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At least 163 records · Page 9

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system—MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. The template-based modeling uses sequence alignment tools with deep multiple sequence alignments to search for structural templates, which are much faster and more accurate than MULTICOM1. The template-free (ab initio or de novo) modeling uses the inter-residue distances predicted by DeepDist to reconstruct tertiary structure models without using any known structure as template. In the blind CASP14 experiment, the average TM-score of the models predicted by our server predictor based on the MULTICOM2 system is 0.720 for 58 TBM (regular) domains and 0.514 for 38 FM and FM/TBM (hard) domains, indicating that MULTICOM2 is capable of predicting good tertiary structures across the board. It can predict the correct fold for 76 CASP14 domains (95% regular domains and 55% hard domains) if only one prediction is made for a domain. The success rate is increased to 3% for both regular and hard domains if five predictions are made per domain. Moreover, the prediction accuracy of the pure template-free structure modeling method on both TBM and FM targets is very close to the combination of template-based and template-free modeling methods. This demonstrates that the distance-based template-free modeling method powered by deep learning can largely replace the traditional template-based modeling method even on TBM targets that TBM methods used to dominate and therefore provides a uniform structure modeling approach to any protein. Finally, on the 38 CASP14 FM and FM/TBM hard domains, MULTICOM2 server predictors (MULTICOM-HYBRID, MULTICOM-DEEP, MULTICOM-DIST) were ranked among the top 20 automated server predictors in the CASP14 experiment. After combining multiple predictors from the same research group as one entry, MULTICOM-HYBRID was ranked no. 5. The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

97 MATHEMATICS AND COMPUTING↗

Disentangling Alzheimer’s disease neurodegeneration from typical brain ageing using machine learning

Abstract Neuroimaging biomarkers that distinguish between changes due to typical brain ageing and Alzheimer’s disease are valuable for determining how much each contributes to cognitive decline. Supervised machine learning models can derive multivariate patterns of brain change related to the two processes, including the Spatial Patterns of Atrophy for Recognition of Alzheimer’s Disease (SPARE-AD) and of Brain Aging (SPARE-BA) scores investigated herein. However, the substantial overlap between brain regions affected in the two processes confounds measuring them independently. We present a methodology, and associated results, towards disentangling the two. T1-weighted MRI scans of 4054 participants (48–95 years) with Alzheimer’s disease, mild cognitive impairment (MCI), or cognitively normal (CN) diagnoses from the Imaging-based coordinate SysTem for AGIng and NeurodeGenerative diseases (iSTAGING) consortium were analysed. Multiple sets of SPARE scores were investigated, in order to probe imaging signatures of certain clinically or molecularly defined sub-cohorts. First, a subset of clinical Alzheimer’s disease patients (n = 718) and age- and sex-matched CN adults (n = 718) were selected based purely on clinical diagnoses to train SPARE-BA1 (regression of age using CN individuals) and SPARE-AD1 (classification of CN versus Alzheimer’s disease) models. Second, analogous groups were selected based on clinical and molecular markers to train SPARE-BA2 and SPARE-AD2 models: amyloid-positive Alzheimer’s disease continuum group (n = 718; consisting of amyloid-positive Alzheimer’s disease, amyloid-positive MCI, amyloid- and tau-positive CN individuals) and amyloid-negative CN group (n = 718). Finally, the combined group of the Alzheimer’s disease continuum and amyloid-negative CN individuals was used to train SPARE-BA3 model, with the intention to estimate brain age regardless of Alzheimer’s disease-related brain changes. The disentangled SPARE models, SPARE-AD2 and SPARE-BA3, derived brain patterns that were more specific to the two types of brain changes. The correlation between the SPARE-BA Gap (SPARE-BA minus chronological age) and SPARE-AD was significantly reduced after the decoupling (r = 0.56–0.06). The correlation of disentangled SPARE-AD was non-inferior to amyloid- and tau-related measurements and to the number of APOE ε4 alleles but was lower to Alzheimer’s disease-related psychometric test scores, suggesting the contribution of advanced brain ageing to the latter. The disentangled SPARE-BA was consistently less correlated with Alzheimer’s disease-related clinical, molecular and genetic variables. By employing conservative molecular diagnoses and introducing Alzheimer’s disease continuum cases to the SPARE-BA model training, we achieved more dissociable neuroanatomical biomarkers of typical brain ageing and Alzheimer’s disease.

