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All sources NASA NTRS DOE OSTI

DOE OSTI2012

A Maximum-Entropy approach for accurate document annotation in the biomedical domain

The increasing number of scientific literature on the Web and the absence of efficient tools used for classifying and searching the documents are the two most important factors that influence the speed of the search and the quality of the results. Previous studies have shown that the usage of ontologies makes it possible to process document and query information at the semantic level, which greatly improves the search for the relevant information and makes one step further towards the Semantic Web. A fundamental step in these approaches is the annotation of documents with ontology concepts, which can also be seen as a classification task. In this paper we address this issue for the biomedical domain and present a new automated and robust method, based on a Maximum Entropy approach, for annotating biomedical literature documents with terms from the Medical Subject Headings (MeSH). The experimental evaluation shows that the suggested Maximum Entropy approach for annotating biomedical documents with MeSH terms is highly accurate, robust to the ambiguity of terms, and can provide very good performance even when a very small number of training documents is used. More precisely, we show that the proposed algorithm obtained an average F-measure of 92.4% (precision 99.41%, recall 86.77%) for the full range of the explored terms (4,078 MeSH terms), and that the algorithm’s performance is resilient to terms’ ambiguity, achieving an average F-measure of 92.42% (precision 99.32%, recall 86.87%) in the explored MeSH terms which were found to be ambiguous according to the Unified Medical Language System (UMLS) thesaurus. Finally, we compared the results of the suggested methodology with a Naive Bayes and a Decision Trees classification approach, and we show that the Maximum Entropy based approach performed with higher F-Measure in both ambiguous and monosemous MeSH terms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Information processing systems, reasoning modules, and reasoning system design methods

Information processing systems, reasoning modules, and reasoning system design methods are described. According to one aspect, an information processing system includes working memory comprising a semantic graph which comprises a plurality of abstractions, wherein the abstractions individually include an individual which is defined according to an ontology and a reasoning system comprising a plurality of reasoning modules which are configured to process different abstractions of the semantic graph, wherein a first of the reasoning modules is configured to process a plurality of abstractions which include individuals of a first classification type of the ontology and a second of the reasoning modules is configured to process a plurality of abstractions which include individuals of a second classification type of the ontology, wherein the first and second classification types are different.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Information processing systems, reasoning modules, and reasoning system design methods

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2016

Information processing systems, reasoning modules, and reasoning system design methods

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Retrofitting Word Embeddings with the UMLS Metathesaurus for Clinical Information Extraction

Deep learning has surged in popularity and proven to be effective for various artificial intelligence applications including information extraction from cancer pathology reports. Since word representation is a core unit that enables deep learning algorithms to understand words and be able to perform NLP, this representation must include as much information as possible to help these algorithms achieve high classification performance. Therefore, in this work in addition to the distributional information of words in large sized corpora, we use UMLS vocabulary resources to enrich the vector space representation of words with the semantic relations between words. These resources provide many terminologies pertaining to cancer. The refined word embeddings are used with a convolutional neural (CNN) model to extract four data elements from cancer pathology reports; ICD-O-3 tumor topography codes, tumor laterality, behavior, and histological grade. We observed that using UMLS vocabulary resources to enrich word embeddings of CNN models consistently outperformed CNN models without pre-training word embeddings and even with pre-trained word embeddings on a domain specific corpus across all four tasks. The results show marginal improvement on the laterality task, but a significant improvement on the other tasks, especially for the macro-f score. Specifically, the improvements are 3%, 13%, and 15% for tumor site, histological grade, and behavior tasks, respectively. This approach is encouraging to enrich word embeddings with more clinical data resources to be used for information abstraction tasks from clinical pathology reports.

Alawad, Mohammed↗

NASA NTRS1991

Rule groupings in expert systems using nearest neighbour decision rules, and convex hulls

Expert System shells are lacking in many areas of software engineering. Large rule based systems are not semantically comprehensible, difficult to debug, and impossible to modify or validate. Partitioning a set of rules found in CLIPS (C Language Integrated Production System) into groups of rules which reflect the underlying semantic subdomains of the problem, will address adequately the concerns stated above. Techniques are introduced to structure a CLIPS rule base into groups of rules that inherently have common semantic information. The concepts involved are imported from the field of A.I., Pattern Recognition, and Statistical Inference. Techniques focus on the areas of feature selection, classification, and a criteria of how 'good' the classification technique is, based on Bayesian Decision Theory. A variety of distance metrics are discussed for measuring the 'closeness' of CLIPS rules and various Nearest Neighbor classification algorithms are described based on the above metric.

