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At least 289 records · Page 16

QLiG: Query Like a Graph For Subgraph Matching

A graph is a natural and flexible modeling approach to represent entities and relationships between them in real-world. A Knowledge Graphs (KG) is a specialized graph with formal and structured representation of facts, relationships, annotated with semantic descriptions. Subgraph matching is one of the fundamental graph problems to identify relationships, interactions and activities of interest within a large graph. A query specification is a collection of abstract components, operations, and constraints to express a pattern. The specification can be implemented in different ways based on underlying data model. Various graph query specifications have been developed over the years and have led to the development of different open-sourced and vendor-specific query languages. Such specification are modeled as an extension of relational algebra used to develop relational query languages such as SQL. Such relational concepts do not inherently support graph queries. There is a need to represent graph queries in terms on graph-based components to expedite query construction by non-database experts. We present a graph-based query approach QLiG (pronounced cleeg), to perform subgraph matching in Labeled Property Graph. We present the query specifications, salient features, and a use case to show functional examples.

Purohit, Sumit↗

Investigating Interruptions: Implications for Flightdeck Performance

A fundamental aspect of multiple task management is attending to new stimuli and integrating associated task requirements into an ongoing task set; this is "interruption management" (IM). Anecdotal evidence and field studies indicate the frequency and consequences of interruptions, however experimental investigations of mechanisms influencing IM are scarce. Interruptions on commercial flightdecks are numerous, of various forms, and have been cited as contributing factors in many aviation incident and accident reports. This research grounds an experimental investigation of flightdeck interruptions in a proposed IM stage model. This model organizes basic research, identifies influencing mechanisms, and suggests appropriate dependent measures for IM. Fourteen airline pilots participated in a flightdeck simulation experiment to investigate the general effects of performing an interrupting task and interrupted procedure, and the effects of specific task factors: (1) modality; (2) embeddedness, or goal-level, of an interruption; (3) strength of association, or coupling-strength, between interrupted tasks; (4) semantic similarity; and (5) environmental stress. General effects of interruptions were extremely robust. All individual task factors significantly affected interruption management, except "similarity." Results extend the Interruption Management model, and are interpreted for their implications for interrupted flightdeck performance and intervention strategies for mitigating their effects on the flightdeck.

Latorella, Kara A.↗

Density Matrix Quantum Circuit Simulation via the BSP Machine on Modern GPU Clusters

As quantum computers evolve, simulations of quantum programs on classical computers will be essential in validating quantum algorithms, understanding the effect of system noise, and design applications for future quantum computers. In this paper, we propose a novel multi-GPU programming model called MG-BSP that constructs a virtual BSP machine on top of modern multi-GPU platforms, and tweak the programming model to build a multi-GPU density matrix quantum simulator. We propose and evaluated a new formulation minimizing communication and prove that the transformation conserves original semantics when noise is introduced. We build the tool-chain to support quantum assembly open standard, synthesize testing quantum circuit, and enable ultra-deep quantum simulation. We evaluated our design on four state-of-the-art multi-GPU platforms including the latest DGX-1 and DGX-2 systems. We demonstrate simulation of 1 million gates in 94 minutes, far deeper circuits than has been demonstrated in prior work. A roofline-model analysis show that we have reached near-optimal performance under memory bound.

Li, Ang↗

Leveraging BERT and Network-Based Attention Analysis for Identifying Treatment Milestones in EHRs

This study introduces a sophisticated data-driven framework for analyzing Electronic Health Records (EHRs) using transformer-based models to identify and disentangle overlapping treatment contexts. The framework leverages a preprocessing pipeline that transforms structured procedural codes into semantically enriched descriptive text, enabling the use of attention mechanisms to cluster medical events into treatment milestones—cohesive and distinct components of care processes. The methodology is rigorously validated using synthetic datasets derived from the MIMIC-III database, designed to simulate the heterogeneity and overlapping procedural contexts characteristic of real-world EHR scenarios. Quantitative evaluation highlights the framework’s robustness in disentangling concurrent care pathways, with attention metrics and unsupervised clustering approaches demonstrating the ability to preserve intra-context relationships while distinguishing inter-context dependencies. By addressing challenges inherent in data heterogeneity, this approach provides a foundation for uncovering complex treatment patterns, advancing clinical decision-making, and optimizing resource allocation in diverse healthcare environments.

