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System, Method and Apparatus for Discovering Phrases in a Database

A phrase discovery is a method of identifying sequences of terms in a database. First, a selection of one or more relevant sequences of terms. such as relevant text, is provided. Next, several shorter sequences of terms, such as phrases, are extracted from the provided relevant sequences of terms. The extracted sequences of terms are then reduced through a culling process. A gathering process then emphasizes the more relevant of the extracted and culled sequences of terms and de-emphasizes the more generic of the extracted and culled sequences of terms. The gathering process can also include iteratively retrieving additional selections of relevant sequences (e.g.. text). extracting and culling additional sequences of terms (e.g.. phrases). emphasizing and de-emphasizing extracted and culled sequences of terms and accumulating all gathered sequences of terms. The resulting gathered sequences of terms are then output.

Michael W McGreevy

polars-dovmed (dovmed) v0.1.0

polars-dovmed is a python package for text search and extraction from NCBI's PubMed Central Open Access subset. It is powered by the polars dataframe library and leverages modern file formats (parquet) to efficiently scan public literature.

Roux, Simon [Lawrence Berkeley National Laboratory

Using the World Wide Web for GIDEP Problem Data Processing at Marshall Space Flight Center

Since April 1997, Marshall Space Flight Center has been using electronic transfer and the web to support our processing of the Government-Industry Data Exchange Program (GIDEP) and NASA ALERT information. Specific aspects include: (1) Extraction of ASCII text information from GIDEP for loading into Word documents for e-mail to ALERT actionees; (2) Downloading of GIDEP form image formats in Adobe Acrobat (.pdf) for internal storage display on the MSFC ALERT web page; (3) Linkage of stored GRDEP problem forms with summary information for access from the MSFC ALERT Distribution Summary Chart or from an html table of released MSFC ALERTs (4) Archival of historic ALERTs for reference by GIDEP ID, MSFC ID, or MSFC release date; (5) On-line tracking of ALERT response status using a Microsoft Access database and the web (6) On-line response to ALERTs from MSFC actionees through interactive web forms. The technique, benefits, effort, coordination, and lessons learned for each aspect are covered herein.

McPherson, John W.

Study of $\langle {p}_{\text{T}}\rangle$ and its higher moments, and extraction of the speed of sound in Pb-Pb collisions with ALICE

Ultrarelativistic heavy-ion collisions produce a state of hot and dense strongly interacting QCD matter called quark-gluon plasma (QGP). On an event-by-event basis, the volume of the QGP in ultracentral collisions is mostly constant, while its total entropy can vary significantly due to quantum fluctuations, leading to variations in the temperature of the system. Exploiting this unique feature of ultracentral collisions allows for the interpretation of the correlation of the mean transverse momentum ($\langle$p T $\rangle$) of produced charged hadrons and the number of charged hadrons as a measure for the speed of sound, c s . This speed is related to the rate at which compression waves travel in the QGP and is determined by fitting the relative increase in $\langle$p T $\rangle$ with respect to the relative change in the average charged-particle density ($\langle$dN ch /dη$\rangle$) measured at mid-rapidity. This study reports the event-average $\langle$p T $\rangle$ of charged particles as well as the variance, skewness, and kurtosis of the event-by-event transverse momentum per charged particle ([p T ]) distribution in ultracentral Pb-Pb collisions at a center-of-mass energy of 5.02 TeV per nucleon pair using the ALICE detector. Different centrality estimators based on charged-particle multiplicity or the transverse energy of the event are used to select ultracentral collisions. By ensuring a pseudorapidity gap between the region used to define the centrality and the region used to perform the measurement, the influence of biases and their potential effects on the rise of the mean transverse momentum is tested. The measured c$^{2}_{s}$ is found to strongly depend on the exploited centrality estimator and ranges between 0.1146±0.0028 (stat.)±0.0065 (syst.) and 0.4374±0.0006 (stat.)±0.0184 (syst.) in natural units. The self-normalized variance shows a steep decrease towards ultracentral collisions, while the self-normalized skewness variables show a maximum, followed by a fast decrease. These non-Gaussian features are understood in terms of the vanishing of the impact-parameter fluctuations contributing to the event-to-event [p T ] distribution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Language Model For Earth Science: Exploring Potential Downstream Applications As Well As Current Challenges

