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At least 163 records · Page 9

Zero-truncated Poisson regression for sparse multiway count data corrupted by false zeros

Abstract We propose a novel statistical inference methodology for multiway count data that is corrupted by false zeros that are indistinguishable from true zero counts. Our approach consists of zero-truncating the Poisson distribution to neglect all zero values. This simple truncated approach dispenses with the need to distinguish between true and false zero counts and reduces the amount of data to be processed. Inference is accomplished via tensor completion that imposes low-rank tensor structure on the Poisson parameter space. Our main result shows that an $N$-way rank-$R$ parametric tensor $\boldsymbol{\mathscr{M}}\in (0,\infty )^{I\times \cdots \times I}$ generating Poisson observations can be accurately estimated by zero-truncated Poisson regression from approximately $IR^2\log _2^2(I)$ non-zero counts under the nonnegative canonical polyadic decomposition. Our result also quantifies the error made by zero-truncating the Poisson distribution when the parameter is uniformly bounded from below. Therefore, under a low-rank multiparameter model, we propose an implementable approach guaranteed to achieve accurate regression in under-determined scenarios with substantial corruption by false zeros. Several numerical experiments are presented to explore the theoretical results.

97 MATHEMATICS AND COMPUTING↗

Evaluating the limitations of Bayesian metabolic control analysis

Bayesian Metabolic Control Analysis (BMCA) is a promising framework for inferring metabolic control coefficients in data-limited scenarios, combining Bayesian inference with linear-logarithmic (lin-log) rate laws. These metabolic control coefficients quantify how changes in enzyme activities affect steady-state fluxes and metabolite concentrations across a metabolic network. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCC), and concentration control coefficients (CCC) under varying data availability conditions using three synthetic metabolic network models. We demonstrate that BMCA predictions are highly dependent on the inclusion of flux and enzyme concentration data, with the omission of these datasets leading to severe inaccuracies. In our synthetic, enzyme-perturbation datasets, external metabolite concentrations had minimal impact and, in some cases, their exclusion improved predictions; when external-nutrient perturbations were introduced and those concentrations were observed, gains were at most modest. Additionally, we find that posterior estimation with both ADVI and HMC can underestimate large-magnitude elasticities in our synthetic settings, with ADVI showing somewhat higher variance under strong up-regulation; thus, recovering |elasticity| ≳ 1.5 remains challenging regardless of the inference engine. ADVI also fails to accurately infer allosteric interactions, even when regulatory effects are strong. While BMCA maintains reasonable accuracy in partially recovering the rankings of the highest FCC values, its estimates of absolute values remain constrained by prior assumptions and data limitations. Our findings reveal the BMCA algorithm’s strengths and weaknesses, providing guidance on its application in metabolic engineering, and highlighting the need for methodological refinements to enhance its predictive capabilities.

59 BASIC BIOLOGICAL SCIENCES↗

Label Assist: Personalized Travel Models for Longitudinal Data Collection

Understanding travel behavior is crucial to transportation decarbonization. OpenPATH is an open-source mobility platform which collects and analyzes human travel behavior at the individual level. The mobile application passively senses trips and prompts users to label them. However, users find the labeling process burdensome; less than half the trips are typically labeled, making much of the data unusable in aggregate analyses of mobility patterns. Prior work has addressed the response fatigue challenge through automated mode inference using sensor data, but sensors cannot capture all aspects of travel behavior. We explore an alternative approach in which we leverage prior user input to predict travel choices in novel trips. We first explore trip clustering methods and develop a novel two-step pipeline using DBSCAN and SVMs to extract realistic geospatial clusters. We then propose two strategies to predict trip labels: (i) clustering trips and extrapolating labels for similar trips, and (ii) random forest classification. The random forest approach is able to achieve - $70-80% accuracy (purpose: 72%, mode: 79%, replaced mode: 81%). These novel approaches to trip classification allow us to increase the rate of user labeling by suggesting predicted labels to be verified by the user. Unlabeled trips can also contribute to aggregate analyses, using label predictions and their associated confidences as a substitute. While there exist other travel survey apps with the ability to infer travel choices, to our knowledge, this is the first paper to describe such a supervised system and rigorously evaluate it.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

