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Likelihood non-Gaussianity in large-scale structure analyses

The standard present-day large-scale structure (LSS) analyses make a major assumption in their Bayesian parameter inference – that the likelihood has a Gaussian form. For summary statistics currently used in LSS, this assumption, even if the underlying density field is Gaussian, cannot be correct in detail. We investigate the impact of this assumption on two recent LSS analyses: the Beutler et al. power spectrum multipole ($P_ℓ$) analysis and the Sinha et al. group multiplicity function ($ζ$) analysis. Using non-parametric divergence estimators on mock catalogues originally constructed for covariance matrix estimation, we identify significant non-Gaussianity in both the $P_ℓ$ and $ζ$ likelihoods. We then use Gaussian mixture density estimation and independent component analysis on the same mocks to construct likelihood estimates that approximate the true likelihood better than the Gaussian pseudo-likelihood. Using these likelihood estimates, we accurately estimate the true posterior probability distribution of the Beutler et al. and Sinha et al. parameters. Likelihood non-Gaussianity shifts the fσ8 constraint by -0.44σ, but otherwise does not significantly impact the overall parameter constraints of Beutler et al. For the $ζ$ analysis, using the pseudo-likelihood significantly underestimates the uncertainties and biases the constraints of the Sinha et al. halo occupation parameters. For log $M_1$ and α, the posteriors are shifted by +0.43σ and -0.51σ and broadened by 42 per cent and 66 per cent, respectively. The divergence and likelihood estimation methods we present provide a straightforward framework for quantifying the impact of likelihood non-Gaussianity and deriving more accurate parameter constraints.

79 ASTRONOMY AND ASTROPHYSICS↗

Flow-based likelihoods for non-Gaussian inference

We investigate the use of data-driven likelihoods to bypass a key assumption made in many scientific analyses, which is that the true likelihood of the data is Gaussian. In particular, we suggest using the optimization targets of flow-based generative models, a class of models that can capture complex distributions by transforming a simple base distribution through layers of nonlinearities. We call these flow-based likelihoods (FBL). We analyze the accuracy and precision of the reconstructed likelihoods on mock Gaussian data, and show that simply gauging the quality of samples drawn from the trained model is not a sufficient indicator that the true likelihood has been learned. We nevertheless demonstrate that the likelihood can be reconstructed to a precision equal to that of sampling error due to a finite sample size. We then apply FBLs to mock weak lensing convergence power spectra, a cosmological observable that is significantly non-Gaussian (NG). We find that the FBL captures the NG signatures in the data extremely well, while other commonly used data-driven likelihoods, such as Gaussian mixture models and independent component analysis, fail to do so. This suggests that works that have found small posterior shifts in NG data with data-driven likelihoods such as these could be underestimating the impact of non-Gaussianity in parameter constraints. By introducing a suite of tests that can capture different levels of NG in the data, we show that the success or failure of traditional data-driven likelihoods can be tied back to the structure of the NG in the data. Here, unlike other methods, the flexibility of the FBL makes it successful at tackling different types of NG simultaneously. Because of this, and consequently their likely applicability across datasets and domains, we encourage their use for inference when sufficient mock data are available for training.

79 ASTRONOMY AND ASTROPHYSICS↗

LIKELIHOOD OF THE POWER SPECTRUM IN COSMOLOGICAL PARAMETER ESTIMATION

The likelihood function is a crucial element of parameter estimation. In analyses of galaxy overdensities and weak lensing shear, one often approximates the likelihood of the power spectrum with a Gaussian distribution. The posterior probability derived from such a likelihood deviates considerably from the exact posterior on the largest scales probed by any survey, where the central limit theorem does not apply. We show that various forms of Gaussian likelihoods can have a significant impact on the estimation of the primordial non-Gaussianity parameter f{sub NL} from the galaxy angular power spectrum. The Gaussian plus log-normal likelihood, which has been applied successfully in analyses of the cosmic microwave background, outperforms the Gaussian likelihoods. Nevertheless, even if the exact likelihood of the power spectrum is used, the estimated parameters may be still biased. As such, the likelihoods and estimators need to be thoroughly examined for potential systematic errors.

