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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Characterizing Quantum Classifier Utility in Natural Language Processing Workflows

Quantum Natural Language Processing (QNLP) develops natural language processing (NLP) models for deployment on quantum computers. We explore feature and data prototype selection techniques to address challenges posed by encoding high dimensional features. Our study builds quantum circuit classifiers that includes classical feature pre-processing, quantum embedding and quantum model training. The quantum models are built on 4 or 6 qubits and the quantum neural network (QNN) uses the established bricklayer design. We compare the dependence of model performance (in terms of accuracy and F1 scores) on feature length, embedding gates and parameterized unitary design. We compare the performance of quantum machine learning models to classical convolution neural network model (CNN) on binary and multi-class classification tasks using two datasets of synthetic features and labels. The first is the ECP-CANDLE P3B3 dataset a corpus of synthetically generated cancer pathology reports. The second dataset is extracted from well-known benchmark dataset (MADELON) - features are generated with a combination of informative, repeated and uninformative features. Both datasets are used for binary classification and multi-class classification with 3 classes. We observe robust, accurate performance from all models on the binary classification tasks, but multiclass classification is a challenge for the quantum models-there is a notable decrease in accuracy when using 3 classes. Overall the performance is comparable in terms of recall and accuracy between QNNs and CNNs, even with large datasets. These results provide a point of comparison between quantum and classical models on real-world datasets.

Hamilton, Kathleen↗
NASA NTRS1983

An overview of computer-based natural language processing

Computer based Natural Language Processing (NLP) is the key to enabling humans and their computer based creations to interact with machines in natural language (like English, Japanese, German, etc., in contrast to formal computer languages). The doors that such an achievement can open have made this a major research area in Artificial Intelligence and Computational Linguistics. Commercial natural language interfaces to computers have recently entered the market and future looks bright for other applications as well. This report reviews the basic approaches to such systems, the techniques utilized, applications, the state of the art of the technology, issues and research requirements, the major participants and finally, future trends and expectations. It is anticipated that this report will prove useful to engineering and research managers, potential users, and others who will be affected by this field as it unfolds.

Gevarter, W. B.↗
NASA NTRS1988

An expert system for natural language processing

A solution to the natural language processing problem that uses a rule based system, written in OPS5, to replace the traditional parsing method is proposed. The advantage to using a rule based system are explored. Specifically, the extensibility of a rule based solution is discussed as well as the value of maintaining rules that function independently. Finally, the power of using semantics to supplement the syntactic analysis of a sentence is considered.

Hennessy, John F.↗
DOE OSTI2021

Clinical Natural Language Processing for Radiation Oncology: A Review and Practical Primer

Natural language processing (NLP), which aims to convert human language into expressions that can be analyzed by computers, is one of the most rapidly developing and widely used technologies in the field of artificial intelligence. Natural language processing algorithms convert unstructured free text data into structured data that can be extracted and analyzed at scale. In medicine, this unlocking of the rich, expressive data within clinical free text in electronic medical records will help untap the full potential of big data for research and clinical purposes. Recent major NLP algorithmic advances have significantly improved the performance of these algorithms, leading to a surge in academic and industry interest in developing tools to automate information extraction and phenotyping from clinical texts. Thus, these technologies are poised to transform medical research and alter clinical practices in the future. Radiation oncology stands to benefit from NLP algorithms if they are appropriately developed and deployed, as they may enable advances such as automated inclusion of radiation therapy details into cancer registries, discovery of novel insights about cancer care, and improved patient data curation and presentation at the point of care. However, challenges remain before the full value of NLP is realized, such as the plethora of jargon specific to radiation oncology, nonstandard nomenclature, a lack of publicly available labeled data for model development, and interoperability limitations between radiation oncology data silos. Successful development and implementation of high quality and high value NLP models for radiation oncology will require close collaboration between computer scientists and the radiation oncology community. Here, we present a primer on artificial intelligence algorithms in general and NLP algorithms in particular; provide guidance on how to assess the performance of such algorithms; review prior research on NLP algorithms for oncology; and describe future avenues for NLP in radiation oncology research and clinics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRSDate not supplied

