8613 Tm [(0.83743)-3907.6(0.75944)-3913.9(0.68886)-7170.2(NA)]TJ -10.5276 -1.2203 TD [(AIC)-8810.7(0.84042)-3907.6(0.76218)-3913.9(0.69590)-3913.9(0.85815)-335.1(\(5.93E-06\))]TJ T* [(GraSM)-7592.7(0.76895)-3907.6(0.67114)-3913.9(0.64938)-7170.2(NA)]TJ T* (GraSM)Tj 6.2762 0 0 6.2762 175.011 285.6755 Tm (RWC)Tj 8.9663 0 0 8.9663 240.6046 287.0361 Tm [(0.76521)-3907.6(0.66967)-3913.9(0.63231)-7170.2(NA)]TJ -10.5276 -1.2266 TD [(simDEF)-7196.7(0.81356)-3907.6(0.72980)-3913.9(0.72644)-3913.9(0.84686)-335.1(\(1.80E-09\))]TJ 0 -1.2203 TD [(W2vGO)-7144.7(0.8246)-4407.5(0.79338)-3913.9(0.71915)-3913.9(0.86571)-335.1(\(4.66E-04\))]TJ T* [(InferSentGO)-5365.7(0.83877)-3907.6(0.76026)-3913.9(0.75343)-3913.9(0.85368)-335.1(\(2.98E-07\))]TJ 0 -1.2267 TD [(AicInferSentGO)-3919.7(0.84830)-3907.6(0.78263)-3913.9(0.74489)-3913.9(0.86871)-335.1(\(2.05E-03\))]TJ -8.0427 -2.0486 TD [(BMA)-5773.7(Resnik)-7748.7(0.85434)-3907.6(0.77871)-3913.9(0.70348)-3913.9(0.86766)-335.1(\(1.24E-03\))]TJ 8.0427 -1.2203 TD (Resnik)Tj 6.2762 0 0 6.2762 173.5936 212.485 Tm (RWC)Tj 8.9663 0 0 8.9663 240.6046 213.8456 Tm [(0.84399)-3907.6(0.75626)-3913.9(0.68595)-7170.2(NA)]TJ -10.5276 -1.2203 TD [(AIC)-8810.7(0.85423)-3907.6(0.77628)-3913.9(0.69902)-3913.9(0.87854)-335.1(\(9.19E-02\))]TJ 0 -1.2267 TD [(GraSM)-7592.7(0.76895)-3907.6(0.67114)-3913.9(0.64938)-7170.2(NA)]TJ 0 -1.2203 TD (GraSM)Tj 6.2762 0 0 6.2762 175.011 179.6031 Tm (RWC)Tj 8.9663 0 0 8.9663 240.6046 180.9638 Tm [(0.74201)-3907.6(0.64989)-3913.9(0.62591)-7170.2(NA)]TJ -10.5276 -1.2203 TD [(simDEF)-7196.7(0.83597)-3907.6(0.74432)-3913.9(0.72863)-3913.9(0.86958)-335.1(\(3.05E-03\))]TJ 0 -1.2266 TD [(W2vGO)-7144.7(0.84296)]TJ /F2 1 Tf 17.6852 0 TD (0.80035)Tj /F1 1 Tf 7.1639 0 TD [(0.71279)-3913.9(0.88170)-335.1(\(2.21E-01\))]TJ -24.849 -1.2203 TD [(InferSentGO)-5365.7(0.84600)-3907.6(0.76548)]TJ /F2 1 Tf 24.849 0 TD (0.76081)Tj /F1 1 Tf 7.1639 0 TD [(0.87503)-335.1(\(2.85E-02\))]TJ -32.0129 -1.2203 TD (AicInferSentGO)Tj /F2 1 Tf 10.5276 0 TD (0.85739)Tj /F1 1 Tf 7.1575 0 TD [(0.79011)-3913.9(0.74139)]TJ /F2 1 Tf 16.6798 0 TD (0.88987)Tj /F1 1 Tf 7.9702 0 0 7.9702 82.0913 119.9622 Tm [(Bold)-329.2(font)-327.9(indicates)-329(the)-329.8(best)-328.9(value)-328.8(in)-335.8(each)-328.5(column.)]TJ 5.9774 0 0 5.3127 82.0913 113.4992 Tm (a)Tj 7.9702 0 0 7.9702 84.7559 109.9842 Tm [(Joint)-265.2(analysis:)-255.9(When)-266.3(comparin)11.9(g)-268.2(genes,)-259.4(we)-264.7(keep)-261.3(their)-263.5(entire)-264.6(GO)-264(annotation)11.8(s,)-268.4(effectiv)10.3(ely)-265.8(treating)-259(the)-265.8(BP,)-260.5(CC,)-267.4(and)-260.2(MF)-263(ontologies)-256.5(as)]TJ -1.3373 -1.2519 TD [(connected)-326.9(GO)-335.2(trees.)]TJ 1.003 -1.2519 TD (*)Tj /F6 1 Tf .4979 0 TD (p)Tj /F1 1 Tf .8322 0 TD [(value)-328.8(of)-333.6(the)-329.8(HanleyMcNe)14.5(il)-334.3(test)-334.5(to)-328.6(compare)-329.2(AUCs)-329.8(of)-326.4(other)-329(methods)-326.2(against)-331.5(BMA)]TJ /F8 1 Tf 34.143 0 TD (+)Tj /F1 1 Tf .5477 0 TD [(AicInferSentGO)14.1(.)]TJ -36.0209 -1.2448 TD -.0215 Tc [(AUCs,)-226.7(area)-228.9(under)-229.1(t)-3.7(he)-228.9(curves)-6.4(;)-224.2(B)-2.8(MA,)-226.7(b)1.9(es)-6.4(t)-224.2(m)-1.6(ax)-225.7(average)-228.9(d)1.9(i)-3.7(s).7(t)-3.7(a)-1.3(nce;)-231.3(BPs,)-226.7(bi)]TJ 27.3002 0 TD -.0219 Tc [(ol)-4.1(ogi)-4.1(cal)-231.7(processes)-6.8(;)-224.6(CCs)-6.8(,)-227.1(cell)-4.1(u)1.5(l)-4.1(a)-1.7(r)-229.5(c)-1.7(omponen)-5.6(t)3(s;)-231.7(GraSM)-4.7(,)-227.1(graph)-5.6(-)5.2(b)-5.6(a)-1.7(sed)]TJ -28.3032 -1.2519 TD 0 Tc [(similarity)-210.6(measure;)-213(MFs,)-204.2(molecular)-208.2(functions;)-210.1(MHD,)-203.1(modied)-209(Hausdorff)-204.7(distance;)-208.1(NA,)-206.1(not)-205.7(available;)-213.6(RWC,)-209.6(random)-203.9(walk)-209.3(contribution.)]TJ /F2 1 Tf 9.9626 0 0 9.9626 74.0976 737.4045 Tm (46)Tj 35.8334 0 TD [(DUO)-8(NG)-339(ET)-335.3(AL.)]TJ ET endstream endobj 33 0 obj <> endobj 34 0 obj <>/ProcSet[/PDF/Text]/ExtGState<>>> endobj 35 0 obj <>stream /GS1 gs BT /F1 1 Tf 9.9626 0 0 9.9626 117.5811 279.1558 Tm 0 0 0 rg 0 Tc 0 Tw 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[(A)12.4(i)19.2(cI)23.2(n)16.3(f)14.3(e)14.5(r)14.3(S)11.4(e)14.5(nt)24.2(G)18.1(O)-630.7(do)26.9(e)14.5(s)-633.6(b)16.3(e)14.5(st)28.7(.)-632(W)13.7(e)-628.5(n)0(o)26.9(t)13.5(e)-628.5(t)13.5(ha)25.1(t)]TJ -25.488 -1.2007 TD -.013 Tc (BMA)Tj /F8 1 Tf 2.2307 0 TD 0 Tc (+)Tj /F1 1 Tf .5349 0 TD -.0144 Tc [(W)-14.4(2)10(vGO,)-305(des)-14.4(p)11.3(ite)-301.5(no)-14.4(t)-291.8(u)1.9(sing)-305.4(info)-14.4(r)10.5(m)-1.6(ation)-299.7(f)-.1(r)-14.4(o)10.5(m)-303.2(t)-.9(he)-301.5(GO)-303.6(tree)-14.4(s)9.5(,)-299.3(wor)-14.4(k)10.5(s)-300.9(q)-14.4(u)12.5(ite)-301.5(well)-302.5(on)-305.4(it)4.8(s)-306.6(o)1.9(wn)-299.7(\(s)-14.4(e)9.5(c).1(on)-14.4(d)-289.1(r)-.1(a)-14.4(n)10.7(k\).)]TJ -1.7641 -1.195 TD 0 Tc [(We)-273.3(use)-272.7(the)-274.3(Hanley)-9.1(McNei)-11.1(l)-271(test)-273.3(to)-271.7(compare)-278(AUC)-9.2(s)-269.4(o)0(f)-271(the)-274.3(othe)-7.6(r)-270.2(methods)-276.4(against)-277.4(BM)-8.2(A)]TJ /F8 1 Tf 34.7465 0 TD (+)Tj /F1 1 Tf .8251 0 TD [(AicInfer)-10.9(SentGO)]TJ -36.5732 -1.2007 TD [(\(Hanl)-8.6(ey)-396(and)-396.7(McNeil,)-401.2(1983\).)-398.8(The)]TJ /F6 1 Tf 14.1239 0 TD (p)Tj /F1 1 Tf .8934 0 TD [(valu)-7.6(es)-397.2(in)-391.3(colu)-7.6(mn)-397.7(6)-393.4(o)0(f)-396.2(Table)-396.9(2)-399.1(show)-395.1(that)-397.3(BMA)]TJ /F8 1 Tf 19.9397 0 TD (+)Tj /F1 1 Tf .552 0 TD [(AicIn)-8.6(ferSent)-9.1(GO)-396.4(is)]TJ -35.509 -1.2007 TD [(slightly)-399.6(better)-396.9(than)-400.2(BMA)]TJ /F8 1 Tf 10.4991 0 TD (+)Tj /F1 1 Tf .552 0 TD [(AIC)-399.9(and)-396.7(BMA)]TJ /F8 1 Tf 6.2312 0 TD (+)Tj /F1 1 Tf .5577 0 TD [(W2vGO)-8.5(,)-393(and)-396.7(is)-392.4(statist)-9.2(ically)-397.7(above)-400(the)-393.8(othe)-7.6(r)-389.7(appro)-7.6(aches)-10.4(.)-393(W)0(e)]TJ -17.8399 -1.2007 TD [(provide)-341.9(the)-336.9(ROC)-334.3(plots)-340.6(for)-336.3(the)-336.9(joint)-336.5(analyses)-341(at)-336.1(our)-334.3(Gi)-8.2(tHub.)]TJ 1.0015 -1.2007 TD [(Our)-321.2(joi)-7.8(nt)-323(analyses)-329.6(did)-323.7(not)-323.7(include)-333.1(Resni)-8.6(k)]TJ 6.9738 0 0 6.9738 290.2109 194.0031 Tm (RWC)Tj 9.9626 0 0 9.9626 306.6519 195.4771 Tm [(,)-324.7(GraSM,)-331.7(and)-322.8(GraS)-10(M)]TJ 6.9738 0 0 6.9738 397.1337 194.0031 Tm (RWC)Tj 9.9626 0 0 9.9626 416.8062 195.4771 Tm [(because)-332.3(the)-325.5(software)-328.8(GOssTo)]TJ -31.0363 -1.2007 TD [(does)-245(not)-238.4(allow)-248.4(the)-240.2(option)-243.4(to)-243.3(combine)-248.5(the)-240.1(three)-245.4(ontologi)-8.7(es.)-238.2(In)-242.5(the)-245.8(experiment)-12.6(,)-239.4(w)0(e)-240.6(reimp)-8.2(lemented)-248.1(Resnik)-242.6(and)]TJ T* [(AIC)-337.3(ourse)-8.8(lves,)-333.5(and)-339.8(changed)-340.7(the)-336.9(source)-341.4(code)-336.7(for)-336.3(simD)-8.8(EF)-330.6(\(see)-339.8(GitHub\))-9.3(.)]TJ /F6 1 Tf 10.959 0 0 10.959 107.6031 147.685 Tm [(3.2.)