79 ASTRONOMY AND ASTROPHYSICS↗

Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary to obtain a more accurate network. All described workflows are implemented as part of the DOE Systems Biology Knowledgebase (KBase) and are publicly available via API or command-line web interface.

59 BASIC BIOLOGICAL SCIENCES↗

Non-Gaussianity in the weak lensing correlation function likelihood – implications for cosmological parameter biases

ABSTRACT We study the significance of non-Gaussianity in the likelihood of weak lensing shear two-point correlation functions, detecting significantly non-zero skewness and kurtosis in 1D marginal distributions of shear two-point correlation functions in simulated weak lensing data. We examine the implications in the context of future surveys, in particular LSST, with derivations of how the non-Gaussianity scales with survey area. We show that there is no significant bias in 1D posteriors of Ωm and σ8 due to the non-Gaussian likelihood distributions of shear correlations functions using the mock data (100 deg2). We also present a systematic approach to constructing approximate multivariate likelihoods with 1D parametric functions by assuming independence or more flexible non-parametric multivariate methods after decorrelating the data points using principal component analysis (PCA). While the use of PCA does not modify the non-Gaussianity of the multivariate likelihood, we find empirically that the 1D marginal sampling distributions of the PCA components exhibit less skewness and kurtosis than the original shear correlation functions. Modelling the likelihood with marginal parametric functions based on the assumption of independence between PCA components thus gives a lower limit for the biases. We further demonstrate that the difference in cosmological parameter constraints between the multivariate Gaussian likelihood model and more complex non-Gaussian likelihood models would be even smaller for an LSST-like survey. In addition, the PCA approach automatically serves as a data compression method, enabling the retention of the majority of the cosmological information while reducing the dimensionality of the data vector by a factor of ∼5.

79 ASTRONOMY AND ASTROPHYSICS↗

Learning likelihood ratios with neural network classifiers

The likelihood ratio is a crucial quantity for statistical inference in science that enables hypothesis testing, construction of confidence intervals, reweighting of distributions, and more. Many modern scientific applications, however, make use of data- or simulation-driven models for which computing the likelihood ratio can be very difficult or even impossible. By applying the so-called “likelihood ratio trick,” approximations of the likelihood ratio may be computed using clever parametrizations of neural network-based classifiers. A number of different neural network setups can be defined to satisfy this procedure, each with varying performance in approximating the likelihood ratio when using finite training data. We present a series of empirical studies detailing the performance of several common loss functionals and parametrizations of the classifier output in approximating the likelihood ratio of two univariate and multivariate Gaussian distributions as well as simulated high-energy particle physics datasets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The simplified likelihood framework

We discuss the simplified likelihood framework as a systematic approximation scheme for experimental likelihoods such as those originating from LHC experiments. We develop the simplified likelihood from the Central Limit Theorem keeping the next-to-leading term in the large N expansion to correctly account for asymmetries. Moreover, we present an efficient method to compute the parameters of the simplified likelihood from Monte Carlo simulations. The approach is validated using a realistic LHC-like analysis, and the limits of the approximation are explored. Finally, we discuss how the simplified likelihood data can be conveniently released in the HepData error source format and automatically built from it, making this framework a convenient tool to transmit realistic experimental likelihoods to the community.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mobile sensing of point-source gas emissions using Bayesian inference: An empirical examination of the likelihood function

This paper evaluates likelihood function forms for Bayesian inference of point-source gas emissions using a mobile sensor. Whereas Bayesian inference has been successfully used to estimate emission rates from time-averaged concentration data measured by stationary sensors, data collected by mobile sensors do not represent ensemble or time-averaged conditions. To examine the potential impact of this contrast, controlled release experiments were conducted with a mobile sensor measuring concentrations repeatedly along transverse cross sections of the downwind plumes. Experiments were conducted with measurements made at different downwind distances, different sensor heights, and with different obstacle states. An examination is made between two commonly-used likelihood functions, the Gaussian and the log-normal. For experiments conducted in the absence of obstacles, the Bayesian estimates using the log-normal likelihood function yield a much smaller bias than those based on the Gaussian likelihood function. This finding is consistent with the non-Gaussian nature of concentration fluctuations near a point-source. For experiments conducted in the presence of obstacles, the Bayesian inference based on the Gaussian likelihood function exhibits a better performance. This can be explained by the enhanced turbulent mixing due to the obstacle-introduced wake eddies. Overall, we find that the selection of the likelihood function can be physically related to the underlying conditions, and the proper selection is critical to ensure the performance of the Bayesian inference for source characterization using mobile sensing data.

