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DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗

DOE OSTI2025

viral_fam_classifier

This code applies publicly available Hidden Markov Model (HMM) profiles to publicly available reference genomes of viruses. It parses the output of these searches to determine bitscore cut-offs for viral taxonomic lineages that may be represented by each HMM. Subsequently, the code will allow the user to classify novel viral sequences using these bitscore cut-offs. This code is a work-in-progress.

Kantor, Rose [Lawrence Livermore National Laborato↗

DOE OSTI2022

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes constituting a segment of a metabolic pathway. The proteins of the shell are unique to BMCs. They also provide selective permeability; this selectivity is dictated by the requirements of their cargo enzymes. We have recently surveyed the wealth of different BMC types and their occurrence in all available genome sequence data by analyzing and categorizing their components found in chromosomal loci using HMM (Hidden Markov Model) protein profiles. To make this a “do-it yourself” analysis for the public we have devised a webserver, BMC Caller (https://bmc-caller.prl.msu.edu), that compares user input sequences to our HMM profiles, creates a BMC locus visualization, and defines the functional type of BMC, if known. Shell proteins in the input sequence data are also classified according to our function-agnostic naming system and there are links to similar proteins in our database as well as an external link to a structure prediction website to easily generate structural models of the shell proteins, which facilitates understanding permeability properties of the shell. Additionally, the BMC Caller website contains a wealth of information on previously analyzed BMC loci with links to detailed data for each BMC protein and phylogenetic information on the BMC shell proteins. Our tools greatly facilitate BMC type identification to provide the user information about the associated organism’s metabolism and enable discovery of new BMC types by providing a reference database of all currently known examples.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Assessing individual movement, habitat use, and behavior of non-breeding marine birds in relation to prey availability in the US Atlantic

Resource availability is a key factor driving marine bird movements and distributions, but direct information on prey availability is difficult to obtain at relevant scales. We present novel methods for describing multi-scale trophic associations, combining movement analyses of marine birds with estimates of forage fish surface aggregations from digital aerial survey data and species occupancy from bottom trawl survey data. We analyzed satellite telemetry data from northern gannets Morus bassanus , red-throated loons Gavia stellata , and long-tailed ducks Clangula hyemalis in the US Atlantic during the non-breeding period. Using discrete-time hidden Markov models to distinguish area-restricted (i.e. putative foraging) from transit movements, we examined how environmental factors influence movement, and how forage fish species distributions and surface aggregations influence habitat use by gannets and loons that have greater dietary reliance. Our results suggest that chlorophyll a concentration significantly affected movement behavior across species, highlighting the importance of higher-productivity areas around estuaries during colder months when regional productivity is low. Though variable across species and seasons, spatial cross-correlation analysis revealed that herring species (Family Clupeidae), including Atlantic menhaden Brevoortia tyrannus , may be important resources; it also showed positive spatial correlations with forage fish aggregations. This suggests that prey patch dynamics and factors driving aggregation formation may be as important as species composition. However, spatial patterns were generally low (<0.3), suggesting a mismatch in spatiotemporal resolution, exemplifying the challenges in quantifying trophic relationships in marine systems. Disentangling predator-prey relationships is critical to understanding the mechanisms driving marine bird behavior in rapidly changing marine systems.

Environmental Sciences & Ecology↗

DOE OSTI2022

The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil ® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the Is PETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as Is PETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Searching for Dark Matter with Superconducting Qubits

Dark matter is an enduring mystery in our quest to understand the fundamental constituents of our universe. Low mass bosons, such the axion or hidden photon, are compelling dark matter candidates. We leverage their potential interactions with electromagnetic fields, whereby the dark matter (of unknown mass) on rare occasion converts into a single photon, to devise a method of detecting these candidates. Current dark matter searches operating at microwave frequencies use a resonant cavity to coherently accumulate the field sourced by the dark matter and a near standard quantum limited (SQL) linear amplifier to read out the cavity signal. To further increase sensitivity to the dark matter signal and enable future searches, sub-SQL detection techniques are required.In this thesis, I report the development of a novel microwave photon counting technique and a new exclusion limit on hidden photon dark matter. We operate a superconducting qubit to make repeated quantum non-demolition measurements of cavity photons and apply a hidden Markov model analysis to reduce the noise to 15.7 dB below the quantum limit, with overall detector performance limited by a residual background of real photons. With the present device, we perform a hidden photon search and constrain the kinetic mixing angle to less than 1.68 x 10-15 in a band around 6.011 GHz (24.86 micro-eV) with an integration time of 8.33 s. This demonstrated noise reduction technique enables future dark matter searches to be sped up by a factor of 1300. By coupling a qubit to an arbitrary quantum sensor, more general sub-SQL metrology is possible with the techniques presented in this work.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Decision system and method for separating faults from attacks