-496.9(Orthologs)]TJ /F1 1 Tf 9.9626 0 0 9.9626 117.5811 129.7133 Tm -.0148 Tc 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[(the)-296(p)1.7(o)-14.6(s)11.1(itive)-296(s).5(et)-297(co)-14.6(n)12.3(t)-1.1(ains)-295.4(o)-14.6(r)10.4(tholo)-14.6(g)12.3(s)-295.4(from)-297.7(t)-1.1(he)-296(two)-294.2(s).5(p)-14.6(e)10.5(cies,)-293.8(w)-2.2(h)-14.6(e)10.5(rea)-14.6(s)-280.9(th)-14.6(e)-285.4(n)1.7(eg)-14.6(a)10.5(tive)-296(s).5(et)-297(con)-14.6(t)9.6(ains)-295.4(ran)-14.6(d)12.3(o)-14.6(m)8.8(l)4.6(y)-294.2(ma)-14.6(t)13.5(c)-14.6(h)10.5(e)-.1(d)]TJ 0 -1.195 TD [(ge)-14.7(n)10.4(e)-.2(s.)-191.5(We)-188(se)-14.7(t)-174.4(t)-1.2(h)-14.7(e)-177.4(size)-14.7(s)-178.5(o)1.6(f)-188.2(t)-1.2(he)-193.7(pos)-14.7(i)8.3(t)4.5(iv)-14.7(e)-177.3(s).4(et)-188.9(an)-14.7(d)-175.6(n)-14.7(e)10.4(g)1.6(ativ)-14.7(e)-177.4(s).4(et)-188.9(to)-186.2(b)-14.7(e)-177.4(eq)-14.7(u)12.2(a)-.2(l.)-185.8(For)-188.2(h)-14.7(u)12.2(m)-1.9(an)-14.7(/)9.5(m)-1.9(ous)-14.7(e)-178.5(d)1.6(ata)-188(s)-14.7(e)9.2(t)-1.2(,)-185.8(w)-2.3(e)-188(h)-14.7(a)10.4(v)1.6(e)-188(1)-14.7(0)12.2(,)-14.7(2)12.6(3)1.6(5)]TJ 0 -1.2007 TD 0 Tc [(p)16.3(a)0(i)28.1(r)14.3(s)-229.6(f)14.3(o)16.3(r)-224.7(e)14.5(a)14.5(c)0(h)-213.9(s)15.1(e)14.5(t)13.5(;)-225.5(f)14.3(o)16.3(r)-224.7(t)13.5(h)0(e)-213.9(h)16.3(u)16.3(m)12.8(an)25.1(/)13.5()17.1(y)-228.4(d)16.3(a)14.5(t)13.5(a)-224.5(s)15.1(et)22.4(,)-222.3(w)12.4(e)-224.5(h)16.3(a)14.5(v)0(e)-213.9(4)16.3(88)26.9(0)-222.7(p)0(a)25.1(i)13.5(r)14.3(s)-223.9(f)14.3(o)16.3(r)-224.7(e)0(a)23.4(c)14.5(h)-222.7(s)0(e)23.9(t)13.5(.)-222.3(W)13.7(e)-224.5(e)14.5(xc)25.1(l)13.5(u)16.3(de)-213.9(R)11.6(e)14.5(s)15.1(n)16.3(i)13.5(k)]TJ 6.9738 0 0 6.9738 486.0849 80.3905 Tm -.022 Tc (RWC)Tj 9.9626 0 0 9.9626 502.1857 81.9212 Tm .2223 Tc [(,G)234.7(r)236.6(a)222.3(S)248.2(M)236.6(,)]TJ -39.6062 -1.2007 TD -.0153 Tc [(an)-15.3(d)-250.1(G)-2.9(raSM)]TJ 6.9738 0 0 6.9738 155.5086 68.4283 Tm -.0179 Tc (RWC)Tj 9.9626 0 0 9.9626 174.274 69.959 Tm 0 Tc 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737.4045 Tm (48)Tj 35.8334 0 TD [(DUO)-8(NG)-339(ET)-335.3(AL.)]TJ ET endstream endobj 39 0 obj <> endobj 40 0 obj <>/ProcSet[/PDF/Text]/ExtGState<>>> endobj 41 0 obj <>stream /GS1 gs BT /F1 1 Tf 9.9626 0 0 9.9626 107.6031 715.4644 Tm 0 0 0 rg 0 Tc 0 Tw [(98)21.2(6,)21.6(61)26.9(5)-234.1(w)0(o)17.3(r)14.3(ds)20(;)-236.8(s)15.1(o,)-223.1(th)18.5(e)-230.2(n)0(u)21.2(m)0(b)17.7(e)14.5(r)-236.1(o)0(f)-225.4(s)15.1(en)19.4(t)13.5(e)0(n)19.4(c)0(e)17.7(s)-235.3(i)13.5(n)-234.1(t)13.5(h)0(e)-225.2(t)0(r)22.2(a)0(i)22.4(n)0(i)18.5(n)0(g)-223.5(d)16.3(at)16.7(a)-230.2(s)0(e)18.3(t)-231.2(is)-227.4(l)13.5(a)0(r)23.2(g)0(e)19.4(r)-236.1(t)13.5(h)0(a)19.4(n)-234.1(t)13.5(h)0(i)18.5(s)-229.6(nu)21.2(mb)17.7(e)14.5(r)0(.)