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At least 253 records · Page 14

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models

The co-expression extrapolation (COXEN) method has been successfully used in multiple studies to select genes for predicting the response of tumor cells to a specific drug treatment. Here, we enhance the COXEN method to select genes that are predictive of the efficacies of multiple drugs for building general drug response prediction models that are not specific to a particular drug. The enhanced COXEN method first ranks the genes according to their prediction power for each individual drug and then takes a union of top predictive genes of all the drugs, among which the algorithm further selects genes whose co-expression patterns are well preserved between cancer cases for building prediction models. We apply the proposed method on benchmark in vitro drug screening datasets and compare the performance of prediction models built based on the genes selected by the enhanced COXEN method to that of models built on genes selected by the original COXEN method and randomly picked genes. Models built with the enhanced COXEN method always present a statistically significantly improved prediction performance (adjusted p-value ≤ 0.05). Our results demonstrate the enhanced COXEN method can dramatically increase the power of gene expression data for predicting drug response.

60 APPLIED LIFE SCIENCES↗

JavaGenes: Evolving Graphs with Crossover

Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

Globus, Al↗

A two step linear statistical technique using leaps and bounds procedure for retrieval of geophysical parameters from microwave radiometric data

A linear statistical technique using a 'leaps and bounds' procedure (Furnival and Wilson, 1974) is developed for retrieving geophysical parameters from remote measurements. It is used for retrieving sea surface temperatures from the Scaning Multichannel Microwave Radiometer (SMMR) on Seasat. The technique uses an efficient algorithm to select the best fixed-size subset of the 10 SMMR channels for linearly retrieving a given geophysical parameter. The 5-channel subset (6.6V, 6.6H 10H, 18V, 21H), where V and H refer to, respectively, the vertical and horizontal polarizations and the numbers are the channel frequencies in gigahertz, gives the minimum rms error in estimating the sea surface temperature. A comparison with ground truth indicates that the algorithm infers the temperature with an rms accuracy of better than 1.5 K under most environmental conditions. A quality control procedure which is seen as holding promise for further improving the accuracy is proposed.

Kakar, R. K.↗

Online Planning Algorithm

AVA v2 software selects goals for execution from a set of goals that oversubscribe shared resources. The term goal refers to a science or engineering request to execute a possibly complex command sequence, such as image targets or ground-station downlinks. Developed as an extension to the Virtual Machine Language (VML) execution system, the software enables onboard and remote goal triggering through the use of an embedded, dynamic goal set that can oversubscribe resources. From the set of conflicting goals, a subset must be chosen that maximizes a given quality metric, which in this case is strict priority selection. A goal can never be pre-empted by a lower priority goal, and high-level goals can be added, removed, or updated at any time, and the "best" goals will be selected for execution. The software addresses the issue of re-planning that must be performed in a short time frame by the embedded system where computational resources are constrained. In particular, the algorithm addresses problems with well-defined goal requests without temporal flexibility that oversubscribes available resources. By using a fast, incremental algorithm, goal selection can be postponed in a "just-in-time" fashion allowing requests to be changed or added at the last minute. Thereby enabling shorter response times and greater autonomy for the system under control.

Rabideau, Gregg R.↗

Selecting representative geological realizations to model subsurface CO 2 storage under uncertainty