According to some embodiments, a plurality of monitoring nodes may each generate a series of current monitoring node values over time that represent a current operation of the industrial asset. A node classification computer may determine, for each monitoring node, a classification result indicating whether each monitoring node is in a normal or abnormal state. A disambiguation engine may receive the classification results from the node classification computer and associate a Hidden Markov Model (“HMM”) with each monitoring node. For each node in an abnormal state, the disambiguation engine may execute the HMM associated with that monitoring node to determine a disambiguation result indicating if the abnormal state is a result of an attack or a fault and output a current status of each monitoring node based on the associated classification result and the disambiguation result.

Giani, Annarita↗

DOE OSTI2025

Model Calibration with Markov Chain Monte Carlo Tutorial

The purpose of this tutorial is to demonstrate how to use Markov chain Monte Carlo (MCMC) to calibrate a model. By calibration, we mean the selection of model parameters (and, when relevant, structures). A common goal in model development and diagnostics is calibration, or the identification of model structures and parameters which are consistent with data. While models can be calibrated through hand-tuning parameters or minimizing simple error metrics such as root-mean-square-error (RMSE), these approaches can underrepresent the probabilistic nature of the data-generating process, as well as the potential for multiple model configurations to be consistent with the data. Probabilistic uncertainty quantification, which is the topic of this notebook, can address these concerns. This tutorial is presented as an appendix to the e-book: Addressing Uncertainty in MultiSector Dynamics Research.

Markov chain Monte Carlo↗

DOE OSTI2022

Reaction–drift–diffusion models from master equations: application to material defects

We present a general method to produce well-conditioned continuum reaction–drift–diffusion equations directly from master equations on a discrete, periodic state space. We assume the underlying data to be kinetic Monte Carlo models (i.e. continuous-time Markov chains) produced from atomic sampling of point defects in locally periodic environments, such as perfect lattices, ordered surface structures or dislocation cores, possibly under the influence of a slowly varying external field. Our approach also applies to any discrete, periodic Markov chain. Here, the analysis identifies a previously omitted non-equilibrium drift term, present even in the absence of external forces, which can compete in magnitude with the reaction rates, thus being essential to correctly capture the kinetics. To remove fast modes which hinder time integration, we use a generalized Bloch relation to efficiently calculate the eigenspectrum of the master equation. A well conditioned continuum equation then emerges by searching for spectral gaps in the long wavelength limit, using an established kinetic clustering algorithm to define a proper reduced, Markovian state space.

36 MATERIALS SCIENCE↗

DOE OSTI2025

PSA 2025 DPRA for Cyber Optimization

Cyberattacks can have many different attack paths, durations, and goals. There are also many different mitigation options involving hardware, software, and/or humans. Evaluating defense options should include quantitative evaluation of overall effectiveness to make cost and risk-informed decisions. Typical cyberattack modeling methods only provide a qualitative evaluation and have difficulty with time dependent scenarios. The main areas of cybersecurity are confidentiality, integrity, and availability. For companies with cyber-physical systems such as advanced nuclear reactors, cyber-related integrity is a requirement set by the U.S. Nuclear Regulatory Commission. But companies are also concerned about availability or reliability as a business case. As cyber threats are evolving to a business-for-hire structure, more attacks focus on disrupting business success and reliability, causing financial and economic stability risk. Companies want reliability analysis while optimizing cost, which requires more than safety modeling methods. Dynamic-state-based and Markov-based modeling provides a method for better cyber scenario modeling with timing and conditional features not found in other numerical evaluation methods. EMRALD (Event Modeling Risk Assessment using Lined Diagrams) is a dynamic risk analysis modeling and simulation tool and has features that reduce modeling issues such as state-base explosion found in Markov-based tools. It has been used to model different time-dependent events including plant behavior and operator procedures. As a general modeling tool, EMRALD can also be used to model cyberattack scenarios with varying mitigation options and quantify effectiveness, producing numerical data for risk-informed decisions. This paper uses EMRALD to demonstrate that dynamic risk analysis can be used for cyber threat modeling to provide insights for design decision-making and optimize defense strategies.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Temporal Characterization and Filtering of Sensor Data to Support Anomaly Detection