-225.1(W)0(e)-227.8(e)14.5(nc)19.4(ou)21.2(nt)24.2(er)17.5(e)14.5(d)]TJ 0 -1.195 TD 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0 TD .3036 Tc ()Tj /F1 1 Tf 1.3828 0 TD 0 Tc [(is)-307.1(the)-308.4(proba)-7.6(bility)-311.5(of)-305.1(ob)-7.2(serving)-309(a)-309.8(term)]TJ /F6 1 Tf 15.5466 0 TD (t)Tj /F1 1 Tf .5861 0 TD (in)Tj -42.4174 -1.8779 TD [(the)-342.6(ontology.)]TJ /F6 1 Tf 5.7304 0 TD .3877 Tc (pt)Tj /F9 1 Tf .5008 0 TD .3036 Tc ()Tj /F1 1 Tf 1.4113 0 TD 0 Tc [(is)-341.2(compute)-9.5(d)-336.5(a)0(s)]TJ /F6 1 Tf 6.4872 0 TD .382 Tc (pt)Tj /F9 1 Tf .5008 0 TD .3036 Tc ()Tj /F8 1 Tf 1.5137 0 TD 0 Tc (=)Tj ET 280.063 423.212 39.912 .39685 re f BT /F1 1 Tf 9.9626 0 0 9.9626 286.6393 427.6912 Tm (freq)Tj /F6 1 Tf 2.0031 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F1 1 Tf -2.2762 -1.3657 TD 0 Tc [(freq)-390.1(root)]TJ /F9 1 Tf 1.6161 0 TD 1.6181 Tc ()Tj /F7 1 Tf 2.5607 .6829 TD 0 Tc (:)Tj /F1 1 Tf .6089 0 TD (freq)Tj /F6 1 Tf 2.0031 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F1 1 Tf 1.4113 0 TD 0 Tc [(is)-341.2(dened)-348.8(as)-340.2(the)-342.6(cum)-7.6(ulative)-341.6(count)-344.1(of)-344.9(term)]TJ /F6 1 Tf 17.7943 0 TD (t)Tj /F1 1 Tf -42.9181 -1.8836 TD [(and)-271.5(its)-276.5(descendants,)-282.8(where)-275.1(freq)]TJ /F6 1 Tf 13.037 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F8 1 Tf 1.5194 0 TD 0 Tc (=)Tj /F1 1 Tf 1.0015 0 TD (count)Tj /F6 1 Tf 2.6177 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F8 1 Tf 1.5194 0 TD 0 Tc (+)Tj /F11 1 Tf 1.1666 .7455 TD (P)Tj /F6 1 Tf 6.9738 0 0 6.9738 319.8613 400.3086 Tm (c)Tj /F9 1 Tf .4471 0 TD (2)Tj /F1 1 Tf .6585 0 TD (child)Tj /F6 1 Tf 2.3982 0 TD (t)Tj /F9 1 Tf -.3821 0 TD .2979 Tc ()Tj /F1 1 Tf 9.9626 0 0 9.9626 351.2692 402.1227 Tm 0 Tc (freq\()Tj /F6 1 Tf 1.9519 0 TD (c)Tj /F1 1 Tf .4496 0 TD (\))Tj /F7 1 Tf .3301 0 TD (:)Tj /F1 1 Tf .5406 0 TD [(whe)-8(re)-272.7(count)]TJ /F6 1 Tf 5.3434 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F1 1 Tf 1.343 0 TD 0 Tc [(is)-272.9(the)-274.3(numb)-6.6(er)-272.8(of)-271(genes)]TJ -34.0295 -1.3088 TD [(annotat)-8.7(ed)-322(with)-319.8(the)-325.5(term)]TJ /F6 1 Tf 10.0495 0 TD (t)Tj /F1 1 Tf .6032 0 TD [(and)-322.7(child)]TJ /F6 1 Tf 4.1655 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F1 1 Tf 1.3942 0 TD 0 Tc [(are)-326.5(the)-319.8(childr)-8.2(en)-322(of)]TJ /F6 1 Tf 7.87 0 TD (t)Tj /F1 1 Tf .2845 0 TD [(.)-319.1(Based)-326.3(on)-320.2(this)-322.7(denition,)-323.8(IC)-389.5(root)]TJ /F9 1 Tf 11.8477 0 TD 1.6238 Tc ()Tj /F8 1 Tf 2.8339 0 TD 0 Tc (=)Tj /F1 1 Tf 1.0015 0 TD [(0)-487.2(and)-322.8(a)]TJ -39.6631 -1.2007 TD [(node)-352(near)-361.4(the)-354(leaves)-355.3(has)-358.1(higher)-352.5(IC)-355.3(than)-354.7(nodes)-353.9(at)-353.2(upp)-8(er)-352.4(levels.)-356.7(To)-354.2(compute)-356.6(a)-355.4(similarity)-360(score)-357.7(of)-350.6(the)-354(GO)]TJ 0 -1.195 TD (terms)Tj /F6 1 Tf 2.5664 0 TD (a)Tj /F1 1 Tf .8308 0 TD (and)Tj /F6 1 Tf 1.7868 0 TD (b)Tj /F1 1 Tf .5008 0 TD [(,)-330.4(w)0(e)-337.3()0(n)-6.4(d)-330.8(the)-336.9(mos)-7(t)-333.6(informat)-9.5(ive)-331.2(com)-7.6(mon)-335.9(ances)-10.4(tor)-331.4(of)-339.2(these)-335.7(two)-339(terms.)]TJ 8.0123 -1.9234 TD [(Resni)-8.6(k)]TJ /F6 1 Tf 3.1753 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7739 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7774 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (=)Tj /F1 1 Tf 3.0786 0 TD (max)Tj /F6 1 Tf 6.9738 0 0 6.9738 313.285 339.1936 Tm (p)Tj /F9 1 Tf .504 0 TD (2)Tj /F1 1 Tf 1.1544 0 TD (par)Tj /F6 1 Tf 1.6747 0 TD (a)Tj /F9 1 Tf -.3902 0 TD .5011 Tc [()501.1(\\)]TJ /F1 1 Tf 1.9348 0 TD 0 Tc (par)Tj /F6 1 Tf 1.6665 0 TD (b)Tj /F9 1 Tf -.3902 0 TD .5092 Tc ()Tj -4.9915 -.0081 TD 5.7678 Tc (fg)Tj /F1 1 Tf 9.9626 0 0 9.9626 373.0393 346.0534 Tm 0 Tc (IC)Tj /F6 1 Tf 1.4682 0 TD (p)Tj /F9 1 Tf -.4666 0 TD .5824 Tc ()Tj /F1 1 Tf 1.3544 0 TD 0 Tc [()-12698.4(\(7\))]TJ -28.999 -2.6177 TD [(where)-309.2(par)]TJ /F6 1 Tf 4.4216 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F1 1 Tf 1.3771 0 TD 0 Tc [(denotes)-308.8(all)-299.8(the)-302.7(ances)-10.4(tors)-304.9(of)-299.4(term)]TJ /F6 1 Tf 13.5321 0 TD (t)Tj /F1 1 Tf .2788 0 TD [(.)