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At least 109 records · Page 6

Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions

Many imaging techniques for biological systems—like fixation of cells coupled with fluorescence microscopy—provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. In this study, these snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Hourly water-carbon interactions modulate decadal water-use efficiency trends inferred from ecosystem-scale measurements

Plant stomatal conductance regulates photosynthesis and transpiration. This physiological link affects ecosystem responses to microclimate and harmonizes carbon, energy, and water exchanges between the biosphere and atmosphere. The relationship between water losses via transpiration and carbon gains via photosynthesis can be quantified by plant water-use efficiency (WUE). While leaf- and ecosystem-scale observations both suggest rising WUE in recent decades, WUE trends inferred from the ecosystem scale are much larger than those inferred from the leaf scale or implied by theory. The unexpectedly large ecosystem-scale WUE trends complicate interpretation of ecophysiological responses to changing environmental conditions. Here, we analyze ecosystem-scale WUE inferred from 40 FLUXNET sites, each with at least 10 years of measurements. Furthermore, our results demonstrate that observed ecosystem-scale WUE trends are more sensitive to hourly weather conditions than longer-term changes in atmospheric carbon dioxide or vapor pressure deficit. Our analysis shows that Earth System Models participating in CMIP6 did not capture the observed WUE sensitivity to inter-site variability and microclimatic conditions. Collectively, our findings suggest that ecosystem-scale WUE trends reflect water-carbon interactions across multiple temporal scales, and disentangling factors contributing to emergent ecosystem responses is needed to infer ecophysiological relationships and model structures from observations.

54 ENVIRONMENTAL SCIENCES↗

Operator inference with roll outs for learning reduced models from scarce and low-quality data

Data-driven modeling has become a key building block in computational science and engineering. However, data that are available in science and engineering are typically scarce, often polluted with noise and affected by measurement errors and other perturbations, which makes learning the dynamics of systems challenging. Here, in this work, we propose to combine data-driven modeling via operator inference with the dynamic training via roll outs of neural ordinary differential equations. Operator inference with roll outs inherits interpretability, scalability, and structure preservation of traditional operator inference while leveraging the dynamic training via roll outs over multiple time steps to increase stability and robustness for learning from low-quality and noisy data. Numerical experiments with data describing shallow water waves and surface quasi-geostrophic dynamics demonstrate that operator inference with roll outs provides predictive models from training trajectories even if data are sampled sparsely in time and polluted with noise of up to 10%.

97 MATHEMATICS AND COMPUTING↗

AI and extreme scale computing to learn and infer the physics of higher order gravitational wave modes of quasi-circular, spinning, non-precessing black hole mergers

We use artificial intelligence (AI) to learn and infer the physics of higher order gravitational wave modes of quasi-circular, spinning, non precessing binary black hole mergers. We trained AI models using 14 million waveforms, produced with the surrogate model NRHybSur3dq8, that include modes up to $\ell$ ≤ 4 and (5,5), except for (4,0) and (4,1), that describe binaries with mass-ratios $\textit{q}$ ≤ 8, individual spins $s^z_{\{1,2\}} \in$[–0.8,0.8], and inclination angle $θ \in$ [0,π]. Our probabilistic AI surrogates can accurately constrain the mass-ratio, individual spins, effective spin, and inclination angle of numerical relativity waveforms that describe such signal manifold. We compared the predictions of our AI models with Gaussian process regression, random forest, k-nearest neighbors, and linear regression, and with traditional Bayesian inference methods through the PyCBC Inference toolkit, finding that AI outperforms all these approaches in terms of accuracy, and are between three to four orders of magnitude faster than traditional Bayesian inference methods. Our AI surrogates were trained within 3.4 hours using distributed training on 1,536 NVIDIA V100 GPUs in the Summit supercomputer.

