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At least 37 records · Page 2

Dynamic pattern matcher using incomplete data

This invention relates generally to pattern matching systems, and more particularly to a method for dynamically adapting the system to enhance the effectiveness of a pattern match. Apparatus and methods for calculating the similarity between patterns are known. There is considerable interest, however, in the storage and retrieval of data, particularly, when the search is called or initiated by incomplete information. For many search algorithms, a query initiating a data search requires exact information, and the data file is searched for an exact match. Inability to find an exact match thus results in a failure of the system or method.

Johnson, Gordon G.↗

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↗

Object/rule integration in CLIPS

This paper gives a brief overview of the C Language Integrated Production System (CLIPS) with a focus on the object-oriented features. The advantages of an object data representation over the traditional working memory element (WME), i.e., facts, are discussed, and the implementation of the Rete inference algorithm in CLIPS is presented in detail. A few methods for achieving pattern-matching on objects with the current inference engine are given, and finally, the paper examines the modifications necessary to the Rete algorithm to allow direct object pattern-matching.

Donnell, Brian L.↗

Integrating an object system into CLIPS: Language design and implementation issues

This paper describes the reasons why an object system with integrated pattern-matching and object-oriented programming facilities is desirable for CLIPS and how it is possible to integrate such a system into CLIPS while maintaining the run-time performance and the low memory usage for which CLIPS is known. The requirements for an object system in CLIPS that includes object-oriented programming and integrated pattern-matching are discussed and various techniques for optimizing the object system and its integration with the pattern-matcher are presented.

Auburn, Mark↗

A study of a multi-pinned phase CCD detector for use as a star tracker

This grant has supported studies of the use of charge coupled devices (CCD's) in star trackers in a number of different areas. Among the tasks we have pursued are the following: (1) radiation modeling and the increase in noise equivalent angle as a result of exposure to protons and bremsstrahlung gamma rays; (2) the development of pattern matching software to identify field locations from a CCD image and a pre-existing map of the local area; (3) observations of various stellar fields from the 24 inch telescope at the Offit Observatory at JHU, primarily to test the pattern matching software (these included crowded fields as well as moving objects, like comets); and (4) tracking of very faint objects to determine the faint limit of the CCD system.

Friedman, Scott D.↗

Interpretable machine learning models classify minerals via spectroscopy

Developing methods to identify mineral species confidently and rapidly from Raman spectral analysis is critical to numerous fields. Traditionally, analysis relies on pattern matching the Raman spectrum of an unknown dataset with a supporting library of well-characterized spectral data, which may prove difficult for environmental samples that are poorly crystalline or phase mixtures. Here, we developed interpretable machine learning models that can classify uranium minerals by secondary oxyanion chemistry and other physicochemical properties based solely on Raman spectra. This new ML method produces a mineral profile of physical and chemical properties for an unknown sample and can rapidly classify or identify unknown minerals from Raman data, without the need for an exact pattern match in a spectral library. Training models are validated by 1. Strong correlation of high confidence model regions with published spectroscopic assignments and 2. Correct classification of a mineral not present in training data. Training data are from the Compendium of Uranium Raman and Infrared Experimental Spectra and available crystallographic information files within the open-source Smart Spectral Matching scientific framework. Physically meaningful classifier models can rapidly identify key structural and chemical information about unknown uranium minerals and the overall methodology is broadly applicable for mineral phases.

Machine learning↗

Leveraging large language models to automate the identification of healthcare access barriers for veterans

Objective: To develop and evaluate an automated system for identifying healthcare barriers focusing on transportation issues in veterans’ clinical notes using large language models (LLMs) and to assess the impact of different prompting strategies on classification performance and explanation consistency. Methods: We developed a hybrid system combining pattern matching for templated notes with LLM analysis for free-text notes. Using 2000 manually annotated clinical notes, we compared four prompting strategies (dual-role short, dual-role long, analysis-first, analysis-only) across Mistral-7B and Llama-3.1 models. We evaluated classification performance using standard metrics and assessed explanation consistency through embedding similarity analysis. Results: The analysis-first strategy achieved superior performance, with Mistral-7B reaching an F1 score of 0.914, outperforming traditional machine learning approaches (GBM: 0.786, BERT: 0.811). LLMs demonstrated higher explanation consistency within models (mean cosine similarity 0.887–0.908) compared to cross-model similarities (0.767–0.872). Pattern matching successfully handled 6.7% of templated notes deterministically. Mistral-7B showed greater internal consistency but higher abstention rates compared to Llama-3.1. Conclusion: Requiring LLMs to analyze evidence before classification improves both accuracy and explanation consistency for identifying transportation barriers in clinical notes. This approach enables automated barrier detection at scale while providing clinically relevant explanations, supporting both population-level healthcare planning and individual patient care decisions.

