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Sharing tuples across independent coordination namespace systems

A system and method for federating a tuple storage database across multiple coordinated namespace (CNS) extended memory storage systems allowing the sharing of tuples and tuple data across independent systems. The method provides a federation service for multiple coordination namespace systems. The method retrieves a tuple from connected independent CNS systems wherein a local CNS Controller sends a read request to the local gatekeeper to retrieve a first tuple and creates a local pending remote record. The local gatekeeper at a requesting node sends a broadcast query to a plurality of remote gatekeepers for the tuple and Remote gatekeepers at remote nodes query in its local CNS for the tuple. The Local gatekeeper process at the requesting node receives results from a plurality of remote gatekeepers for the said tuple and selects one remote gatekeeper to receive the requested tuple and broadcasts a read for tuple data with selected gatekeeper.

Jacob, Philip↗

Key Questions for the Quantum Machine Learner to Ask Themselves

Within the last several years quantum machine learning (QML) has begun to mature; however, many open questions remain. Rather than review open questions, in this perspective piece I will discuss my view about how we should approach problems in QML. In particular I will list a series of questions that I think we should ask ourselves when developing quantum algorithms for machine learning. These questions focus on what the definition of quantum ML is, what is the proper quantum analogue of QML algorithms is, how one should compare QML to traditional ML and what fundamental limitations emerge when trying to build QML protocols. As an illustration of this process I also provide information theoretic arguments that show that amplitude encoding can require exponentially more queries to a quantum model to determine membership of a vector in a concept class than classical bit-encodings would require; however, if the correct analogue is chosen then both the quantum and classical complexities become polynomially equivalent. This example underscores the importance of asking ourselves the right questions when developing and benchmarking QML algorithms.

Wiebe, Nathan O.↗

Scalable Pattern Matching in Metadata Graphs via Constraint Checking

Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: They do not scale to process large graphs and/or support only a restricted set of search templates or usage scenarios. Moreover, the algorithms at the core of the existing techniques are not suitable for today’s graph processing infrastructures relying on horizontal scalability and shared-nothing clusters, as most of these algorithms are inherently sequential and difficult to parallelize. In this article we present an algorithmic pipeline that bases pattern matching on constraint checking. The key intuition is that each vertex and edge participating in a match has to meet a set of constraints implicitly specified by the search template. These constraints can be verified independently and typically are less expensive to compute than searching the full template. The pipeline we propose generates these constraints and iterates over them to eliminate all the vertices and edges that do not participate in any match, thus reducing the background graph to a subgraph that is the union of all template matches—the complete set of all vertices and edges that participate in at least one match. Additional analysis can be performed on this annotated, reduced graph, such as full match enumeration, match counting, or computing vertex/edge centrality. Furthermore, a vertex-centric formulation for constraint checking algorithms exists, and this makes it possible to harness existing high-performance, vertex-centric graph processing frameworks. This technique (i) enables highly scalable pattern matching in metadata (labeled) graphs; (ii) supports arbitrary patterns with 100% precision; (iii) enables tradeoffs between precision and time-to-solution, while always selects all vertices and edges that participate in matches, thus offering 100% recall; and (iv) supports a set of popular data analytics scenarios. We implement our approach on top of HavoqGT, an open-source asynchronous graph processing framework, and demonstrate its advantages through strong and weak scaling experiments on massive scale real-world (up to 257 billion edges) and synthetic (up to 4.4 trillion edges) labeled graphs, respectively, and at scales (1,024 nodes / 36,864 cores), orders of magnitude larger than used in the past for similar problems. This article serves two purposes: First, it synthesises the knowledge accumulated during a long-term project. Second, it presents new system features, usage scenarios, optimizations, and comparisons with related work that strengthen the confidence that pattern matching based on iterative pruning via constraint checking is an effective and scalable approach in practice. The new contributions include the following: (i) We demonstrate the ability of the constraint checking approach to efficiently support two additional search scenarios that often emerge in practice, interactive incremental search and exploratory search. (ii) We empirically compare our solution with two additional state-of-the-art systems, Arabsque and TriAD. (iii) We show the ability of our solution to accommodate a more diverse range of datasets with varying properties, e.g., scale, skewness, label distribution, and match frequency. (iv) We introduce or extend a number of system features (e.g., work aggregation, load balancing, and the ability to cap the generated traffic) and design optimizations and demonstrate their advantages with respect to improving performance and scalability. (v) We present bottleneck analysis and insights into artifacts that influence performance. (vi) We present a theoretical complexity argument that motivates the performance gains we observe.