79 ASTRONOMY AND ASTROPHYSICS↗

Flow over an espresso cup: inferring 3-D velocity and pressure fields from tomographic background oriented Schlieren via physics-informed neural networks

Tomographic background oriented Schlieren (Tomo-BOS) imaging measures density or temperature fields in three dimensions using multiple camera BOS projections, and is particularly useful for instantaneous flow visualizations of complex fluid dynamics problems. We propose a new method based on physics-informed neural networks (PINNs) to infer the full continuous three-dimensional (3-D) velocity and pressure fields from snapshots of 3-D temperature fields obtained by Tomo-BOS imaging. The PINNs seamlessly integrate the underlying physics of the observed fluid flow and the visualization data, hence enabling the inference of latent quantities using limited experimental data. In this hidden fluid mechanics paradigm, we train the neural network by minimizing a loss function composed of a data mismatch term and residual terms associated with the coupled Navier–Stokes and heat transfer equations. We first quantify the accuracy of the proposed method based on a two-dimensional synthetic data set for buoyancy-driven flow, and subsequently apply it to the Tomo-BOS data set, where we are able to infer the instantaneous velocity and pressure fields of the flow over an espresso cup based only on the temperature field provided by the Tomo-BOS imaging. Moreover, we conduct an independent PIV experiment to validate the PINN inference for the unsteady velocity field at a centre plane. To explain the observed flow physics, we also perform systematic PINN simulations at different Reynolds and Richardson numbers and quantify the variations in velocity and pressure fields. Furthermore, the results in this paper indicate that the proposed deep learning technique can become a promising direction in experimental fluid mechanics.

97 MATHEMATICS AND COMPUTING↗

Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

Abstract Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific GRNs are limited in their ability to integrate scRNA-seq and scATAC-seq measurements and to model network dynamics on a cell lineage. To address this challenge, we have developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the GRN for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated and real datasets, we show that scMTNI is a broadly applicable framework for linear and branching lineages that accurately infers GRN dynamics and identifies key regulators of fate transitions for diverse processes such as cellular reprogramming and differentiation.

59 BASIC BIOLOGICAL SCIENCES↗

Automating Bayesian inference and design to quantify acoustic particle levitation

Self-propulsion of micro- and nanoparticles powered by ultrasound provides an attractive strategy for the remote manipulation of colloidal matter using biocompatible energy inputs. Quantitative understanding of particle motion and its dependence on size, shape, and composition requires accurate characterization of the acoustic field, which depends sensitively on the experimental setup. Here, we show how automated experiments based on Bayesian inference and design can accurately and efficiently characterize the acoustic field within resonant chambers used to propel acoustic nanomotors. Repeated cycles of observation, inference, and design (OID) are guided by a physical model that describes the rate at which levitating particles approach the nodal plane. Using video microscopy, we observe the relaxation of tracer particles to this plane following the application of the acoustic field. We use sequential Monte Carlo methods to infer model parameters such as the amplitude and frequency of the resonant chamber while accounting for particle-level measurement noise and population-level heterogeneity in the field. Guided by simulated outcomes, we select the optimal design for the next experiment as to maximize the information gain in the relevant parameters. We show how this iterative process serves to discriminate between competing hypotheses and efficiently converges to accurate parameter estimates using only few automated experiments. We discuss the need for model criticism to ensure the validity of the guiding model throughout automated cycles of observation, inference, and design. Furthermore, this work demonstrates how Bayesian methods can learn the parameters of nonlinear, hierarchical models used to describe video microscopy data of active colloids.

42 ENGINEERING↗

Inference of the optical depth to reionization τ from Planck CMB maps with convolutional neural networks

The optical depth to reionization, τ, is the least constrained parameter of the cosmological Λ cold dark matter (ΛCDM) model. To date, its most precise value is inferred from large-scale polarized cosmic microwave background (CMB) power spectra from the High Frequency Instrument (HFI) aboard the Planck satellite. These maps are known to contain significant contamination by residual non-Gaussian systematic effects, which are hard to model analytically. Therefore, robust constraints on τ are currently obtained through an empirical cross-spectrum likelihood built from simulations. In this paper, we present a likelihood-free inference of τ from polarized Planck HFI maps which, for the first time, is fully based on neural networks (NNs). NNs have the advantage of not requiring an analytical description of the data and can be trained on state-of-the-art simulations, combining the information from multiple channels. By using Gaussian sky simulations and Planck SRoll2 simulations, including CMB, noise, and residual instrumental systematic effects, we trained, tested, and validated NN models considering different setups. We inferred the value of τ directly from Stokes Q and U maps at ~4° pixel resolution, without computing angular power spectra. On Planck data, we obtained τ NN = 0.0579 ± 0.0082, which is compatible with current EE cross-spectrum results but with a ~30% larger uncertainty, which can be assigned to the inherent nonoptimality of our estimator and to the retraining procedure applied to avoid biases. While this paper does not improve on current cosmological constraints on τ, our analysis represents a first robust application of NN-based inference on real data, and highlights its potential as a promising tool for complementary analysis of near-future CMB experiments, also in view of the ongoing challenge to achieve the first detection of primordial gravitational waves.