Carbon capture and storage (CCS) is one of the quickest and most effective solutions for reducing carbon emissions. The majority of subsurface storage occurs in saline aquifers, for which geological information is lacking which in turn results in geological uncertainty. To evaluate uncertainty in CO 2 injection projections, the use of multiple geological realizations (GRs) has been practiced very commonly. In this approach, hundreds or thousands of high-resolution GRs is used that quickly becomes computationally expensive. This issue can be addressed with representative geological realizations (RGRs) that preserve the uncertainty domain of the ensemble GRs. Here, in this study, we propose the use of unsupervised machine learning (UML) frameworks, including dissimilarity measurement, dimensionality reduction, clustering and sampling algorithms ta select a predetermined number of RGRs. We compare the simulation outputs of the RGR sets and the ensemble using the Kolmogorov–Smirnov (KS) test to select the best UML. The UML frameworks and their associated selection processes are evaluated using a saline aquifer with a single CO 2 injection well and 200 GRs with varying uncertain petrophysical characteristics. The best UML framework is selected to use only 5% of the GRs while maintaining the uncertainty domain of the ensemble GRs. In addition, the best UML framework is tested using a saline aquifer with three CO 2 injection wells and varied GRs. The results show that our proposed UML framework can be used to choose RGRs, capturing the whole uncertainty domain. Our approach leads to a significant reduction in the computational cost associated with scenario testing, decision-making, and development planning for CO 2 storage sites under geological uncertainty.

58 GEOSCIENCES↗

TPSAS-NF1676L-12441-DND

The increasing presence of airport surface surveillance technologies has spawned a strong interest in airport surface traffic management research; the vast majority has assumed that the airport’s runway configuration is known and constant. Tactical Runway Configuration Management (TRCM), one component of NASA’s System Oriented Runway Management concept, plans the airport configuration to optimize traffic efficiency for the forecast weather, traffic, and other factors. While planning runway configuration can provide benefit and is required by other automation concepts, larger benefits are possible by planning other airport configuration decisions, such as runway assignment policies, that are currently made manually by controllers. A laboratory prototype of the TRCM algorithm which selects optimal airport configuration schedules has been implemented and studied within a simulation environment. The presentation will describe simulation results for several airports, under various weather and traffic conditions. The sequence of airport configurations recommended by TRCM result in significantly less delay than the airport configurations that were actually used by controllers, illustrating both the potential benefit from airport configuration optimization and the ability of TRCM to provide effective airport configuration schedules. The application to several, distinct airports demonstrates the approach is capable of handling the differences between airports with a common algorithm, while providing decision support that respects the current procedures at those airports. Consequently, TRCM is able to be deployed to any airport within the current National Airspace System. The TRCM algorithmic approach is also extensible to future operational scenarios. NASA is in the process of transferring the initial TRCM technology to the FAA. Future research will extend the concept and algorithm to provide coordinated plans for metroplex airports and study NextGen applications.

Stephen Atkins↗

TPSAS-NF1676L-12263-DND

The increasing presence of airport surface surveillance technologies has spawned a strong interest in airport surface traffic management research; the vast majority has assumed that the airport’s runway configuration is known and constant. Tactical Runway Configuration Management (TRCM), one component of NASA’s System Oriented Runway Management concept, plans the airport configuration to optimize traffic efficiency for the forecast weather, traffic, and other factors. While planning runway configuration can provide benefit and is required by other automation concepts, larger benefits are possible by planning other airport configuration decisions, such as runway assignment policies, that are currently made manually by controllers. A laboratory prototype of the TRCM algorithm which selects optimal airport configuration schedules has been implemented and studied within a simulation environment. The presentation will describe simulation results for several airports, under various weather and traffic conditions. The sequence of airport configurations recommended by TRCM result in significantly less delay than the airport configurations that were actually used by controllers, illustrating both the potential benefit from airport configuration optimization and the ability of TRCM to provide effective airport configuration schedules. The application to several, distinct airports demonstrates the approach is capable of handling the differences between airports with a common algorithm, while providing decision support that respects the current procedures at those airports. Consequently, TRCM is able to be deployed to any airport within the current National Airspace System. The TRCM algorithmic approach is also extensible to future operational scenarios. NASA is in the process of transferring the initial TRCM technology to the FAA. Future research will extend the concept and algorithm to provide coordinated plans for metroplex airports and study NextGen applications.

Stephen Atkins↗

Accommodation of practical constraints by a linear programming jet select

An experimental spacecraft control system will be incorporated into the Space Shuttle flight software and exercised during a forthcoming mission to evaluate its performance and handling qualities. The control system incorporates a 'phase space' control law to generate rate change requests and a linear programming jet select to compute jet firings. Posed as a linear programming problem, jet selection must represent the rate change request as a linear combination of jet acceleration vectors where the coefficients are the jet firing times, while minimizing the fuel expended in satisfying that request. This problem is solved in real time using a revised Simplex algorithm. In order to implement the jet selection algorithm in the Shuttle flight control computer, it was modified to accommodate certain practical features of the Shuttle such as limited computer throughput, lengthy firing times, and a large number of control jets. To the authors' knowledge, this is the first such application of linear programming. It was made possible by careful consideration of the jet selection problem in terms of the properties of linear programming and the Simplex algorithm. These modifications to the jet select algorithm may by useful for the design of reaction controlled spacecraft.

Bergmann, E.↗

Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate

Background: One of the European Union directives indicates that 10% of all fuels must be bio-synthesized by 2020. In this regard, biobutanol—natively produced by clostridial strains—poses as a promising alternative biofuel. One possible approach to overcome the difculties of the industrial exploration of the native producers is the expression of more suitable pathways in robust microorganisms such as Escherichia coli. The enumeration of novel pathways is a powerful tool, allowing to identify non-obvious combinations of enzymes to produce a target compound. Results: This work describes the in silico driven design of E. coli strains able to produce butanol via 2-oxoglutarate by a novel pathway. This butanol pathway was generated by a hypergraph algorithm and selected from an initial set of 105,954 diferent routes by successively applying diferent flters, such as stoichiometric feasibility, size and novelty. The implementation of this pathway involved seven catalytic steps and required the insertion of nine heterologous genes from various sources in E. coli distributed in three plasmids. Expressing butanol genes in E. coli K12 and cultivation in High-Density Medium formulation seem to favor butanol accumulation via the 2-oxoglutarate pathway. The maximum butanol titer obtained was 85±1 mg L-1 by cultivating the cells in bioreactors. Conclusions: In this work, we were able to successfully translate the computational analysis into in vivo applications, designing novel strains of E. coli able to produce n-butanol via an innovative pathway. Our results demonstrate that enumeration algorithms can broad the spectrum of butanol producing pathways. This validation encourages further research to other target compounds.

09 BIOMASS FUELS↗

Enhanced Contact Graph Routing (ECGR) MACHETE Simulation Model

Contact Graph Routing (CGR) for Delay/Disruption Tolerant Networking (DTN) space-based networks makes use of the predictable nature of node contacts to make real-time routing decisions given unpredictable traffic patterns. The contact graph will have been disseminated to all nodes before the start of route computation. CGR was designed for space-based networking environments where future contact plans are known or are independently computable (e.g., using known orbital dynamics). For each data item (known as a bundle in DTN), a node independently performs route selection by examining possible paths to the destination. Route computation could conceivably run thousands of times a second, so computational load is important. This work refers to the simulation software model of Enhanced Contact Graph Routing (ECGR) for DTN Bundle Protocol in JPL's MACHETE simulation tool. The simulation model was used for performance analysis of CGR and led to several performance enhancements. The simulation model was used to demonstrate the improvements of ECGR over CGR as well as other routing methods in space network scenarios. ECGR moved to using earliest arrival time because it is a global monotonically increasing metric that guarantees the safety properties needed for the solution's correctness since route re-computation occurs at each node to accommodate unpredicted changes (e.g., traffic pattern, link quality). Furthermore, using earliest arrival time enabled the use of the standard Dijkstra algorithm for path selection. The Dijkstra algorithm for path selection has a well-known inexpensive computational cost. These enhancements have been integrated into the open source CGR implementation. The ECGR model is also useful for route metric experimentation and comparisons with other DTN routing protocols particularly when combined with MACHETE's space networking models and Delay Tolerant Link State Routing (DTLSR) model.