Hwang, Gyujoon↗

Robotics Plan in Support of DOME Testbed Operations

Various robotic tooling options have been evaluated for the NRIC DOME concept of operations (ConOps). Framatome was contracted to develop a wide-ranging list of commercial off the shelf (COTS) and custom robotic systems to be considered for performing the DOME ConOps functions. Subsequent project tasks from Framatome narrowed down the list and scored the most viable options. The abbreviated list, and associated scoring, has been reviewed and assessed to provide formal recommendations for the robotic ConOps functions of DOME. The overhead telescoping mast & Kraft arm assembly is recommended as the primary system for reactor demobilization and removal. The estimated cost is $\$700$K with a timeline to develop and deliver of about 2.5 years. The mast & Kraft arm would still require an overhead lift system for mobilization and installation. Either the refurbished polar crane or a new gantry crane delivery platform could both serve as the overhead lift and delivery system. The estimated costs for the refurbishment polar crane and new gantry crane systems are, respectively, $\$4.4$M and $\$3$M with about 2.5 years to develop and deliver. A Brokk + Kraft crawler & arm is recommended as a secondary robotic system to support the overhead mast & Kraft arm system. The Brokk + Kraft crawler & arm would cost an estimated $\$726$k and would take about 1.5 years to develop and deliver. The Boston Dynamics SPOT robot is also recommended for the in-service monitoring during experimentation operations. The estimated cost is $\$220$K with a timeline to deliver of 8-14 months. The Elios 3 aerial drone is recommended to perform large area radiation dose rate mapping and visual inspections. The estimated cost is a $\$100$K and will also need about 8-14 months to develop and deliver. A mockup rig is also recommended to be procured an employed to test & verify the robotic capabilities as well as provide needed training for operations personnel. It is estimated that a mockup rig would cost about $\$500$k and would take up to a year to develop and build.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Synoptic scale forecast skill and systematic errors in the MASS 2.0 model

The synoptic scale performance characteristics of MASS 2.0 are determined by comparing filtered 12-24 hr model forecasts to same-case forecasts made by the National Meteorological Center's synoptic-scale Limited-area Fine Mesh model. Characteristics of the two systems are contrasted, and the analysis methodology used to determine statistical skill scores and systematic errors is described. The overall relative performance of the two models in the sample is documented, and important systematic errors uncovered are presented.

Koch, S. E.↗

Infrared low-level wind shear work

Results of field experiments for the detection of clear air disturbance and low level wind shear utilizing an infrared airborne system are given in vugraph form. The hits, misses and nuisance alarms scores are given. Information is given on the infrared spatial resolution technique. The popular index of aircraft hazard (F= WX over g - VN over AS) is developed for a remote temperature sensor.

Adamson, Pat↗

Signal Processing Methods for Removing the Effects of Whole Body Vibration upon Speech

Humans may be exposed to whole-body vibration in environments where clear speech communications are crucial, particularly during the launch phases of space flight and in high-performance aircraft. Prior research has shown that high levels of vibration cause a decrease in speech intelligibility. However, the effects of whole-body vibration upon speech are not well understood, and no attempt has been made to restore speech distorted by whole-body vibration. In this paper, a model for speech under whole-body vibration is proposed and a method to remove its effect is described. The method described reduces the perceptual effects of vibration, yields higher ASR accuracy scores, and may significantly improve intelligibility. Possible applications include incorporation within communication systems to improve radio-communication systems in environments such a spaceflight, aviation, or off-road vehicle operations.