Classification of Notices to Airmen using Natural Language Processing

This paper establishes the feasibility of using Natural Language Processing (NLP) to classify NOTAMs or Notices to Airmen – a pilot messaging framework to gather real-time situational awareness. Present day air mobility operations heavily rely on NOTAMs. However, pilots often have difficulty interpreting NOTAMs due to the sheer volume of inapplicable messages and unclear abbreviations. Using NLP, the presented study analyzes the accuracy of classifying NOTAMs and, thereby, the efficiency of generating actionable interpretations in real time. To this effect, efficacies of four NLP neural network architectures were analyzed, including three Recurrent Neural Networks (RNNs) with GloVe, Word2Vec, and FastText word embeddings, and one trained Bi-Directional Encoder Representations from Transformers (BERT) model. The four neural networks were trained and evaluated on three open-source datasets of varying text lengths, vocabularies, and grammars, taken from e-commerce product descriptions, social media tweets, and unstructured descriptions for data and analytics services on open data marketplaces such as NASA’s Data and Reasoning Fabric (DRF) platform. This provided cross-analysis of each neural network architecture’s performance per text type. The best performing architecture, BERT, was then fine-tuned on a collection of open-source NOTAM data. Post-training, a real-time NOTAM classification service was implemented to draw inference on new NOTAMs using the trained model, which demonstrated close to 99% accuracy in classification. This modular classification service is envisioned to be integrated with a data and analytics delivery platform, such as the DRF, thus availing real-time contextualization of NOTAMs to air mobility clients, humans, and machines for enhanced decision making.

Aiden C. Szeto↗
NASA NTRSDate not supplied

Classification of Notices to Airmen using Natural Language Processing

This paper establishes the feasibility of using Natural Language Processing (NLP) to classify NOTAMs or Notices to Airmen – a pilot messaging framework to gather real-time situational awareness. Present day air mobility operations heavily rely on NOTAMs. However, pilots often have difficulty interpreting NOTAMs due to the sheer volume of inapplicable messages and unclear abbreviations. Using NLP, the presented study analyzes the accuracy of classifying NOTAMs and, thereby, the efficiency of generating actionable interpretations in real time. To this effect, efficacies of four NLP neural network architectures were analyzed, including three Recurrent Neural Networks (RNNs) with GloVe, Word2Vec, and FastText word embeddings, and one trained Bi-Directional Encoder Representations from Transformers (BERT) model. The four neural networks were trained and evaluated on three open-source datasets of varying text lengths, vocabularies, and grammars, taken from e-commerce product descriptions, social media tweets, and unstructured descriptions for data and analytics services on open data marketplaces such as NASA’s Data and Reasoning Fabric (DRF) platform. This provided cross-analysis of each neural network architecture’s performance per text type. The best performing architecture, BERT, was then fine-tuned on a collection of open-source NOTAM data. Post-training, a real-time NOTAM classification service was implemented to draw inference on new NOTAMs using the trained model, which demonstrated close to 99% accuracy in classification. This modular classification service is envisioned to be integrated with a data and analytics delivery platform, such as the DRF, thus availing real-time contextualization of NOTAMs to air mobility clients, humans, and machines for enhanced decision making.

Aiden Szeto↗
DOE OSTI2020

Data-driven materials research enabled by natural language processing and information extraction

Given the emergence of data science and machine learning throughout all aspects of society, but particularly in the scientific domain, there is increased importance placed on obtaining data. Data in materials science are particularly heterogeneous, based on the significant range in materials classes that are explored and the variety of materials properties that are of interest. This leads to data that range many orders of magnitude, and these data may manifest as numerical text or image-based information, which requires quantitative interpretation. The ability to automatically consume and codify the scientific literature across domains - enabled by techniques adapted from the field of natural language processing - therefore has immense potential to unlock and generate the rich datasets necessary for data science and machine learning. This review focuses on the progress and practices of natural language processing and text mining of materials science literature and highlights opportunities for extracting additional information beyond text contained in figures and tables in articles. Here, we discuss and provide examples for several reasons for the pursuit of natural language processing for materials, including data compilation, hypothesis development, and understanding the trends within and across fields. Current and emerging natural language processing methods along with their applications to materials science are detailed. We, then, discuss natural language processing and data challenges within the materials science domain where future directions may prove valuable.

