J Chem Inf Model - Applicability domains for classification problems: Benchmarking of distance to models for Ames mutagenicity set.

Tópicos

{ perform(999) metric(946) measur(919) }
{ model(2656) set(1616) predict(1553) }
{ error(1145) method(1030) estim(1020) }
{ system(1050) medic(1026) inform(1018) }
{ system(1976) rule(880) can(841) }
{ clinic(1479) use(1117) guidelin(835) }
{ data(3008) multipl(1320) sourc(1022) }
{ can(774) often(719) complex(702) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ method(1557) propos(1049) approach(1037) }
{ compound(1573) activ(1297) structur(1058) }
{ data(2317) use(1299) case(1017) }
{ use(1733) differ(960) four(931) }
{ estim(2440) model(1874) function(577) }
{ data(1737) use(1416) pattern(1282) }
{ measur(2081) correl(1212) valu(896) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ concept(1167) ontolog(924) domain(897) }
{ algorithm(1844) comput(1787) effici(935) }
{ data(1714) softwar(1251) tool(1186) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ gene(2352) biolog(1181) express(1162) }
{ activ(1138) subject(705) human(624) }
{ implement(1333) system(1263) develop(1122) }
{ method(2212) result(1239) propos(1039) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ imag(1057) registr(996) error(939) }
{ sequenc(1873) structur(1644) protein(1328) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ extract(1171) text(1153) clinic(932) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ 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) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ research(1085) discuss(1038) issu(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ 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) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The estimation of accuracy and applicability of QSAR and QSPR models for biological and physicochemical properties represents a critical problem. The developed parameter of "distance to model" (DM) is defined as a metric of similarity between the training and test set compounds that have been subjected to QSAR/QSPR modeling. In our previous work, we demonstrated the utility and optimal performance of DM metrics that have been based on the standard deviation within an ensemble of QSAR models. The current study applies such analysis to 30 QSAR models for the Ames mutagenicity data set that were previously reported within the 2009 QSAR challenge. We demonstrate that the DMs based on an ensemble (consensus) model provide systematically better performance than other DMs. The presented approach identifies 30-60% of compounds having an accuracy of prediction similar to the interlaboratory accuracy of the Ames test, which is estimated to be 90%. Thus, the in silico predictions can be used to halve the cost of experimental measurements by providing a similar prediction accuracy. The developed model has been made publicly available at http://ochem.eu/models/1 .

Resumo Limpo

estim accuraci applic qsar qspr model biolog physicochem properti repres critic problem develop paramet distanc model dm defin metric similar train test set compound subject qsarqspr model previous work demonstr util optim perform dm metric base standard deviat within ensembl qsar model current studi appli analysi qsar model ame mutagen data set previous report within qsar challeng demonstr dms base ensembl consensus model provid systemat better perform dms present approach identifi compound accuraci predict similar interlaboratori accuraci ame test estim thus silico predict can use halv cost experiment measur provid similar predict accuraci develop model made public avail httpochemeumodel

Resumos Similares

J Chem Inf Model - Rank order entropy: why one metric is not enough. ( 0,80465024723243 )
J Chem Inf Model - Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions. ( 0,684793207643315 )
Neural Comput - Improved similarity measures for small sets of spike trains. ( 0,671271209551112 )
J Chem Inf Model - Time-split cross-validation as a method for estimating the goodness of prospective prediction. ( 0,661271589434297 )
J Chem Inf Model - GRID-based three-dimensional pharmacophores II: PharmBench, a benchmark data set for evaluating pharmacophore elucidation methods. ( 0,653121028937883 )
J Chem Inf Model - Study of chromatographic retention of natural terpenoids by chemoinformatic tools. ( 0,651280905817472 )
