Comput. Biol. Med. - Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics.

Tópicos

{ model(3480) simul(1196) paramet(876) }
{ problem(2511) optim(1539) algorithm(950) }
{ first(2504) two(1366) second(1323) }
{ health(1844) social(1437) communiti(874) }
{ implement(1333) system(1263) develop(1122) }
{ method(1219) similar(1157) match(930) }
{ chang(1828) time(1643) increas(1301) }
{ method(1557) propos(1049) approach(1037) }
{ use(976) code(926) identifi(902) }
{ assess(1506) score(1403) qualiti(1306) }
{ analysi(2126) use(1163) compon(1037) }
{ model(3404) distribut(989) bayesian(671) }
{ take(945) account(800) differ(722) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ concept(1167) ontolog(924) domain(897) }
{ howev(809) still(633) remain(590) }
{ studi(1119) effect(1106) posit(819) }
{ spatial(1525) area(1432) region(1030) }
{ state(1844) use(1261) util(961) }
{ model(2656) set(1616) predict(1553) }
{ can(774) often(719) complex(702) }
{ system(1976) rule(880) can(841) }
{ sequenc(1873) structur(1644) protein(1328) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2675) segment(2577) method(1081) }
{ algorithm(1844) comput(1787) effici(935) }
{ control(1307) perform(991) simul(935) }
{ general(901) number(790) one(736) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ perform(1367) use(1326) method(1137) }
{ medic(1828) order(1363) alert(1069) }
{ cost(1906) reduc(1198) effect(832) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ framework(1458) process(801) describ(734) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ 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) }
{ compound(1573) activ(1297) structur(1058) }
{ blood(1257) pressur(1144) flow(957) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The aim of inverse modeling is to capture the systems dynamics through a set of parameterized Ordinary Differential Equations (ODEs). Parameters are often required to fit multiple repeated measurements or different experimental conditions. This typically leads to a multi-objective optimization problem that can be formulated as a non-convex optimization problem. Modeling of glucose utilization of Lactococcus lactis bacteria is considered using in vivo Nuclear Magnetic Resonance (NMR) measurements in perturbation experiments. We propose an ODE model based on a modified time-varying exponential decay that is flexible enough to model several different experimental conditions. The starting point is an over-parameterized non-linear model that will be further simplified through an optimization procedure with regularization penalties. For the parameter estimation, a stochastic global optimization method, particle swarm optimization (PSO) is used. A regularization is introduced to the identification, imposing that parameters should be the same across several experiments in order to identify a general model. On the remaining parameter that varies across the experiments a function is fit in order to be able to predict new experiments for any initial condition. The method is cross-validated by fitting the model to two experiments and validating the third one. Finally, the proposed model is integrated with existing models of glycolysis in order to reconstruct the remaining metabolites. The method was found useful as a general procedure to reduce the number of parameters of unidentifiable and over-parameterized models, thus supporting feature selection methods for parametric models.

Resumo Limpo

aim invers model captur system dynam set parameter ordinari differenti equat ode paramet often requir fit multipl repeat measur differ experiment condit typic lead multiobject optim problem can formul nonconvex optim problem model glucos util lactococcus lacti bacteria consid use vivo nuclear magnet reson nmr measur perturb experi propos ode model base modifi timevari exponenti decay flexibl enough model sever differ experiment condit start point overparameter nonlinear model will simplifi optim procedur regular penalti paramet estim stochast global optim method particl swarm optim pso use regular introduc identif impos paramet across sever experi order identifi general model remain paramet vari across experi function fit order abl predict new experi initi condit method crossvalid fit model two experi valid third one final propos model integr exist model glycolysi order reconstruct remain metabolit method found use general procedur reduc number paramet unidentifi overparameter model thus support featur select method parametr model

Resumos Similares