Anastasiadis, Stergios↗

DOE OSTI2023

Computer Vision: EO Imaging & Video Tasks, Metrics, and Datasets [Slides]

Classification is an assignment of an image to a certain category. Localization is identified by the box surrounding the object in the image. Object detection detects instances of semantic objects of a certain class. Semantic segmentation categorizes all the pixels of an image into classes of objects. Instance segmentation identifies each instance of each object in the image. Panoptic (i.e., showing or seeing everything at once) segmentation is a combination of semantic and instance segmentation and classifies all the pixels in the image.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1992

Towards an Effective Theory of Reformulation: Semantics - Part 1

This paper describes an investigation into the structure of representations of sets of actions, utilizing semigroup theory. The goals of this project are twofold: to shed light on the relationship between tasks and representations, leading to a classification of tasks according to the representations they admit; and to develop techniques for automatically transforming representations so as to improve problem-solving performance. A method is demonstrated for automatically generating serial algorithms for representations whose actions form a finite group. This method is then extended to representations whose actions form a finite inverse semigroup.

Benjamin, D. Paul↗

DOE OSTI2012

Semantic Features for Classifying Referring Search Terms

When an internet user clicks on a result in a search engine, a request is submitted to the destination web server that includes a referrer field containing the search terms given by the user. Using this information, website owners can analyze the search terms leading to their websites to better understand their visitors needs. This work explores some of the features that can be used for classification-based analysis of such referring search terms. We present initial results for the example task of classifying HTTP requests countries of origin. A system that can accurately predict the country of origin from query text may be a valuable complement to IP lookup methods which are susceptible to the obfuscation of dereferrers or proxies. We suggest that the addition of semantic features improves classifier performance in this example application. We begin by looking at related work and presenting our approach. After describing initial experiments and results, we discuss paths forward for this work.

99 GENERAL AND MISCELLANEOUS↗

NASA NTRSDate not supplied

Expanding NeMO-Net Machine Learning Capabilities for Citizen Science

NASA NeMO-Net, the neural multi-modal observation and training network for global coral reef assessment, is an open-source deep convolutional neural network and interactive active learning training software aiming to accurately assess the present and past dynamics of coral reef ecosystems through determination of percent living cover and morphology as well as mapping of spatial distribution. We present an interactive citizen science video game, released this April, for desktop and iOS devices where users interactively label morphology classifications over mm-scale 3D coral reef imagery captured using diver photomosaic imagery, the UAV enabled NASA FluidCam instrument, and satellite datasets. To date, the application has had over 40,000 downloads and over 60,000 unique coral reef classifications, each filtered through a user-based rating and expert evaluation system. We also present results from NeMO-Net’s convolutional neural network (CNN) models used to semantically segment 2D satellite imagery as well as projections of 3D coral reconstructions using user input data as training datasets. Fusing datasets using machine learning from multiple remote sensing platforms presents novel methodologies for assessing the health of coral ecosystems, which are critically endangered by a changing climate. In partnering with Mission Blue, the National Oceanic and Atmospheric Administration (NOAA), and the Living Oceans Foundation (LOF), NeMO-Net leverages an international consortium of subject matter experts to provide both proper training for citizen scientists and the generation of a labeled datasets to ingest into machine learning algorithms for global coral reef identification.

