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1.0015 -1.2007 TD
[(Hen)-8(ce,)-386.7(supervis)-9.3(ed)-384.6(methods)-390.2(sp)20(ec)12(i)13.5(a)0(l)16.7(i)0(z)16.7(e)0(d)-367.5(i)0(n)-362.8(t)0(h)18.5(e)-378.1(de)19.4(te)16.7(ct)16.7(io)18.5(n)-376.3(o)0(f)-362(r)0(e)17.5(g)0(u)15.5(l)0(a)16.7(t)13.5(or)13.6(y)-370.7(e)0(l)16.7(e)0(m)15.9(e)0(n)19.4(t)0(s)-369.7(t)13.5(yp)15.5(ic)16.7(al)16.7(l)13.5(y)-376.3(pe)19.4(rf)17.3(or)13.6(m)-374.2(m)0(u)17.7(c)0(h)]TJ
-1.0015 -1.2007 TD
[(be)13.8(tt)21.4(er)17.5(.)-279.2(T)10.8(o)-279.6(o)0(b)15.5(t)13.5(ai)16.7(n)-279.6(g)0(o)15.5(o)0(d)-263.3(c)0(l)16.7(a)0(s)12.6(s)0(i)23()0(c)14.5(a)0(t)16.7(i)0(o)18.5(n)-273.9(pe)13.8(rf)17.3(or)19.3(ma)15.9(nc)19.4(es)-272(of)-265.3(un)15.5(su)20(pe)13.8(rv)19.3(is)17.3(ed)-270.8(H)12.4(M)0(M)11.6(s)-275.1(th)18.5(e)-281.4(n)0(u)21.2(m)0(b)17.7(e)0(r)-272.7(o)0(f)-265.3(h)0(i)18.5(d)0(d)15.5(e)0(n)-270.8(s)0(t)23(a)0(t)16.7(e)0(s)-272(o)0(f)19.3(t)0(e)16.7(n)]TJ
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[(ta)16.7(ti)15.7(on)21.2(s)-229.6(w)0(h)17.3(e)0(r)17.5(e)-230.2(si)17.3(ng)15.5(l)13.5(e)-230.2(ch)13.8(r)14.3(o)0(m)12(a)0(t)22.4(i)0(n)-220.5(sta)-8(tes)-241.3(are)-246.8(repr)-8.8(esent)-11.3(ed)-242.3(by)-240.5(mul)-8.6(tiple)-247.2(sta)-8(tes)-241.3(of)-242.5(the)-240.2(HM)-7.4(M.)-242.1(Figu)-10.7(re)-238.6(1)-239.8(i)0(l)-7.1(lustra)-9.4(tes)-247(this)]TJ
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0 -1.195 TD
[(to)-288.8(dete)-9.4(rmine)-287(the)-291.4(optim)-7.2(al)-284.9(set)-286.9(of)-288(para)-8.6(meter)-10(s)-280.8(i)0(t)-285.9(i)0(s)-284.3(nece)-14.1(ssary)-288.8(to)-283.1(lea)-8.6(rn)-282.3(an)-9(d)-279.6(eval)-9.4(uate)-288.2(a)-287.1(large)-291(numb)-6.6(er)-284.1(o)-6.5(f)-281.6(differ)-9.4(ent)]TJ
0 -1.2007 TD
[(mod)-11.5(els,)-338.5(eff)-8(ect)-8.6(ively)-341.2(negat)-10.1(ing)-340.8(the)-336.9(pres)-8(u)-6.5(med)-337.7(sim)-9.8(plici)-8.2(ty.)]TJ
1.0015 -1.2007 TD
[(ChroMo)-7.5(dule)-263.7(\(Won)-269.3(et)-262.1(al.,)-262.9(2013\))-261.9(is)-261.6(a)-264.3(supervis)-9.3(ed)-259.4(alter)-9.2(native)-264.1(that)-266.4(models)-264.2(the)-262.9(spat)-8.8(ial)-260(distribut)-9.7(ion)-261.1(of)-265.3(features)]TJ
-1.0015 -1.2007 TD
[(at)-358.9(chromat)-11.5(in)-351.4(sta)-8(tes)-355.2(with)-359.6(leftrig)-8.7(ht)-357.1(structure)-9.7(d)-353.6(H)0(M)-7.4(M)0(s)-357.5(that)-357.5(are)-355(com)-7.6(monly)-357.2(used)-358.8(in)-357.1(speec)-10.4(h)-353.6(recogniti)-9.3(on)-354.3(\(Ra-)]TJ
T*