Comput Math Methods Med - Analytical solutions for the mathematical model describing the formation of liver zones via Adomian's method. ( 0,857061615567877 )
Comput Math Methods Med - Dynamics analysis and simulation of a modified HIV infection model with a saturated infection rate. ( 0,794719183406478 )
IEEE Trans Image Process - Reinitialization-free level set evolution via reaction diffusion. ( 0,787488345186463 )
Comput Methods Programs Biomed - An efficient passive planar micromixer with ellipse-like micropillars for continuous mixing of human blood. ( 0,781402696223917 )
Brief. Bioinformatics - Choosing appropriate models for protein-protein interaction networks: a comparison study. ( 0,778465127026511 )
Neural Comput - Effect of phase response curve skewness on synchronization of electrically coupled neuronal oscillators. ( 0,777474531464606 )
J Integr Bioinform - An advanced environment for hybrid modeling of biological systems based on modelica. ( 0,777023268017009 )
Comput Math Methods Med - ModeLang: a new approach for experts-friendly viral infections modeling. ( 0,764626687421693 )
Comput. Biol. Med. - Modelling and simulating reaction-diffusion systems using coloured Petri nets. ( 0,763054144808341 )
Comput Biol Chem - An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology. ( 0,762894281899898 )
Comput. Biol. Med. - ODE/PDE analysis of corneal curvature. ( 0,761127298478829 )
Comput Methods Programs Biomed - Solving delay differential equations in S-ADAPT by method of steps. ( 0,759651445820416 )
Comput Methods Programs Biomed - Reprint of Pharmacokinetic modelling of the anti-malarial drug artesunate and its active metabolite dihydroartemisinin. ( 0,743093258494738 )
Comput Math Methods Med - Modeling schistosomiasis and HIV/AIDS codynamics. ( 0,742612148417067 )
Med Biol Eng Comput - A fluid-structure interaction model of the aortic valve with coaptation and compliant aortic root. ( 0,742224480590295 )
Comput Math Methods Med - Solutions of a linearized mathematical model for capillary formation in tumor angiogenesis: an initial data perturbation approximation. ( 0,739144875666709 )
Comput Math Methods Med - A theoretical model for the transmission dynamics of the Buruli ulcer with saturated treatment. ( 0,735604546879208 )
Comput Biol Chem - A stochastic evolution model for residue Insertion-Deletion Independent from Substitution. ( 0,7345591357864 )
Comput Methods Programs Biomed - Innovative model to simulate exhalation phase in human respiratory system. ( 0,732591856266984 )
Comput Methods Programs Biomed - Functionality of the baroreceptor nerves in heart rate regulation. ( 0,731338208149254 )
IEEE Trans Image Process - Box relaxation schemes in staggered discretizations for the dual formulation of total variation minimization. ( 0,729817696988853 )
IEEE Trans Pattern Anal Mach Intell - Bi-polynomial Modeling of Low-frequency Reflectances. ( 0,725311288840306 )
Comput Math Methods Med - Numerical solutions for a model of tissue invasion and migration of tumour cells. ( 0,720693588885961 )
Comput Math Methods Med - Modeling innate immune response to early Mycobacterium infection. ( 0,7200288026372 )
Comput Math Methods Med - Computational modeling of microabscess formation. ( 0,71750587221521 )
Comput Math Methods Med - Noninvasive monitoring of hepatic damage from hepatitis C virus infection. ( 0,715615362737377 )
Comput Methods Programs Biomed - Development of a computer algorithm for feedback controlled electrical nerve fiber stimulation. ( 0,715327780922963 )
Comput Math Methods Med - Mathematical modeling of transmission dynamics and optimal control of vaccination and treatment for hepatitis B virus. ( 0,713724391629719 )
Comput Math Methods Med - Numerical stability of partitioned approach in fluid-structure interaction for a deformable thin-walled vessel. ( 0,712621369896709 )
Neural Comput - Analytical integrate-and-fire neuron models with conductance-based dynamics and realistic postsynaptic potential time course for event-driven simulation strategies. ( 0,712615693545634 )
Comput. Biol. Med. - Network and Nakamura tridiagonal computational simulation of electrically-conducting biopolymer micro-morphic transport phenomena. ( 0,70904495489031 )
Comput. Biol. Med. - Semi-computational simulation of magneto-hemodynamic flow in a semi-porous channel using optimal homotopy and differential transform methods. ( 0,708941338815985 )
IEEE Trans Neural Netw Learn Syst - Discrete-Time Zhang Neural Network for Online Time-Varying Nonlinear Optimization With Application to Manipulator Motion Generation. ( 0,708205745697238 )