54 ENVIRONMENTAL SCIENCES↗

Is Primary Prostate Cancer Treatment Influenced by Likelihood of Extraprostatic Disease? A Surveillance, Epidemiology and End Results Patterns of Care Study

Purpose: To examine the patterns of primary treatment in a recent population-based cohort of prostate cancer patients, stratified by the likelihood of extraprostatic cancer as predicted by disease characteristics available at diagnosis. Methods and Materials: A total of 157,371 patients diagnosed from 2004 to 2008 with clinically localized and potentially curable (node-negative, nonmetastatic) prostate cancer, who have complete information on prostate-specific antigen, Gleason score, and clinical stage, were included. Patients with clinical T1/T2 disease were grouped into categories of <25%, 25%-50%, and >50% likelihood of having extraprostatic disease using the Partin nomogram. Clinical T3/T4 patients were examined separately as the highest-risk group. Logistic regression was used to examine the association between patient group and receipt of each primary treatment, adjusting for age, race, year of diagnosis, marital status, Surveillance, Epidemiology and End Results database region, and county-level education. Separate models were constructed for primary surgery, external-beam radiotherapy (RT), and conservative management. Results: On multivariable analysis, increasing likelihood of extraprostatic disease was significantly associated with increasing use of RT and decreased conservative management. Use of surgery also increased. Patients with >50% likelihood of extraprostatic cancer had almost twice the odds of receiving prostatectomy as those with <25% likelihood, and T3-T4 patients had 18% higher odds. Prostatectomy use increased in recent years. Patients aged 76-80 years were likely to be managed conservatively, even those with a >50% likelihood of extraprostatic cancer (34%) and clinical T3-T4 disease (24%). The proportion of patients who received prostatectomy or conservative management was approximately 50% or slightly higher in all groups. Conclusions: There may be underutilization of RT in older prostate cancer patients and those with likely extraprostatic disease. Because more than half of prostate cancer patients do not consult with a radiation oncologist, a multidisciplinary consultation may affect the treatment decision-making process.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Planck 2018 results. V. CMB power spectra and likelihoods

We describe the legacy Planck cosmic microwave background (CMB) likelihoods derived from the 2018 data release. The overall approach is similar in spirit to the one retained for the 2013 and 2015 data release, with a hybrid method using different approximations at low ( ℓ < 30) and high ( ℓ ≥ 30) multipoles, implementing several methodological and data-analysis refinements compared to previous releases. With more realistic simulations, and better correction and modelling of systematic effects, we can now make full use of the CMB polarization observed in the High Frequency Instrument (HFI) channels. The low-multipole EE cross-spectra from the 100 GHz and 143 GHz data give a constraint on the ΛCDM reionization optical-depth parameter τ to better than 15% (in combination with the TT low- ℓ data and the high- ℓ temperature and polarization data), tightening constraints on all parameters with posterior distributions correlated with τ . We also update the weaker constraint on τ from the joint TEB likelihood using the Low Frequency Instrument (LFI) channels, which was used in 2015 as part of our baseline analysis. At higher multipoles, the CMB temperature spectrum and likelihood are very similar to previous releases. A better model of the temperature-to-polarization leakage and corrections for the effective calibrations of the polarization channels (i.e., the polarization efficiencies) allow us to make full use of polarization spectra, improving the ΛCDM constraints on the parameters θ MC , ω c , ω b , and H 0 by more than 30%, and n s by more than 20% compared to TT-only constraints. Extensive tests on the robustness of the modelling of the polarization data demonstrate good consistency, with some residual modelling uncertainties. At high multipoles, we are now limited mainly by the accuracy of the polarization efficiency modelling. Using our various tests, simulations, and comparison between different high-multipole likelihood implementations, we estimate the consistency of the results to be better than the 0.5 σ level on the ΛCDM parameters, as well as classical single-parameter extensions for the joint likelihood (to be compared to the 0.3 σ levels we achieved in 2015 for the temperature data alone on ΛCDM only). Minor curiosities already present in the previous releases remain, such as the differences between the best-fit ΛCDM parameters for the ℓ < 800 and ℓ > 800 ranges of the power spectrum, or the preference for more smoothing of the power-spectrum peaks than predicted in ΛCDM fits. These are shown to be driven by the temperature power spectrum and are not significantly modified by the inclusion of the polarization data. Overall, the legacy Planck CMB likelihoods provide a robust tool for constraining the cosmological model and represent a reference for future CMB observations.

