SEARCH · Search NASA

Results for “evolutionary algorithm”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10

All sources NASA NTRS DOE OSTI

DOE OSTI2019

Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis

Lignin is a bountiful biopolymer of phenylpropanoid monomers that is critical for plant structure and function. Based on the abundance of lignin in the biosphere and interest in lignin valorization, a more comprehensive understanding of lignin biosynthesis is imperative. We introduce an open-source software toolkit, Lignin-KMC, that combines kinetic Monte Carlo and first-principles calculations of radical coupling events to model lignin biosynthesis in silico. Lignification is simulated using the Gillespie algorithm with rates derived from density functional theory calculations of individual fragment couplings. Using this approach, we confirm experimental findings regarding the impact of lignification conditions on the polymer structure such as (1) the positive correlation between sinapyl alcohol fraction and depolymerization yield and (2) the primarily benzodioxane linked structure of C-lignin. Furthermore, we identify the in planta monolignol supply rate as a possible control mechanism for lignin biosynthesis based on evolutionary stresses. These examples not only highlight the robustness of our modeling framework but also motivate future studies of new lignin types, unexplored monolignol chemistries, and lignin structure predictions, all with an overarching aim of developing a more comprehensive molecular understanding of native lignin, which, in turn, can accelerate the biological and chemistry communities interested in this important biopolymer.

09 BIOMASS FUELS↗

DOE OSTI2018

Regional surname affinity: A spatial network approach

Abstract Objective We investigate surname affinities among areas of modern‐day China, by constructing a spatial network, and making community detection. It reports a geographical genealogy of the Chinese population that is result of population origins, historical migrations, and societal evolutions. Materials and methods We acquire data from the census records supplied by China's National Citizen Identity Information System, including the surname and regional information of 1.28 billion registered Chinese citizens. We propose a multilayer minimum spanning tree (MMST) to construct a spatial network based on the matrix of isonymic distances, which is often used to characterize the dissimilarity of surname structure among areas. We use the fast unfolding algorithm to detect network communities. Results We obtain a 10‐layer MMST network of 362 prefecture nodes and 3,610 edges derived from the matrix of the Euclidean distances among these areas. These prefectures are divided into eight groups in the spatial network via community detection. We measure the partition by comparing the inter‐distances and intra‐distances of the communities and obtain meaningful regional ethnicity classification. Discussion The visualization of the resulting communities on the map indicates that the prefectures in the same community are usually geographically adjacent. The formation of this partition is influenced by geographical factors, historic migrations, trade and economic factors, as well as isolation of culture and language. The MMST algorithm proves to be effective in geo‐genealogy and ethnicity classification for it retains essential information about surname affinity and highlights the geographical consanguinity of the population.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Online evolutionary neural architecture search for multivariate non-stationary time series forecasting

Time series forecasting (TSF) is one of the most important tasks in data science. TSF models are usually pre-trained with historical data and then applied on future unseen datapoints. However, real-world time series data is usually non-stationary and models trained offline usually face problems from data drift. Models trained and designed in an offline fashion can not quickly adapt to changes quickly or be deployed in real-time. To address these issues, this work presents the Online NeuroEvolution-based Neural Architecture Search (ONE-NAS) algorithm, which is a novel neural architecture search method capable of automatically designing and dynamically training recurrent neural networks (RNNs) for online forecasting tasks. Without any pre-training, ONE-NAS utilizes populations of RNNs that are continuously updated with new network structures and weights in response to new multivariate input data. ONE-NAS is tested on real-world, large-scale multivariate wind turbine data as well as the univariate Dow Jones Industrial Average (DJIA) dataset. These results demonstrate that ONE-NAS outperforms traditional statistical time series forecasting methods, including online linear regression, fixed long short-term memory (LSTM) and gated recurrent unit (GRU) models trained online, as well as state-of-the-art, online ARIMA strategies. Additionally, results show that utilizing multiple populations of RNNs which are periodically repopulated provide significant performance improvements, allowing this online neural network architecture design and training to be successful.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype–phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ω C , which measures the error-corrected convergence rate of protein evolution. While ω C distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype–phenotype associations, even in lineages that diverged for hundreds of millions of years.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Evolutionary multi-objective optimization and Pareto-frontal uncertainty quantification of interatomic forcefields for thermal conductivity simulations