Neural Comput - Computing confidence intervals for point process models. ( 0,70609762661283 )
Comput Math Methods Med - Variational principles for buckling of microtubules modeled as nonlocal orthotropic shells. ( 0,705595655315943 )
Comput. Biol. Med. - Examples of testing global identifiability of biological and biomedical models with the DAISY software. ( 0,704410549940126 )
Comput. Biol. Med. - Computing the stability of steady-state solutions of mathematical models of the electrical activity in the heart. ( 0,698624296386789 )
Comput Math Methods Med - Global hopf bifurcation on two-delays leslie-gower predator-prey system with a prey refuge. ( 0,693703790697767 )
Comput Math Methods Med - Uncertainty quantification in simulations of epidemics using polynomial chaos. ( 0,690231954434675 )
Neural Comput - Cross-talk induces bifurcations in nonlinear models of synaptic plasticity. ( 0,689145166639945 )
Med Biol Eng Comput - CSF dynamic analysis of a predictive pulsatility-based infusion test for normal pressure hydrocephalus. ( 0,680452717645262 )
Comput Math Methods Med - Optimal control of HIV/AIDS in the workplace in the presence of careless individuals. ( 0,680029183851883 )
J. Comput. Biol. - Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible? ( 0,679391961698162 )
J Chem Inf Model - Full and partial agonism of ionotropic glutamate receptors indicated by molecular dynamics simulations. ( 0,678269685983624 )
J Clin Monit Comput - The standard strong ion difference, standard total titratable base, and their relationship to the Boston compensation rules and the Van Slyke equation for extracellular fluid. ( 0,678196877509249 )
Comput Methods Programs Biomed - Design of a framework for modeling, integration and simulation of physiological models. ( 0,676018661038598 )
Comput Methods Programs Biomed - Parametric-based brain Magnetic Resonance Elastography using a Rayleigh damping material model. ( 0,674011914314975 )
Comput Methods Programs Biomed - Simulating and analysing infectious disease data in a heterogeneous population with migration. ( 0,673482755510662 )
Comput Math Methods Med - A numerical method of reduced complexity for simulating vascular hemodynamics using coupled 0D lumped and 1D wave propagation models. ( 0,666758473784475 )
IEEE Trans Image Process - Efficiency of semi-implicit schemes for anisotropic diffusion in the hypercube. ( 0,665908109911048 )
Comput. Biol. Med. - epiModel: a system to build automatically systems of differential equations of compartmental type-epidemiological models. ( 0,66521274785898 )
Wiley Interdiscip Rev Syst Biol Med - A conceptual framework for computational models of Achilles tendon homeostasis. ( 0,664802183527093 )
IEEE Trans Vis Comput Graph - Paraglide: Interactive Parameter Space Partitioning for Computer Simulations. ( 0,663586117705963 )
Lifetime Data Anal - An extended cure model and model selection. ( 0,661019751096732 )
Comput Methods Programs Biomed - Modelling the Double Peak Phenomenon in pharmacokinetics. ( 0,660913040967034 )
J Chem Inf Model - Fitting of dihedral terms in classical force fields as an analytic linear least-squares problem. ( 0,658670690527488 )
IEEE Trans Neural Netw Learn Syst - Stochastic Stability of Delayed Neural Networks With Local Impulsive Effects. ( 0,658444453507052 )
IEEE Trans Image Process - Additive log-logistic model for networked video quality assessment. ( 0,65760411704984 )
Comput Math Methods Med - Dynamics of Mycobacterium and bovine tuberculosis in a human-buffalo population. ( 0,654334429964095 )
Comput. Biol. Med. - An implicit evolution scheme for active contours and surfaces based on IIR filtering. ( 0,651631712307269 )
Comput Math Methods Med - Effects of maximal sodium and potassium conductance on the stability of Hodgkin-Huxley model. ( 0,650901626209465 )
Comput. Biol. Med. - A synergic simulation-optimization approach for analyzing biomolecular dynamics in living organisms. ( 0,650470793642377 )
Comput Math Methods Med - Towards patient-specific modeling of coronary hemodynamics in healthy and diseased state. ( 0,64870346142799 )
Neural Comput - Theoretical and evolutionary parameter tuning of neural oscillators with a double-chain structure for generating rhythmic signals. ( 0,646060025171773 )
IEEE Trans Image Process - Fast cartoon + texture image filters. ( 0,64566237151863 )
IEEE Trans Image Process - New class tiling design for dot-diffused halftoning. ( 0,644776746866755 )
Comput. Biol. Med. - Density-based Monte Carlo filter and its applications in nonlinear stochastic differential equation models. ( 0,643969361513941 )