NeMO-Net↗

NASA NTRSDate not supplied

Expanding NeMO-Net Machine Learning Capabilities for Citizen Science

NASA NeMO-Net, the neural multi-modal observation and training network for global coral reef assessment, is an open-source deep convolutional neural network and interactive active learning training software aiming to accurately assess the present and past dynamics of coral reef ecosystems through determination of percent living cover and morphology as well as mapping of spatial distribution. We present an interactive citizen science video game, released this April, for desktop and iOS devices where users interactively label morphology classifications over mm-scale 3D coral reef imagery captured using diver photomosaic imagery, the UAV enabled NASA FluidCam instrument, and satellite datasets. To date, the application has had over 40,000 downloads and over60,000 unique coral reef classifications, each filtered through a user-based rating and expert evaluation system. We also present results from NeMO-Net’s convolutional neural network (CNN) models used to semantically segment 2D satellite imagery as well as projections of 3D coral reconstructions using user input data as training datasets. Fusing datasets using machine learning from multiple remote sensing platforms presents novel methodologies for assessing the health of coral ecosystems, which are critically endangered by a changing climate. In partnering with Mission Blue, the National Oceanic and Atmospheric Administration (NOAA), and the Living Oceans Foundation (LOF), NeMO-Net leverages an international consortium of subject matter experts to provide both proper training for citizen scientists and the generation of a labeled datasets to ingest into machine learning algorithms for global coral reef identification.

NeMO-Net↗

DOE OSTI2026

Creating a Training Dataset for Semantic Segmentation of Canal Networks for Irrigation Modernization

Canal infrastructure has provided critical irrigation water to the western United States for over a century. To continue providing vital water resources to the semi-arid West, irrigation systems must undergo maintenance and modernization. Many canal companies are resource-constrained, and because funding opportunities often require detailed knowledge of existing infrastructure, they can struggle to secure financial capital. We address this problem by creating training data for a semantic segmentation deep learning model to map canal networks throughout the western United States. To create a diverse and robust training dataset, we labelled 1-m NAIP imagery with the locations of no canals, wet canals, and dry/vegetated canals. Since creating these datasets is time consuming, we first developed a preprocessing methodology to identify canals within our four study areas. We used NAIP imagery and provided canal centerline data to buffer, standardize, and cluster the imagery, automating the labeling process as much as possible. However, this still required manual cleaning and manual classification of canal type. Challenges arose when canals were interrupted (e.g., road culverts or piped sections) or when nearby features shared similar characteristics (e.g., irrigated fields, trees, and shadows). Combining automated preprocessing with manual refinement produced four detailed canal masks to be used in the semantic segmentation model developed by Richard Tapia.

13 - HYDRO ENERGY↗

DOE OSTI2017

Measuring, Predicting and Visualizing Short-Term Change in Word Representation and Usage in VKontakte Social Network

Language in social media is extremely dynamic: new words emerge, trend and disappear, while the meaning of existing words can fluctuate over time. This work addresses several important tasks of visualizing and predicting short term text representation shift, i.e. the change in a word’s contextual semantics. We study the relationship between short-term concept drift and representation shift on a large social media corpus – VKontakte collected during the Russia-Ukraine crisis in 2014 – 2015. We visualize short-term representation shift for example keywords and build predictive models to forecast short-term shifts in meaning from previous meaning as well as from concept drift. We show that short-term representation shift can be accurately predicted up to several weeks in advance and that visualization provides insight into meaning change. Our approach can be used to explore and characterize specific aspects of the streaming corpus during crisis events and potentially improve other downstream classification tasks including real-time event forecasting in social media.

concept drift↗

DOE OSTI2022

SeqMask: Behavior Extraction Over Cyber Threat Intelligence Via Multi-Instance Learning

Abstract Identification and extraction of Tactics, Techniques and Procedures (TTPs) for Cyber Threat Intelligence (CTI) restore the full picture of cyber attacks and guide the analysts to assess the system risk. Existing frameworks can hardly provide uniform and complete processing mechanisms for TTPs information extraction without adequate knowledge background. A multi-instance learning approach named SeqMask is proposed in this paper as a solution. SeqMask extracts behavior keywords from CTI evaluated by the semantic impact, and predicts TTPs labels by conditional probabilities. Still, the framework has two mechanisms to determine the validity of keywords. One using expert experience verification. The other verifies the distortion of the classification effect by blocking existing keywords. In the experiments, SeqMask reached 86.07% and 73.99% in F1 scores for TTPs classifications. For the top 20% of keywords, the expert approval rating is 92.20%, where the average repetition of keywords whose scores between 100% and 90% is 60.02%. Particularly, when the top 65% of the keywords were blocked, the F1 decreased to about 50%; when removing the top 50%, the F1 was under 31%. Further, we also validate the possibility of extracting TTPs from full-size CTI and malware whose F1 are improved by 2.16% and 0.81%.