79 ASTRONOMY AND ASTROPHYSICS↗

Interpreting the electron temperature inferred from x-ray continuum emission for direct-drive inertial confinement fusion implosions on OMEGA

In this paper, we present a theoretical framework for interpreting the hot-spot electron temperature ($T_e$) inferred from hard (10- to 20-keV) x-ray continuum emission for inertial confinement fusion implosions on OMEGA. We first show that the inferred $T_e$ represents the emission-weighted, harmonic mean of the hot-spot $T_e$ distribution, both spatially and temporally. A scheme is then provided for selecting a photon energy of which the emission weighting approximates neutron weighting. Simulations are then used to quantify the predicted relationship between the inferred T e , neutron-weighted T i , and implosion performance on OMEGA. In an ensemble of 1-D simulations, it was observed that hot-spot thermal nonequilibrium precluded a sufficiently unique mapping between the inferred $T_e$ and neutron-weighted T i . In 3-D simulations with low-harmonic-mode perturbations (i.e., laser beam power imbalance, target offset, and beam port geometry departures from spherical symmetry) and laser imprint (1 max = 200).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Soil incubation methods lead to large differences in inferred methane production temperature sensitivity

Abstract Quantifying the temperature sensitivity of methane (CH 4 ) production is crucial for predicting how wetland ecosystems will respond to climate warming. Typically, the temperature sensitivity (often quantified as a Q 10 value) is derived from laboratory incubation studies and then used in biogeochemical models. However, studies report wide variation in incubation-inferred Q 10 values, with a large portion of this variation remaining unexplained. Here we applied observations in a thawing permafrost peatland (Stordalen Mire) and a well-tested process-rich model ( ecosys ) to interpret incubation observations and investigate controls on inferred CH 4 production temperature sensitivity. We developed a field-storage-incubation modeling approach to mimic the full incubation sequence, including field sampling at a particular time in the growing season, refrigerated storage, and laboratory incubation, followed by model evaluation. We found that CH 4 production rates during incubation are regulated by substrate availability and active microbial biomass of key microbial functional groups, which are affected by soil storage duration and temperature. Seasonal variation in substrate availability and active microbial biomass of key microbial functional groups led to strong time-of-sampling impacts on CH 4 production. CH 4 production is higher with less perturbation post-sampling, i.e. shorter storage duration and lower storage temperature. We found a wide range of inferred Q 10 values (1.2–3.5), which we attribute to incubation temperatures, incubation duration, storage duration, and sampling time. We also show that Q 10 values of CH 4 production are controlled by interacting biological, biochemical, and physical processes, which cause the inferred Q 10 values to differ substantially from those of the component processes. Terrestrial ecosystem models that use a constant Q 10 value to represent temperature responses may therefore predict biased soil carbon cycling under future climate scenarios.

54 ENVIRONMENTAL SCIENCES↗

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↗

Map-based cosmology inference with lognormal cosmic shear maps

ABSTRACT Most cosmic shear analyses to date have relied on summary statistics (e.g. ξ+ and ξ−). These types of analyses are necessarily suboptimal, as the use of summary statistics is lossy. In this paper, we forward-model the convergence field of the Universe as a lognormal random field conditioned on the observed shear data. This new map-based inference framework enables us to recover the joint posterior of the cosmological parameters and the convergence field of the Universe. Our analysis properly accounts for the covariance in the mass maps across tomographic bins, which significantly improves the fidelity of the maps relative to single-bin reconstructions. We verify that applying our inference pipeline to Gaussian random fields recovers posteriors that are in excellent agreement with their analytical counterparts. At the resolution of our maps – and to the extent that the convergence field can be described by the lognormal model – our map posteriors allow us to reconstruct all summary statistics (including non-Gaussian statistics). We forecast that a map-based inference analysis of LSST-Y10 data can improve cosmological constraints in the σ8–Ωm plane by $\approx\!{30}{{\ \rm per\ cent}}$ relative to the currently standard cosmic shear analysis. This improvement happens almost entirely along the $S_8=\sigma _8\Omega _{\rm m}^{1/2}$ directions, meaning map-based inference fails to significantly improve constraints on S8.