The use of deep learning techniques to build transformer language models such as SciBERT and GPT3 have transformed the natural language technology (NLT) landscape. These new NLTs are being used in speech to text and vice versa, auto-mated text classification, sentiment analysis, topic modeling, text summarization, and cognitive assistants. While Earth science has no shortage of unstructured data such as journal and conference papers, little efforts have focused on harnessing NLTs for knowledge extraction and supporting the scientific process. This paper surveys the use of language models in different science. BERT-E, a new Earth science-specific language model, is presented. BERT-E is generated using a transfer learning solution. A language model that has already been trained for general Science (SciBERT) is fine-tuned using abstracts and full text extracted from various Earth science-related articles. A downstream keywords classification application is used for evaluation, and the use of BERT-E shows improved performance. The need to develop a robust set of benchmarks in evaluating the language model such as BERT-E is discussed. Finally, example applications are presented to inspire additional ideas for applications using domain-specific language models.

R Ramachandran

Indirect Measurement of the 23 Na(p, γ) 24 Mg Direct Capture Reaction Rate via ( 3 He,d) Spectroscopy

The cross section of the $^{23}\text{Na}(p,γ)^{24}\text{Mg}$ reaction is dominated by direct capture at low energies relevant for stellar burning. Such cross sections can be constrained using spectroscopic factors($C^2S$) or asymptotic normalization coefficients(ANCs) from transfer reactions. In this work, the $^{23}\text{Na}(^3\text{He},d)^{24}\text{Mg}$ reaction was measured at $E_{lab}=21$ MeV to extract spectroscopic factors for $^{24}\text{Mg}$ states with excitation energies in $E_x=7 - 12$ MeV using the Enge split-pole spectrograph at the Triangle Universities Nuclear Laboratory. A new non-resonant astrophysical S factor and the direct capture reaction rate for the $^{23}\text{Na}(p,γ)$ reaction are calculated and presented based on this measurement. The new rate at $T<0.04$ GK is 43$\%$ smaller than in previous studies. Rigorous treatments of uncertainties are presented using a Bayesian Markov Chain Monte Carlo (MCMC) method. Finally, sources of uncertainties for computing the direct capture cross section are also discussed in detail.

electromagnetic moments

Experiences with Text Mining Large Collections of Unstructured Systems Development Artifacts at JPL

Often repositories of systems engineering artifacts at NASA's Jet Propulsion Laboratory (JPL) are so large and poorly structured that they have outgrown our capability to effectively manually process their contents to extract useful information. Sophisticated text mining methods and tools seem a quick, low-effort approach to automating our limited manual efforts. Our experiences of exploring such methods mainly in three areas including historical risk analysis, defect identification based on requirements analysis, and over-time analysis of system anomalies at JPL, have shown that obtaining useful results requires substantial unanticipated efforts - from preprocessing the data to transforming the output for practical applications. We have not observed any quick 'wins' or realized benefit from short-term effort avoidance through automation in this area. Surprisingly we have realized a number of unexpected long-term benefits from the process of applying text mining to our repositories. This paper elaborates some of these benefits and our important lessons learned from the process of preparing and applying text mining to large unstructured system artifacts at JPL aiming to benefit future TM applications in similar problem domains and also in hope for being extended to broader areas of applications.

text mining

A Summary of Advances in Document Summarization from 2023-2024

In computer science, Document Summarization is the task of condensing some quantity of text and related content through automated means. In this document, we review recent literature in text summarization. “Hybrid” extractive-abstractive approaches continue to be explored. Some of the latest efforts have also sought to enable users to adjust summaries with queries or other structure and begun to test reinforcement-learning style agentic LLM-based solutions.