Kim, Minsu [ORNL] (ORCID:0000000224185535)↗

Procedure Parsing: A Method for Parsing Handwritten Documents into Computer-Based Procedures

The nuclear industry is heavily procedure driven, where almost everything has a step-by-step instruction that is expected to be followed in detail. Historically, these procedures were printed on paper copies. Recently, the industry transitioned towards electronic copies (i.e., PDFs on tablets). One major drive for this transition is the introduction of human error and loss of situation awareness when using paper copies. However, electronic copies of documents inherently have the same error traps as their paper cousins. Therefore, there is an increased interest in a way to utilize the information in the step-by-step guidance, but to present it in a dynamic manner that guides the user and adapts to any encountered conditions. Researchers at Idaho National Laboratory propose a flexible, automated method based on document parsing and augmented by natural language processing (NLP) techniques, to address these shortcomings and capitalize on these recent advancements in machine learning. The proposed method provides a cost-effective solution for computer-assisted procedure parsing of hand-written control room procedures, originally authored in Word or PDF formats, into instructions that can be displayed as computer-based procedures (CBP) in a modern graphical user interface. The researchers devised, implemented and demonstrated the Operating Procedure Extender for Novel Systems (OPENS) method in 2020. The key to OPENS is to map the original procedure text into a context-free grammar, tying content to equipment, locations, and other steps, actions, etc. This formal grammar is then used to isolate and define keywords and actions verbs, such as “measure” or “evaluate” and tie them to specific equipment referenced within that step or located in other steps, substeps, actions, subactions and tables throughout the procedure. OPENS generates an abstract syntax tree from the document which it uses to store a copy of this information in the open-standard, machine-readable and human-readable file formats XML and JSON. The XML is useful to preserve the relational aspects of the procedure for referencing tables and branching information so the user can be directed to the next appropriate active step based on the values entered for that step and previous steps. The JSON is useful for storing and exchanging data objects used to track responses to previous steps and state changes in simulated environments. In future iterations, these formats can also be used for storing more detailed information about input during plant operation or simulation. The techniques the researcher developed could further be improved by integration of recent advancements in machine learning. NLP methods could standardize documents, correct for grammatical error, and provide automated semantic validation. The researcher expects that self-supervised techniques applied to collections of natural language instructions could strengthen the model with broader context. All these methods together give us a practical way to automatically extract protocols from documents and user interactions, empowering researchers, procedure writers and nuclear operators while moving the industry forward.

99 GENERAL AND MISCELLANEOUS↗

Simulation and Verification of Synchronous Set Relations in Rewriting Logic

This paper presents a mathematical foundation and a rewriting logic infrastructure for the execution and property veri cation of synchronous set relations. The mathematical foundation is given in the language of abstract set relations. The infrastructure consists of an ordersorted rewrite theory in Maude, a rewriting logic system, that enables the synchronous execution of a set relation provided by the user. By using the infrastructure, existing algorithm veri cation techniques already available in Maude for traditional asynchronous rewriting, such as reachability analysis and model checking, are automatically available to synchronous set rewriting. The use of the infrastructure is illustrated with an executable operational semantics of a simple synchronous language and the veri cation of temporal properties of a synchronous system.

Rocha, Camilo↗

NASA's ATM Ontology: Semantic Integration and Querying Across NAS Data Sources

NASA is developing an Air Traffic Management (ATM) Ontology as part of an advanced prototyping activity that demonstrates the utility of semantic technologies for integrating, querying, and searching over various sources of heterogeneous ATM data. The ontology encodes an overarching data model that functions as the backbone upon which to overlay data from multiple sources published by FAA, NOAA, NASA, and others. The integrated data can be queried to produce results not achievable using any single source alone. The ontology incorporates flight data, weather data, traffic management advisory data, airport delay data, and national airspace infrastructure data for a very limited spatial and temporal slice of airspace operations (one day of operations at a major airport).

air traffic management↗

Formal Methods in the Development of Highly Assured Software for Unmanned Aircraft Systems

In traditional software development methodologies, operational and functional requirements of systems are often specified in structured natural language notations. These restricted notations provide good documentation support, but only provide limited support for semantic analysis. These notations are generally not rich enough to unambiguously specify the requirements of safety-critical systems that, for example, involve complex numerical computations or that interact with the physical environment. Examples of these safety-critical systems are autonomous vehicles such as unmanned aircraft systems. This talk advocates the use of expressive formal logics, such as higher-order logic, to specify the operational and functional requirement of unmanned systems and to prove the correctness of these requirements. Semantic analysis of requirements written in higher-order logic is supported through the use of interactive theorem provers. Formal models serve as ideal reference implementations of functional requirements. Hence, formal logics enable software validation techniques where software implementations can be checked against functional requirements in a mechanical way. The Formal Methods group in the Safety-Critical Avionics Systems Branch at NASA Langley Research Center has conducted research on the development and application of formal verification techniques to safety-critical applications of interest to NASA for more than 30 years. This talk illustrates the use of formal methods in the development of highly-assured autonomous unmanned aircraft systems.