97 MATHEMATICS AND COMPUTING↗

Semantic Framework for Spatial Query Reformulation for Disaster Monitoring Applications

In disasters, since time is of the essence, quick decision making based on actionable insights is desired. In our earlier work, we have demonstrated that the spatial relationships-based queries can play a vital role in the disaster response phase. However, we found that the utilization of spatial relationships rules (i.e. encoded spatial knowledge) via rule reasoning process do not scale well with the increased number of image regions. Most of the available Resource Description Framework (RDF) triplestores do not support rule reasoning due to the computational complexity and undecidable nature of the rule reasoning process. In this paper, we propose an alternative approach for utilizing spatial knowledge encoded in the form of spatial relationship rules. The proposed approach reformulates the spatial query by expanding it with the configuration encoded in the corresponding spatial relationship rule. The preliminary results are promising and show the applicability of the proposed approach during the time critical events such as flood disaster.

Kurte, Kuldeep↗

SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing

Abstract Human immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and evolution studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web-servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for large-scale local HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analyzing full-length genomes or partial HIV-1 genomic regions (GAG, POL, and ENV) and recognizes more than ninety circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy/releases.

Araújo, Pedro M. M.↗

System and method of storing and analyzing information

A system and method of storing and analyzing information is disclosed. The system includes a compiler layer to convert user queries to data parallel executable code. The system further includes a library of multithreaded algorithms, processes, and data structures. The system also includes a multithreaded runtime library for implementing compiled code at runtime. The executable code is dynamically loaded on computing elements and contains calls to the library of multithreaded algorithms, processes, and data structures and the multithreaded runtime library.

Feo, John T.↗

Data-driven wind turbine wake modeling via probabilistic machine learning

Wind farm design primarily depends on the variability of the wind turbine wake flows to the atmospheric wind conditions and the interaction between wakes. Physics-based models that capture the wake flow field with high-fidelity are computationally very expensive to perform layout optimization of wind farms, and, thus, data-driven reduced-order models can represent an efficient alternative for simulating wind farms. In this work, we use real-world light detection and ranging (LiDAR) measurements of wind-turbine wakes to construct predictive surrogate models using machine learning. Specifically, we first demonstrate the use of deep autoencoders to find a low-dimensional latent space that gives a computationally tractable approximation of the wake LiDAR measurements. Then, we learn the mapping between the parameter space and the (latent space) wake flow fields using a deep neural network. Additionally, we also demonstrate the use of a probabilistic machine learning technique, namely, Gaussian process modeling, to learn the parameter-space-latent-space mapping in addition to the epistemic and aleatoric uncertainty in the data. Finally, to cope with training large datasets, we demonstrate the use of variational Gaussian process models that provide a tractable alternative to the conventional Gaussian process models for large datasets. Furthermore, we introduce the use of active learning to adaptively build and improve a conventional Gaussian process model predictive capability. Overall, we find that our approach provides accurate approximations of the wind-turbine wake flow field that can be queried at an orders-of-magnitude cheaper cost than those generated with high-fidelity physics-based simulations.

Deep neural networks↗

Optimized self-designing key-value storage engine

Embodiments of the invention utilize an optimized key-value storage engine to strike the optimal balance between cloud-cost and performance and supports queries, including updates, lookups, range queries, inserts, and read-modify-writes. Cloud cost is manifested in purchasing both storage and processing resources. The improved approach has the ability to self-design and instantiate holistic configurations given a workload, a cloud budget, and optionally performance goals and a set of Service Level Agreement (SLA) specifications. A configuration reflects an optimized storage engine design in terms of, for example, the individual data structures design (in-memory and on-disk) in the engine as well as their algorithms and interactions, a cloud provider, and the exact virtual machines to be used.

Idreos, Stratos↗

Risk-Informed Condition Evaluation of Solar-centered Energy Generation and Distribution Networks through Bayesian Learning and Inference

We develop a methodology based on Bayesian inference over Probabilistic Graphical Models (PGMs) to understand and quantify risk in solar-centered grids using targeted measurements and learned system behavior. Being non-prescriptive but, rather, able to infer system behavior and, ultimately, address risk queries from data, our machine learning-type paradigm is tailored for diverse topologies and threat scenarios often associated with distributed energy generation and photovoltaic distributed energy resources (PV-DERs) in particular. We describe algorithmic processes for: (i) learning the structure of PGMs that result from attack-prone PV-DER-proliferated distribution systems, (ii) quantifying cause-effect relationships, and (iii) evaluating risk queries based on diverse evidence. The contributions are illustrated on a residential grid subject to output impairment attacks on its PV-DER infrastructure.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Efficient fully-coherent quantum signal processing algorithms for real-time dynamics simulation