-302(Resnik)]TJ /F6 1 Tf 3.7216 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7774 Tc ()Tj /F1 1 Tf 2.851 0 TD 0 Tc [(ranges)-307.2(from)-306.4(0)-296.7(t)0(o)]TJ /F9 1 Tf 7.0563 0 TD (1)Tj /F1 1 Tf 1.2974 0 TD [(becau)-9.2(se)-306.1(the)-302.7(probability)]TJ /F6 1 Tf -33.7677 -1.195 TD .3877 Tc (pt)Tj /F9 1 Tf .5008 0 TD .3036 Tc ()Tj /F1 1 Tf 1.4056 0 TD 0 Tc [(range)-9.4(s)-332(from)-340.6(0)-330.8(t)0(o)-334.3(1)0(.)]TJ -.9048 -1.2007 TD [(In)-316.5(this)-322.7(model,)-325.2(the)-319.8(simi)-7.6(larity)-323.9(score)-323.5(between)-324.7(a)-321.2(G)0(O)-322.4(term)]TJ /F6 1 Tf 22.5232 0 TD (t)Tj /F1 1 Tf .6032 0 TD [(and)-322.7(itself)-319.4(is)-324.2(not)-318(1.)-319.8(Second,)-326.4(when)]TJ /F6 1 Tf 13.7654 0 TD (a)Tj /F1 1 Tf .8194 0 TD (and)Tj /F6 1 Tf 1.7698 0 TD (b)Tj /F1 1 Tf .8194 0 TD (have)Tj -41.302 -1.2007 TD [(only)-358.6(the)]TJ /F6 1 Tf 3.7216 0 TD (root)Tj /F1 1 Tf 2.0258 0 TD [(as)-351.6(a)-355.4(com)-7.6(mon)-352.9(ances)-10.4(tor,)-354.5(then)-360.4(Resnik)]TJ /F6 1 Tf 15.0686 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F8 1 Tf 2.9989 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (0)Tj /F7 1 Tf .5008 0 TD (:)Tj /F1 1 Tf .626 0 TD [(This)-359.6(is)-352.6(problem)-9.7(atic)-359.3(because)-360.8(leaf)-358.5(nodes)-359.6(are)]TJ -25.5506 -1.2007 TD [(more)-317.6(informative)-317.9(than)-314.9(othe)-7.6(r)-310(type)-7.6(s)-309.2(o)0(f)-310.8(nodes.)-320.2(Consider)-320.1(the)-314.1(example)-318.6(in)-311.6(Song)-315.3(et)-313.4(al.)-313.7(\(2014\).)-316.2(Here,)-314.5(the)]TJ /F6 1 Tf 40.5509 0 TD (root)Tj /F1 1 Tf 1.9803 0 TD (is)Tj -42.5312 -1.2007 TD [(the)-234.5(only)-239.1(common)-241(ances)-10.4(tor)-234.7(of)-236.8(the)-234.5(pair)]TJ /F6 1 Tf 15.1482 0 TD (a)Tj /F1 1 Tf .7341 0 TD (and)Tj /F6 1 Tf 1.6844 0 TD (b)Tj /F1 1 Tf .7398 0 TD [(and)-237.4(the)-234.5(pair)]TJ /F6 1 Tf 4.9451 0 TD (c)Tj /F1 1 Tf .6829 0 TD (and)Tj /F6 1 Tf 1.6844 0 TD (d)Tj /F1 1 Tf .5008 0 TD [(.)-233.7(Nex)-8(t,)-231.5(suppos)-7(e)-235.9(that)]TJ /F6 1 Tf 8.1261 0 TD (a)Tj /F1 1 Tf .7341 0 TD (and)Tj /F6 1 Tf 1.6844 0 TD (b)Tj /F1 1 Tf .7341 0 TD [(are)-241.1(leaf)-239(nodes,)]TJ /F6 1 Tf -37.3983 -1.2007 TD (c)Tj /F1 1 Tf .7341 0 TD [(is)-284.3(the)-285.7(pare)-8.6(nt)-283.1(of)]TJ /F6 1 Tf 6.3848 0 TD (a)Tj /F1 1 Tf .5008 0 TD (,)Tj /F6 1 Tf .5349 0 TD (d)Tj /F1 1 Tf .7853 0 TD [(is)-284.3(the)-291.4(parent)-291.7(of)]TJ /F6 1 Tf 6.3848 0 TD (b)Tj /F1 1 Tf .5065 0 TD [(,)-279.2(and)]TJ /F6 1 Tf 2.2648 0 TD (root)Tj /F1 1 Tf 1.9575 0 TD [(is)-284.3(the)-291.4(parent)-286(o)-6.5(f)-281.6(both)]TJ /F6 1 Tf 8.4562 0 TD (c)Tj /F1 1 Tf .7341 0 TD (and)Tj /F6 1 Tf 1.7299 0 TD (d)Tj /F1 1 Tf .5065 0 TD [(.)