97 MATHEMATICS AND COMPUTING

Information Extraction for System-Software Safety Analysis: Calendar Year 2007 Year-End Report

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis on the models to identify possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations; 4) perform discrete-time-based simulation on the models to investigate scenarios where these paths may play a role in failures and mishaps; and 5) identify resulting candidate scenarios for software integration testing. This paper describes new challenges in a NASA abort system case, and enhancements made to develop the integrated tool set.

Malin, Jane T.

PDF Entity Annotation Tool (PEAT)

While different text mining approaches – including the use of Artificial Intelligence (AI) and other machine based methods - continue to expand at a rapid pace, the tools used by researchers to create the labeled datasets required for training, modeling, and evaluation remain rudimentary. Labeled datasets contain the target attributes the machine is going to learn; for example, training an algorithm to delineate between images of a car or truck would generally require a set of images with a quantitative description of the underlying features of each vehicle type. Development of labeled textual data that can be used to build natural language machine learning models for scientific literature is not currently integrated into existing manual workflows used by domain experts. Published literature is rich with important information, such as different types of embedded text, plots, and tables that can all be used as inputs to train ML/natural language processing (NLP) models, when extracted and prepared in machine readable formats. Currently, both normalized data extraction of use to domain experts and extraction to support development of ML/NLP models are labor intensive and cumbersome manual processes. Automatic extraction of data and information from formats such as PDFs that are optimized for layout and human readability, not machine readability. The PDF (Portable Document Format) Entity Annotation Tool (PEAT) was developed with the goal of allowing users to annotate publications within their current print format, while also allowing those annotations to be captured in a machine-readable format. One of the main issues with traditional annotation tools is that they require transforming the PDF into plain text to facilitate the annotation process. While doing so lessens the technical challenges of annotating data, the user loses all structure and provenance that was inherent in the underlying PDF. Also, textual data extraction from PDFs can be an error prone process. Challenges include identifying sequential blocks of text and a multitude of document formats (multiple columns, font encodings, etc.). As a result of these challenges, using existing tools for development of NLP/ML models directly from PDFs is difficult because the generated outputs are not interoperable. We created a system that allows annotations to be completed on the original PDF document structure, with no plain text extraction. The result is an application that allows for easier and more accurate annotations. In addition, by including a feature that grants the user the ability to easily create a schema, we have developed a system that can be used to annotate text for different domain-centric schemas of relevance to subject matter experts. Different knowledge domains require distinct schemas and annotation tags to support machine learning.

97 MATHEMATICS AND COMPUTING

A Decision Support System to Compile Environmental Mitigations from Hydropower Licensing Documents

The process of deciphering, extracting, and compiling information from texts dense with domain-specific terminology and technical jargon is a challenging endeavor. It demands considerable expertise and deep knowledge in the respective field, resulting in a labor-intensive process when executed by humans. Furthermore, the task of identifying multiple class labels in extensive texts presents a challenge due to intra- and inter-reader variability, making the process time-consuming and costly.We’re introducing a user-friendly graphical interface, fortified with a BERT model-powered decision support system. This advanced system aims to augment efficiency, curtail data collection time, and sustain high precision in data acquisition. It is instrumental in deciphering and synthesizing intricate texts teeming with a spectrum of expressions, even within similar mitigation categories. Such tasks traditionally demand substantial human effort and specialized knowledge in the domain.Our system is specifically engineered for the task of extracting environmental mitigation information to promote sustainable hydropower development from licenses issued by the Federal Energy Regulatory Commission (FERC). These license documents are comprehensive, each containing over 15,000 words and requiring the identification of 135 different class labels. We anticipate that our system will boost reading speed, improve the consistency of classification outputs among readers, and contribute to the development of a robust scientific database of environmental mitigations associated with the 2,000+ non-federal hydropower facilities licensed by FERC in the United States.