Predictive Molecular Dynamics simulations of thermal transport require forcefields that can simultaneously reproduce several structural, thermodynamic and vibrational properties of materials like lattice constants, phonon density of states, and specific heat. This requires a multi-objective optimization approach for forcefield parameterization. Existing methodologies for forcefield parameterization use ad-hoc and empirical weighting schemes to convert this into a single-objective optimization problem. Here, we provide and describe software to perform multi-objective optimization of Stillinger–Weber forcefields (SWFF) for two-dimensional layered materials using the recently developed 3rd generation non-dominated sorting genetic algorithm (NSGA-III). NSGA-III converges to the set of optimal forcefields lying on the Pareto front in the multi-dimensional objective space. This set of forcefields is used for uncertainty quantification of computed thermal conductivity due to variability in the forcefield parameters. We demonstrate this new optimization scheme by constructing a SWFF for a representative two-dimensional material, 2H-MoSe 2 and quantifying the uncertainty in their computed thermal conductivity.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Deep representation learning improves prediction of LacI-mediated transcriptional repression

Significance The understanding of protein function increases with new experimental and evolutionary datasets. A major challenge is to apply machine learning to these datasets to capture essential features of protein function. Here, we analyze the experimentally determined repression function for tens of thousands of mutants of the LacI protein. This study provides a continuous, noncategorical repression value across a majority of all single mutations and for thousands of higher-order mutations. To develop a top-performing model for the prediction of repression by LacI, we compare several leading variant effect prediction algorithms. A deep representation learning paradigm, first trained across millions of proteins from all known protein families and then fine-tuned using LacI experimental data, offers the highest predictive performance of repression function.

42 ENGINEERING↗

DOE OSTI2023

Finding Your Niche: An Evolutionary Approach to HPC Topologies

Traditional interconnection network design approaches focus on building general network topologies by optimizing the bisection bandwidth or minimizing the network’s diameter to reduce the maximum distance between any two nodes, thus amortizing the overall execution time of the HPC workloads. While such network topologies may accommodate a wide variety of applications in general, this may result in sub-optimal performance for many frequently-executed or dynamic workloads. In this paper, instead of focusing on designing an all-encompassing, general-purpose network topology, we develop a methodology to design customized network interconnects, evolved by “finding” the optimal topologies for a particular target workload given by its communication and contention profiles. To this end, we implement a Genetic Algorithm (GA)-based approach for network topology design tailored to improve the overall execution time of a particular workload of interest. We conducted extensive experiments with well-known motifs in physics-based workloads (Sweep3D and FFT), as well as with a representative graph application (MiniVite), using the well-known Structural Simulation Toolkit (SST) Macroscale Element Library (SST/macro) simulator for network interconnect evaluation. We demonstrate that our genetic algorithm-based approach is robust enough to find the underlying optimal topology of a particular workload.

network interconnects, graph search, meta-heuristi↗

DOE OSTI2019

Intelligent Reservoir Generation for Liquid State Machines using Evolutionary Optimization

Neuromorphic Computing is a burgeoning field of research. Many groups are exploring hardware architectures and theoretical ideas about spiking recurrent neural networks. The overarching goal is to exploit the low power promise of these neuromorphic systems. However, it is difficult to train spiking recurrent neural networks (SRNNs) to perform tasks and make efficient use of neuromorphic hardware. Reservoir Computing is an attractive methodology because it requires no tuning of weights for the reservoir itself. Yet, to find optimal reservoirs, manual tuning of hyperparameters such as hidden neurons, synaptic density, and natural structure is still required. Because of this, researchers often have to generate and evaluate many networks, which can result in non-trivial amounts of computation. This paper employs the reservoir computing technique (specifically liquid state machines) and genetic algorithms in order to develop useful networks that can be deployed on neuromorphic hardware. We build on past work in reservoir computing and genetic algorithms to demonstrate the power of combining these two techniques and the advantage it can provide over manually tuning reservoirs for use on classification tasks. We discuss the complexities of determining whether or not to use the genetic algorithms approach for liquid state machine generation.

