Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2410.11976

Multiple Gaussian process models based global sensitivity analysis and efficient optimization of in vitro mRNA transcription process

Min Tao·Adithya Nair·Ioanna Kalospyrou·Robert A Milton·Mabrouka Maamra·Zoltan Kis·Joan Cordiner·Solomon F Brown
View original source ↗Read source document ↗Export metadata ↓

Abstract

The in vitro transcription (IVT) process is a critical step in RNA production. To ensure the efficiency of RNA manufacturing, it is essential to optimize and identify its key influencing factors. In this study, multiple Gaussian Process (GP) models are used to perform efficient optimization and global sensitivity analysis (GSA). Firstly, multiple GP models were constructed using the data from multiple experimental replicates, accurately capturing the complexities of the IVT process. Then GSA was conducted to determine the dominant reaction factors, specifically the concentrations of reactants NTP and Mg across all data-driven models. Concurrently, a multi-start optimization algorithm was applied to these GP models to identify optimal operational conditions that maximize RNA yields across all surrogate models. These optimized conditions are subsequently validated through additional experimental data.

Explore related subjects

q-bio.QMmath.OC

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Min Tao, Adithya Nair, Ioanna Kalospyrou, Robert A Milton, Mabrouka Maamra, Zoltan Kis, Joan Cordiner, Solomon F Brown. 2024-10-20. Multiple Gaussian process models based global sensitivity analysis and efficient optimization of in vitro mRNA transcription process. https://arxiv.org/abs/2410.11976

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Lightning-fast adaptive immune receptor similarity search by symmetric deletion lookup

An individual's adaptive immune receptor (AIR) repertoire records immune history due to the receptors' antigen specificity. Reading this record requires computational approaches for inferring receptor function from sequence, as the diversity of possible receptor-antigen pairs vastly outstrips experimental knowledge. Identification of AIRs with similar sequence and thus putatively similar function is a common performance bottleneck in these approaches. Here, we benchmark the runtime scaling of five algorithmic approaches to radius-based search for Levenshtein neighbors. We show that a symmetric deletion lookup approach, originally proposed for spell-checking, is particularly scalable. We introduce SymScan and XTNeighbor, optimized CPU and GPU software implementing a parallelized variant of the algorithm. For one million input sequences, these tools identify all sequence pairs that differ by one or two edits in seconds, orders of magnitude faster than existing approaches. We demonstrate how symmetric deletion lookup can be integrated as a pre-filtering step in T cell receptor metaclone discovery and B cell receptor lineage identification. Our contribution is poised to greatly accelerate existing analysis pipelines and enable processing of immunosequencing data at scale.

q-bio.QM↗
arXiv2026

Implication of modelling choices on connectivity estimation: A comparative analysis

Landscape connectivity is an important field with important conservation implications. Connectivity modelling is a useful tool to inform and guide landscape planning. However, it involves assumptions and methodological decisions which ultimately impact connectivity outcomes. In order to understand the implications of modelling choices on final connectivity estimations, we compare two landscape characterisation approaches - expert knowledge and species distribution models - and three movements models - least-cost paths, circuit theory and an individual-based movement simulator. The implementation of the models and the construction of the analyses scope highlighted conceptual and methodological differences that made the comparison difficult. Landscape characterisation appears as the principal factor determining connectivity outcomes. Therefore, the confrontation between expert knowledge and species distribution models is critical to leverage points of convergence and complementarity between these two approaches. Conceptual differences between movement models are reported on connectivity map and habitat patch contribution estimations. In the want of data and protocol design specifically to validate connectivity models, approaches that integrate stochastic and behavioural processes, bring a more realistic perspective to connectivity estimation.

q-bio.QM↗
arXiv2026

Triplication: an important component of the modern scientific method

A scientific-study protocol (defined) is designed to deliver results from which inductive inference is allowed. In the nineteenth century, triplication was introduced into the plant sciences and Fisher's p<0.05 rule (1925) incorporated into triple-result protocols designed to counter random/systematic errors which contribute to real-world variability. The aims of the present study were to: (1) classify replication protocols; (2) assess their prevalence in plant-science studies (published during one twenty-first-century year; for defined variable construct); (3) explore triplication rationale. Methods: a plant-sciences protocol-prevalence report was produced; experimental/associational-study proportions analyzed; and real-world-data proxies used to show confidence-interval-width patterns with increasing replicate number. Results: 25% plant-science studies analyzed showed triplication, including 11% triple-result protocols (including greater replicate numbers: 48%;17%, respectively). Theoretical considerations indicated that even if systematic errors predominate, (previously-known) square-root rules sometimes apply, contributing to triplication importance (exemplified by real-world-data proxies). Conclusions: The defined protocols, with minor modifications, should provide the means for assessment of most sciences. Triplication was extensively applied in studies analysed and there are strong methodological reasons why triplication, rather than duplication/quadruplication, is the appropriate standard: triple-result protocols: (a) effectively reduce false positives to acceptable levels; (b) give qualitatively-different information (shape) from duplication; (c) have a large efficiency advantage (concerning confidence-interval widths) over quadruplication. The application of batch replication is not, primarily, a statistical problem and cannot effectively be replaced by simulation.

q-bio.QM↗