-279.2(One)-292.5(would)-289.3(then)-286.4(expec)-9.2(t)-288.1(that)]TJ -31.4801 -1.2007 TD [(Resni)-8.6(k)]TJ /F6 1 Tf 3.3404 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F7 1 Tf 2.8282 0 TD 0 Tc (<)Tj /F6 1 Tf 1.0528 0 TD [(Resnik)-581(c)]TJ /F1 1 Tf 3.7045 0 TD ()Tj /F6 1 Tf .7739 0 TD (d)Tj /F9 1 Tf -1.6104 0 TD 1.7603 Tc ()Tj /F10 1 Tf 2.5323 0 TD 0 Tc (;)Tj /F1 1 Tf .6032 0 TD [(however)-9.1(,)-330.4(one)-339.8(would)-340.6(obtain)-336.3(Resni)-8.6(k)]TJ /F6 1 Tf 14.6816 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7739 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7774 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (=)Tj /F1 1 Tf 1.0015 0 TD (Resnik)Tj /F6 1 Tf 3.1696 0 TD (c)Tj /F1 1 Tf .4496 0 TD ()Tj /F6 1 Tf .7796 0 TD (d)Tj /F9 1 Tf -1.6161 0 TD 1.7603 Tc ()Tj /F8 1 Tf 2.9762 0 TD 0 Tc (=)Tj /F1 1 Tf 1.0015 0 TD (0)Tj /F7 1 Tf .5008 0 TD (:)Tj /F6 1 Tf 10.959 0 0 10.959 107.6031 212.9952 Tm [(5.2.)-496.9(AIC)-332.1(method)]TJ /F1 1 Tf 9.9626 0 0 9.9626 117.5811 195.0803 Tm [(The)-316.9(AIC)-320.2(method)-319.9(by)-314.5(Song)-320.9(et)-313.4(al.)-319.4(\(2014\))-315.8(ame)-9.4(nds)-316.5(the)-314.1(two)-322(problems)-318.9(in)-317.3(the)-319.8(Resnik)-322.3(method.)-320.3(To)-314.3(encode)-322.9(the)]TJ -1.0015 -1.2007 TD [(fact)-330(that)-329(leaf)-330(nodes)-331.2(are)-332.2(more)-329(informat)-9.5(ive,)-325.9(AIC)-331.6(denes)-332.9(a)-326.9(know)-7(ledge)-328.8(functi)-8.2(on)-325.9(of)-327.9(term)]TJ /F6 1 Tf 35.1164 0 TD (t)Tj /F1 1 Tf .6089 0 TD (as)Tj /F6 1 Tf 1.1609 0 TD .4066 Tc (kt)Tj /F9 1 Tf .4666 0 TD .3036 Tc ()Tj /F8 1 Tf 1.5194 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (1)Tj /F7 1 Tf .5065 0 TD (=)Tj /F1 1 Tf .5008 0 TD (IC)Tj /F6 1 Tf 1.3828 0 TD (t)Tj /F9 1 Tf -.3813 0 TD .3036 Tc ()Tj /F1 1 Tf 1.0698 0 TD 0 Tc (,)Tj -42.9466 -1.2007 TD [(which)-274.1(is)-267.2(used)-273.5(to)-266.1(measur)-9.1(e)-270(its)-265.1(sem)-8.8(antic)-269(weight)]TJ /F6 1 Tf 18.4886 0 TD [(sw)-388.7(t)]TJ /F9 1 Tf 1.0528 0 TD .3036 Tc ()Tj /F8 1 Tf 1.5194 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (1)Tj /F7 1 Tf .6032 0 TD (=)Tj /F1 1 Tf .9845 0 TD (1)Tj /F8 1 Tf 1.1097 0 TD (+)Tj /F1 1 Tf 1.0015 0 TD (exp)Tj /F8 1 Tf 2.0031 0 TD (-)Tj /F6 1 Tf .717 0 TD .4123 Tc (kt)Tj /F9 1 Tf .4723 0 TD .3036 Tc ()Tj -1.7413 0 TD 2.4261 Tc ()Tj -3.9492 0 TD 6.7623 Tc ()Tj /F1 1 Tf 7.5343 0 TD 0 Tc [(.)-267.8(Here)]TJ /F6 1 Tf 2.7372 0 TD (sw)Tj /F1 1 Tf 1.4397 0 TD (root)Tj /F9 1 Tf -.387 0 TD 1.6181 Tc ()Tj /F8 1 Tf 2.8339 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (1)Tj /F7 1 Tf .5008 0 TD (:)Tj /F1 1 Tf .5406 0 TD [(Seman)-10.1(tic)]TJ -39.4526 -1.2007 TD (value)Tj /F6 1 Tf 2.5152 0 TD [(sv)-391.5(t)]TJ /F9 1 Tf .8365 0 TD .3036 Tc ()Tj /F1 1 Tf 1.4113 0 TD 0 Tc (of)Tj /F6 1 Tf 1.1723 0 TD (t)Tj /F1 1 Tf .6146 0 TD [(is)-341.2(then)-337.7(dened)-343.1(as)]TJ /F6 1 Tf 7.5343 0 TD [(sv)-391.5(t)]TJ /F9 1 Tf .8365 0 TD .3036 Tc ()Tj /F8 1 Tf 1.5194 0 TD 0 Tc (=)Tj /F11 1 Tf 1.1609 .7512 TD (P)Tj /F6 1 Tf 6.9738 0 0 6.9738 295.0865 157.3795 Tm (p)Tj /F9 1 Tf .504 0 TD (2)Tj /F1 1 Tf .6585 0 TD (path)Tj /F6 1 Tf 2.1218 0 TD (t)Tj /F9 1 Tf -.3902 0 TD .306 Tc ()Tj /F6 1 Tf 9.9626 0 0 9.9626 326.0409 159.1937 Tm 0 Tc (sw)Tj /F1 1 Tf 1.0527 0 TD (\()Tj /F6 1 Tf .3357 0 TD (p)Tj /F1 1 Tf .5008 0 TD (\))Tj /F7 1 Tf .3301 0 TD (:)Tj /F1 1 Tf .6089 0 TD [(Fun)-7.2(ction)-341.2(path)]TJ /F6 1 Tf 6.0263 0 TD (t)Tj /F9 1 Tf -.387 0 TD .3036 Tc ()Tj /F1 1 Tf 1.4113 0 TD 0 Tc [(contain)-8.7(s)-337.7(every)-339.4(ances)-10.4(tor)-337.1(of)]TJ /F6 1 Tf 11.1136 0 TD (t)Tj /F1 1 Tf -42.9181 -1.2007 TD [(and)-351.2(the)-348.3(term)]TJ /F6 1 Tf 5.571 0 TD (t)Tj /F1 1 Tf .6317 0 TD [(itself.)