Yoon, Hong-Jun [ORNL] (ORCID:0000000254505878)

MechBERT: Language Models for Extracting Chemical and Property Relationships about Mechanical Stress and Strain

Language models are transforming materials-aware naturallanguage processing by enabling the extraction of dynamic, context-rich information from unstructured text, thus, moving beyond the limitations of traditional information-extraction methods. Moreover, small language models are on the rise because some of them can perform better than large language models (LLMs) when given domain-specific questionanswer tasks, especially about an application area that relies on a highly specialized vernacular, such as materials science. We therefore present a new class of MechBERT language models for understanding mechanical stress and strain in materials. These employ Bidirectional Encoder Representations for transformer (BERT) architectures. We showcase four MechBERT models, all of which were pretrained on a corpus of documents that are textually rich in chemicals and their stress–strain properties and were fine-tuned on question-answering tasks. We evaluated the level of performance of our models on domain-specific as well as general English-language question-answer tasks and also explored the influence of the size and type of BERT architectures on model performance. We find that our MechBERT models outperform BERT-based models of the same size and maintain relevancy better than much larger BERT-based models when tasked with domain-specific question-answering tasks within the stress–strain engineering sector. These small language models also enable much faster processing and require a much smaller fraction of data to pretrain them, affording them greater operational efficiency and energy sustainability than LLMs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women

Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.

Research & Experimental Medicine

Extracting Material Property Measurements from Scientific Literature with Limited Annotations

Extracting material property data from scientific text is pivotal for advancing data-driven research in chemistry and materials science; however, the extensive annotation effort required to produce training data for named entity recognition (NER) models for this task often makes it a barrier to extracting specialized data sets. Here, in this work, we present a comparative study of the conventional, supervised NER methodology to alternative few-shot learning architectures and large language model (LLM)-based approaches that mitigate the need to label large training data sets. We find that the best-performing LLM (GPT-4o) not only excels in directly extracting relevant material properties based on limited examples but also enhances supervised learning through data augmentation. We supplement our findings with error and data quality assessments to provide a nuanced understanding of factors that impact property measurement extraction.

36 MATERIALS SCIENCE

Natural Language Processing Methods for Air Traffic Management Text and Speech Data

This presentation discusses two efforts of the NARI AI/ML Intern team during the Fall 2021 OSTEM Internship term. For Letters of Agreement (LoA), we have studied how LoAs are structured and explored the question ‘What is an LoA constraint?’ To do this, our approach is data-driven, iterative, and assisted by machine learning when available. In this presentation, we will walk through our tasks of manually scanning through documents, performing a preliminary entity labelling task, and our unsupervised analysis on LoA procedures sections. After this research phase, we define the smallest constraint unit in an LoA, and start to perform entity extraction. Looking towards constraint extraction, we are also exploring the use of a one-class support vector machine (OneClassSVM) model to identify patterns within the data. The second effort of our team this term is focused on Air Traffic Control System Command Center (ATCSCC) advisory meetings, and the subsequent advisory documents that get published from their content. These advisory documents are important to give readily accessible summaries of daily operations, so that data centers, airline officials, and other stakeholders can easily understand the context of these meetings in real time. In applying machine learning to this scenario, two natural language processing tasks are used. First is developing machine learning models to convert the meeting speech data into text. With this text, use of extractive and abstractive text summarization models are used to automatically generate preliminary versions of the advisory documents.

Natural Language Processing

KAM (Knowledge Acquisition Module): A tool to simplify the knowledge acquisition process

Analysts, knowledge engineers and information specialists are faced with increasing volumes of time-sensitive data in text form, either as free text or highly structured text records. Rapid access to the relevant data in these sources is essential. However, due to the volume and organization of the contents, and limitations of human memory and association, frequently: (1) important information is not located in time; (2) reams of irrelevant data are searched; and (3) interesting or critical associations are missed due to physical or temporal gaps involved in working with large files. The Knowledge Acquisition Module (KAM) is a microcomputer-based expert system designed to assist knowledge engineers, analysts, and other specialists in extracting useful knowledge from large volumes of digitized text and text-based files. KAM formulates non-explicit, ambiguous, or vague relations, rules, and facts into a manageable and consistent formal code. A library of system rules or heuristics is maintained to control the extraction of rules, relations, assertions, and other patterns from the text. These heuristics can be added, deleted or customized by the user. The user can further control the extraction process with optional topic specifications. This allows the user to cluster extracts based on specific topics. Because KAM formalizes diverse knowledge, it can be used by a variety of expert systems and automated reasoning applications. KAM can also perform important roles in computer-assisted training and skill development. Current research efforts include the applicability of neural networks to aid in the extraction process and the conversion of these extracts into standard formats.