[(bine)-7.6(r,)-304.7(1989\).)-313.5(Howeve)-10.3(r,)-304.7(the)-308.4(construc)-9.9(tion)-310.2(of)-305.1(a)-309.8(model)-307.8(require)-9.9(s)-303.6(a)-309.8(training)-314.1(set)-309.6(for)-307.8(each)-310(chromat)-11.5(in)-305.9(state.)-310.4(As)-308.2(an)]TJ
T*
[(alter)-9.2(native)-355.1(to)-351.4(the)-348.3(HM)-7.4(M-based)-355.5(methods)-8.9(,)-353.2(Segway)-352.7(\(H)-7.4(offman)-355.3(et)-347.5(al.,)-354(2012a,b)-6.7(\))-349.9(allow)-9.4(s)-349.1(t)0(o)-345.7(com)-7.6(pute)-354.7(segmenta-)]TJ
T*
[(tio)-7.8(ns)-298.6(based)-304.5(on)-297.4(arbitrar)-9.7(y)-296.7(hidden)-305(processe)-10.1(s,)-298.2(as)-300.4(long)-301.7(as)-300.4(the)-297.1(mode)-8.4(l)-299.4(can)-301.8(be)-299.2(represe)-10.2(nted)-297.8(as)-300.4(a)-298.5(d)0(y)-7.2(namic)-303.9(Bayesian)]TJ
T*
[(networ)-9.3(k.)-359.7(It)-364.8(operate)-9.7(s)-360.5(o)0(n)-360(a)-366.7(single)-365.9(base-pair)-367.2(reso)-8(lution)-365.7(and)-362.6(with)-365.3(its)-361.8(defa)-8.6(ult)-360.6(model)-364.7(com)-7.6(putes)-362.4(segm)-9.6(entations)]TJ
0 -1.195 TD
[(that)-306.3(are)-309.4(even)-308.2(more)-306.2(ne-grai)-9.9(ned)-300(than)-309.2(those)-305.5(of)-305.1(Chrom)-8.3(HMM)-306(and)-305.7(EpiCSeg)-309.5(\(Hoff)-8(man)-303.5(et)-302(al.,)-308.4(2012a\).)-304.6(Se)-8.2(gway)]TJ
0 -1.2007 TD
[(mode)-8.4(ls)-290(are)-286.7(typi)-8.6(cally)-291.7(trained)-295.3(on)-286.1(a)-287.1(small)-294.7(fraction)-292.3(of)-288(the)-291.4(avai)-9.4(lable)-291.8(data,)-288.6(due)-294.3(to)-288.8(the)-285.7(com)-7.6(putational)-295.4(comp)-8.4(lexity)]TJ
T*
[(of)-339.2(the)-336.9(inference)-345.1(algorithm)-341.1(and)-334.1(the)-336.9(high)-335.9(data)-339.4(reso)-8(lution.)]TJ
1.0015 -1.2007 TD
[(A)-266.5(different)-272.3(appro)-7.6(ach)-267.6(is)-261.6(imple)-9(mented)-270.5(in)-260.4(Stat)-9.6(eHub-Stat)-9.7(ePaintR)-268.8(\(C)-8.2(oetzee)-270.6(et)-262.2(al.,)-268.6(2018\).)-267.9(Instead)-270.9(of)-265.3(inferring)]TJ
-1.0015 -1.2007 TD
[(chrom)-11.1(atin)-323.3(states)-329(de)-322(novo)-321.7(ever)-8.6(y)-319.4(time)-326.9(a)-321.2(segment)-10.7(ation)-324.1(is)-324.2(compute)-9.5(d,)-319.8(the)-325.5(method)-325.6(imple)-9(ments)-326.1(a)-321.2(model)-324.9(of)-322.2(our)]TJ
T*
[(cu)13.8(rr)17.3(en)19.4(t)-282.4(u)0(n)15.5(d)0(e)19.4(r)0(s)18.1(t)0(a)16.7(n)0(d)15.5(i)0(n)18.5(g)-285.3(of)-271(ch)13.8(ro)19.3(ma)15.9(ti)21.4(n)-285.3(s)0(t)17.3(a)0(t)16.7(e)-287.1(ch)19.4(ar)17.5(ac)17.7(te)16.7(ri)16.5(st)17.3(i)13.5(c)0(s)12.6(.)-279.2(In)-276.7(pa)13.8(r)14.3(t)0(i)15.7(c)0(u)19.4(l)0(a)16.7(r)0(,)-276.3(t)0(h)18.5(e)-287.1(m)12.8(o)0(d)15.5(e)0(l)-273.5(e)0(n)13.8(c)0(o)19.4(d)0(e)13.8(s)-280.8(fo)19.3(r)-287.3(e)0(a)17.7(c)0(h)-276.5(c)0(h)19.4(r)0(o)13.6(m)12.8(at)16.7(in)]TJ
