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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring the ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6/15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

Maximum likelihood decoding analysis of accumulate-repeat-accumulate codes

In this paper, the performance of the repeat-accumulate codes with (ML) decoding are analyzed and compared to random codes by very tight bounds. Some simple codes are shown that perform very close to Shannon limit with maximum likelihood decoding.

LDPC codes turbo-like codes maximum likelihood dec↗
DOE OSTI2026

The DESI DR1 peculiar velocity survey: growth rate measurements from the maximum likelihood fields method

We present the constraint on the growth rate of structure from the combination of DESI DR1 BGS sample, Fundamental Plane, and Tully-Fisher peculiar velocity catalogues using the maximum likelihood fields method. The combined catalogue contains 415,523 galaxy redshifts and 76,616 peculiar velocity measurements. To handle the large amount of data in the DESI DR1 peculiar velocity catalogue, we significantly improve the computational efficiency by rewriting the algorithm with JAX. After removing outliers and Tully-Fisher galaxies that are affected by systematics, we find fσ 8 = 0.483 -0.043 +0.080 (stat) ± 0.018(sys), consistent within 1σ with the power spectrum and correlation function analysis using the same dataset. Combining all three measurements with appropriate correlations, the consensus measurement is fσ 8 (z eff = 0.07) = 0.450±0.055, consistent with Planck +ΛCDM cosmology (fσ 8 = 0.449±0.008). Combining with the high redshift growth rate of structure measurements from DESI ShapeFit, the constraint on the growth index is γ = 0.58±0.11, consistent with GR.

cosmic flows↗
DOE OSTI2024

Dark energy survey year 3 results: likelihood-free, simulation-based w CDM inference with neural compression of weak-lensing map statistics

We present simulation-based cosmological wcold dark matter (wCDM) inference using dark energy survey year 3 weak-lensing maps, via neural data compression of weak-lensing map summary statistics: power spectra, peak counts, and direct map-level compression/inference with convolutional neural networks (CNN). Using simulation-based inference, also known as likelihood-free or implicit inference, we use forward-modelled mock data to estimate posterior probability distributions of unknown parameters. This approach allows all statistical assumptions and uncertainties to be propagated through the forward-modelled mock data; these include sky masks, non-Gaussian shape noise, shape measurement bias, source galaxy clustering, photometric redshift uncertainty, intrinsic galaxy alignments, non-Gaussian density fields, neutrinos, and non-linear summary statistics. We include a series of tests to validate our inference results. This paper also describes the Gower Street simulation suite: 791 full-sky pkdgrav3 dark matter simulations, with cosmological model parameters sampled with a mixed active-learning strategy, from which we construct over 3000 mock dark energy survey lensing data sets. For wCDM inference, for which we allow –1 < w < –$\frac{1}{3}$⁠, our most constraining result uses power spectra combined with map-level (CNN) inference. Using gravitational lensing data only, this map-level combination gives Ω m = 0.283$^{+0.020}_{–0.027}$⁠, S 8 = 0.804$^{+0.025}_{–0.017⁠}$, and w < –0.80 (with a 68 per cent credible interval); compared to the power spectrum inference, this is more than a factor of two improvement in dark energy parameter (Ω⁠ DE , w⁠) precision.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

A Latent-Variable Formulation of the Poisson Canonical Polyadic Tensor Model: Maximum Likelihood Estimation and Fisher Information

We establish parameter inference for the Poisson canonical polyadic (PCP) tensor model through a latent-variable formulation. Our approach exploits the observation that any random PCP tensor can be derived by marginalizing an unobservable random tensor of one dimension larger. The loglikelihood of this larger dimensional tensor, referred to as the “complete” loglikelihood, is comprised of multiple rank one PCP loglikelihoods. Using this methodology, we first derive maximum likelihood estimators for the PCP model and demonstrate that several existing algorithms for fitting non-negative matrix and tensor factorizations are Expectation-Maximization algorithms. Next, we derive the observed and expected Fisher information matrices for the PCP model. The Fisher information provides us crucial insights into the well-posedness of the tensor model, such as the role that tensor rank plays in identifiability and indeterminacy. For the special case of rank one PCP models, we demonstrate that these results are greatly simplified.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Likelihood-Based Particle Identification in SBND

Accurate particle identification is crucial in any high-energy physics experiment, allowing scientists to understand the unique interactions and mechanisms at play in a detector. In this project, I develop and study a likelihood-based particle identification (PID) algorithm for the Short-Baseline Near Detector, which offers a more physically motivated strategy for PID.

Vanderwaal, Sophia [U. Alabama, Huntsville]↗
DOE OSTI2026

Red Noise–based False Alarm Thresholds for Astrophysical Periodograms via Whittle’s Approximation to the Likelihood

Astronomers who search for periodic signals using Lomb–Scargle periodograms rely on false alarm level (FAL) estimates to identify statistically significant peaks. Although FALs are often calculated from white noise models, many astronomical time series suffer from red noise. Prewhitening is a statistical technique in which a continuum model is subtracted from the log power spectrum estimate, after which the observer can proceed with a white-noise treatment. Here we present a prewhitening-based method of calculating frequency-dependent FALs. We fit power laws and autoregressive models of order 1 to each Lomb–Scargle periodogram by minimizing the Whittle approximation to the negative log-likelihood (NLL), then calculate FALs based on the best-fit model power spectrum. Our technique is a novel extension of the Whittle NLL to datasets with uneven time sampling. We demonstrate FAL calculations using observations of α Cen B, GJ 581, HD 192310, synthetic data from the radial velocity (RV) fitting challenge, and Kepler observations of a differential rotator. The Kepler data analysis shows that only true rotation signals are detected by red noise FALs, while white noise FALs suggest all spurious peaks in the low-frequency range are significant. A high-frequency sinusoid injected into α Cen B logR$'$ HK observations exceeds the 1% red noise FAL despite having only 8.9% of the power of the dominant rotation signal. In a periodogram of HD 192310 RVs, peaks associated with differential rotation and planets are detected against the 5% red noise FAL without iterative model fitting or subtraction. The software for calculating red noise–based FALs is available on GitHub.

Astrostatistics (1882)↗