J Chem Inf Model - Using random forest to model the domain applicability of another random forest model. ( 0,642696180032217 )
J Chem Inf Model - Comparative studies on some metrics for external validation of QSPR models. ( 0,637321427081908 )
J Chem Inf Model - Three useful dimensions for domain applicability in QSAR models using random forest. ( 0,636462618900402 )
Artif Intell Med - Training artificial neural networks directly on the concordance index for censored data using genetic algorithms. ( 0,635072720225163 )
J Biomed Inform - Transfer learning based clinical concept extraction on data from multiple sources. ( 0,630076004351744 )
J Chem Inf Model - Prediction of active site cleft using support vector machines. ( 0,611748769858066 )
Int J Health Geogr - A linear programming model for preserving privacy when disclosing patient spatial information for secondary purposes. ( 0,611479387189137 )
J Chem Inf Model - Development of novel 3D-QSAR combination approach for screening and optimizing B-Raf inhibitors in silico. ( 0,608663892701974 )
BMC Med Inform Decis Mak - Measuring preferences for analgesic treatment for cancer pain: how do African-Americans and Whites perform on choice-based conjoint (CBC) analysis experiments? ( 0,605636791648817 )
J Chem Inf Model - iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. ( 0,605159043267181 )
Artif Intell Med - Fuzzy model identification of dengue epidemic in Colombia based on multiresolution analysis. ( 0,602203222729326 )
IEEE Trans Image Process - Two-dimensional approach to full-reference image quality assessment based on positional structural information. ( 0,599799776198877 )
J Chem Inf Model - Does rational selection of training and test sets improve the outcome of QSAR modeling? ( 0,59638613762505 )
J Chem Inf Model - Best of both worlds: combining pharma data and state of the art modeling technology to improve in Silico pKa prediction. ( 0,596017647213229 )
AMIA Annu Symp Proc - Effect of data combination on predictive modeling: a study using gene expression data. ( 0,589220683867026 )
J Chem Inf Model - A new approach to radial basis function approximation and its application to QSAR. ( 0,585770053596915 )
IEEE Trans Image Process - Toward an impairment metric for stereoscopic video: a full-reference video quality metric to assess compressed stereoscopic video. ( 0,584386270264975 )
J. Med. Internet Res. - Outsourcing medical data analyses: can technology overcome legal, privacy, and confidentiality issues? ( 0,580270370358579 )
J Chem Inf Model - Beyond the scope of Free-Wilson analysis: building interpretable QSAR models with machine learning algorithms. ( 0,579786331942576 )
J Am Med Inform Assoc - Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery. ( 0,577967865366326 )
J Chem Inf Model - RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes. ( 0,577652321305426 )
Comput. Biol. Med. - Similarity measure for quality control of dental CAD/CAM-applications. ( 0,577578770732005 )
J Chem Inf Model - Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes. ( 0,572842347538401 )
BMC Med Inform Decis Mak - Concordance and predictive value of two adverse drug event data sets. ( 0,571808086634054 )
IEEE Trans Image Process - Co-transduction for shape retrieval. ( 0,568724844503667 )
J Biomed Inform - MysiRNA: improving siRNA efficacy prediction using a machine-learning model combining multi-tools and whole stacking energy (G). ( 0,56795932104708 )
Brief. Bioinformatics - Letter to the editor: Stability of Random Forest importance measures. ( 0,567290740096027 )
IEEE Trans Image Process - View-based discriminative probabilistic modeling for 3D object retrieval and recognition. ( 0,565611204192416 )
AMIA Annu Symp Proc - Advanced proficiency EHR training: effect on physicians' EHR efficiency, EHR satisfaction and job satisfaction. ( 0,56232268633246 )
Comput Methods Programs Biomed - Predicting body fat percentage based on gender, age and BMI by using artificial neural networks. ( 0,561758162063893 )
J Chem Inf Model - How accurately can we predict the melting points of drug-like compounds? ( 0,561045430605177 )
J Chem Inf Model - Pharmacophore assessment through 3-D QSAR: evaluation of the predictive ability on new derivatives by the application on a series of antitubercular agents. ( 0,560682926238365 )