Segui, John S.↗

Development of multi-objective core optimization framework and application to sodium-cooled fast test reactors

The optimization of a Sodium-cooled Fast Reactor (SFR) core is a challenging process, due to the large number of design parameters, the nonlinearities among inputs and outputs, and the complicated correlation among output parameters. This study attempts to develop a generalized framework for the SFR core optimization by coupling the sensitivity analysis, advanced optimization algorithm, and optionally the surrogate modeling. The framework is built based on the fast reactor modeling capability of the Argonne Reactor Computation (ARC) suite and the sensitivity analysis and optimization modules embedded in the DAKOTA code, both have been integrated within the NEAMS Workbench. The genetic algorithm is selected as the optimization method for its robustness, while the option of surrogate modeling is also explored to alleviate the computational burden caused by employing the ARC direct core physics simulation and thus enhance the efficiency of the optimization. Finally, the normalized deviations of performance parameters of the near-optimal solution from those of the ideal core are calculated and used as criteria to down select the final core design. The developed framework is applied to the Advanced Burner Test Reactor (ABTR) core, and optimal solutions are determined by balancing various objectives simultaneously, including peak fast flux, core volume, power, reactivity swing, plutonium mass feed, while at the same time satisfying the predefined constraints due to safety or economics considerations. The optimal ABTR core design obtained using the direct physical simulation and surrogated model are compared and discussed. It is found that using the accurately constructed surrogate models can significantly reduce the required computational time while maintaining satisfactory accuracy.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Data acquisition and slow control interface for the Mu2e experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10000 over existing limits. The Mu2e Trigger and Data Acquisition System (TDAQ) uses otsdaq as the online Data Acquisition System (DAQ) solution. Developed at Fermilab, otsdaq integrates both the artdaq DAQ and the art analysis frameworks for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability and provides a multi-user, web-based, interface accessible through a web browser. The data stream from the detector subsystems is read by a software filter algorithm that selects events which are combined with the data flux coming from a cosmic ray veto system. The Detector Control System (DCS) has been developed using the Experimental Physics and Industrial Control System (EPICS) open source platform for monitoring, controlling, alarming, and archiving. The DCS system has been integrated into otsdaq. A prototype of the TDAQ and the DCS systems has been built at Fermilab's Feynman Computing Center. In this study, we report on the progress of the integration of this prototype in the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Wasserstein Normalized Autoencoder for Anomaly Detection in ProtoDUNE Vertical-Drift Detector

ProtoDUNE Vertical Drift needs a selective triggering algorithm. The detector sits on Earth's surface, so cosmic activity dominates its data. Our goal in this paper is to trigger on neutrino events more robustly than the current deployed Analog-to-Digital Converter Simple Window (ADCSW) model and, eventually, search for signals of Beyond Standard Model (BSM) physics at DUNE as our ultimate North Star objective. As a step towards this goal, we evaluate a Wasserstein Normalized Autoencoder (WNAE) on simulated collection-plane only windows of shape $1\times10\times10$ where Neutrinos act as our BSM-proxy and Cosmic-ray Muons serve as our learned background. The network parameters are fitted using only cosmic-ray muon events as background in order to maintain an unsupervised pipeline. Training uses finite-step Langevin $x^-$ samples, positive-sample reconstruction energy, and an empirical sliced $2$-Wasserstein objective to learn a normalized Boltzmann energy model. We then calibrate on a nominal $5\,\mathrm{Hz}$ operating threshold calculated from cosmic validation data. Both WNAE and ADCSW accept 311 of 194,083 held-out cosmic background events at this $5\,\mathrm{Hz}$ threshold. We found that WNAE accepts 9,677 of 34,634 neutrino-proxy events $(27.9\pm0.24)\%$, compared with 10,076 $(29.1\pm0.24)\%$ for ADCSW, an observed WNAE-minus-ADCSW difference of $-1.15\%$. At another nominal $2\,\mathrm{Hz}$ target threshold, the corresponding efficiencies are $(20.5\pm0.22)\%$ and $(22.6\pm0.22)\%$, respectively. Of the WNAE-selected neutrino proxies at $5\,\mathrm{Hz}$, $(20.8\pm0.4)\%$ of the classified neutrino-proxy events are unique to WNAE, where the uncertainty is an absolute binomial standard error of $0.4\%$.