Thinking Bayesian for plasma physicists

Bayesian statistics offers a powerful technique for plasma physicists to infer knowledge from the heterogeneous data types encountered. To explain this power, a simple example, Gaussian Process Regression, and the application of Bayesian statistics to inverse problems are explained. The likelihood is the key distribution because it contains the data model, or theoretic predictions, of the desired quantities. By using prior knowledge, the distribution of the inferred quantities of interest based on the data given can be inferred. Because it is a distribution of inferred quantities given the data and not a single prediction, uncertainty quantification is a natural consequence of Bayesian statistics. The benefits of machine learning in developing surrogate models for solving inverse problems are discussed, as well as progress in quantitatively understanding the errors that such a model introduces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Instantiation of HCML Demonstrating Bayesian Predictive Modeling for Attentional Control

The research team developed models of Attentional Control (AC) that are unique to existing modeling approaches in the literature. The goal was to enable the research team to (1) make predictions about AC and human performance in real-world scenarios and (2) to make predictions about individual characteristics based on human data. First, the team developed a proof-of-concept approach for representing an experimental design and human subjects data in a Bayesian model, then demonstrated an ability to draw inferences about conditions of interest relevant to real-world scenarios. Ultimately, this effort was successful, and we were able to make reasonable (meaning supported by behavioral data) inferences about conditions of interest to develop a risk model for AC (where risk is defined as a mismatch between AC and attentional demand). The team additionally defined a path forward for a human-constrained machine learning (HCML) approach to make predictions about an individual's state based on performance data. The effort represents a successful first step in both modeling efforts and serves as a basis for future work activities. Numerous opportunities for future work have been defined.

97 MATHEMATICS AND COMPUTING↗

An Experimental Investigation of Students’ Learning Effects When Using a Simplified Nuclear Simulator

Securing enough data has been a main challenge in human reliability analysis (HRA). Many researchers and institutes have made a lot of efforts for collecting HRA data to produce reasonable human error probabilities (HEPs) as well as reduce the uncertainty of HRA quantification. Representatively, U.S. Nuclear Regulatory Commission (U.S. NRC), Korea Atomic Energy Research Institute (KAERI) and Idaho National Laboratory (INL) have led lots of empirical research regarding the HRA data collection. The U.S. NRC and KAERI have mainly carried out full-scope simulator research collecting HRA data through experiments using full-scope simulators with actual operators. In contrast, INL has experimentally collected the data using simplified simulators and student operators. INL has proposed the Simplified Human Error Experimental Program (SHEEP) framework to complement full-scope data collection efforts by suggesting a way to infer full-scope data based on experimental data collected from students operating simplified simulators, specifically the Rancor Microworld Simulator (Rancor) and the Compact Nuclear Simulator (CNS). The aim of the SHEEP framework is to lower the entry point for collecting useful HRA data by securing large sample sizes at a reasonable amount of cost and labor while also guaranteeing a high degree of freedom when designing experiments. The authors’ previous research investigated whether data collected from the SHEEP framework could support a representative full-scope study. Besides, human performance differences between professional and student operators when using Rancor and CNS have been analyzed to understand the lack of fidelity of the simplified simulators and student operators within the SHEEP study. As a follow up research, this study experimentally investigates students’ learning effects and the performance trends over a certain period when using Rancor. This study aims to find out 1) how much training or education is required to collect HRA data from non-experts (i.e., students) when using Rancor and 2) how much differences there are in human performance measures between students and professional operators. In this study, a longitudinal experiment is developed. The four experiment trials with two weeks interval are carried out for sixteen undergraduate students majoring nuclear engineering at Chosun University. Totally four scenarios randomly selected from ten Rancor scenarios are used in each experiment trial. Four human performance measurements (i.e., workload, situation awareness, time and error) are considered in the experiment. Lastly, the trend of students’ performance is compared with operator data having been collected from the previous experiment.

99 GENERAL AND MISCELLANEOUS↗

An Empirical Study on the Use of the Rancor Microworld Simulator to Support Full-scope Data Collection

A lack of data has been identified as a major challenge in human reliability analysis (HRA). Accordingly, several institutes and researchers have tried to collect HRA data from different data sources such as actual historical measurements, expert judgements, or simulator studies. While the most recent studies predominantly focus on collecting data using full-scope simulators with actual operators, Idaho National Laboratory (INL) has begun to collect HRA data using a simplified simulator, i.e., the Rancor Microworld simulator, with student participants. Full-scope studies have been known to have several intrinsic challenges to securing enough quantity of the data due to many reasons like the high cost for performing experiments or requiring actual operators’ cooperation. The ultimate goal of INL’s effort aims to infer actual operators’ data collected from a full-scope simulator on the basis of microworld data with student subjects as well as collect additional data that could be missed in the full-scope research. As a first step to achieve this goal, this paper projects an experimental plan for investigating the differences in human performance between individuals in two groups: 1) an actual operator and 2) a student when using the Rancor Microworld simulator. A randomized factorial experiment design has been developed with two independent variables, i.e., type of scenario and type of subject. Six human performance measures, i.e., 1) time, 2) error, 3) workload, 4) situation awareness, 5) patterns of attention and 6) the number of manipulations were selected. A couple of scenarios and their procedures available to the Rancor Microworld simulator have been developed.

