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EcoQBNs: First Application of Ecological Modeling with Quantum Bayesian Networks.

ABSTRACT: A recent advancement in modeling was the development of quantum Bayesian networks (QBNs). QBNs generally differ from BNs by substituting traditional Bayes calculus in probability tables with the quantum amplification wave functions. QBNs can solve a variety of problems which are unsolvable by, or are too complex for, traditional BNs. These include problems with feedback loops and temporal expansions; problems with non-commutative dependencies in which the order of the specification of priors affects the posterior outcomes; problems with intransitive dependencies constituting the circular dominance of the outcomes; problems in which the input variables can affect each other, even if they are not causally linked (entanglement); problems in which there may be >1 dominant probability outcome dependent on small variations in inputs (superpositioning); and problems in which the outcomes are nonintuitive and defy traditional probability calculus (Parrondo's paradox and the violation of the Sure Thing Principle). I present simple examples of these situations illustrating problems in prediction and diagnosis, and I demonstrate how BN solutions are infeasible, or at best require overly-complex latent variable structures. I then argue that many problems in ecology and evolution can be better depicted with ecological QBN (EcoQBN) modeling. The situations that fit these kinds of problems include noncommutative and intransitive ecosystems responding to suites of disturbance regimes with no specific or single climax condition, or that respond differently depending on the specific sequence of the disturbances (priors). Case examples are presented on the evaluation of habitat conditions for a bat species, representing state-transition models of a boreal forest under disturbance, and the entrainment of auditory signals among organisms. I argue that many current ecological analysis structures-such as state-and-transition models, predator-prey dynamics, the evolution of symbiotic relationships, ecological disturbance models, and much more-could greatly benefit from a QBN approach. I conclude by presenting EcoQBNs as a nascent field needing the further development of the quantum mathematical structures and, eventually, adjuncts to existing BN modeling shells or entirely new software programs to facilitate model development and application.

SUBMITTER: Marcot BG

PROVIDER: S-EPMC8069849 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The causal pathways of stressors that lead to impacts on individuals, populations, and communities of organisms are useful to know for designing alternatives that manage or remediate ecological risks. The ecological risk assessment (ERA) framework (USEPA, 1998b) can help to identify and prioritize management of risks. One key product of the problem formulation step in an ERA, that captures and represents causal knowledge, is the conceptual site model (CSM). The CSM is a graphical depiction of the risk environment that traces the fate and transport pathways of contaminants from sources of contamination (e.g., a leaking storage tank) to receptors (i.e., the ecological endpoints of concern in the risk assessment). The CSM guides the development of methods for assessing ecological risk scenarios and for remediation design alternatives. The qualitative and quantitative aspects of Bayesian networks may support CSM development and risk characterization. Bayesian networks provide a graphical platform geared toward probabilistic modeling making them important candidates for calculating risks in environmental assessments. The diagrammatic representation of causal Bayesian networks (i.e., the directed acyclic graphs) also adds explanatory depth for developing the evidence-base for risk characterization and remediation interventions. We call these qualitative graphs conceptual Bayesian networks (CBNs). The components of CBNs can be used to represent the variables and relationships between sources of contamination, media transfer, bioaccumulation, and risk. The connections help to compose, piece together, and explore hypothesized relationships that bring about high-risk scenarios. Causal pathway analysis of the CBNs provides visualizations of exposure pathways from initial and intermediate sources to receptors. Remediation options that would interrupt or stop the transport of contaminants to ecological receptors can then be identified. Even if the CBN is not quantified, the structures can support mechanistic and statistical designs for exposure and effects analysis and risk characterization and evaluate information needs for resolving uncertainties. This paper will examine these and other unexplored benefits of CBNs to assessment and management of contaminated sites.

Project description:BackgroundThe combination of genotypic and genome-wide expression data arising from segregating populations offers an unprecedented opportunity to model and dissect complex phenotypes. The immense potential offered by these data derives from the fact that genotypic variation is the sole source of perturbation and can therefore be used to reconcile changes in gene expression programs with the parental genotypes. To date, several methodologies have been developed for modeling eQTL data. These methods generally leverage genotypic data to resolve causal relationships among gene pairs implicated as associates in the expression data. In particular, leading studies have augmented Bayesian networks with genotypic data, providing a powerful framework for learning and modeling causal relationships. While these initial efforts have provided promising results, one major drawback associated with these methods is that they are generally limited to resolving causal orderings for transcripts most proximal to the genomic loci. In this manuscript, we present a probabilistic method capable of learning the causal relationships between transcripts at all levels in the network. We use the information provided by our method as a prior for Bayesian network structure learning, resulting in enhanced performance for gene network reconstruction.ResultsUsing established protocols to synthesize eQTL networks and corresponding data, we show that our method achieves improved performance over existing leading methods. For the goal of gene network reconstruction, our method achieves improvements in recall ranging from 20% to 90% across a broad range of precision levels and for datasets of varying sample sizes. Additionally, we show that the learned networks can be utilized for expression quantitative trait loci mapping, resulting in upwards of 10-fold increases in recall over traditional univariate mapping.ConclusionsUsing the information from our method as a prior for Bayesian network structure learning yields large improvements in accuracy for the tasks of gene network reconstruction and expression quantitative trait loci mapping. In particular, our method is effective for establishing causal relationships between transcripts located both proximally and distally from genomic loci.

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EcoQBNs: First Application of Ecological Modeling with Quantum Bayesian Networks.

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