J. Comput. Biol. - Balancing the robustness and predictive performance of biomarkers.

Tópicos

{ assess(1506) score(1403) qualiti(1306) }
{ method(1557) propos(1049) approach(1037) }
{ take(945) account(800) differ(722) }
{ drug(1928) target(777) effect(648) }
{ perform(1367) use(1326) method(1137) }
{ result(1111) use(1088) new(759) }
{ estim(2440) model(1874) function(577) }
{ imag(2830) propos(1344) filter(1198) }
{ sampl(1606) size(1419) use(1276) }
{ can(774) often(719) complex(702) }
{ network(2748) neural(1063) input(814) }
{ data(1737) use(1416) pattern(1282) }
{ framework(1458) process(801) describ(734) }
{ learn(2355) train(1041) set(1003) }
{ studi(1119) effect(1106) posit(819) }
{ model(2656) set(1616) predict(1553) }
{ cost(1906) reduc(1198) effect(832) }
{ gene(2352) biolog(1181) express(1162) }
{ method(1969) cluster(1462) data(1082) }
{ detect(2391) sensit(1101) algorithm(908) }
{ sequenc(1873) structur(1644) protein(1328) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ concept(1167) ontolog(924) domain(897) }
{ care(1570) inform(1187) nurs(1089) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ first(2504) two(1366) second(1323) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
{ process(1125) use(805) approach(778) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
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{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ data(3963) clinic(1234) research(1004) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ decis(3086) make(1611) patient(1517) }
{ activ(1452) weight(1219) physic(1104) }
{ method(2212) result(1239) propos(1039) }

Resumo

Recent studies have highlighted the importance of assessing the robustness of putative biomarkers identified from experimental data. This has given rise to the concept of stable biomarkers, which are ones that are consistently identified regardless of small perturbations to the data. Since stability is not by itself a useful objective, we present a number of strategies that combine assessments of stability and predictive performance in order to identify biomarkers that are both robust and diagnostically useful. Moreover, by wrapping these strategies around logistic regression classifiers regularized by the elastic net penalty, we are able to assess the effects of correlations between biomarkers upon their perceived stability. We use a synthetic example to illustrate the properties of our proposed strategies. In this example, we find that: (i) assessments of stability can help to reduce the number of false-positive biomarkers, although potentially at the cost of missing some true positives; (ii) combining assessments of stability with assessments of predictive performance can improve the true positive rate; and (iii) correlations between biomarkers can have adverse effects on their stability and hence must be carefully taken into account when undertaking biomarker discovery. We then apply our strategies in a proteomics context to identify a number of robust candidate biomarkers for the human disease HTLV1-associated myelopathy/tropical spastic paraparesis (HAM/TSP).

Resumo Limpo

recent studi highlight import assess robust putat biomark identifi experiment data given rise concept stabl biomark one consist identifi regardless small perturb data sinc stabil use object present number strategi combin assess stabil predict perform order identifi biomark robust diagnost use moreov wrap strategi around logist regress classifi regular elast net penalti abl assess effect correl biomark upon perceiv stabil use synthet exampl illustr properti propos strategi exampl find assess stabil can help reduc number falseposit biomark although potenti cost miss true posit ii combin assess stabil assess predict perform can improv true posit rate iii correl biomark can advers effect stabil henc must care taken account undertak biomark discoveri appli strategi proteom context identifi number robust candid biomark human diseas htlvassoci myelopathytrop spastic paraparesi hamtsp

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