J Chem Inf Model - Impact of template choice on homology model efficiency in virtual screening. ( 0,547531379423113 )
Int J Comput Assist Radiol Surg - Three-dimensional skeletonization and symbolic description in vascular imaging: preliminary results. ( 0,544550633665072 )
IEEE Trans Image Process - Incremental N-mode SVD for large-scale multilinear generative models. ( 0,542554322929631 )
J Chem Inf Model - Criterion for evaluating the predictive ability of nonlinear regression models without cross-validation. ( 0,540354635905585 )
BMC Med Inform Decis Mak - Regression tree construction by bootstrap: model search for DRG-systems applied to Austrian health-data. ( 0,54023436236579 )
IEEE Trans Vis Comput Graph - Quartic Box-Spline Reconstruction on the BCC Lattice. ( 0,539810482847905 )
J Chem Inf Model - Statistical analysis and compound selection of combinatorial libraries for soluble epoxide hydrolase. ( 0,537912537618887 )
AMIA Annu Symp Proc - Motivating the additional use of external validity: examining transportability in a model of glioblastoma multiforme. ( 0,537453471890571 )
J Chem Inf Model - Interpretable, probability-based confidence metric for continuous quantitative structure-activity relationship models. ( 0,534986938857025 )
Brief. Bioinformatics - Evaluating template-based and template-free protein-protein complex structure prediction. ( 0,533105331475951 )
Int J Health Geogr - Incorporating geographical factors with artificial neural networks to predict reference values of erythrocyte sedimentation rate. ( 0,531888212888926 )
J. Comput. Biol. - The complexity of the dirichlet model for multiple alignment data. ( 0,529179968033583 )
IEEE Trans Image Process - A multisize superpixel approach for salient object detection based on multivariate normal distribution estimation. ( 0,527619209967991 )
J Chem Inf Model - Applicability Domain ANalysis (ADAN): a robust method for assessing the reliability of drug property predictions. ( 0,527464690435995 )
J Am Med Inform Assoc - Harvest: an open platform for developing web-based biomedical data discovery and reporting applications. ( 0,52741841064931 )
J Chem Inf Model - Stochastic proximity embedding on graphics processing units: taking multidimensional scaling to a new scale. ( 0,526528731780608 )
J Chem Inf Model - Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets. ( 0,525848655001975 )
IEEE Trans Image Process - Neighborhood Supported Model Level Fuzzy Aggregation for Moving Object Segmentation. ( 0,525007057987594 )
Int J Comput Assist Radiol Surg - Assessing performance in brain tumor resection using a novel virtual reality simulator. ( 0,523391337971795 )
J Chem Inf Model - Applicability domain based on ensemble learning in classification and regression analyses. ( 0,523183665421104 )
Int J Comput Assist Radiol Surg - Optimized order estimation for autoregressive models to predict respiratory motion. ( 0,521438977507878 )
IEEE Trans Image Process - Spatial statistics of image features for performance comparison. ( 0,521018219519543 )
J. Med. Internet Res. - A case study of the New York City 2012-2013 influenza season with daily geocoded Twitter data from temporal and spatiotemporal perspectives. ( 0,520990188536085 )
J Chem Inf Model - In silico prediction of total human plasma clearance. ( 0,520803423279291 )
J Chem Inf Model - In silico prediction of chemical Ames mutagenicity. ( 0,520229477037277 )
Comput. Biol. Med. - A prediction model of substrates and non-substrates of breast cancer resistance protein (BCRP) developed by GA-CG-SVM method. ( 0,517925916535027 )
J Chem Inf Model - QSAR modeling of imbalanced high-throughput screening data in PubChem. ( 0,517563678671751 )
J Chem Inf Model - In silico prediction of aqueous solubility using simple QSPR models: the importance of phenol and phenol-like moieties. ( 0,516007173369542 )
J Chem Inf Model - Robust scoring functions for protein-ligand interactions with quantum chemical charge models. ( 0,515478637975679 )
J Chem Inf Model - Assessing relative bioactivity of chemical substances using quantitative molecular network topology analysis. ( 0,514942451717046 )
J. Comput. Biol. - An almost optimal algorithm for generalized threshold group testing with inhibitors. ( 0,513432564913245 )