Formal Methods↗

The semantics of fuzzy logic

Summarized here are the results of recent research on the conceptual foundations of fuzzy logic. The focus is primarily on the principle characteristics of a model that quantifies resemblance between possible worlds by means of a similarity function that assigns a number between 0 and 1 to every pair of possible worlds. Introduction of such a function permits one to interpret the major constructs and methods of fuzzy logic: conditional and unconditional possibility and necessity distributions and the generalized modus ponens of Zadeh on the basis of related metric relationships between subsets of possible worlds.

Ruspini, Enrique H.↗

Watermarks in stream processing systems: semantics and comparative analysis of Apache Flink and Google cloud dataflow

Streaming data processing is an exercise in taming disorder: from oftentimes huge torrents of information, we hope to extract powerful and timely analyses. But when dealing with streaming data, the unbounded and temporally disordered nature of real-world streams introduces a critical challenge: how does one reason about the completeness of a stream that never ends? In this paper, we present a comprehensive definition and analysis of watermarks, a key tool for reasoning about temporal completeness in infinite streams.First, we describe what watermarks are and why they are important, highlighting how they address a suite of stream processing needs that are poorly served by eventually-consistent approaches:• Computing a single correct answer, as in notifications.• Reasoning about a lack of data, as in dip detection.• Performing non-incremental processing over temporal subsets of an infinite stream, as in statistical anomaly detection with cubic spline models.• Safely and punctually garbage collecting obsolete inputs and intermediate state.• Surfacing a reliable signal of overall pipeline health.Second, we describe, evaluate, and compare the semantically equivalent, but starkly different, watermark implementations in two modern stream processing engines: Apache Flink and Google Cloud Dataflow.

Akidau, Tyler↗

The AutoBayes Program Synthesis System: System Description

AUTOBAYES is a fully automatic program synthesis system for the statistical data analysis domain. Its input is a concise description of a data analysis problem in the form of a statistical model; its output is optimized and fully documented C/C++ code which can be linked dynamically into the Matlab and Octave environments. AUTOBAYES synthesizes code by a schema-guided deductive process. Schemas (i.e., code templates with associated semantic constraints) are applied to the original problem and recursively to emerging subproblems. AUTOBAYES complements this approach by symbolic computation to derive closed-form solutions whenever possible. In this paper, we concentrate on the interaction between the symbolic computations and the deductive synthesis process. A statistical model specifies for each problem variable (i.e., data or parameter) its properties and dependencies in the form of a probability distribution, A typical data analysis task is to estimate the best possible parameter values from the given observations or measurements. The following example models normal-distributed data but takes prior information (e.g., from previous experiments) on the data's mean value and variance into account.

Fischer, Bernd↗

Evaluating MPI resource usage summary statistics

The Message Passing Interface (MPI) remains the dominant programming model for scientific applications running on today’s high-performance computing (HPC) systems. This dominance stems from MPI’s powerful semantics for inter-process communication that has enabled scientists to write applications for simulating important physical phenomena. MPI does not, however, specify how messages and synchronization should be carried out. Those details are typically dependent on low-level architecture details and the message characteristics of the application. Therefore, analyzing an application’s MPI resource usage is critical to tuning MPI’s performance on a particular platform. The result of this analysis is typically a discussion of the mean message sizes, queue search lengths and message arrival times for a workload or set of workloads. While a discussion of the arithmetic mean in MPI resource usage might be the most intuitive summary statistic, it is not always the most accurate in terms of representing the underlying data. In this paper, we analyze MPI resource usage for a number of key MPI workloads using an existing MPI trace collector and discrete-event simulator. Our analysis demonstrates that the average, while easy and efficient to calculate, is a useful metric for characterizing latency and bandwidth measurements, but may not be a good representation of application message sizes, match list search depths, or MPI inter-operation times. Additionally, we show that the median and mode are superior choices in many cases. We also observe that the arithmetic mean is not the best representation of central tendency for data that are drawn from distributions that are multi-modal or have heavy tails. Furthermore, the results and analysis of our work provide valuable guidance on how we, as a community, should discuss and analyze MPI resource usage data for scientific applications.