IEEE Trans Image Process - Vectorial total variation-based regularization for variational image registration. ( 0,64328732339243 )
J. Comput. Biol. - An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. ( 0,643123378631667 )
Comput. Biol. Med. - Mathematical modeling of brain glioma growth using modified reaction-diffusion equation on brain MR images. ( 0,640518273535385 )
Comput. Biol. Med. - Numerical investigation into blood clotting at the bone-dental implant interface in the presence of an electrical stimulus. ( 0,640372651342424 )
Lifetime Data Anal - Bayesian dynamic regression models for interval censored survival data with application to children dental health. ( 0,639727862320772 )
Comput. Biol. Med. - Phase lagging model of brain response to external stimuli-modeling of single action potential. ( 0,638142358435462 )
Brief. Bioinformatics - Investigating biocomplexity through the agent-based paradigm. ( 0,63782234165523 )
Comput Methods Programs Biomed - A therapy parameter-based model for predicting blood glucose concentrations in patients with type 1 diabetes. ( 0,637618558644206 )
Neural Comput - A calcium-based simple model of multiple spike interactions in spike-timing-dependent plasticity. ( 0,63671274928767 )
Neural Comput - Integration of reinforcement learning and optimal decision-making theories of the basal ganglia. ( 0,635757548315357 )
Wiley Interdiscip Rev Syst Biol Med - Influenza A virus infection kinetics: quantitative data and models. ( 0,63217169175117 )
Comput. Biol. Med. - A compartment model of alveolar-capillary oxygen diffusion with ventilation-perfusion gradient and dynamics of air transport through the respiratory tract. ( 0,631754740300483 )
J Chem Inf Model - Exploiting domain knowledge for improved quantitative high-throughput screening curve fitting. ( 0,63130566415867 )
J Integr Bioinform - From binary to multivalued to continuous models: the lac operon as a case study. ( 0,629340858182609 )
Comput Methods Programs Biomed - On the use of continuous glucose monitoring systems to design optimal clinical tests for the identification of type 1 diabetes models. ( 0,629217053811078 )
J Clin Monit Comput - Simulating physiological interactions in a hybrid system of mathematical models. ( 0,627820048363124 )
Comput Biol Chem - Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. ( 0,627692448114119 )
Comput Math Methods Med - Global stability analysis of SEIR model with holling type II incidence function. ( 0,625507117676622 )
Comput Math Methods Med - A meshfree method for simulating myocardial electrical activity. ( 0,622959573576582 )
Neural Comput - Active data collection for efficient estimation and comparison of nonlinear neural models. ( 0,621679042100687 )
Comput Math Methods Med - Disease control of delay SEIR model with nonlinear incidence rate and vertical transmission. ( 0,620676986543092 )
IEEE Trans Image Process - Rate-distortion analysis of dead-zone plus uniform threshold scalar quantization and its application--part I: fundamental theory. ( 0,619485054482494 )
J Med Syst - A mathematical programming model for scheduling of nurses' labor shifts. ( 0,619217355399575 )
Comput Methods Programs Biomed - Biomechanical analyses of static and dynamic fixation techniques of retrograde interlocking femoral nailing using nonlinear finite element methods. ( 0,618689316691532 )
Comput Math Methods Med - Complexity analysis and parameter estimation of dynamic metabolic systems. ( 0,618262142365649 )
IEEE Trans Image Process - Optimizing a tone curve for backward-compatible high dynamic range image and video compression. ( 0,61749713536306 )
IEEE Trans Neural Netw Learn Syst - Finite-Horizon Approximate Optimal Guaranteed Cost Control of Uncertain Nonlinear Systems With Application to Mars Entry Guidance. ( 0,616138428046854 )
J Integr Bioinform - Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient. ( 0,615786715315465 )
Neural Comput - MOSAIC for multiple-reward environments. ( 0,613915018258681 )
Comput Methods Programs Biomed - Accounting for large deformations in real-time simulations of soft tissues based on reduced-order models. ( 0,611498249857337 )
Comput. Biol. Med. - On a reusable and multilevel methodology for modeling and simulation of pharmacokinetic-physiological systems: a preliminary study. ( 0,610943950212691 )
Comput Math Methods Med - Spongiosa primary development: a biochemical hypothesis by Turing patterns formations. ( 0,609767997856324 )
Comput Math Methods Med - Nonlinear radon transform using Zernike moment for shape analysis. ( 0,609524748353395 )