Healthcare access barriers↗

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗

Sentinel

Network intrusion detection systems (NIDS) are commonplace in network security but they frequently employ algorithms that are computational demanding requiring hardware and software with significant power requirements. Two examples of such resource-intensive algorithms used for network security are regular expression matching and broader signature pattern matching which are commonly used in deep packet inspection (DPI). Network security algorithms that have large power requirements may be a challenge for low-power internet-of-things (IoT) environments, which generally lack the power resources to implement complex security measures like computationally expensive DPI at the edge. Furthermore, IoT environments incorporating 5G standalone networks have network latency constraints beyond just power that make DPI at the edge even more difficult. Programmable logic is ideally suited for machine learning inference for DPI because of its deep instruction level parallelism and single-cycle memory access. Machine learning approaches for DPI have been explored before using the programmable logic of field programmable gate arrays (FPGA) as a potential solution for NIDS approaches that would be power-suitable for IoT. However, those previous programmable logic NIDS approaches utilize either a supervised or unsupervised learning model. Sentinel utilizes the ensemble of these two machine learning approaches known as a semi-supervised approach which has shown promise in NIDS implementations. Sentinel provides a programmable logic implementation of a semi-supervised approach for DPI which operates at much lower power and latency than a GPU implementation with negligible loss of accuracy due to quantization through a logistic regressor.

Anderson, MatthewW [Idaho National Laboratory (INL↗

QA4, a language for artificial intelligence.

Introduction of a language for problem solving and specifically robot planning, program verification, and synthesis and theorem proving. This language, called question-answerer 4 (QA4), embodies many features that have been found useful for constructing problem solvers but have to be programmed explicitly by the user of a conventional language. The most important features of QA4 are described, and examples are provided for most of the material introduced. Language features include backtracking, parallel processing, pattern matching, set manipulation, and pattern-triggered function activation. The language is most convenient for use in an interactive way and has extensive trace and edit facilities.

Derksen, J. A. C.↗

Embedding CLIPS in a database-oriented diagnostic system

This paper describes the integration of C Language Production Systems (CLIPS) into a powerful portable maintenance aid (PMA) system used for flightline diagnostics. The current diagnostic target of the system is the Garrett GTCP85-180L, a gas turbine engine used as an Auxiliary Power Unit (APU) on some C-130 military transport aircraft. This project is a database oriented approach to a generic diagnostic system. CLIPS is used for 'many-to-many' pattern matching within the diagnostics process. Patterns are stored in database format, and CLIPS code is generated by a 'compilation' process on the database. Multiple CLIPS rule sets and working memories (in sequence) are supported and communication between the rule sets is achieved via the export and import commands. Work is continuing on using CLIPS in other portions of the diagnostic system and in re-implementing the diagnostic system in the Ada language.

Conway, Tim↗

Using discrete Bayesian networks for diagnosing and isolating cross-level faults in HVAC systems

Fault detection and diagnosis (FDD) technologies are critical to ensure satisfactory building performance, such as reducing energy wastes and negative impacts on occupant comfort and productivity. Existing FDD technologies mainly focus on component-level FDD solutions, which could lead to mis-diagnosis of cross-level faults in heating, ventilating, and air-conditioning (HVAC) systems. Cross-level faults are those faults that occur in one component or subsystem, but cause operational abnormalities in other components or subsystems, and result in a building level performance degradation. How to effectively diagnose the root cause of a cross-level fault is the focus of this study. Here, this paper presents a novel discrete Bayesian Network (DisBN)-based method for diagnosing cross-level faults in an HVAC system commonly used in commercial buildings. A two-level DisBN structure model is developed in this study. The parameters used in the DisBN model are obtained either from expert knowledge or through machine-learning strategies from normal system operation data. Meanwhile, the probability parameters are discretized to incorporate the uncertainties associated with typical expert knowledge. Thus, the developed DisBN method addresses the challenges many other BN based FDD methods face, i.e., the lack of fault data for BN parameter training. The developed DisBN represents causal relationships between a fault and its cross-level system impacts (i.e., fault symptoms or fault indicators) by considering how fault impacts propagate across different levels in an HVAC system. A weather and schedule information-based Pattern Matching (WPM) method is employed to automatically create WPM baseline data sets for each incoming real time snapshot data from the building systems. Consequently, BN inference and real-time diagnostics are achieved by comparing incoming snapshot data and the WPM baseline data set. The proposed method is evaluated using experimental fault data collected in a campus building. Fault diagnosis results demonstrate that the WPM-DisBN method is effective at locating the root causes of cross-level faults in an HVAC system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Reproducing the Photospheric Magnetic Field Evolution During the Rise of Cycle 24 with Flux Transport by Supergranules