Here, we present an approach for characterizing complex temporal behavior in the sensor measurements of a system in order to support detection of anomalies in that system. We first characterize typical behavior by extending a hidden Markov model-based approach to time series alignment. We then use a trace of that learned behavior to develop a particle filter that enables efficient estimation of the filtering distribution on the state space. This produces filtered residuals that can then be used in an anomaly detection framework. Our motivating example is the daily behavior of a building’s heating, ventilation, and air conditioning (HVAC) system, using sensor measurements that arrive every minute and induce a state space with 15,120 states. We provide an end-to-end demonstration of our approach showing improved performance of anomaly detection after application of alignment and filtering compared to the unaligned data. The proposed model is implemented as a computationally efficient R package alignts (align time series) built with R and Fortran 95 with OpenMP support.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Induced Markov chain for wind farm generation forecasting

Systems and methods for forecasting power generation in a wind farm are disclosed. The systems and methods utilize an induced Markov chain model to generate a forecast of power generation of the wind farm. The forecast is at least one of a point forecast or a distributional forecast. Additionally, the systems and methods modify at least one of: (i) a generation of electricity at a power plant coupled to a common power grid as the wind farm; or (ii) a distribution of electricity in the common power grid based on the forecast of power generation of the wind farm. In an exemplary approach, utilizing the induced Markov chain model to generate the forecast may include determining a series of time adjacent power output measurements based on historical wind power measurements and calculating a time series of difference values based on the series of time adjacent power output measurements.

17 WIND ENERGY↗

DOE OSTI2020

A Deep Generative Model for Non-Intrusive Identification of EV Charging Profiles

The proliferation of electric vehicles (EVs) brings environmental benefits and technical challenges to power grids. An identification algorithm which can accurately extract individual EV charging profiles out of widely available smart meter measurements has attracted great interests. This paper proposes a non-intrusive identification framework for EV charging profile extraction, which is driven by deep generative models (DGM). First, the proposed DGM is designed as a representation layer embedded into the Markov process and used to model the joint probability distribution of available time-series data. A novel contribution is to approximate posterior distributions by neural networks whose parameters are obtained by variational inference and supervised learning. Second, the EV charging status is inferred from the DGM via dynamic programming. Lastly, the desired EV charging profile can be reconstructed by the rated power of EV models and inferred status. Compared with the benchmark Hidden Markov Models, the proposed framework can better handle noise in data with less computational complexity and better overall accuracy performances with smaller recall. The proposed framework is validated by numerical experiments on the Pecan Street dataset.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2022

Calibrating uncertain parameters in melt pool simulations of additive manufacturing

Melt pool scale numerical modeling of additive manufacturing (AM) processes can provide predictive capabilities and theoretical insight into the process-property-structure-performance relationships for AM parts. Despite capabilities of numerical models to solve complex multi-physics problems, it is often important to consider a tradeoff between detailed physics and computational cost. Therefore, sources of uncertainty in both experimental conditions and the parameters needed for modeling require models to be validated against empirical evidence. Here, a method is proposed to calibrate uncertain parameters used in continuum-scale melt pool models for powder bed fusion (PBF) AM. Both a simplified heat transfer model and a heat transfer and fluid flow model were investigated. A surrogate model and Markov chain-based optimization algorithm calibrated melt pool geometry for models within experimental variation of the target melt pool width and depth from the NIST AM-Bench 2018-02 dataset. The melt pool temperature distributions, solidification parameters, and simulated multi-layer solidification microstructures were compared between the two models. Similar results from both models indicate that calibrated, lower fidelity numerical models may be used in place of higher fidelity models to generate melt pool solidification data. Finally, these calibrated models therefore enable lower computational cost melt pool simulations without a noticeable decrease in simulation accuracy for grain-scale microstructure simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Performing Numerical Analysis of Cybersecurity Options Using Dynamic Risk Analysis Tool EMRALD