human response to vibration↗

Deep Learning Method for Detecting Precursors to Adverse Events

With the recent advancements in Deep Learning methods, the ability to model large complex heterogeneous data sets are fundamentally changing industry and research. Coupled with hardware improvements, and ease of implementation, a wide variety of deep neural network architectures can quickly be developed to solve a sweeping range of problems such as: object detection in images, automatic healthcare diagnosis using heterogenous data sources, real time language translating and sentence prediction, upscaling low resolution images, and forecasting of multivariate timeseries. Generally, many of these architectures outperform classical machine learning approaches in their respective tasks, however, this typically comes at a cost of interpretability. These black box algorithms generally suffer from lack of transparency in both model complexity as well as the rationale behind the prediction. This lack of comprehension, is driving an emerging area of interest in “Explainable AI”. An algorithm called: “Deep Temporal Multiple Instance Learning”1 was a recently developed to identify precursors to adverse events and has been applied in the aviation domain. The deep learning architecture is designed to capture the evolution of the probability of the outcome over the time preceding the adverse event using a multiple instance learning approach as illustrated in Figure 1. Precursors are defined when the probability of the event has exceeded a threshold at some point in the timeseries, at which point, a sensitivity analysis is performed to determine contributing factors. The contributing factors are used to explain and define the precursor during the periods where the probability score is high. The identified contributing factors are then presented to subject matter experts to provide objective insights into the leading factors associated with the particular adverse event. The algorithm has been tested on flight data from a commercial airline and has the ability to discover precursors to known adverse events that take the form of safety critical operations, such as unstable approach events on final approach. Apart from detecting precursors to adverse events, the converse can also be leveraged to discover corrective actions. These positive actions manifest themselves as periods in the timeseries when the precursor score has been lowered from an elevated state; meaning that if the system had been left uncorrected, it would have eventually reached the adverse event state. Characterizing these state changes can help identify successful interventions that may not have been known before. Policy makers and procedure designers can use this additional knowledge to craft more safety and efficient resilient procedures for future operations and therefore improve the overall performance of the National Airspace.

Matthews, Bryan L.↗

In vivo testing confirms a blunting of the human cell-mediated immune mechanism during space flight

The cell-mediated immune (CMI) mechanism was evaluated in 10 space shuttle astronauts by measuring their delayed-type hypersensitivity response to seven common recall antigens. The Multitest CMI test system was used to administer antigens of tetanus, diphtheria, Streptococcus, Proteus, old tuberculin, Candida, and Trichophyton to the forearm 46 h before nominal mission termination; readings were conducted 2 h after landing. The mean number of reactions was reduced from 4.5 preflight to 3.0 inflight, and the mean reaction score was reduced from 21.4 to 13.7 mm inflight. The data presented suggest that the CMI system is still being degraded by space flight conditions on day 4 and that between day 5 and day 10, the depression maximizes and the system begins to adjust to the new conditions. The relation of these in vivo findings to previously reported in vitro results is discussed.

Taylor, G. R.↗

A Corrected Score Function Framework for Modelling Circadian Gene Expression

Many biological processes display oscillatory behaviour based on an approximately 24 h internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic studies have identified associations between gene expression during a 24 h period and an individual's health. A challenge with analysing data from these studies is that each individual's internal timing system is offset relative to the 24 h day-night cycle, where day–night cycle time is recorded for each collected sample. Laboratory procedures can accurately determine each individual's offset and determine the internal time of sample collection. However, these laboratory procedures are labour-intensive and expensive. Here, in this paper, we propose a corrected score function framework to obtain a regression model of gene expression given internal time when the offset of each individual is too burdensome to determine. A feature of this framework is that it does not require the probability distribution generating offsets to be symmetric with a mean of zero. Simulation studies validate the use of this corrected score function framework for cosinor regression, which is prevalent in circadian transcriptomic studies. Illustrations with data from three circadian transcriptomic studies further demonstrate that the proposed framework consistently mitigates bias relative to using a score function that does not account for this offset.