97 MATHEMATICS AND COMPUTING↗

VerifyIO: Verifying Adherence to Parallel I/O Consistency Semantics

VerifyIO is a tool designed for verifying I/O consistency semantics in High-Performance Computing (HPC) applications. It addresses the challenges of ensuring correctness and portability across different I/O consistency models, such as POSIX, Commit, Session, and MPI-IO. By analyzing execution traces, detecting conflicts, and verifying synchronization adherence, VerifyIO provides actionable insights for both application developers and I/O library designers.

Wang, Chen [Lawrence Livermore National Laboratory↗

Molecular Vision - Multimodal, multitask retrieval of molecular structure from measured signatures for reference-free compound identification

We are currently at risk of generating false conclusions based on limited methods to identify small molecules in biological systems and in chemical forensics. By definition, the chemical structures of novel small molecules have not been determined, let alone measured or synthesized. Currently, unambiguous structure determination of small molecules is constrained by the time and effort needed to isolate compounds and perform de novo structure elucidation using laboratory-based methods, significantly extending the time to inform mitigation strategies. To address this gap, we have developed a deep learning approach to directly map molecular structure to experimental signatures. We aim to unify measurement technologies employed in untargeted small molecule identification studies—such as infrared (IR) spectrometry, tandem mass spectrometry (MS/MS), ion mobility spectrometry-derived collision cross section (CCS)—through use of a multimodal, multitask deep learning architecture. Where existing methods require direct generation of information-rich spectra and/or properties, an inherently difficult task, we will simplify molecular signature-based identification by posing the problem as a recognition or retrieval task. The model is thus presented with relevant endpoints – structure and one or more molecular signatures – and need only determine whether they are semantically related. Thus, our approach offers the following advantages over existing techniques: (i) circumvents difficulties associated with direct generation of molecular signatures from structure and structure from signatures; (ii) incorporates multiple molecular signatures simultaneously, as available, to support identification; and (iii) enables rapid computation of structural embeddings toward broad coverage of known chemical space. Taken together, the approach removes the need to explicitly obtain or compute reference spectra, representing a powerful method for compound identification that requires only experimentally observed signatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.

60 APPLIED LIFE SCIENCES↗

Bridging the Gap Between Requirements and Model Analysis : Evaluation on Ten Cyber-Physical Challenge Problems

Formal verfication and simulation are powerful tools to validate requirements against complex systems. [Problem] Requirements are developed in early stages of the software lifecycle and are typically written in ambiguous natural language. There is a gap between such requirements and formal notations that can be used by verification tools, and lack of support for proper association of requirements with software artifacts for verification. [Principal idea] We propose to write requirements in an intuitive, structured natural language with formal semantics, and to support formalization and model/code verification as a smooth, well-integrated process. [Contribution] We have developed an end-to-end, open source requirements analysis framework that checks Simulink models against requirements written in structured natural language. Our framework is built in the Formal Requirements Elicitation Tool (fret); we use fret's requirements language named fretish, and formalization of fretish requirements in temporal logics. Our proposed framework contributes the following features: 1) automatic extraction of Simulink model information and association of fretish requirements with target model signals and components; 2) translation of temporal logic formulas into synchronous dataflow cocospec specifications as well as Simulink monitors, to be used by verification tools; we establish correctness of our translation through extensive automated testing; 3) interpretation of counterexamples produced by verification tools back at requirements level. These features support a tight integration and feedback loop between high level requirements and their analysis. We demonstrate our approach on a major case study: the Ten Lockheed Martin Cyber-Physical, aerospace-inspired challenge problems.

Mavridou, Anastasia↗

A simple modern correctness condition for a space-based high-performance multiprocessor

A number of U.S. national programs, including space-based detection of ballistic missile launches, envisage putting significant computing power into space. Given sufficient progress in low-power VLSI, multichip-module packaging and liquid-cooling technologies, we will see design of high-performance multiprocessors for individual satellites. In very high speed implementations, performance depends critically on tolerating large latencies in interprocessor communication; without latency tolerance, performance is limited by the vastly differing time scales in processor and data-memory modules, including interconnect times. The modern approach to tolerating remote-communication cost in scalable, shared-memory multiprocessors is to use a multithreaded architecture, and alter the semantics of shared memory slightly, at the price of forcing the programmer either to reason about program correctness in a relaxed consistency model or to agree to program in a constrained style. The literature on multiprocessor correctness conditions has become increasingly complex, and sometimes confusing, which may hinder its practical application. We propose a simple modern correctness condition for a high-performance, shared-memory multiprocessor; the correctness condition is based on a simple interface between the multiprocessor architecture and a high-performance, shared-memory multiprocessor; the correctness condition is based on a simple interface between the multiprocessor architecture and the parallel programming system.

Probst, David K.↗