Reynolds, John↗

DOE OSTI2024

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Evolutionary Biology↗

DOE OSTI2020

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗

DOE OSTI2025

Functional protein mining with conformal guarantees

Molecular structure prediction and homology detection offer promising paths to discovering protein function and evolutionary relationships. However, current approaches lack statistical reliability assurances, limiting their practical utility for selecting proteins for further experimental and in-silico characterization. To address this challenge, we introduce a statistically principled approach to protein search leveraging principles from conformal prediction, offering a framework that ensures statistical guarantees with user-specified risk and provides calibrated probabilities (rather than raw ML scores) for any protein search model. Our method (1) lets users select many biologically-relevant loss metrics (i.e. false discovery rate) and assigns reliable functional probabilities for annotating genes of unknown function; (2) achieves state-of-the-art performance in enzyme classification without training new models; and (3) robustly and rapidly pre-filters proteins for computationally intensive structural alignment algorithms. Our framework enhances the reliability of protein homology detection and enables the discovery of uncharacterized proteins with likely desirable functional properties.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Parallel derivative-free optimization for simulation-based design of behind-the-meter energy systems

In this work, the integrated design and dispatch of behind-the-meter or distributed resources (e.g. stationary battery storage and solar PV generation) is considered. A simulation-based framework is employed, generating high-fidelity results with closed-loop predictive control at a fine resolution, at the expense of high computational cost (several minutes to a few hours per design point). To address this challenge, parallel derivative-free design methods are considered. Four methods are compared, including state-of-the-art surrogate-based methods (Radial-Basis Functions and Gaussian processes) and sampling strategies, an evolutionary-based method, and a simple sequential grid refinement method. As a case study, two types of design problem with increasing complexity are considered, namely, the design of behind-the-meter resources (three design variables) and the inclusion of grid capacity (four design variables). The second yields a constrained design problem for which violations can only be determined after solving the computationally expensive simulation. For the three-dimensional case, all methods present a good performance, achieving a solution within 1% of the optimum after the first iteration, with the sequential grid refinement exhibiting the fastest convergence and achieving the best final objective value. This indicates that the parallel evaluation of multiple sampling points may be more important than the choice of method for small decision spaces. For the four-dimensional constrained case, the Genetic Algorithm presents the best tradeoff between performance and computational effort, while the rough objective function terrain generated by constraint violation penalties reduces the performance of surrogate-based methods. Contour plots with flat regions indicate flexibility in the optimal design and highlight the importance of characterizing the solution space.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning

Abstract The Structural Classification of Proteins—extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Enhanced resonant ultrasound spectroscopy for measurement of the elastic properties of multi-material systems

Understanding the elastic properties of materials is critical for their safe incorporation and predictable performance. Current methods of bulk elastic characterization often have notable limitations for in situ structural applications, with usage restricted to simple geometries and material distributions. To address these existing issues, this study sought to expand the capabilities of resonant ultrasound spectroscopy (RUS), an established nondestructive evaluation method, to include the characterization of isotropic multi-material samples. In this work, finite-element-based RUS analysis consisted of numerical simulations and experimental testing of composite samples comprised of material pairs with varying elasticity and density contrasts. Utilizing genetic algorithm inversion and mode matching, our results demonstrate that elastic properties of multi-material samples can be reliably identified within several percent of known or nominal values using a minimum number of identified resonance modes, given sample mass is held consistent. The accurate recovery of material properties for composite samples of varying material similarity and geometry expands the pool of viable samples for RUS and advances the method towards in situ inspection and evaluation.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Measuring photometric redshifts for high-redshift radio source surveys

With the advent of deep, all-sky radio surveys, the need for ancillary data to make the most of the new, high-quality radio data from surveys like the Evolutionary Map of the Universe (EMU), GaLactic and Extragalactic All-sky Murchison Widefield Array survey eXtended, Very Large Array Sky Survey, and LOFAR Two-metre Sky Survey is growing rapidly. Radio surveys produce significant numbers of Active Galactic Nuclei (AGNs) and have a significantly higher average redshift when compared with optical and infrared all-sky surveys. Thus, traditional methods of estimating redshift are challenged, with spectroscopic surveys not reaching the redshift depth of radio surveys, and AGNs making it difficult for template fitting methods to accurately model the source. Machine Learning (ML) methods have been used, but efforts have typically been directed towards optically selected samples, or samples at significantly lower redshift than expected from upcoming radio surveys. This work compiles and homogenises a radio-selected dataset from both the northern hemisphere (making use of Sloan Digital Sky Survey optical photometry) and southern hemisphere (making use of Dark Energy Survey optical photometry). We then test commonly used ML algorithms such as k-Nearest Neighbours (kNN), Random Forest, ANNz, and GPz on this monolithic radio-selected sample. We show that kNN has the lowest percentage of catastrophic outliers, providing the best match for the majority of science cases in the EMU survey. We note that the wider redshift range of the combined dataset used allows for estimation of sources up to z = 3 before random scatter begins to dominate. When binning the data into redshift bins and treating the problem as a classification problem, we are able to correctly identify ≈ 76% of the highest redshift sources—sources at redshift z > 2.51 —as being in either the highest bin (z > 2.51) or second highest (z = 2.25).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