Gettig, Gary A.

NASA Taxonomies for Searching Problem Reports and FMEAs

Many types of hazard and risk analyses are used during the life cycle of complex systems, including Failure Modes and Effects Analysis (FMEA), Hazard Analysis, Fault Tree and Event Tree Analysis, Probabilistic Risk Assessment, Reliability Analysis and analysis of Problem Reporting and Corrective Action (PRACA) databases. The success of these methods depends on the availability of input data and the analysts knowledge. Standard nomenclature can increase the reusability of hazard, risk and problem data. When nomenclature in the source texts is not standard, taxonomies with mapping words (sets of rough synonyms) can be combined with semantic search to identify items and tag them with metadata based on a rich standard nomenclature. Semantic search uses word meanings in the context of parsed phrases to find matches. The NASA taxonomies provide the word meanings. Spacecraft taxonomies and ontologies (generalization hierarchies with attributes and relationships, based on terms meanings) are being developed for types of subsystems, functions, entities, hazards and failures. The ontologies are broad and general, covering hardware, software and human systems. Semantic search of Space Station texts was used to validate and extend the taxonomies. The taxonomies have also been used to extract system connectivity (interaction) models and functions from requirements text. Now the Reconciler semantic search tool and the taxonomies are being applied to improve search in the Space Shuttle PRACA database, to discover recurring patterns of failure. Usual methods of string search and keyword search fall short because the entries are terse and have numerous shortcuts (irregular abbreviations, nonstandard acronyms, cryptic codes) and modifier words cannot be used in sentence context to refine the search. The limited and fixed FMEA categories associated with the entries do not make the fine distinctions needed in the search. The approach assigns PRACA report titles to problem classes in the taxonomy. Each ontology class includes mapping words - near-synonyms naming different manifestations of that problem class. The mapping words for Problems, Entities and Functions are converted to a canonical form plus any of a small set of modifier words (e.g. non-uniformity NOT + UNIFORM.) The report titles are parsed as sentences if possible, or treated as a flat sequence of word tokens if parsing fails. When canonical forms in the title match mapping words, the PRACA entry is associated with the corresponding Problem, Entity or Function in the ontology. The user can search for types of failures associated with types of equipment, clustering by type of problem (e.g., all bearings found with problems of being uneven: rough, irregular, gritty ). The results could also be used for tagging PRACA report entries with rich metadata. This approach could also be applied to searching and tagging failure modes, failure effects and mitigations in FMEAs. In the pilot work, parsing 52K+ truncated titles (the test cases that were available), has resulted in identification of both a type of equipment and type of problem in about 75% of the cases. The results are displayed in a manner analogous to Google search results. The effort has also led to the enrichment of the taxonomy, adding some new categories and many new mapping words. Further work would make enhancements that have been identified for improving the clustering and further reducing the false alarm rate. (In searching for recurring problems, good clustering is more important than reducing false alarms). Searching complete PRACA reports should lead to immediate improvement.

Malin, Jane T.

Algorithms for software development version control and change detection

Simple computer algorithms for processing source program and text data files in order to extract change detection, version control, version history, and current status information are described. These algorithms presuppose that it is possible to attach to each record of the source files a 6-character code, placed within delimiters that will cause the compiler, or other using program, to ignore this code field. The code contains a 2-character code for a character-by-character position-sensitive checksum of the record, another for the record number in the file, and a third for the data on which the encoding took place. Once the source file has been thus encoded, it is possible to detect the following transactions on the file since the most recent version coding; (1) addition of new records (having no version code), (2) modification of existing records, (3) deletion of a number of records, (4) movement and/or duplication of existing records, and (5) modification and duplication of records. In addition, it is possible to extract a version history of the number of records created or modified by date. A special file listing program is described which prints the file records without showing the version codes, but places a "change bar" at the right margin whenever a change is detected. The program also provides a list of changed pages and a version history.

Tausworthe, R. C.