T*
[(st)17.3(at)16.7(e)-292.8(t)0(h)18.5(e)-292.8(se)12.6(t)-288.1(o)0(f)-288(f)0(e)17.5(a)0(t)16.7(u)0(r)19.3(e)0(s)-283.3(t)0(h)18.5(a)0(t)-284.9(a)0(r)17.5(e)-292.8(po)15.5(si)23(ti)15.7(ve)19.4(ly)-283.1(or)-288(ne)19.4(ga)19.4(ti)15.7(ve)19.4(ly)-283.1(as)12.6(so)20(ci)16.7(at)16.7(ed)-282.2(wi)14.5(t)13.5(h)-296.7(th)18.5(at)-284.9(st)17.3(at)22.4(e.)-287.5(T)10.8(h)0(e)-287.8(m)12.8(et)16.7(ho)15.5(d)-291(i)0(s)-284.3(c)0(e)17.7(r)0(t)16.5(a)0(i)16.7(n)0(l)18.5(y)-291(a)]TJ
T*
[(st)17.3(ep)-236.6(to)18.5(wa)15.5(rd)-236.8(th)18.5(e)-241.6(r)0(i)16.5(g)0(h)15.5(t)-242.5(di)18.5(re)17.5(ct)16.7(io)18.5(n,)-234.5(bu)21.2(t)-248.2(i)13.5(t)-248.2(a)0(l)16.7(s)0(o)-230.3(d)0(o)15.5(e)0(s)-237.8(n)0(o)21.2(t)-242.5(mo)17.7(de)13.8(l)-242.5(t)0(h)18.5(e)-247.2(sp)20(at)16.7(ia)16.7(l)-242.5(d)0(i)18.5(s)0(t)17.3(r)0(i)16.5(b)0(u)21.2(t)0(i)15.7(o)0(n)-234.8(o)0(f)-231.1(f)0(e)11.8(a)0(t)22.4(u)0(r)13.6(e)0(s)-232.1(a)0(r)17.5(o)0(u)15.5(n)0(d)-234.8(c)0(h)19.4(r)0(o)13.6(m)12.8(at)16.7(in)]TJ
0 -1.195 TD
[(st)17.3(at)16.7(es)-317.5(an)19.4(d,)-314.1(th)18.5(er)17.5(ef)17.5(or)13.6(e,)-315.9(pr)19.3(od)21.2(uc)13.8(es)-311.8(hi)12.8(gh)21.2(ly)-317.3(fr)17.3(ag)19.4(me)15.9(nt)18.5(ed)-316.3(se)18.3(gm)17.7(en)19.4(ta)16.7(ti)15.7(on)21.2(s,)-315.3(si)17.3(mi)14.9(la)16.7(r)-321.4(t)0(o)-317.3(t)13.5(ho)15.5(se)-317.5(of)-310.8(un)15.5(su)20(pe)13.8(rv)19.3(is)17.3(ed)-316.3(HM)15.3(Ms)18.1(.)]TJ
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[(FIG.)-410.7(1.)]TJ
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4.1921 0 TD
[(Genome)-407.1(segmentations.)-413.8(Typical)-407.6(genome)-410.1(segmentation)-410.2(\(s1\))-409.1(where)-413(the)-403.3(promoter)-409.6(is)-408.9(fragmented)-413.5(into)-404.4(many)]TJ
-4.1921 -1.2266 TD
[(different)-269.2(segments.)-266.7(In)-267.2(this)-266.5(example,)-267.2(the)-264.2(optimal)-267.5(segmentation)-264.8(\(s2\))-263.7(shows)-268.8(a)-267.5(single)-261.6(active)-271.6(promoter)-264.2(segment)-263.1(\(PA\))-270.7(with)-262.3(a)]TJ
0 -1.2203 TD
[(transcribed)-338.8(region)-334.9(to)-331.8(the)-333.8(left)-339.9(and)-329.7(no)-334.1(signal)-337.5(to)-331.8(the)-333.8(right.)]TJ
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9.9626 0 0 9.9626 74.0976 737.4045 Tm
[(2)-30877.7(BEN)-10(NER)-339.2(AND)-338.4(VINGR)-8.9(ON)]TJ
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