Zheng, Jake [U. Chicago (main)] (ORCID:00090002189↗

Wasserstein Normalized Autoencoder for Anomaly Detection in ProtoDUNE Vertical-Drift Detector

ProtoDUNE Vertical Drift needs a selective triggering algorithm. The detector sits on Earth's surface, so cosmic activity dominates its data. Our goal in this paper is to trigger on neutrino events more robustly than the current deployed Analog-to-Digital Converter Simple Window (ADCSW) model and, eventually, search for signals of Beyond Standard Model (BSM) physics at DUNE as our ultimate North Star objective. As a step towards this goal, we evaluate a Wasserstein Normalized Autoencoder (WNAE) on simulated collection-plane only windows of shape $1\times10\times10$ where Neutrinos act as our BSM-proxy and Cosmic-ray Muons serve as our learned background. The network parameters are fitted using only cosmic-ray muon events as background in order to maintain an unsupervised pipeline. Training uses finite-step Langevin $x^-$ samples, positive-sample reconstruction energy, and an empirical sliced $2$-Wasserstein objective to learn a normalized Boltzmann energy model. We then calibrate on a nominal $5\,\mathrm{Hz}$ operating threshold calculated from cosmic validation data. Both WNAE and ADCSW accept 311 of 194,083 held-out cosmic background events at this $5\,\mathrm{Hz}$ threshold. We found that WNAE accepts 9,677 of 34,634 neutrino-proxy events $(27.9\pm0.24)\%$, compared with 10,076 $(29.1\pm0.24)\%$ for ADCSW, an observed WNAE-minus-ADCSW difference of $-1.15\%$. At another nominal $2\,\mathrm{Hz}$ target threshold, the corresponding efficiencies are $(20.5\pm0.22)\%$ and $(22.6\pm0.22)\%$, respectively. Of the WNAE-selected neutrino proxies at $5\,\mathrm{Hz}$, $(20.8\pm0.4)\%$ of the classified neutrino-proxy events are unique to WNAE, where the uncertainty is an absolute binomial standard error of $0.4\%$.

Zheng, Jake [Chicago U.] (ORCID:0009000218901379)↗

Recursive Branching Simulated Annealing Algorithm

This innovation is a variation of a simulated-annealing optimization algorithm that uses a recursive-branching structure to parallelize the search of a parameter space for the globally optimal solution to an objective. The algorithm has been demonstrated to be more effective at searching a parameter space than traditional simulated-annealing methods for a particular problem of interest, and it can readily be applied to a wide variety of optimization problems, including those with a parameter space having both discrete-value parameters (combinatorial) and continuous-variable parameters. It can take the place of a conventional simulated- annealing, Monte-Carlo, or random- walk algorithm. In a conventional simulated-annealing (SA) algorithm, a starting configuration is randomly selected within the parameter space. The algorithm randomly selects another configuration from the parameter space and evaluates the objective function for that configuration. If the objective function value is better than the previous value, the new configuration is adopted as the new point of interest in the parameter space. If the objective function value is worse than the previous value, the new configuration may be adopted, with a probability determined by a temperature parameter, used in analogy to annealing in metals. As the optimization continues, the region of the parameter space from which new configurations can be selected shrinks, and in conjunction with lowering the annealing temperature (and thus lowering the probability for adopting configurations in parameter space with worse objective functions), the algorithm can converge on the globally optimal configuration. The Recursive Branching Simulated Annealing (RBSA) algorithm shares some features with the SA algorithm, notably including the basic principles that a starting configuration is randomly selected from within the parameter space, the algorithm tests other configurations with the goal of finding the globally optimal solution, and the region from which new configurations can be selected shrinks as the search continues. The key difference between these algorithms is that in the SA algorithm, a single path, or trajectory, is taken in parameter space, from the starting point to the globally optimal solution, while in the RBSA algorithm, many trajectories are taken; by exploring multiple regions of the parameter space simultaneously, the algorithm has been shown to converge on the globally optimal solution about an order of magnitude faster than when using conventional algorithms. Novel features of the RBSA algorithm include: 1. More efficient searching of the parameter space due to the branching structure, in which multiple random configurations are generated and multiple promising regions of the parameter space are explored; 2. The implementation of a trust region for each parameter in the parameter space, which provides a natural way of enforcing upper- and lower-bound constraints on the parameters; and 3. The optional use of a constrained gradient- search optimization, performed on the continuous variables around each branch s configuration in parameter space to improve search efficiency by allowing for fast fine-tuning of the continuous variables within the trust region at that configuration point.