-353.9(Usually,)]TJ /F6 1 Tf 6.3279 0 TD [(sv)-391.5(a)]TJ /F9 1 Tf .8365 0 TD .5027 Tc ()Tj /F7 1 Tf 1.5535 0 TD 0 Tc (<)Tj /F6 1 Tf 1.0471 0 TD [(sv)-391.5(b)]TJ /F9 1 Tf .8365 0 TD .5027 Tc ()Tj /F1 1 Tf 1.6218 0 TD 0 Tc [(when)-350.2(term)]TJ /F6 1 Tf 4.7118 0 TD (a)Tj /F1 1 Tf .8479 0 TD [(is)-346.9(near)-8.6(er)-346.7(to)-351.4(the)-354(root)-349.2(than)]TJ /F6 1 Tf 10.6299 0 TD (b)Tj /F1 1 Tf .5008 0 TD [(.)-353.2(Song)-349.4(et)-347.5(al.)-353.6(\(2014\))]TJ -35.1164 -1.2007 TD [(dene)-336.7(their)-343.2(similarity)-342.9(score)-340.6(of)-333.6(two)-333.3(GO)-339.4(terms)]TJ /F6 1 Tf 18.9552 0 TD (a)Tj /F1 1 Tf .8365 0 TD (and)Tj /F6 1 Tf 1.7811 0 TD (b)Tj /F1 1 Tf .8365 0 TD (as)Tj -9.3723 -2.7656 TD (AIC)Tj /F6 1 Tf 2.1055 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F8 1 Tf 2.9989 0 TD 0 Tc (=)Tj ET 296.107 109.984 107.603 .39685 re f BT /F1 1 Tf 9.9626 0 0 9.9626 296.107 116.1638 Tm (2)Tj /F11 1 Tf .6658 .7512 TD (P)Tj /F6 1 Tf 6.9738 0 0 6.9738 313.2282 113.3291 Tm (p)Tj /F9 1 Tf .504 0 TD (2)Tj /F1 1 Tf 1.1544 0 TD (path)Tj /F6 1 Tf 2.1218 0 TD (a)Tj /F9 1 Tf -.3902 0 TD .5011 Tc [()501.1(\\)]TJ /F1 1 Tf 1.9348 0 TD 0 Tc (path)Tj /F6 1 Tf 2.1137 0 TD (b)Tj /F9 1 Tf -.3821 0 TD .5011 Tc ()Tj -5.902 -.0081 TD 6.6702 Tc (fg)Tj /F6 1 Tf 9.9626 0 0 9.9626 379.729 116.1638 Tm 0 Tc [(sw)-474.1(p)]TJ /F9 1 Tf 1.0528 0 TD .5881 Tc ()Tj /F6 1 Tf -6.8742 -1.5364 TD 0 Tc [(sv)-391.5(a)]TJ /F9 1 Tf .8365 0 TD .5027 Tc ()Tj /F8 1 Tf 1.7185 0 TD 0 Tc (+)Tj /F6 1 Tf .9958 0 TD [(sv)-385.8(b)]TJ /F9 1 Tf .8365 0 TD .497 Tc ()Tj /F7 1 Tf 4.0118 .6886 TD 0 Tc (:)Tj /F1 1 Tf 12.1379 0 TD (\(8\))Tj -41.0289 -2.5892 TD -.0124 Tc [(AI)-12.4(C)]TJ /F6 1 Tf 2.0827 0 TD 0 Tc (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F1 1 Tf 2.7315 0 TD 0 Tc [(r)14.3(a)0(n)19.4(g)0(e)19.4(s)-161.3(fr)17.3(om)-153(0)-165.8(t)13.5(o)-165.8(1)0(.)-154.8(I)0(n)-157.2(t)13.5(hi)18.5(s)-167(m)12.8(od)21.2(el)22.4(,)-165.4(A)12.4(IC)]TJ /F6 1 Tf 14.8296 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (a)Tj /F9 1 Tf -1.6673 0 TD 1.7831 Tc ()Tj /F8 1 Tf 2.9989 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (1)Tj /F7 1 Tf .5008 0 TD (:)Tj /F1 1 Tf .4496 0 TD [(Wh)18.7(en)]TJ /F6 1 Tf 2.5323 0 TD (a)Tj /F1 1 Tf .6658 0 TD -.0145 Tc [(an)-14.5(d)]TJ /F6 1 Tf 1.5877 0 TD 0 Tc (b)Tj /F1 1 Tf .6658 0 TD [(ha)19.4(ve)-157(on)21.2(l)13.5(y)-165.8(t)13.5(h)0(e)]TJ /F6 1 Tf 5.315 0 TD [(ro)20(ot)]TJ /F1 1 Tf 1.7982 0 TD [(as)-158.2(t)13.5(h)0(e)-157(c)0(o)19.5(m)12.8(mo)23.4(n)]TJ -37.3812 -1.2007 TD [(an)19.4(c)14.5(e)0(s)18.3(t)13.5(or)19.3(,)-245.1(t)0(h)18.5(e)14.5(n)-251.2(A)0(I)21(C)]TJ /F6 1 Tf 7.779 0 TD (a)Tj /F1 1 Tf .5008 0 TD ()Tj /F6 1 Tf .7796 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7774 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (=)Tj /F1 1 Tf .9958 0 TD (2)Tj /F7 1 Tf .5065 0 TD (=)Tj /F6 1 Tf .882 0 TD [(sv)-380.1(a)]TJ /F9 1 Tf .8251 0 TD .5027 Tc ()Tj /F8 1 Tf 1.7185 0 TD 0 Tc (+)Tj /F6 1 Tf .9958 0 TD [(sv)-380.1(b)]TJ /F9 1 Tf .8251 0 TD .5027 Tc ()Tj -4.7459 0 TD 5.6356 Tc ()Tj /F1 1 Tf 6.4019 0 TD 0 Tc [(,)-250.8(w)12.4(hi)18.5(ch)-236.6(de)19.4(pe)19.4(n)16.3(d)0(s)-241.7(o)0(n)-234.8(w)0(h)17.3(e)0(r)23.2(e)]TJ /F6 1 Tf 10.5104 0 TD (a)Tj /F1 1 Tf .7455 0 TD [(an)19.4(d)]TJ /F6 1 Tf 1.673 0 TD (b)Tj /F1 1 Tf .7512 0 TD [(ar)23.2(e)-252.9(o)0(n)-234.8(t)0(h)18.5(e)-247.2(GO)-242.7(t)13.5(r)0(e)17.5(e)14.5(.)]TJ /F2 1 Tf -32.476 66.9948 TD [(SEMANT)-12.2(IC)-336.7(SIMILA)-11.7(RITY)-335.5(OF)-340.6(GO)-338.6(DEFINITIO)-14(NS)-19750.9(49)]TJ ET endstream endobj 42 0 obj <> 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7.5855 0 TD (U)Tj /F8 1 Tf .8877 0 TD (=)Tj /F1 1 Tf .717 0 TD [(Disj)-8(Anc\(a\))]TJ /F9 1 Tf 4.7573 0 TD ([)Tj /F1 1 Tf .9617 0 TD [(DisjAnc\(b\))-10.9(.)]TJ /F6 1 Tf 5.0589 0 TD (c)Tj /F1 1 Tf 7.4718 0 0 6.641 483.6471 621.2975 Tm (1)Tj 9.9626 0 0 9.9626 490.3936 622.9416 Tm [(is)-301.4(a)]TJ -41.7857 -1.2007 TD [(com)-7.6(mon)-279(disjunc)-8.1(tive)-277.8(ances)-10.4(tor)-274.5(of)]TJ /F6 1 Tf 13.2248 0 TD (a)Tj /F1 1 Tf .7739 0 TD (and)Tj /F6 1 Tf 1.7242 0 TD (b)Tj /F1 1 Tf .7796 0 TD [(if)-279.4(for)-273.7(each)-281.6(com)-7.6(mon)-279(ancestor)]TJ /F6 1 Tf 11.8762 0 TD (c)Tj /F1 1 Tf 7.4718 0 0 6.641 361.3038 609.3353 Tm (2)Tj 9.9626 0 0 9.9626 367.7668 610.9794 Tm (of)Tj /F6 1 Tf 1.1153 0 TD (a)Tj /F1 1 Tf .7739 0 TD (and)Tj /F6 1 Tf 1.7242 0 TD (b)Tj /F1 1 Tf .7796 0 TD [(where)-280.7(IC)]TJ /F6 1 Tf 4.1143 0 TD (c)Tj /F1 1 Tf 6.9738 0 0 6.9738 457.0015 609.5054 Tm (1)Tj /F9 1 Tf 9.9626 0 0 9.9626 448.6676 610.9794 Tm .8555 Tc ()Tj /F7 1 Tf 1.9006 0 TD 0 Tc (<)Tj /F6 1 Tf 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[(GO)-373.6(terms,)-368.2(RW)-8.8(C)-364(i)0(s)-369.7(a)0(n)-367.5(edge-)-9.4(based)-367.1(appro)-7.6(ach)-370.1(that)-368.9(analyzes)-375.7(the)-371(shared)-369.8(childr)-8.2(en)-367.5(of)-367.7(two)-373.2(GO)-367.9(terms)]TJ /F6 1 Tf 40.0216 0 TD (a)Tj /F1 1 Tf .865 0 TD (and)Tj /F6 1 Tf 1.8153 0 TD (b)Tj /F1 1 Tf -42.7019 -1.195 TD [(\(Y)-7.4(ang)-425.2(et)-421.5(al.,)-427.9(2012\).)-427.3(In)-424.6(brief,)-428.1(in)-419.7(the)-427.9(RWC)-429.7(paradigm,)-428(GO)-430.5(terms)-424.8(with)-427.9(more)-425.7(com)-7.6(mon)-426.9(children)-426.9(are)-428.9(more)]TJ 0 -1.2007 TD [(deem)-10.2(ed)-333.4(to)-334.3(be)-339.1(more)-334.7(simi)-7.6(lar.)]TJ 1.0015 -1.2007 TD [(Den)-8(e)]TJ /F6 1 Tf 3.0388 0 TD (N)Tj 7.4718 0 0 6.641 120.9826 464.655 Tm (c)Tj /F1 1 Tf 9.9626 0 0 9.9626 128.0126 466.3558 Tm [(as)-368.7(the)-371(numb)-6.6(er)-369.5(of)-367.7(genes)-372.8(annotat)-8.7(ed)-367.5(by)-365.7(ter)-8.8(m)]TJ /F6 1 Tf 17.948 0 TD (c)Tj /F1 1 Tf .4496 0 TD 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0 TD (is)Tj -19.1885 -2.1169 TD (RWC)Tj /F6 1 Tf 2.9477 0 TD (a)Tj /F1 1 Tf .5065 0 TD ()Tj /F6 1 Tf .7739 0 TD (b)Tj /F9 1 Tf -1.6616 0 TD 1.7774 Tc ()Tj /F8 1 Tf 2.9932 0 TD 0 Tc (=)Tj /F11 1 Tf 1.2462 .9503 TD (X)Tj /F6 1 Tf 6.9738 0 0 6.9738 266.2865 398.7779 Tm (i)Tj /F1 1 Tf .2845 0 TD ()Tj /F6 1 Tf .4959 0 TD (j)Tj /F9 1 Tf .2845 0 TD (2)Tj /F6 1 Tf .6585 0 TD (L)Tj 9.9626 0 0 9.9626 283.8046 409.3794 Tm (W)Tj 6.9738 0 0 6.9738 292.9322 413.518 Tm (a)Tj /F9 1 Tf -.1138 -.9918 TD (1)Tj /F1 1 Tf 9.9626 0 0 9.9626 299.6219 409.3794 Tm (\()Tj /F6 1 Tf .3301 0 TD (i)Tj /F1 1 Tf .2845 0 TD (\))Tj /F6 1 Tf .3357 0 TD (W)Tj 6.9738 0 0 6.9738 318.2172 413.518 Tm (b)Tj /F9 1 Tf -.1219 -.9918 TD (1)Tj /F1 1 Tf 9.9626 0 0 9.9626 324.8503 409.3794 Tm (\()Tj /F6 1 Tf .3357 0 TD (j)Tj /F1 1 Tf .2845 0 TD (\)score\()Tj /F6 1 Tf 2.7827 0 TD (i)Tj /F1 1 Tf .2845 0 TD ()Tj /F6 1 Tf .6658 0 TD (j)Tj /F1 1 Tf .2845 0 TD [(\))-11062.2(\(11\))]TJ -29.8071 -2.9534 TD 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