Fitting a defect non-linear model with or without prior, distinguishing nuclear reaction products as an example

A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens

An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.

A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens

An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.

Practicalities of Bayesian network modeling for nuclear data evaluation with the nucdataBaynet package

Bayesian networks are a helpful abstraction in the modelization of the relationships between different variables for the purpose of uncertainty quantification. They are therefore especially well suited for the application to nuclear data evaluation to accurately model the relationships of experimental and nuclear models. Constraints, such as sum rules and the non-negativity of cross sections, can be rigorously taken into account in Bayesian inference within Bayesian networks. This contribution elaborates on the practical aspects of the construction of Bayesian networks with the nucdataBaynet package for the purpose of nuclear data evaluation.

A first sketch: Construction of model defect priors inspired by dynamic time warping

Model defects are known to cause biased nuclear data evaluations if they are not taken into account in the evaluation procedure. We suggest a method to construct prior distributions for model defects for reaction models using neighboring isotopes of 56Fe as an example. A model defect is usually a function of energy and describes the difference between the model prediction and the truth. Of course, neither the truth nor the model defect are accessible. A Gaussian process (GP) enables to define a probability distribution on possible shapes of a model defect by referring to intuitively understandable concepts such as smoothness and the expected magnitude of the defect. Standard specifications of GPs impose a typical length-scale and amplitude valid for the whole energy range, which is often not justified, e.g., when the model covers both the resonance and statistical range. In this contribution, we show how a GP with energy-dependent length-scales and amplitudes can be constructed from available experimental data. The proposed construction is inspired by a technique called dynamic time warping used, e.g., for speech recognition. We demonstrate the feasibility of the data-driven determination of model defects by inferring a model defect of the nuclear models code TALYS for (n,p) reactions of isotopes with charge number between 20 and 30. The newly introduced GP parametrization besides its potential to improve evaluations for reactor relevant isotopes, such as 56Fe, may also help to better understand the performance of nuclear models in the future.

Formulation of Model Defects Suitable for the Resonance Regime

A method to account for model deficiencies in nuclear data evaluations in the resonance regime is proposed. The method follows the ideas of Schnabel and coworkers and relies on Gaussian processes with a novel problemadapted ansatz for the covariance matrix of model uncertainties extending the formalism to the energy region of resonances. The method was used to evaluate a set of schematic but realistic neutron reaction data generated by an R-matrix code and a well defined model defect. Using the extended ansatz for model defects the Bayesian evaluation successfully recovered the built-in model defect in size and structure thus demonstrating the applicability of the method.