Ge, Wenhan↗

DOE OSTI2021

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

Abstract Inhibiting protein kinases (PKs) that cause cancers has been an important topic in cancer therapy for years. So far, almost 8% of >530 PKs have been targeted by FDA-approved medications, and around 150 protein kinase inhibitors (PKIs) have been tested in clinical trials. We present an approach based on natural language processing and machine learning to investigate the relations between PKs and cancers, predicting PKs whose inhibition would be efficacious to treat a certain cancer. Our approach represents PKs and cancers as semantically meaningful 100-dimensional vectors based on word and concept neighborhoods in PubMed abstracts. We use information about phase I-IV trials in ClinicalTrials.gov to construct a training set for random forest classification. Our results with historical data show that associations between PKs and specific cancers can be predicted years in advance with good accuracy. Our tool can be used to predict the relevance of inhibiting PKs for specific cancers and to support the design of well-focused clinical trials to discover novel PKIs for cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Figure Descriptive Text Extraction Using Ontological Representation

Abstract Experimental research publications provide figure form resources including graphs, charts, and any type of images to effectively support and convey methods and results. To describe figures, authors add captions, which are often incomplete, and more descriptions reside in body text. This work presents a method to extract figure descriptive text from the body of scientific articles. We adopted ontological semantics to aid concept recognition of figure-related information, which generates human- and machine-readable knowledge representations from sentences. Our results show that conceptual models bring an improvement in figure descriptive sentence classification over word-based approaches.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2005

Spoken Language Processing in the Clarissa Procedure Browser

Clarissa, an experimental voice enabled procedure browser that has recently been deployed on the International Space Station, is as far as we know the first spoken dialog system in space. We describe the objectives of the Clarissa project and the system's architecture. In particular, we focus on three key problems: grammar-based speech recognition using the Regulus toolkit; methods for open mic speech recognition; and robust side-effect free dialogue management for handling undos, corrections and confirmations. We first describe the grammar-based recogniser we have build using Regulus, and report experiments where we compare it against a class N-gram recogniser trained off the same 3297 utterance dataset. We obtained a 15% relative improvement in WER and a 37% improvement in semantic error rate. The grammar-based recogniser moreover outperforms the class N-gram version for utterances of all lengths from 1 to 9 words inclusive. The central problem in building an open-mic speech recognition system is being able to distinguish between commands directed at the system, and other material (cross-talk), which should be rejected. Most spoken dialogue systems make the accept/reject decision by applying a threshold to the recognition confidence score. NASA shows how a simple and general method, based on standard approaches to document classification using Support Vector Machines, can give substantially better performance, and report experiments showing a relative reduction in the task-level error rate by about 25% compared to the baseline confidence threshold method. Finally, we describe a general side-effect free dialogue management architecture that we have implemented in Clarissa, which extends the "update semantics'' framework by including task as well as dialogue information in the information state. We show that this enables elegant treatments of several dialogue management problems, including corrections, confirmations, querying of the environment, and regression testing.

Rayner, M.↗

NASA NTRSDate not supplied

Developing Natural Language Processing and Supervised Learning Techniques to Classify Mars Tasks

As NASA's Human Research Program (HRP) prepares for long-duration Mars missions, understanding astronaut tasks is crucial. This study, conducted at NASA Glenn Research Center (GRC), employed Natural Language Processing (NLP) and machine learning techniques to analyze and classify Mars tasks. A list of 1,058 Mars tasks was provided by HRP experts including binary labeling of 18 Human System Task Categories (HSTCs). We developed an NLP model using Google's BERT language model to capture the semantic and syntactic nuances of these tasks. Supervised training was initially applied to a subset of the NLP-analyzed tasks to assess the model's effectiveness in classifying the remaining tasks. Incorporating HSTC descriptions significantly enhanced the classification accuracy for 9 out of the 18 HSTCs and reduced training time. To address the issue of severe class imbalance in the HSTC data, we introduced innovative weighting and sampling techniques for data augmentation. We then fine-tune BERT to implement a pairwise relatedness scoring method, allowing us to cluster tasks based on their relatedness and similarity, getting a step closer to labeling the tasks without supervision. In this presentation we guide you through data preprocessing, deciphering key syntax components using BERT, and performing supervised classification of the Mars tasks. This work showcases the potential use of advanced NLP techniques to analyze Mars missions to be incorporated into various crew health and performance analyses.

GenAI↗