36 MATERIALS SCIENCE↗
NASA NTRS2022

Natural Language Processing Techniques for Intelligent Knowledge Management of Safety Reports

Safety, failure, and incident reports are common artifacts across various domains, including aviation and wildfire response. These reports are often mandatory to submit, resulting in the culmination of large repositories of text-based documents. Simultaneously, these reports and corresponding repositories are often only manually analyzed and queried by users via out-of-date search engines. As a consequence, we have been developing the Manager for Intelligent Knowledge Access (MIKA) toolkit, which uses natural language processing to improve information access and reuse. In this presentation, we discuss natural language processing techniques for knowledge discovery and apply these methods to a repository of aerial wildfire mishap reports. Two methods are used for knowledge discovery: topic modeling and named-entity recognition. We use topic modeling to identify hazards and perform a trend analysis to produce a data-driven risk matrix. A custom named-entity recognition model, build from fine tuning a pre-trained language model, is used to identify failure modes, failure causes, failure effects, control processes, and recommendations to aid in failure modes and effects analysis (FMEA). Throughout the presentation, we discuss and apply natural language processing techniques to better leverage the vast amount of information contained in report repositories.

Machine learning↗
DOE OSTI2024

Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools

The study of protein-protein interactions (PPIs) provides insight into various biological mechanisms, including the binding of antibodies to antigens, enzymes to inhibitors or promoters, and receptors to ligands. Recent studies of PPIs have led to significant biological breakthroughs. For example, the study of PPIs involved in the human:SARS-CoV-2 viral infection mechanism aided in the development of the SARS-CoV-2 vaccines. Though several databases exist for the manual curation of PPI networks, text mining methods have been routinely demonstrated as useful alternatives for newly studied or understudied species where databases are incomplete. Here, the relationship extraction (RE) performance of several open-source classical text processing, machine learning (ML)-based natural language processing (NLP), and large language model (LLM)-based NLP tools were compared. Overall, our results indicated that networks derived from classical methods tend to have high true positive rates at the expense of having overconnected-networks, ML-based NLP methods have lower true positive rates but networks with the closest structures to the target network, and LLM-based NLP methods tend to exist in-between the two other approaches, with variable performances. Finally, the selection of a specific NLP approach should be tied to the needs of a study and text availability, as models varied in performance due to the amount of text provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Automated detection of mild cognitive impairment and dementia from voice recordings: A natural language processing approach

Automated computational assessment of neuropsychological tests would enable widespread, cost-effective screening for dementia. A novel natural language processing approach is developed and validated to identify different stages of dementia based on automated transcription of digital voice recordings of subjects’ neuropsychological tests conducted by the Framingham Heart Study (n = 1084). Transcribed sentences from the test were encoded into quantitative data and several models were trained and tested using these data and the participants’ demographic characteristics. Average area under the curve (AUC) on the held-out test data reached 92.6%, 88.0%, and 74.4% for differentiating Normal cognition from Dementia, Normal or Mild Cognitive Impairment (MCI) from Dementia, and Normal from MCI, respectively. The proposed approach offers a fully automated identification of MCI and dementia based on a recorded neuropsychological test, providing an opportunity to develop a remote screening tool that could be adapted easily to any language.

neuropsychological↗
DOE OSTI2023

AD – Elog Data Search Using Natural Language Processing Techniques

The goal of this project is to develop and evaluate a Machine Learning model using natural language processing techniques to categorize AD E-Log entries efficiently. AD E-Logs, which play a vital role in Fermilab's projects as a system to record and manage various data, often suffer from slow search processing and imprecise results. To address this issue, we preprocessed the data and employed the Doc2Vec model for training. The resulting model enables us to identify and retrieve the most relevant entries, thus enhancing user experience in accessing desired information.