RG-CAT: Detection pipeline and catalogue of radio galaxies in the EMU pilot survey

Abstract We present source detection and catalogue construction pipelines to build the first catalogue of radio galaxies from the 270$\rm deg^2$pilot survey of the Evolutionary Map of the Universe (EMU-PS) conducted with the Australian Square Kilometre Array Pathfinder (ASKAP) telescope. The detection pipeline uses Gal-DINO computer vision networks (Gupta et al. 2024, PASA, 41, e001) to predict the categories of radio morphology and bounding boxes for radio sources, as well as their potential infrared host positions. The Gal-DINO network is trained and evaluated on approximately 5 000 visually inspected radio galaxies and their infrared hosts, encompassing both compact and extended radio morphologies. We find that the Intersection over Union (IoU) for the predicted and ground-truth bounding boxes is larger than 0.5 for 99% of the radio sources, and 98% of predicted host positions are within$3^{\prime \prime}$of the ground-truth infrared host in the evaluation set. The catalogue construction pipeline uses the predictions of the trained network on the radio and infrared image cutouts based on the catalogue of radio components identified using theSelavysource finder algorithm. Confidence scores of the predictions are then used to prioritiseSelavycomponents with higher scores and incorporate them first into the catalogue. This results in identifications for a total of 211 625 radio sources, with 201 211 classified as compact and unresolved. The remaining 10 414 are categorised as extended radio morphologies, including 582 FR-I, 5 602 FR-II, 1 494 FR-x (uncertain whether FR-I or FR-II), 2 375 R (single-peak resolved) radio galaxies, and 361 with peculiar and other rare morphologies. Each source in the catalogue includes a confidence score. We cross-match the radio sources in the catalogue with the infrared and optical catalogues, finding infrared cross-matches for 73% and photometric redshifts for 36% of the radio galaxies. The EMU-PS catalogue and the detection pipelines presented here will be used towards constructing catalogues for the main EMU survey covering the full southern sky.

Astronomy & Astrophysics↗

DOE OSTI2020

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

Abstract Background A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. Results Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp 614 Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro 323 Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. Conclusions These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Nearby stellar substructures in the Galactic halo from DESI Milky Way Survey Year 1 Data Release

We report five nearby ($d_{\mathrm{helio}} < 5$ kpc) stellar substructures in the Galactic halo from a subset of 138 661 stars in the Dark Energy Spectroscopic Instrument (DESI) Milky Way Survey Year 1 Data Release. With an unsupervised clustering algorithm, HDBSCAN*, these substructures are independently identified in Integrals of Motion ($E_{\rm tot}$, $L_{\rm z}$, $\log {J_r}$, $\log {J_z}$) space and Galactocentric cylindrical velocity space ($V_{R}$, $V_{\phi }$, $V_{z}$). We associate all identified clusters with known nearby substructures (Helmi streams, M18-Cand10/MMH-1, Sequoia, Antaeus, and ED-2) previously reported in various studies. With metallicities precisely measured by DESI, we confirm that the Helmi streams, M18-Cand10, and ED-2 are chemically distinct from local halo stars. We have characterized the chemodynamic properties of each dynamic group, including their metallicity dispersions, to associate them with their progenitor types (globular cluster or dwarf galaxy). Our approach for searching substructures with HDBSCAN* reliably detects real substructures in the Galactic halo, suggesting that applying the same method can lead to the discovery of new substructures in future DESI data. With more stars from future DESI data releases and improved astrometry from the upcoming Gaia Data Release 4, we will have a more detailed blueprint of the Galactic halo, offering a significant improvement in our understanding of the formation and evolutionary history of the Milky Way Galaxy.

dynamics↗