79 ASTRONOMY AND ASTROPHYSICS↗

COSMIC MICROWAVE BACKGROUND LIKELIHOOD APPROXIMATION FOR BANDED PROBABILITY DISTRIBUTIONS

We investigate sets of random variables that can be arranged sequentially such that a given variable only depends conditionally on its immediate predecessor. For such sets, we show that the full joint probability distribution may be expressed exclusively in terms of uni- and bivariate marginals. Under the assumption that the cosmic microwave background (CMB) power spectrum likelihood only exhibits correlations within a banded multipole range, Δl{sub C}, we apply this expression to two outstanding problems in CMB likelihood analysis. First, we derive a statistically well-defined hybrid likelihood estimator, merging two independent (e.g., low- and high-l) likelihoods into a single expression that properly accounts for correlations between the two. Applying this expression to the Wilkinson Microwave Anisotropy Probe (WMAP) likelihood, we verify that the effect of correlations on cosmological parameters in the transition region is negligible in terms of cosmological parameters for WMAP; the largest relative shift seen for any parameter is 0.06σ. However, because this may not hold for other experimental setups (e.g., for different instrumental noise properties or analysis masks), but must rather be verified on a case-by-case basis, we recommend our new hybridization scheme for future experiments for statistical self-consistency reasons. Second, we use the same expression to improve the convergence rate of the Blackwell-Rao likelihood estimator, reducing the required number of Monte Carlo samples by several orders of magnitude, and thereby extend it to high-l applications.

79 ASTRONOMY AND ASTROPHYSICS↗

Effect of radiance-to-reflectance transformation and atmosphere removal on maximum likelihood classification accuracy of high-dimensional remote sensing data

Many analysis algorithms for high-dimensional remote sensing data require that the remotely sensed radiance spectra be transformed to approximate reflectance to allow comparison with a library of laboratory reflectance spectra. In maximum likelihood classification, however, the remotely sensed spectra are compared to training samples, thus a transformation to reflectance may or may not be helpful. The effect of several radiance-to-reflectance transformations on maximum likelihood classification accuracy is investigated in this paper. We show that the empirical line approach, LOWTRAN7, flat-field correction, single spectrum method, and internal average reflectance are all non-singular affine transformations, and that non-singular affine transformations have no effect on discriminant analysis feature extraction and maximum likelihood classification accuracy. (An affine transformation is a linear transformation with an optional offset.) Since the Atmosphere Removal Program (ATREM) and the log residue method are not affine transformations, experiments with Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data were conducted to determine the effect of these transformations on maximum likelihood classification accuracy. The average classification accuracy of the data transformed by ATREM and the log residue method was slightly less than the accuracy of the original radiance data. Since the radiance-to-reflectance transformations allow direct comparison of remotely sensed spectra with laboratory reflectance spectra, they can be quite useful in labeling the training samples required by maximum likelihood classification, but these transformations have only a slight effect or no effect at all on discriminant analysis and maximum likelihood classification accuracy.

Hoffbeck, Joseph P.↗

Improved Nested Sampling and Surrogate-Enabled Comparison With Other Marginal Likelihood Estimators