99 GENERAL AND MISCELLANEOUS↗

Zero-Truncated Poisson Tensor Decomposition for Sparse Count Data

We propose a novel statistical inference paradigm for zero-inflated multiway count data that dispenses with the need to distinguish between true and false zero counts. Our approach ignores all zero entries and applies zero-truncated Poisson regression on the positive counts. Inference is accomplished via tensor completion that imposes low-rank structure on the Poisson parameter space. Our main result shows that an $\textit{N}$-way rank-R parametric tensor 𝓜 ϵ (0, ∞) $I$Χ∙∙∙Χ$I$ generating Poisson observations can be accurately estimated from approximately $IR^2 \text{log}^2_2(I)$ non-zero counts for a nonnegative canonical polyadic decomposition. Several numerical experiments are presented demonstrating that our zero-truncated paradigm is comparable to the ideal scenario where the locations of false zero counts are known $\textit{a priori}$.

97 MATHEMATICS AND COMPUTING↗

Hybrid Star Models in the Light of New Multimessenger Data

Abstract Recent astrophysical mass inferences of compact stars HESS J1731-347 and PSR J0952-0607, with extremely small and large masses respectively, as well as the measurement of the neutron skin of Ca in the CREX experiment challenge and constrain the models of dense matter. We examine the concept of hybrid stars—objects containing quark cores surrounded by nucleonic envelopes—as models that account for these new data along with other inferences. We employ a family of 81 nucleonic equations of state (EOSs) with variable skewness and slope of symmetry energy at saturation density and a constant speed-of-sound EOS for quark matter. For each nucleonic EOS, a family of hybrid EOSs is generated by varying the transition density, the energy jump, and the speed of sound. These models are tested against the data from GW170817 and J1731-347, which favor low-density soft EOS and J0592-0607 and J0740+6620, which require high-density stiff EOS. The addition of J0592-0607's mass measurement to the constraints has no significant impact on the parameter space of the admissible EOS, but allows us to explore the potential effect of pulsars more massive than J0740+6620, if such exists. We then examine the occurrence of twin configurations and quantify the ranges of masses and radii that they can possess. It is shown that including J1731-347 data favors EOSs that predict low-mass twins with M ≲ 1.3 M ⊙ that can be realized if the deconfinement transition density is low. If combined with large speed of sound in quark matter such models allow for maximum masses of hybrid stars in 2.0–2.6 M ⊙ .

Astronomy & Astrophysics↗

Evaluating the limitations of Bayesian metabolic control analysis

AbstractBayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements.Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

Shin, Janis (ORCID:0000000216572455)↗

A non-linear solution to the S 8 tension – II. Analysis of DES Year 3 cosmic shear

ABSTRACT Weak galaxy lensing surveys have consistently reported low values of the S8 parameter compared to the Planck lambda cold dark matter (ΛCDM) cosmology. Amon & Efstathiou used KiDS-1000 cosmic shear measurements to propose that this tension can be reconciled if the matter fluctuation spectrum is suppressed more strongly on non-linear scales than assumed in state-of-the-art hydrodynamical simulations. In this paper, we investigate cosmic shear data from the Dark Energy Survey (DES) Year 3. The non-linear suppression of the matter power spectrum required to resolve the S8 tension between DES and the Planck ΛCDM model is not as strong as inferred using KiDS data, but is still more extreme than predictions from recent numerical simulations. An alternative possibility is that non-standard dark matter contributes to the required suppression. We investigate the redshift and scale dependence of the suppression of the matter power spectrum. If our proposed explanation of the S8 tension is correct, the required suppression must extend into the mildly non-linear regime to wavenumbers $k\sim 0.2 \, h\, {\rm Mpc}^{-1}$. In addition, all measures of S8 using linear scales should agree with the Planck ΛCDM cosmology, an expectation that will be testable to high precision in the near future.

