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Razeen Shaikh

dblp:425/3214 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2023
0009-0006-5584-3402ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Theoretical computer science
1 paper
Mathematical optimization · 100%

Topics — the 5 heaviest of 5, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › systems biology
parameter estimation
0.712023
ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models · Bioinform. 2023
Bioinformatics and computational biology
systems biology
0.712023
ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models · Bioinform. 2023
Mathematical optimization
continuous optimization
0.212023
ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models · Bioinform. 2023
Mathematical optimization › multi-objective optimization
evolutionary algorithm
0.212023
ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models · Bioinform. 2023
Mathematical optimization
global optimization
0.212023
ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models · Bioinform. 2023

Methods — techniques the papers use, named apart from their topics

stochastic ranking · 1.3linear least squares · 1.3evolutionary strategy · 1.3
YearPublicationVenuePosition
2023 ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models
abstract
MOTIVATION: Mathematical models in systems biology help generate hypotheses, guide experimental design, and infer the dynamics of gene regulatory networks. These models are characterized by phenomenological or mechanistic parameters, which are typically hard to measure. Therefore, efficient parameter estimation is central to model development. Global optimization techniques, such as evolutionary algorithms (EAs), are applied to estimate model parameters by inverse modeling, i.e. calibrating models by minimizing a function that evaluates a measure of the error between model predictions and experimental data. EAs estimate model parameters "fittest individuals" by generating a large population of individuals using strategies like recombination and mutation over multiple "generations." Typically, only a few individuals from each generation are used to create new individuals in the next generation. Improved Evolutionary Strategy by Stochastic Ranking (ISRES), proposed by Runnarson and Yao, is one such EA that is widely used in systems biology to estimate parameters. ISRES uses information at most from a pair of individuals in any generation to create a new population to minimize the error. In this article, we propose an efficient evolutionary strategy, ISRES+, which builds on ISRES by combining information from all individuals across the population and across all generations to develop a better understanding of the fitness landscape. RESULTS: ISRES+ uses the additional information generated by the algorithm during evolution to approximate the local neighborhood around the best-fit individual using linear least squares fits in one and two dimensions, enabling efficient parameter estimation. ISRES+ outperforms ISRES and results in fitter individuals with a tighter distribution over multiple runs, such that a typical run of ISRES+ estimates parameters with a higher goodness-of-fit compared with ISRES. AVAILABILITY AND IMPLEMENTATION: Algorithm and implementation: Github-https://github.com/gtreeves/isres-plus-bandodkar-2022.
Prasad U. Bandodkar, Razeen Shaikh, Gregory T. Reeves
Bioinform.2