Estimating marginal likelihood is of central importance to Bayesian model selection and/or model averaging. The nested sampling method has been recently used together with the Metropolis-Hasting (M-H) sampling algorithm for estimating marginal likelihood. This study develops a new implementation of nested sampling by using the DiffeRential Evolution Adaptive Metropolis (DREAMzs) sampling algorithm. The two implementations of nested sampling are evaluated for four models of a synthetic groundwater flow modeling. The DREAMzs-based nested sampling outperforms the M-H-based nested sampling in terms of their accuracy, convergence, efficiency, and stability, which is attributed to the fact that DREAMzs is more robust than M-H for parameter sampling. The nested sampling method is also compared with four other methods (arithmetic mean, harmonic mean, stabilized harmonic mean, and thermodynamic integration) commonly used for estimating marginal likelihood and posterior probability of the four groundwater models. The comparative study requires hundreds of millions of model executions, which would not be possible without using surrogate models to replace the original models. Using the arithmetic mean estimator as the reference, the comparison reveals that thermodynamic integration outperforms nested sampling in terms of accuracy and stability, whereas nested sampling is more computationally efficient to reach to convergence. Here, the harmonic mean and stabilized harmonic mean methods give the worst marginal likelihood estimation. Accurate marginal likelihood estimation is important for accurate estimation of posterior model probability and better predictive performance of Bayesian model averaging.

54 ENVIRONMENTAL SCIENCES↗

Planck 2013 results. XV. CMB power spectra and likelihood

This paper presents the Planck 2013 likelihood, a complete statistical description of the two-point correlation function of the CMB temperature fluctuations that accounts for all known relevant uncertainties, both instrumental and astrophysical in nature. We use this likelihood to derive our best estimate of the CMB angular power spectrum from Planck over three decades in multipole moment, &ell;, covering 2 &le; &ell; &le; 2500. The main source of uncertainty at &ell; &le; 1500 is cosmic variance. Uncertainties in small-scale foreground modelling and instrumental noise dominate the error budget at higher &ell;s. For &ell; < 50, our likelihood exploits all Planck frequency channels from 30 to 353 GHz, separating the cosmological CMB signal from diffuse Galactic foregrounds through a physically motivated Bayesian component separation technique. At &ell; &le; 50, we employ a correlated Gaussian likelihood approximation based on a fine-grained set of angular cross-spectra derived from multiple detector combinations between the 100, 143, and 217 GHz frequency channels, marginalising over power spectrum foreground templates. We validate our likelihood through an extensive suite of consistency tests, and assess the impact of residual foreground and instrumental uncertainties on the final cosmological parameters. We find good internal agreement among the high-&ell; cross-spectra with residuals below a few &mu;K 2 at &ell; ≲ 1000, in agreement with estimated calibration uncertainties. We compare our results with foreground-cleaned CMB maps derived from all Planck frequencies, as well as with cross-spectra derived from the 70 GHz Planck map, and find broad agreement in terms of spectrum residuals and cosmological parameters. We further show that the best-fit CDM cosmology is in excellent agreement with preliminary Planck EE and TE polarisation spectra. We find that the standard ΛCDM cosmology is well constrained by Planck from the measurements at &ell; ≲ 1500. One specific example is the spectral index of scalar perturbations, for which we report a 5.4σ deviation from scale invariance, n s = 1. Increasing the multipole range beyond &ell; ≃ 1500 does not increase our accuracy for the ΛCDM parameters, but instead allows us to study extensions beyond the standard model. We find no indication of significant departures from the ΛCDM framework. Finally, we report a tension between the Planck best-fit ΛCDM model and the low-&ell; spectrum in the form of a power deficit of 5&ndash;10% at &ell; ≲ 40, with a statistical significance of 2.5&ndash;3σ. Without a theoretically motivated model for this power deficit, we do not elaborate further on its cosmological implications, but note that this is our most puzzling finding in an otherwise remarkably consistent data set.

79 ASTRONOMY AND ASTROPHYSICS↗

Planck 2015 results: XI. CMB power spectra, likelihoods, and robustness of parameters