59 BASIC BIOLOGICAL SCIENCES↗

A score-based diffusion model approach for adaptive learning of stochastic partial differential equation solutions

In this paper, we propose a novel framework for adaptively learning the time-evolving solutions of stochastic partial differential equations (SPDEs) using score-based diffusion models within a recursive Bayesian inference setting. SPDEs play a central role in modeling complex physical systems under uncertainty, but their numerical solutions often suffer from model errors and reduced accuracy due to incomplete physical knowledge and environmental variability. To address these challenges, we encode the governing physics into the score function of a diffusion model using simulation data and incorporate observational information via a likelihood-based correction in a reverse-time stochastic differential equation. This enables adaptive learning through iterative refinement of the solution as new data becomes available. To improve computational efficiency in high-dimensional settings, we introduce the ensemble score filter, a training-free approximation of the score function designed for real-time inference. Numerical experiments on benchmark SPDEs demonstrate the accuracy and robustness of the proposed method under sparse and noisy observations.

97 MATHEMATICS AND COMPUTING↗

Optimal band selection for target detection with a LWIR multispectral imager

Multispectral imaging can offer many benefits in cost, complexity, resolution, size, weight, and power, relative to hyperspectral imaging. When designing a multispectral system, spectral bandpasses can be selected using optimization algorithms configured to maximally separate target detection scores between target and background regions. A hyperspectral image (HSI) can serve as the source of data from which band groupings can be tested for optimality. The output of an adaptive cosine estimator target detection algorithm is used in an objective function. Three optimization algorithms are compared: particle swarm, dual annealing, and differential evolution. A global optimum is also found using a brute force approach on the Livermore Computing Syrah supercomputer. Three materials are investigated: calcite, gypsum, and limestone. This is done for 3-, 4-, and 5-band systems. The data originate from a longwave infrared HSI of a material display board. The optimization algorithms were run 30 times for every scenario. Performance statistics (maximum, minimum, mean, standard deviation, and median) based on the separation values are given. Additional characterization was performed using receiver operator characteristic (ROC) curves and the area under the ROC curve. While good performance was obtained for the three optimization algorithms, the dual annealing algorithm produced the highest and most consistent detection separation scores on average.

47 OTHER INSTRUMENTATION↗

Food Acceptability, Menu Fatigue, and Aversion During the Sirius-21 Analog Mission

Spaceflight food systems are closed systems, meaning they are restricted to the variety and quantity of food launched within resource limitations of the mission. The acceptability of the food system has been linked to caloric intake and associated nutritional benefits. ISS crew members receive substantial personal food preferences (around 25% of their total intake) but have noted in debriefs that they would prefer more food variety and preference for the length of the missions and they tire of certain foods over six months. Limits on variety and personal preference are expected to increase as missions become further from Earth. It is possible that menu fatigue leads to decreases in acceptability and increased aversion to available foods that may contribute to the body mass loss often experienced by spaceflight crews. However, the impact of repeat food consumption on acceptability has not yet been systematically investigated across potential spaceflight food systems. Limited variety and crew preferences within food categories may have more severe physical and behavioral health and performance consequences as mission duration increases. Characterizing the relationship between food acceptability and mission duration will contribute to defining requirements for an acceptable food system that will support crew health and performance on long duration missions. This study evaluated acceptability of the food system used in the SIRIUS-21 8-month mission in Moscow, Russia. To capture in situ scoring of repeat consumption experiences, we administered a weekly food acceptability questionnaire to all 5 crewmembers throughout the mission. Crewmembers scored foods they consumed at 3 meals every 6 days on a 9-point hedonic scale and provided open-ended feedback regarding food context, attributes, and the meal. The sequence was intended to capture all days in the 7-day menu cycle. The repetition was intended to target repeat food ratings that may provide insight into onset of menu fatigue where they might stop eating some foods or limit their choices to their favorites. Every 30 days crewmembers completed two additional surveys to characterize the food system, any changes to the food system, and their experience with the food system. Data collection is complete. Data are currently being assessed by descriptive statistics and visualizations of the ratings over time. The primary goal is to look for trends in the trajectories of ratings of the food items over time – both within and between individuals – to determine if there are substantial decreases in acceptability across all foods, or within specific food categories (e.g., vegetables). The number of times a particular item is scored provides some information on the frequency of consumption (preference), and the overall number of unique items can give a measure of overall variety. We will assess whether individuals were more likely to have more observations on food items that are rated higher, and whether those who rated foods higher had more or less overall variety. Since the data are composed of longitudinal subjective ratings, repeated measures techniques will be used to quantify trends over time and how these may relate to preference and variety. We will assess how these trends relate to their characterization of and experience with the SIRIUS-21 food system. We will also provide content analysis of any additional feedback collected on the open-ended questions and debrief interviews.