Comput Methods Programs Biomed - Kinetic modelling of haemodialysis removal of myoglobin in rhabdomyolysis patients. ( 0,510674057002419 )
IEEE Trans Image Process - Linear time distances between fuzzy sets with applications to pattern matching and classification. ( 0,510385585505497 )
J Am Med Inform Assoc - Automated extraction of ejection fraction for quality measurement using regular expressions in Unstructured Information Management Architecture (UIMA) for heart failure. ( 0,509384022346627 )
Comput Biol Chem - Ranking of microRNA target prediction scores by Pareto front analysis. ( 0,509345148429208 )
J Chem Inf Model - Real external predictivity of QSAR models: how to evaluate it? Comparison of different validation criteria and proposal of using the concordance correlation coefficient. ( 0,508378250592302 )
J Chem Inf Model - CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. ( 0,507450269661527 )
J Chem Inf Model - Building a three-dimensional model of CYP2C9 inhibition using the Autocorrelator: an autonomous model generator. ( 0,505599568011225 )
Med Biol Eng Comput - Development of a comprehensive musculoskeletal model of the shoulder and elbow. ( 0,50549577921979 )
Comput. Aided Surg. - Evaluation of a computational model to predict elbow range of motion. ( 0,505249472386017 )
Artif Intell Med - Improved cosine similarity measures of simplified neutrosophic sets for medical diagnoses. ( 0,50385331675966 )
Med Biol Eng Comput - Application of the RIMARC algorithm to a large data set of action potentials and clinical parameters for risk prediction of atrial fibrillation. ( 0,503505903943834 )
Brief. Bioinformatics - An empirical assessment of validation practices for molecular classifiers. ( 0,502556757852999 )
Spat Spatiotemporal Epidemiol - Spatial modelling of disease using data- and knowledge-driven approaches. ( 0,50247181816518 )
J Clin Monit Comput - Evaluation of a computer program for non-invasive determination of pulmonary shunt and ventilation-perfusion mismatch. ( 0,501880410858771 )
J. Comput. Biol. - Population model-based inter-diplotype similarity measure for accurate diplotype clustering. ( 0,5015855847819 )
IEEE Trans Image Process - Efficient algorithm for level set method preserving distance function. ( 0,501538077790235 )
AMIA Annu Symp Proc - Predicting the dengue incidence in Singapore using univariate time series models. ( 0,500877967160417 )
Artif Intell Med - Image partitioning and illumination in image-based pose detection for teleoperated flexible endoscopes. ( 0,500411992339068 )
IEEE J Biomed Health Inform - Identifying mammalian MicroRNA targets based on supervised distance metric learning. ( 0,497833957415243 )
Int J Health Geogr - Modelling zoonotic diseases in humans: comparison of methods for hantavirus in Sweden. ( 0,497540554078801 )
J Chem Inf Model - Optimizing predictive performance of CASE Ultra expert system models using the applicability domains of individual toxicity alerts. ( 0,496625373948964 )
Comput Methods Programs Biomed - Privacy-preserving Kruskal-Wallis test. ( 0,496174951781072 )
Med Decis Making - Developing a tuberculosis transmission model that accounts for changes in population health. ( 0,495384769831919 )
Med Biol Eng Comput - Novel non-invasive method of measurement of endothelial function: enclosed-zone flow-mediated dilatation (ezFMD). ( 0,495206797971667 )
J Chem Inf Model - Ligand and structure-based classification models for prediction of P-glycoprotein inhibitors. ( 0,494206928465119 )
J Chem Inf Model - Coping with unbalanced class data sets in oral absorption models. ( 0,49339317949325 )
J Chem Inf Model - Combined 3D-QSAR, molecular docking, and molecular dynamics study on piperazinyl-glutamate-pyridines/pyrimidines as potent P2Y12 antagonists for inhibition of platelet aggregation. ( 0,492822584221945 )
IEEE Trans Image Process - 3-D object retrieval and recognition with hypergraph analysis. ( 0,492627938476913 )
IEEE Trans Pattern Anal Mach Intell - Improved Iris Recognition Through Fusion of Hamming Distance and Fragile Bit Distance. ( 0,491348633901091 )
J Chem Inf Model - Prediction of linear cationic antimicrobial peptides based on characteristics responsible for their interaction with the membranes. ( 0,491327271153713 )
J Chem Inf Model - Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening. ( 0,488198666107299 )