This study presents the Planck 2015 likelihoods, statistical descriptions of the 2-point correlationfunctions of the cosmic microwave background (CMB) temperature and polarization fluctuations that account for relevant uncertainties, both instrumental and astrophysical in nature. They are based on the same hybrid approach used for the previous release, i.e., a pixel-based likelihood at low multipoles (ℓ< 30) and a Gaussian approximation to the distribution of cross-power spectra at higher multipoles. The main improvements are the use of more and better processed data and of Planck polarization information, along with more detailed models of foregrounds and instrumental uncertainties. The increased redundancy brought by more than doubling the amount of data analysed enables further consistency checks and enhanced immunity to systematic effects. It also improves the constraining power of Planck, in particular with regard to small-scale foreground properties. Progress in the modelling of foreground emission enables the retention of a larger fraction of the sky to determine the properties of the CMB, which also contributes to the enhanced precision of the spectra. Improvements in data processing and instrumental modelling further reduce uncertainties. Extensive tests establish the robustness and accuracy of the likelihood results, from temperature alone, from polarization alone, and from their combination. For temperature, we also perform a full likelihood analysis of realistic end-to-end simulations of the instrumental response to the sky, which were fed into the actual data processing pipeline; this does not reveal biases from residual low-level instrumental systematics. Even with the increase in precision and robustness, the ΛCDM cosmological model continues to offer a very good fit to the Planck data. The slope of the primordial scalar fluctuations, n s , is confirmed smaller than unity at more than 5σ from Planck alone. We further validate the robustness of the likelihood results against specific extensions to the baseline cosmology, which are particularly sensitive to data at high multipoles. For instance, the effective number of neutrino species remains compatible with the canonical value of 3.046. For this first detailed analysis of Planck polarization spectra, we concentrate at high multipoles on the E modes, leaving the analysis of the weaker B modes to future work. At low multipoles we use temperature maps at all Planck frequencies along with a subset of polarization data. These data take advantage of Planck’s wide frequency coverage to improve the separation of CMB and foreground emission. Within the baseline ΛCDM cosmology this requires τ = 0.078 ± 0.019 for the reionization optical depth, which is significantly lower than estimates without the use of high-frequency data for explicit monitoring of dust emission. At high multipoles we detect residual systematic errors in E polarization, typically at the μK 2 level; we therefore choose to retain temperature information alone for high multipoles as the recommended baseline, in particular for testing non-minimal models. Finally and nevertheless, the high-multipole polarization spectra from Planck are already good enough to enable a separate high-precision determination of the parameters of the ΛCDM model, showing consistency with those established independently from temperature information alone.

79 ASTRONOMY AND ASTROPHYSICS↗

Effect of likelihood misspecification in Gaussian process-driven autonomous experimentation

In recent years, several groups have designed Autonomous Experiment (AE) models with the aim of using them as an alternative method for neutron scattering scanning. In an AE, Gaussian processes (GPs) are most frequently used due to their interpretability, their non-parametric nature, their universal approximation, and their closed-form predictive distribution. GPs have two key components, namely, the model for the likelihood of a neutron count knowing the underlying dynamic structure factor and the acquisition function. In this paper, we investigate the impact, on the quality of an AE, of the likelihood and acquisition function choices, in energy scans and (Q, ω) ones, with respect to the signal-over-noise ratio. While we hypothesized that the quality of GP predictions would decrease when the normal to Poisson likelihood approximation breaks down at low count rates, we found that the use of the correct Poisson likelihood does not improve the quality of the data collected, as well as yields very poor results in (Q, ω) scans at low count rates. In fact, the best results are obtained with a combination of normal likelihood, including the observation noise, and the change in variance acquisition function. In addition, we find that the performance, or quality of the predictive distribution, is a misleading measure of efficiency, that is, of the quality of the data collected.

Perryman, David Elliott [Inst. Laue-Langevin (ILL)↗

Amortized simulation-based frequentist inference for tractable and intractable likelihoods

Abstract High-fidelity simulators that connect theoretical models with observations are indispensable tools in many sciences. If the likelihood is known, inference can proceed using standard techniques. However, when the likelihood is intractable or unknown, a simulator makes it possible to infer the parameters of a theoretical model directly from real and simulated observations when coupled with machine learning. We introduce an extension of the recently proposed likelihood-free frequentist inference ( LF2I ) approach that makes it possible to construct confidence sets with the p -value function and to use the same function to check the coverage explicitly at any given parameter point. Like LF2I , this extension yields provably valid confidence sets in parameter inference problems for which a high-fidelity simulator is available. The utility of our algorithm is illustrated by applying it to three pedagogically interesting examples: the first is from cosmology, the second from high-energy physics and astronomy, both with tractable likelihoods, while the third, with an intractable likelihood, is from epidemiology 3 3 Code to reproduce all of our results is available on https://github.com/AliAlkadhim/ALFFI . .

Computer Science↗

Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Evolutionary Biology↗