Simulating the unitary dynamics of a quantum system is a fundamental problem of quantum mechanics, in which quantum computers are believed to have significant advantage over their classical counterparts. One prominent such instance is the simulation of electronic dynamics, which plays an essential role in chemical reactions, non-equilibrium dynamics, and material design. These systems are time-dependent, which requires that the corresponding simulation algorithm can be successfully concatenated with itself over different time intervals to reproduce the overall coherent quantum dynamics of the system. In this paper, we quantify such simulation algorithms by the property of being fully-coherent: the algorithm succeeds with arbitrarily high success probability 1 − δ while only requiring a single copy of the initial state. Here we subsequently develop fully-coherent simulation algorithms based on quantum signal processing (QSP), including a novel algorithm that circumvents the use of amplitude amplification while also achieving a query complexity additive in time t, ln(1/δ), and ln(1/ϵ) for error tolerance ϵ: $Θ‖\mathscr{H}‖|t|+ln(1/ϵ)+ln(1/δ)$. Furthermore, we numerically analyze these algorithms by applying them to the simulation of the spin dynamics of the Heisenberg model and the correlated electronic dynamics of an H2 molecule. Since any electronic Hamiltonian can be mapped to a spin Hamiltonian, our algorithm can efficiently simulate time-dependent ab initio electronic dynamics in the circuit model of quantum computation. Accordingly, it is also our hope that the present work serves as a bridge between QSP-based quantum algorithms and chemical dynamics, stimulating a cross-fertilization between these exciting fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

59 BASIC BIOLOGICAL SCIENCES↗

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗

The Design and Implementation of a Secure Datastore Based on Ethereum Smart Contract

In this paper, we present a secure datastore based on an Ethereum smart contract. Our research is guided by three research questions. First, we will explore to what extend a smart-contract-based datastore should resemble a traditional database system. Second, we will investigate how to store the data in a smart-contract-based datastore for maximum flexibility while minimizing the gas consumption. Third, we seek answers regarding whether or not a smart-contract-based datastore should incorporate complex processing such as data encryption and data analytic algorithms. The proposed smart-contract-based datastore aims to strike a good balance between several constraints: (1) smart contracts are publicly visible, which may create a confidentiality concern for the data stored in the datastore; (2) unlike traditional database systems, the Ethereum smart contract programming language (i.e., Solidity) offers very limited data structures for data management; (3) all operations that mutate the blockchain state would incur financial costs and the developers for smart contracts must make sure sufficient gas is provisioned for every smart contract call, and ideally, the gas consumption should be minimized. Our investigation shows that although it is essential for a smart-contract-based datastore to offer some basic data query functionality, it is impractical to offer query flexibility that resembles that of a traditional database system. Furthermore, we propose that data should be structured as tag-value pairs, where the tag serves as a non-unique key that describes the nature of the value. We also conclude that complex processing should not be allowed in the smart contract due to the financial burden and security concerns. The tag-based secure datastore designed this way also defines its applicative perimeter, i.e., only applications that align with our strategy would find the proposed datastore a good fit. Those that would rather incur higher financial cost for more data query flexibility and/or less user burden on data pre- and post-processing would find the proposed database too restrictive.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities

The execution and analysis of complex experiments are challenged by the vast dimensionality of the underlying parameter spaces. Although an increase in data-acquisition rates should allow broader querying of the parameter space, the complexity of experiments and the subtle dependence of the model function on input parameters remains daunting owing to the sheer number of variables. New strategies for autonomous data acquisition are being developed, with one promising direction being the use of Gaussian process regression (GPR). GPR is a quick, non-parametric and robust approximation and uncertainty quantification method that can be applied directly to autonomous data acquisition. We review GPR-driven autonomous experimentation and illustrate its functionality using real-world examples from large experimental facilities in the USA and France. We introduce the basics of a GPR-driven autonomous loop with a focus on Gaussian processes, and then shift the focus to the infrastructure that needs to be built around GPR to create a closed loop. Finally, the case studies we discuss show that Gaussian-process-based autonomous data acquisition is a widely applicable method that can facilitate the optimal use of instruments and facilities by enabling the efficient acquisition of high-value datasets.