Bolcar, Matthew↗

Modeling household online shopping demand in the U.S.: a machine learning approach and comparative investigation between 2009 and 2017

Despite the rapid growth of online shopping and research interest in the relationship between online and in-store shopping, national-level modeling and investigation of the demand for online shopping with a prediction focus remain limited in the literature. Here, this paper differs from prior work and leverages two recent releases of the U.S. National Household Travel Survey (NHTS) data for 2009 and 2017 to develop machine learning (ML) models, specifically gradient boosting machine (GBM), for predicting household-level online shopping purchases. The NHTS data allow for not only conducting nationwide investigation but also at the level of households, which is more appropriate than at the individual level given the connected consumption and shopping needs of members in a household. We follow a systematic procedure for model development including employing Recursive Feature Elimination algorithm to select input variables (features) in order to reduce the risk of model overfitting and increase model explainability. Among several ML models, GBM is found to yield the best prediction accuracy. Extensive post-modeling investigation is conducted in a comparative manner between 2009 and 2017, including quantifying the importance of each input variable in predicting online shopping demand, and characterizing value-dependent relationships between demand and the input variables. In doing so, two latest advances in machine learning techniques, namely Shapley value-based feature importance and Accumulated Local Effects plots, are adopted to overcome inherent drawbacks of the popular techniques in current ML modeling. The modeling and investigation are performed at the national level, with a number of findings obtained. The models developed and insights gained can be used for online shopping-related freight demand generation and may also be considered for evaluating the potential impact of relevant policies on online shopping demand.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Aspects of Solvers for Large-Scale Coupled Problems in Porous Media

This report summarizes solution strategies for discrete systems occurring in the simulation of processes in the subsurface. The focus is on scalable solvers for large and coupled systems. The goal of this work is to enable researchers to select suitable algorithms and parameter settings to efficiently solve their problems. The work provides an overview of existing methods, highlighting their features, potential, and also frequent pitfalls. Numerical examples are provided for single phase flow, density driven flow and poroelasticity.Aspects of multiphase flow are discussed briefly; a detailed discussion of reactive transport is beyond the scope of the article. Future trends are discussed.

97 MATHEMATICS AND COMPUTING↗

Investigations of Association Among Atmospheric Radionuclide Measurements

Large networks producing frequent atmospheric radionuclide measurements have additional power in characterizing and localizing radionuclide release events over the analysis done with four or fewer samples. However, adding unrelated samples to an analysis dilutes that advantage, unless models are extended to account for this complexity. A key steppingstone to obtaining network power is to select a group of related sample measurements that are associated with a release event. Such collections of measurements can be assembled by an analyst, or perhaps they can be selected by algorithm. The authors explore, using a year of atmospheric transport calculations and realistic sensor sensitivities, the potential for a computed radionuclide association tool.

Eslinger, Paul W.↗