Grace L. Douglas↗

Deep learning for drag force modelling in dilute, poly-dispersed particle-laden flows with irregular-shaped particles

Here, this study applies machine learning-based approaches to develop a drag force model for irregular-shaped particles in incompressible flows. The particle-laden flows are studied through an in-house particle-resolved direct numerical simulation (PR-DNS) at low-intermediate Reynolds numbers (Re). We utilize the PR-DNS to obtain drag force coefficients and flow fields of single particles. A variational auto-encoder model is used to obtain latent vectors to represent the geometrical features of the particles, and artificial neural networks (ANN) are developed to predict drag force coefficients and flow fields of the single particles. This study applies a pairwise interaction extended point-particle (PIEP) model to obtain the coefficients assuming the flow fields of neighboring particles can be linearly superposed. The PIEP method shows significant improvement on prediction for a few neighbored particles. In addition, the results reveal R2 scores of 0.56-0.62 and errors of 9.1-10.0 % for the dilute, polydispersed systems with a volume fraction of 0.5 %.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integrated Landscape Management to Reduce Biomass Feedstock Access Costs

Using geospatial, machine learning, and optimization techniques, a field scoring and design framework known as the bioenergy Landscape Environmental Assessment and Design System (bioLEADS) was developed and used to show through modelling that it is possible to reduce biomass feedstock access costs, improve field revenue, and shift intensive row crop production away from subfield areas susceptible to erosion and low in soil organic carbon. The purpose of bioLEADS is to automate agricultural field selection and subfield allocation to perennial energy crop production while incorporating reduced biomass feedstock access costs to support attaining the U.S. Department of Energy (DOE) Bioenergy Technologies Office (BETO) cost targets.

09 BIOMASS FUELS↗

Discovering Strong Gravitational Lenses in the Dark Energy Survey with Interactive Machine Learning and Crowd-sourced Inspection with Space Warps

We conduct a search for strong gravitational lenses in the Dark Energy Survey (DES) Year 6 imaging data. We implement a pre-trained Vision Transformer (ViT) for our machine learning (ML) architecture and adopt interactive machine learning to construct a training sample with multiple classes to address common types of false positives. Our ML model reduces ∼236 million DES cutout images to 22,564 targets of interest, including ∼85% of previously reported galaxy–galaxy lens candidates discovered in DES. These targets were visually inspected by citizen scientists, who ruled out ∼90% as false positives. Of the remaining 2618 candidates, 149 were expert-classified as “definite” lenses and 516 as “probable” lenses, for a total of 665 systems, with 147 of these candidates being newly identified. Additionally, we trained a second ViT to find double-source plane lens systems, finding at least one double-source system. Our main ViT excels at identifying galaxy–galaxy lenses, consistently assigning high scores to candidates with high expert assessments. The top 800 ViT-scored images include ∼100 of our “definite” lens candidates. This selection is an order of magnitude higher in purity than previous convolutional neural-network-based lens searches and demonstrates the feasibility of applying our methodology for discovering large samples of lenses in future surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Spoken Language Processing in the Clarissa Procedure Browser