79 ASTRONOMY AND ASTROPHYSICS↗

Probabilistic inference of the structure and orbit of Milky Way satellites with semi-analytic modelling

Semi-analytic modelling furnishes an efficient avenue for characterizing dark matter haloes associated with satellites of Milky Way-like systems, as it easily accounts for uncertainties arising from halo-to-halo variance, the orbital disruption of satellites, baryonic feedback, and the stellar-to-halo mass (SMHM) relation. We use the SatGen semi-analytic satellite generator, which incorporates both empirical models of the galaxy–halo connection as well as analytic prescriptions for the orbital evolution of these satellites after accretion onto a host to create large samples of Milky Way-like systems and their satellites. By selecting satellites in the sample that match observed properties of a particular dwarf galaxy, we can infer arbitrary properties of the satellite galaxy within the cold dark matter paradigm. For the Milky Way’s classical dwarfs, we provide inferred values (with associated uncertainties) for the maximum circular velocity v max and the radius r max at which it occurs, varying over two choices of baryonic feedback model and two prescriptions for the SMHM relation. While simple empirical scaling relations can recover the median inferred value for v max and r max , this approach provides realistic correlated uncertainties and aids interpretability. We also demonstrate how the internal properties of a satellite’s dark matter profile correlate with its orbit, and we show that it is difficult to reproduce observations of the Fornax dwarf without strong baryonic feedback. Furthermore, the technique developed in this work is flexible in its application of observational data and can leverage arbitrary information about the satellite galaxies to make inferences about their dark matter haloes and population statistics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Exogeological inferences from white dwarf pollutants: the impact of stellar physics

Many white dwarfs have accreted material from their own planetary systems. These objects can be used to infer the composition of exoplanetary material and identify evidence for key geological processes. However, the white dwarf atmospheric physics distorts the inferred material composition away from the true composition, mainly through differential atomic diffusion of the accreted metals. Correcting for this effect is essential, but is dependent on various physical assumptions associated with the white dwarf itself. We first focus on the effect of assumptions related to convective overshoot and thermohaline mixing on the atomic diffusion time-scales. For white dwarfs with H-dominated atmospheres between 12000 K and 18000 K⁠, we find that including a complete treatment of convective overshoot decreases the inferred Fe and O abundances in accreted material. For these white dwarfs, we also find that including thermohaline mixing decreases Fe and O abundances. For He-dominated systems, the effect of convective overshoot is comparatively minor. We then explore the overall effect of other physical assumptions by comparing publicly available grids of diffusion time-scales. We find that the choice of model grid can have a large impact for white dwarfs with He-dominated atmospheres, notably on the inferred core to mantle ratio of accreted material. We identify several systems for which the geological interpretation is robust against these systematics. We also present a ‘discrepancy metric’ which can be used to estimate the potential impact of changing the stellar physics without requiring detailed modelling.

Astronomy and AstroPhysics↗

Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs

When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source’s infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model—which make use of different information within a tree—suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.

59 BASIC BIOLOGICAL SCIENCES↗

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

Inference of neutrino flavor evolution through data assimilation and neural differential equations

The evolution of neutrino flavor in dense environments such as core-collapse supernovae and binary compact object mergers constitutes an important and unsolved problem. Its solution has potential implications for the dynamics and heavy-element nucleosynthesis in these environments. In this paper, we build upon recent work to explore inference-based techniques for the estimation of model parameters and neutrino flavor evolution histories. Here, we combine data assimilation, ordinary differential equation solvers, and neural networks to craft an inference approach tailored for nonlinear dynamical systems. Using this architecture, and a simple two-neutrino-beam, two-flavor model, we compare the performances of nine different optimization algorithms and expand upon previous assessments of the efficacy of inference for tackling problems in flavor evolution. We find that employing this new architecture, together with evolutionary optimization algorithms, accurately captures flavor histories in the small-scale model and allows us to quickly explore both model parameters and initial flavor content. In future work we plan to extend these inference techniques to large numbers of neutrinos.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