We simulate the transport of magnetic flux in the Sun s photosphere by an evolving pattern of cellular horizontal flows (supergranules). Characteristics of the simulated flow pattern match observed characteristics including the velocity power spectrum, cell lifetimes, and cell pattern motion in longitude and latitude. Simulations using an average, and north-south symmetric, meridional motion of the cellular pattern produce polar magnetic fields that are too weak in the North and too strong in the South. Simulations using cellular patterns with meridional motions that evolve with the observed changes in strength and north-south asymmetry will be analyzed to see if they reproduce the polar field evolution observed during the rise of Cycle 24.

Hathaway, David H.↗

Radiative lifetime-encoded unicolour security tags using perovskite nanocrystals

Traditional fluorescence-based tags, used for anticounterfeiting, rely on primitive pattern matching and visual identification; additional covert security features such as fluorescent lifetime or pattern masking are advantageous if fraud is to be deterred. Herein, we present an electrohydrodynamically printed unicolour multi-fluorescent-lifetime security tag system composed of lifetime-tunable lead-halide perovskite nanocrystals that can be deciphered with both existing time-correlated single-photon counting fluorescence-lifetime imaging microscopy and a novel time-of-flight prototype. We find that unicolour or matching emission wavelength materials can be prepared through cation-engineering with the partial substitution of formamidinium for ethylenediammonium to generate “hollow” formamidinium lead bromide perovskite nanocrystals; these materials can be successfully printed into fluorescence-lifetime-encoded-quick-read tags that are protected from conventional readers. Furthermore, we also demonstrate that a portable, cost-effective time-of-flight fluorescence-lifetime imaging prototype can also decipher these codes. A single comprehensive approach combining these innovations may be eventually deployed to protect both producers and consumers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hierarchical Pattern Classifier

Hierarchical pattern classifier reduces number of comparisons between input and memory vectors without reducing detail of final classification by dividing classification process into coarse-to-fine hierarchy that comprises first "grouping" step and second classification step. Three-layer neural network reduces computation further by reducing number of vector dimensions in processing. Concept applicable to pattern-classification problems with need to reduce amount of computation necessary to classify, identify, or match patterns to desired degree of resolution.

Yates, Gigi L.↗

Investigation of Jupiter's Equatorial Hotspots and Plumes Using Cassini ISS Observations

We present updated analysis of Jupiter's equatorial meteorology from Cassini observations. For two months preceding the spacecraft's closest approach, the ISS onboard regularly imaged the atmosphere. We created time-lapse movies from this period in order to analyze the dynamics of equatorial 5-micron hot spots and their interactions with adjacent latitudes. Hot spots are quasi-stable, rectangular dark areas on visible-wavelength images, with defined eastern edges that sharply contrast with surrounding clouds, but a diffuse western edge serving as a nebulous boundary with adjacent equatorial plumes. Hot spots exhibit significant variations in size and shape over timescales of days and weeks. Some of these changes correspond with passing vortex systems from adjacent latitudes interacting with hot spots. Strong anticyclonic gyres present to the south and southeast of the dark areas appear to circulate into hot spots. Impressive, bright white plumes occupy spaces in between hot spots. Compact cirrus-iike 'scooter' clouds flow rapidly through the plumes before disappearing within the dark areas. This raises the possibility that the plumes and fast-moving clouds are at higher altitudes, because their speed does not match previously published zonal wind profiles. Most profiles represent the drift speed of the hot spots at their latitude from pattern matching of the entire longitudinal image strip. If a downward branch of an equatorially-trapped Rossby waves controls the overall appearance of hot spots, however, the westward phase velocity of the wave leads to underestimates of the true jet stream speed. Instead, our expanded data set demonstrating the rapid flow of these scooter clouds may be more illustrative of the actual jet stream speed at these latitudes. This research was supported by a NASA JDAP grant and the NASA Postdoctoral Program.

Choi, David S.↗

NASA's Software Bank (NETS)

NETS (A Neural Network Development Tool) is a software system for mimicking the human brain. It is used in a University of Arkansas project in pattern matching of chemical systems. If successful, chemists would be able to identify mixtures of compounds without long and costly separation procedures. Using NETS, the group has trained the computer to recognize pattern relationships in a known compound and associate the results to an unknown compound. The research appears to be promising.

Source record↗