Clarissa, an experimental voice enabled procedure browser that has recently been deployed on the International Space Station, is as far as we know the first spoken dialog system in space. We describe the objectives of the Clarissa project and the system's architecture. In particular, we focus on three key problems: grammar-based speech recognition using the Regulus toolkit; methods for open mic speech recognition; and robust side-effect free dialogue management for handling undos, corrections and confirmations. We first describe the grammar-based recogniser we have build using Regulus, and report experiments where we compare it against a class N-gram recogniser trained off the same 3297 utterance dataset. We obtained a 15% relative improvement in WER and a 37% improvement in semantic error rate. The grammar-based recogniser moreover outperforms the class N-gram version for utterances of all lengths from 1 to 9 words inclusive. The central problem in building an open-mic speech recognition system is being able to distinguish between commands directed at the system, and other material (cross-talk), which should be rejected. Most spoken dialogue systems make the accept/reject decision by applying a threshold to the recognition confidence score. NASA shows how a simple and general method, based on standard approaches to document classification using Support Vector Machines, can give substantially better performance, and report experiments showing a relative reduction in the task-level error rate by about 25% compared to the baseline confidence threshold method. Finally, we describe a general side-effect free dialogue management architecture that we have implemented in Clarissa, which extends the "update semantics'' framework by including task as well as dialogue information in the information state. We show that this enables elegant treatments of several dialogue management problems, including corrections, confirmations, querying of the environment, and regression testing.

Rayner, M.↗

An Information Theoretic Approach to Identify Dominant Voltage Influencers for Unbalanced Distribution Systems

Smart distribution grid with multiple renewable energy sources can experience random voltage fluctuations due to variable generation, which may result in voltage violations. Traditional voltage control algorithms are inadequate to handle fast voltage variations. Therefore, new dynamic control methods are being developed that can significantly benefit from the knowledge of dominant voltage influencer (DVI) nodes. DVI nodes for a particular node of interest refer to nodes that have a relatively high impact on the voltage fluctuations at that node. Conventional power flow-based algorithms to identify DVI nodes are computationally complex, which limits their use in real-time applications. This paper proposes a novel information theoretic voltage influencing score (VIS) that quantifies the voltage influencing capacity of nodes with DERs/active loads in a three phase unbalanced distribution system. VIS is then employed to rank the nodes and identify the DVI set. VIS is derived analytically in a computationally efficient manner and its efficacy to identify DVI nodes is validated using the IEEE 37-node test system. It is shown through experiments that KL divergence and Bhattacharyya distance are effective indicators of DVI nodes with an identifying accuracy of more than 90%. Additionally, the computation burden is also reduced by an order of 5, thus providing the foundation for efficient voltage control.

42 ENGINEERING↗

Modeling and Simulation Credibility Assessment of Finite Element Models for Fall From Heights Injury Scenarios

Finite element (FE) computational models of the whole human body are being used to investigate the injury modalities and mechanisms arising from suited astronauts’ ExtraVehicular Activities (EVAs). These FE whole body models – simplified Elemance and THUMS pedestrian versions – have undergone a series of verification and validation (V&V) assessments for applications in automotive, domestic, and contact sports arenas. However, the FE models’ Modeling and Simulation (M&S) credibility assessments for simulating suited astronaut injuries due to fall from heights in altered gravity environments are limited. The current study evaluates the M&S credibility of simplified Elemance and THUMS pedestrian FE models based on eight credibility factors – data pedigree, input pedigree, code verification, solution verification, conceptual validation, referent validation, results uncertainty, and results robustness – as per NASA-STD-7009A [1]. These credibility factors were assigned ordinal scores ranging between 0 to 4, with a score of 0 in the case of insufficient evidence and 4 when all data for the model is known, used appropriately, and traceable to the Real-World System (RWS) with acceptable accuracy, precision, and uncertainty. The credibility factor sufficiency thresholds were assigned upon guidance from NASA EVA subject matter experts. The factor scores were ascertained through the evaluation of M&S credibility assessment procedures described in the published literature and FE model reports. The M&S credibility scores for the Elemance and THUMS FE models vary between 1 and 3 for data pedigree, input pedigree, and referent validation credibility factors, and between 0 and 1 for code verification, solution verification, conceptual validation, results uncertainty and results robustness. The results show that these FE models are credible for simulating fall from heights injury scenarios in specific kinematic and kinetic ranges that correlate with highway and contact sports-related external conditions. Multiple credibility elevation strategies are prescribed to improve the Elemance and THUMS models’ credibility for use in the EVA fall from height injury scenarios.

R A Perkins↗