Preston, Calvin (ORCID:0000000281136916)↗

The impact of tomographic redshift bin width errors on cosmological probes

ABSTRACT Systematic errors in the galaxy redshift distribution n(z) can propagate to systematic errors in the derived cosmology. We characterize how the degenerate effects in tomographic bin widths and galaxy bias impart systematic errors on cosmology inference using observational data from the Deep Lens Survey. For this we use a combination of galaxy clustering and galaxy–galaxy lensing. We present two end-to-end analyses from the catalogue level to parameter estimation. We produce an initial cosmological inference using fiducial tomographic redshift bins derived from photometric redshifts, then compare this with a result where the redshift bins are empirically corrected using a set of spectroscopic redshifts. We find that the derived parameter S8 ≡ σ8(Ωm/.3)1/2 decreases from $0.841^{+0.062}_{-0.061}$ to $0.781^{0.061}_{0.054}$ upon correcting the n(z) errors in the second method.

79 ASTRONOMY AND ASTROPHYSICS↗

Real-time Anomaly Detection for Liquid Argon Time Projection Chambers

We present a real-time anomaly detection framework for liquid argon time projection chambers (LArTPCs), targeting applications in particle physics experiments such as the Short Baseline Near Detector (SBND) or the future Deep Underground Neutrino Experiment (DUNE). These experiments employ detectors that generate and stream high-resolution but sparse images of neutrino and other particle interactions. Our approach utilizes anomaly detection with autoencoders, compressed through knowledge distillation (KD), to enable the detection of anomalous signals in the data through efficient inference on resource-constrained hardware. The framework is targeted for deployment on computing platforms equipped with field-programmable gate arrays (FPGAs), GPUs, or CPUs, allowing low-latency selection of relevant activity directly from the raw detector data stream. We demonstrate that our approach is suitable for the detection and localization of anomalously "high-multiplicity" activity, and outline promising applications for LArTPC online data filtering and triggering.

FOS: Physical sciences↗

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.

59 BASIC BIOLOGICAL SCIENCES↗

Hydra: computer vision for data quality monitoring

Hydra, initially developed for Hall-D in 2019, is a system that utilizes computer vision to perform near real time data quality monitoring. Since then, it has been deployed across all experimental halls at Jefferson Lab, with the CLAS12 collaboration in Hall-B being the first outside of GlueX to fully utilize Hydra. The system comprises back end processes that manage the models, their inferences, and the data flow. Finally, the front-end components, accessible via web pages, allow detector experts and shift crews to view and interact with the system.

47 OTHER INSTRUMENTATION↗

Laser-Plasma Spectroscopy of Hydroxyl with Applications

This article discusses laser-induced laboratory-air plasma measurements and analysis of hydroxyl (OH) ultraviolet spectra. The computations of the OH spectra utilize line strength data that were developed previously and that are now communicated for the first time. The line strengths have been utilized extensively in interpretation of recorded molecular emission spectra and have been well-tested in laser-induced fluorescence applications for the purpose of temperature inferences from recorded data. Moreover, new experiments with Q-switched laser pulses illustrate occurrence of molecular recombination spectra for time delays of the order of several dozen of microseconds after plasma initiation. The OH signals occur due to the natural humidity in laboratory air. Centrifugal stretching of the Franck-Condon factors and r-centroids are included in the process of determining the line strengths that are communicated as a Supplementary File. Laser spectroscopy applications of detailed OH computations include laser-induced plasma and combustion analyses, to name but two applications. This work also includes literature references that address various diagnosis applications.

47 OTHER INSTRUMENTATION↗

A Representation Fusion Framework for Decoupling Diagnostic Information in Multimodal Learning

Modern medicine increasingly relies on multimodal data, ranging from clinical notes to imaging and genomics, to guide diagnosis and treatment. However, integrating these heterogeneous data sources in a principled and interpretable manner remains a major challenge. We present MODES (Multi-mOdal Disentangled Embedding Space), a representation fusion framework that explicitly separates shared and modality-specific factors of variation, offering a structured latent space for multimodal information that improves both prediction and interpretability. By leveraging pre-trained unimodal foundation models, MODES mitigates the dependency on extensive paired datasets, crucial in data-scarce clinical settings. We introduce a masking strategy that optimizes representation dimensionality by eliminating low-information dimensions, to achieve compact, information-rich representations. Our framework demonstrates superior performance in predicting diagnoses and phenotypes compared to unimodal and conventional fusion models. MODES also enables robust diagnostic inference in missing data scenarios, offering an opportunity toward interpretable and efficient multimodal diagnostics in personalized healthcare.

60 APPLIED LIFE SCIENCES↗