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Catalyst: Fast and flexible modeling of reaction networks.
Publication Type: Academic Journal
Source(s): PLoS computational biology [PLoS Comput Biol] 2023 Oct 18; Vol. 19 (10), pp. e1011530. Date of Electronic Publication: 2023 Oct 18 (Print Publication: 2023).
Abstract: We introduce Catalyst.jl, a flexible and feature-filled Julia library for modeling and high-performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating stochastic chemical kinetics (jump process), chemical Langevin equatio...
Microbial interactions in theory and practice: when are measurements compatible with models?
Publication Type: Academic Journal
Source(s): Current opinion in microbiology [Curr Opin Microbiol] 2023 Oct; Vol. 75, pp. 102354. Date of Electronic Publication: 2023 Jul 06.
Abstract: Most predictive models of ecosystem dynamics are based on interactions between organisms: their influence on each other's growth and death. We review here how theoretical approaches are used to extract interaction measurements from experimental data in...
An in-depth investigation of the influence of sample size on PCA-MLR, PMF, and FA-NNC source apportionment results.
Publication Type: Academic Journal
Source(s): Environmental geochemistry and health [Environ Geochem Health] 2023 Aug; Vol. 45 (8), pp. 5841-5855. Date of Electronic Publication: 2023 May 13.
Abstract: The mechanism by which parameters influence the source apportionment results of receptor models is not well understood. Three mature receptor models, namely, principal component analysis-multiple linear regression (PCA-MLR), positive matrix factorizati...
Quantifying tissue growth, shape and collision via continuum models and Bayesian inference.
Publication Type: Academic Journal
Source(s): Journal of the Royal Society, Interface [J R Soc Interface] 2023 Jul; Vol. 20 (204), pp. 20230184. Date of Electronic Publication: 2023 Jul 19.
Abstract: Although tissues are usually studied in isolation, this situation rarely occurs in biology, as cells, tissues and organs coexist and interact across scales to determine both shape and function. Here, we take a quantitative approach combining data from ...
Relationship between prediction accuracy and feature importance reliability: An empirical and theoretical study.
Publication Type: Academic Journal
Source(s): NeuroImage [Neuroimage] 2023 Jul 01; Vol. 274, pp. 120115. Date of Electronic Publication: 2023 Apr 23.
Abstract: There is significant interest in using neuroimaging data to predict behavior. The predictive models are often interpreted by the computation of feature importance, which quantifies the predictive relevance of an imaging feature. Tian and Zalesky (2021)...
Diagnosing and Handling Common Violations of Missing at Random.
Publication Type: Academic Journal
Source(s): Psychometrika [Psychometrika] 2023 Dec; Vol. 88 (4), pp. 1123-1143. Date of Electronic Publication: 2023 Jan 04.
Abstract: Ignorable likelihood (IL) approaches are often used to handle missing data when estimating a multivariate model, such as a structural equation model. In this case, the likelihood is based on all available data, and no model is specified for the missing...
Empirical Quantification of Predictive Uncertainty Due to Model Discrepancy by Training with an Ensemble of Experimental Designs: An Application to Ion Channel Kinetics.
Publication Type: Academic Journal
Source(s): Bulletin of mathematical biology [Bull Math Biol] 2023 Nov 24; Vol. 86 (1), pp. 2. Date of Electronic Publication: 2023 Nov 24.
Abstract: When using mathematical models to make quantitative predictions for clinical or industrial use, it is important that predictions come with a reliable estimate of their accuracy (uncertainty quantification). Because models of complex biological systems ...
Generalized Stressors on Hive and Forager Bee Colonies.
Publication Type: Academic Journal
Source(s): Bulletin of mathematical biology [Bull Math Biol] 2023 Oct 12; Vol. 85 (11), pp. 112. Date of Electronic Publication: 2023 Oct 12.
Abstract: Hive-forming bees play an integral role in promoting agricultural sustainability and ecosystem preservation. The recent worldwide decline of several species of bees, and in particular, the honeybee in the United States, highlights the value in understa...
A Test to Distinguish Monotone Homogeneity from Monotone Multifactor Models.
Publication Type: Academic Journal
Source(s): Psychometrika [Psychometrika] 2023 Jun; Vol. 88 (2), pp. 387-412. Date of Electronic Publication: 2023 Mar 18.
Abstract: The goodness-of-fit of the unidimensional monotone latent variable model can be assessed using the empirical conditions of nonnegative correlations (Mokken in A theory and procedure of scale-analysis, Mouton, The Hague, 1971), manifest monotonicity (Ju...
Simulating contact networks for livestock disease epidemiology: a systematic review.
Publication Type: Academic Journal
Source(s): Journal of the Royal Society, Interface [J R Soc Interface] 2023 May; Vol. 20 (202), pp. 20220890. Date of Electronic Publication: 2023 May 17.
Abstract: Contact structure among livestock populations influences the transmission of infectious agents among them. Models simulating realistic contact networks therefore have important applications for generating insights relevant to livestock diseases. This s...