Muse, Amiin↗
NASA NTRSDate not supplied

Knowledge Discovery for Early Failure Assessment of Complex Engineered Systems Using Natural Language Processing

Emerging complex engineered systems may have unexpected safety issues due to novel operational environments, increasing autonomy, human-machine interaction, and other factors. To prevent failures in operation or testing that necessitate costly redesign, it is desirable to predict likely failure modes early in the design process. Information about past engineering failures in natural language format presents one possible solution by enabling the retrieval of information that can inform new designs. However, identifying documents containing usable information and extracting the required information can be prohibitively time-consuming when implemented at scale. In this research, an automated natural language processing (NLP) framework is proposed to discover relevant knowledge from documents containing failure-related design information. The framework is applied to NASA’s Lessons Learned Information System (LLIS),which is publicly available. Documents containing usable information are filtered using two different NLP-based models. Next, from the identified usable documents, a failure taxonomy is extracted using a partitioned hierarchical topic modeling approach. Partitions of the document describe different sections of the failure taxonomy – i.e., failure, cause of failure, and recommendations – as indicated by the structure of the original document. The extracted failure taxonomy can be leveraged in early design failure assessment methods. Moreover, the framework can be used to identify documents containing usable failure-related design information from other databases and extract relevant information from these documents.

Documentation and Information Science↗
NASA NTRSDate not supplied

Knowledge Discovery for Early Failure Assessment of Complex Engineered Systems Using Natural Language Processing

Emerging complex engineered systems may have unexpected safety issues due to novel operational environments, increasing autonomy, human-machine interaction, and other factors. To prevent failures in operation or testing that necessitate costly redesign, it is desirable to predict likely failure modes early in the design process. Information about past engineering failures in natural language format presents one possible solution by enabling the retrieval of information that can inform new designs. However, identifying documents containing usable information and extracting the required information can be prohibitively time-consuming when implemented at scale. In this research, an automated natural language processing (NLP) framework is proposed to discover relevant knowledge from documents containing failure-related design information. The framework is applied to NASA’s Lessons Learned Information System (LLIS),which is publicly available. Documents containing usable information are filtered using two different NLP-based models. Next, from the identified usable documents, a failure taxonomy is extracted using a partitioned hierarchical topic modeling approach. Partitions of the document describe different sections of the failure taxonomy – i.e., failure, cause of failure, and recommendations – as indicated by the structure of the original document. The extracted failure taxonomy can be leveraged in early design failure assessment methods. Moreover, the framework can be used to identify documents containing usable failure-related design information from other databases and extract relevant information from these documents.

Documentation and Information Science↗
NASA NTRS2019

Understanding Machine Learning in Earth Science: A Natural Language Processing Approach

Machine learning (ML) is being increasingly utilized in Earth science research. Benefits of ML include efficiency, reduction of human error, and ability to extract hidden patterns within data. However, the mutual lack of each other’s domain knowledge by ML and Earth science stands as a barrier to timely and effective implementation. Earth science, in particular, faces challenges in generating sample data, compared to those of traditional ML problems such as face recognition or stock predictions, where data is abundant and not lacking in ground truth, which is necessary for labeling. Earth science data are more varying in formats, such as HDF5 and image resolutions, and are not standardized across instruments, even within a given Earth science discipline. Previous studies have been done to outline the specific challenges that Earth science faces with ML, while others have focused on using existing publications to mine information efficiently. Other resources such as Scikit-Learn have developed decision trees for choosing appropriate machine learning algorithms, but application within Earth science subjects becomes much more complex. For the current study, we propose a methodology and tool that aids in implementation of ML in Earth science using natural language processing (NLP). Our work comprises three main parts: (1) analyzing existing publications related to ML and Earth science, using natural language processing: (2) extracting from the publications information on ML models subjects in Earth Science: and (3) visualizing the extracted relationships as a network graph. The resulting network graph should aid the Earth science communities in applying optimal ML algorithms and guiding data preparation through visualization of similar studies. The network graph and analysis of document similarity will be the basis of our next step, which is to develop a decision tree for selecting optimal machine learning methodologies for specified Earth science applications.