Cyberattacks can have many different attack paths, durations, and goals. There are also many different mitigation options involving hardware, software, and/or humans. Considering a cyber threat should involve defense-in-depth methods and a quantitative or numerical evaluation of overall effectiveness against dynamic, time-dependent attacks to make cost and risk-informed decisions. Typical cyberattack modeling methods only provide a qualitative evaluation. The main areas of cybersecurity are confidentiality, integrity, and availability. For companies with cyber-physical systems such as advanced nuclear reactors, cyber-related safety is a requirement set by North American Electric Reliability and the U.S. Nuclear Regulatory Commission. They are also concerned about availability or reliability as a business case. As cyber threats are evolving to a business-for-hire structure, more attacks may focus on disrupting business success and reliability, causing financial and economic stability risk. Companies want to know business reliability and recovery from those threats, and that requires modeling physical behavior of the targets. Dynamic-state-based and Markov-based modeling provides a method for better cyber scenario modeling with different tools having issues such as state-base explosion. Dynamic modeling enables time and conditional features not found in other numerical evaluation methods. EMRALD (Event Modeling Risk Assessment using Lined Diagrams) is a dynamic risk analysis modeling and simulation tool and has features that reduce modeling issues. It has been used to model different time-dependent events including plant behavior and operator procedures. As a general modeling tool, EMRALD can also be used to model cyberattack scenarios with varying mitigation options and quantify effectiveness, producing numerical data for risk-informed decisions. This paper uses EMRALD to demonstrate that dynamic numerical risk analysis can be used for cyber threat modeling to provide insights for design decision-making and optimize defense strategies. Keywords: cyber modeling; cyber-physical systems; numerical cyber modeling

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Attention Enabled Multi-Agent DRL for Decentralized Volt-VAR Control of Active Distribution System Using PV Inverters and SVCs

This paper proposes attention enabled multi-agent deep reinforcement learning (MADRL) framework for active distribution network decentralized Volt-VAR control. Using the unsupervised clustering, the whole distribution system can be decomposed into several sub-networks according to the voltage and reactive power sensitivity relationships. Then, the distributed control problem of each sub-network is modeled as Markov games and solved by the improved MADRL algorithm, where each sub-network is modeled as an adaptive agent. An attention mechanism is developed to help each agent focus on specific information that is mostly related to the reward. All agents are centrally trained offline to learn the optimal coordinated Volt-VAR control strategy and executed in a decentralized manner to make online decisions with only local information. Compared with other distributed control approaches, the proposed method can effectively deal with uncertainties, achieve fast decision makings, and significantly reduce the communication requirements. Comparison results with model-based and other data-driven methods on IEEE 33-bus and 123-bus systems demonstrate the benefits of the proposed approach.

distribution network↗

DOE OSTI2020

Probabilistic Power Consumption Modeling for Commercial Buildings Using Logistic Regression Markov Chain

The total energy consumed by buildings takes up to 40% of U.S. energy use, in which a large portion is contributed by commercial buildings. Building performance optimization is desirable but requires accurate building models with uncertainties taken into account. This paper proposes a novel probabilistic modeling method using Logistic Regression Markov Chain (LRMC). The LRMC model enhances the performance of traditional Markov Chain (MC) models by adopting time-variant transition matrices calibrated using logistic regression with exogenous inputs. Compared with existing building models, the proposed model produces accurate multi-step modeling results with full probability distribution. The proposed probabilistic building model is tested using actual commercial building measurements and modeling performance is evaluated with two probabilisitc metrics. The results show that the LRMC model has higher accuracy than traditional MC model and Logistic Regression (LR) model in that it yields lower error scores under both evaluation metrics.

Building modeling↗

DOE OSTI2023

Quantum logic gate synthesis as a Markov decision process

Reinforcement learning has witnessed recent applications to a variety of tasks in quantum programming. The underlying assumption is that those tasks could be modeled as Markov decision processes (MDPs). Here, we investigate the feasibility of this assumption by exploring its consequences for single-qubit quantum state preparation and gate compilation. By forming discrete MDPs, we solve for the optimal policy exactly through policy iteration. We find optimal paths that correspond to the shortest possible sequence of gates to prepare a state or compile a gate, up to some target accuracy. Our method works in both the absence and presence of noise and compares favorably to other quantum compilation methods, such as the Ross–Selinger algorithm. This work provides theoretical insight into why reinforcement learning may be successfully used to find optimally short gate sequences in quantum programming.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