36 MATERIALS SCIENCE↗

Adaptive Spatially Aware I/O for Multiresolution Particle Data Layouts

Large-scale simulations on nonuniform particle distributions that evolve over time are widely used in cosmology, molecular dynamics, and engineering. Such data are often saved in an unstructured format that neither preserves spatial locality nor provides metadata for accelerating spatial or attribute subset queries, leading to poor performance of visualization tasks. Furthermore, the parallel I/O strategy used typically writes a file per process or a single shared file, neither of which is portable or scalable across different HPC systems. We present a portable technique for scalable, spatially aware adaptive aggregation that preserves spatial locality in the output. We evaluate our approach on two supercomputers, Stampede2 and Summit, and demonstrate that it outperforms prior approaches at scale, achieving up to 2.5× faster writes and reads for nonuniform distributions. Furthermore, the layout written by our method is directly suitable for visual analytics, supporting low-latency reads and attribute-based filtering with little overhead.

Usher, Will↗

Two-Stage Estimation and Variance Modeling for Latency-Constrained Variational Quantum Algorithms

The quantum approximate optimization algorithm (QAOA) has enjoyed increasing attention in noisy, intermediate-scale quantum computing with its application to combinatorial optimization problems. QAOA has the potential to demonstrate a quantum advantage for NP-hard combinatorial optimization problems. As a hybrid quantum-classical algorithm, the classical component of QAOA resembles a simulation optimization problem in which the simulation outcomes are attainable only through a quantum computer. The simulation that derives from QAOA exhibits two unique features that can have a substantial impact on the optimization process: (i) the variance of the stochastic objective values typically decreases in proportion to the optimality gap, and (ii) querying samples from a quantum computer introduces an additional latency overhead. In this paper, we introduce a novel stochastic trust-region method derived from a derivative-free, adaptive sampling trust-region optimization method intended to efficiently solve the classical optimization problem in QAOA by explicitly taking into account the two mentioned characteristics. The key idea behind the proposed algorithm involves constructing two separate local models in each iteration: a model of the objective function and a model of the variance of the objective function. Exploiting the variance model allows us to restrict the number of communications with the quantum computer and also helps navigate the nonconvex objective landscapes typical in QAOA optimization problems. In conclusion, we numerically demonstrate the superiority of our proposed algorithm using the SimOpt library and Qiskit when we consider a metric of computational burden that explicitly accounts for communication costs.

Derivative-free Optimization↗

Ontologies at Work: Analyzing Information Requirements for Model Predictive Control in Buildings

Model Predictive Control (MPC) has shown significant potential for improving energy efficiency, indoor air quality and occupant comfort of buildings. MPC-based control algorithms have also shown the ability to shift loads and optimize for multiple objectives, including but not limited to reducing the green-house gas emissions, energy costs and peak demand. However, one of the main implementation challenges of these control algorithms is the integration and configuration effort needed to deploy a supervisory MPC controller in a building. By assigning standardized references to information sources and control points in buildings, existing studies have shown that semantic ontologies and corresponding queries have the potential to ease the deployment of such controllers. Yet, the use of semantic information to ease the deployment processes of MPC controllers is still limited. In this paper, we review three MPC experiments and synthesize the information requirements of these optimization problems. We then turn to existing and upcoming semantic ontologies such as Brick, SAREF and ASHRAE Standard 223 to represent these requirements, evaluating their potential to support the implementation of an MPC controller. This investigation concludes with a discussion of existing opportunities and open questions that the community should explore to support more streamlined MPC implementations.

Prakash, Anand Krishnan↗

Large Language Models (LLMs) for Energy Systems Research

The integration of Large Language Models (LLMs) in energy systems research promises transformative results, as demonstrated in this work, particularly in the realms of information retrieval and legal document analysis. We have developed a chat-based interface, specifically designed to query an extensive corpus of technical reports from the National Renewable Energy Laboratory (NREL). This interface capitalizes on the natural language processing capabilities of LLMs, providing future consumers of NREL research with a user-friendly platform to access and extract valuable information from technical documents, thus enhancing the dissemination of research to the public. In addition to information retrieval, we have employed LLMs to extract renewable energy siting ordinances from a variety of legal documents, a task traditionally driven by significant human labor. This automated extraction not only supports the ongoing development of the high-impact NREL siting ordinance database but also ensures the database's accuracy and comprehensiveness. Crucially, we have augmented the performance of LLMs through the integration of a decision tree framework, resulting in a substantial improvement in extraction accuracy. Comparative analysis with manual efforts has shown that this approach not only rivals but also significantly surpasses human accuracy, heralding increased reliability in legal document analysis for energy systems research. To democratize access to these advancements and foster collaborative research, we introduce the "Energy Language Model" (ELM), an open-source software package. ELM encapsulates the methodologies and tools developed in this work, providing researchers and practitioners with a robust toolkit to conduct similar analyses within their respective domains. Through these contributions, this work underscores the immense potential of LLMs in revolutionizing energy systems research, improving accuracy, efficiency, and accessibility in the field.

automation↗