Zheng, Laura↗
NASA NTRS2019

Simplifying NASA Earth Science Data and Information Access Through Natural Language Processing Based Data Analysis and Visualization

NASA Earth science data collected from satellites, model assimilation, airborne missions, and field campaigns, are large, complex and evolving. Such characteristics pose great challenges for end users (e.g., Earth science and applied science users, students, citizen scientists), particularly for those who are unfamiliar with NASA's EOSDIS and thus unable to access and utilize datasets effectively. For example, a novice user may simply ask: what is the total rainfall for a flooding event in my county yesterday? For an experienced user (e.g., algorithm developer), a question can be: how did my rainfall product perform, compared to ground observations, during a flooding event? Nonetheless, with rapid information technology development such as natural language processing, it is possible to develop simplified Web interfaces and back-end processing components to handle such questions and deliver answers in terms of text, data, or graphic results directly to users.In this presentation, we describe the main challenges for end users with different levels of expertise in accessing and utilizing NASA Earth science data. Surveys reveal that most non-professional users normally do not want to download and handle raw data as well as conduct heavy-duty data processing tasks. Often they just want some simple graphics or data for various purposes. To them, simple and intuitive user interfaces are sufficient because complicated ones can be difficult and time-consuming to learn. Professionals also want such interfaces to answer many questions from datasets. One solution is to develop a natural language based search box like Google and the search results can be text, data, graphics and more. Now the challenge is, with natural language processing, can we design a system to process a scientific question typed in by a user? In this presentation, we describe our plan for such a prototype. The workflow is: 1) extract needed information (e.g., variables, spatial and temporal information, processing methods, etc.) from the input, 2) process the data in the backend, and 3) deliver the results (data or graphics) to the user.

Liu, Zhong↗
DOE OSTI2023

Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions

Background. During drug development, it is essential to gather information about the change of clinical exposure of a drug (object) due to the pharmacokinetic (PK) drug-drug interactions (DDIs) with another drug (precipitant). While many natural language processing (NLP) methods for DDI have been published, most were designed to evaluate if (and what kind of) DDI relationships exist in the text, without identifying the direction of DDI (object vs. precipitant drug). Here we present a method for the automatic identification of the directionality of a PK DDI from literature or drug labels. Methods. We reannotated the Text Analysis Conference (TAC) DDI track 2019 corpus for identifying the direction of a PK DDI and evaluated the performance of a fine-tuned BioBERT model on this task by following the training and validation steps prespecified by TAC. Results. This initial attempt showed the model achieved an F-score of 0.82 in identifying sentences as containing PK DDI and an F-score of 0.97 in identifying object versus precipitant drugs in those sentences. Discussion and conclusion. Despite a growing list of NLP methods for DDI extraction, most of them use a common set of corpora to perform general purpose tasks (e.g., classifying a sentence into one of several fixed DDI categories). There is a lack of coordination between the drug development and biomedical informatics method development community to develop corpora and methods to perform specific tasks (e.g., extract clinical exposure changes due to PK DDI). We hope that our effort can encourage such a coordination so that more “fit for purpose” NLP methods could be developed and used to facilitate the drug development process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identifying COVID-19 cases and extracting patient reported symptoms from Reddit using natural language processing

We used social media data from “covid19positive” subreddit, from 03/2020 to 03/2022 to identify COVID-19 cases and extract their reported symptoms automatically using natural language processing (NLP). We trained a Bidirectional Encoder Representations from Transformers classification model with chunking to identify COVID-19 cases; also, we developed a novel QuadArm model, which incorporates Question-answering, dual-corpus expansion, Adaptive rotation clustering, and mapping, to extract symptoms. Our classification model achieved a 91.2% accuracy for the early period (03/2020-05/2020) and was applied to the Delta (07/2021–09/2021) and Omicron (12/2021–03/2022) periods for case identification. We identified 310, 8794, and 12,094 COVID-positive authors in the three periods, respectively. The top five common symptoms extracted in the early period were coughing (57%), fever (55%), loss of sense of smell (41%), headache (40%), and sore throat (40%). During the Delta period, these symptoms remained as the top five symptoms with percent authors reporting symptoms reduced to half or fewer than the early period. During the Omicron period, loss of sense of smell was reported less while sore throat was reported more. Our study demonstrated that NLP can be used to identify COVID-19 cases accurately and extracted symptoms efficiently.

60 APPLIED LIFE SCIENCES↗