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Corley, Courtney D.

Publications and source records attributed to Corley, Courtney D..

At least 19 records

Fuzzy Simplicial Networks: A Topology-Inspired Model to Improve Task Generalization in Few-shot Learning

Deep learning has shown great success in settings with massive amounts of data but has struggled when data is limited. Few-shot learning algorithms, which seek to address this limitation, are designed to generalize well to new tasks with limited data. Typically, models are evaluated on unseen classes and datasets that are defined by the same fundamental task as they are trained for (e.g. category membership). One can also ask how well a model can generalize to fundamentally different tasks within a fixed dataset (for example: moving from category membership to tasks that involve detecting object orientation or quantity). To formalize this kind of shift we define a notion of “independence of tasks” and identify three new sets of labels for established computer vision datasets that test a model's ability to generalize to tasks which draw on orthogonal attributes in the data. We use these datasets to investigate the failure modes of metric-based few-shot models. Based on our findings, we introduce a new few-shot model called Fuzzy Simplicial Networks (FSN) which leverages a construction from topology to more flexibly represent each class from limited data. In particular, FSN models can not only form multiple representations for a given class but can also begin to capture the low-dimensional structure which characterizes class manifolds in the encoded space of deep networks. We show that FSN outperforms state-of-the-art models on the challenging tasks we introduce in this paper while remaining competitive on standard few-shot benchmarks.

deep learning↗

Prototypical Region Proposal Networks for Few-Shot Localization and Classification

Recently proposed few-shot image classification methods have generally focused on use cases where the objects to be classified are the central subject of images. Despite success on benchmark vision datasets aligned with this use case, these methods typically fail on use cases involving densely-annotated, busy images: images common in the wild where objects of relevance are not the central subject, instead appearing potentially occluded, small, or among other incidental objects belonging to other classes of potential interest. To localize relevant objects, we employ a prototype-based few-shot segmentation model which compares the encoded features of unlabeled query images with support class centroids to produce region proposals indicating the presence and location of support set classes in a query image. These region proposals are then used as additional conditioning input to few-shot image classifiers. We develop a framework to unify the two stages (segmentation and classification) into an end-to-end classification model---PRoPnet---and empirically demonstrate that our methods improve accuracy on image datasets with natural scenes containing multiple object classes.

Skomski, Steven E.↗

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.

Colby, Sean M.↗

Deep Learning for Scientific Discovery

Deep learning has positively impacted fields were perceptive tasks are paramount, such as computer vision and natural language processing. Tremendous strides have also been made in deep reinforcement learning towards robotics and gaming. Given the success in these fields, it is apparent that deep learning may also accelerate scientific discovery. Herein, we discuss several topic areas where modern representation learning is driving innovation. This article presents a) learning non-linear models from data, b) learning scientific laws from models, c) deep learning on graphs, and d) approaches to scalable deep learning.

deep learning, scientific computing, koopman, mate↗

Forecasting influenza-like illness dynamics for military populations using neural networks and social media

This work is the first to take advantage of recurrent neural networks to predict influenza-like-illness (ILI) dynamics from various linguistic signals extracted from social media data. Unlike other approaches that rely on timeseries analysis of historical ILI data [1, 2] and the state-of-the-art machine learning models [3, 4], we build and evaluate the predictive power of Long Short Term Memory (LSTMs) architectures capable of nowcasting (predicting in \real-time") and forecasting (predicting the future) ILI dynamics in the 2011 { 2014 influenza seasons. To build our models we integrate information people post in social media e.g., topics, stylistic and syntactic patterns, emotions and opinions, and communication behavior. We then quantitatively evaluate the predictive power of different social media signals and contrast the performance of the-state-of-the-art regression models with neural networks. Finally, we combine ILI and social media signals to build joint neural network models for ILI dynamics prediction. Unlike the majority of the existing work, we specifically focus on developing models for local rather than national ILI surveillance [1], specifically for military rather than general populations [3] in 26 U.S. and six international locations. Our approach demonstrates several advantages: (a) Neural network models learned from social media data yield the best performance compared to previously used regression models. (b) Previously under-explored language and communication behavior features are more predictive of ILI dynamics than syntactic and stylistic signals expressed in social media. (c) Neural network models learned exclusively from social media signals yield comparable or better performance to the models learned from ILI historical data, thus, signals from social media can be potentially used to accurately forecast ILI dynamics for the regions where ILI historical data is not available. (d) Neural network models learned from combined ILI and social media signals significantly outperform models that rely solely on ILI historical data, which adds to a great potential of alternative public sources for ILI dynamics prediction. (e) Location-specific models outperform previously used location-independent models e.g., U.S. only. (f) Prediction results significantly vary across geolocations depending on the amount of social media data available and ILI activity patterns.

60 APPLIED LIFE SCIENCES↗

Beyond Fine Tuning: Adding capacity to leverage few labels

In this paper we present a technique to train neural network models on small amounts of data. Current methods for training neural networks on small amounts of rich data typically rely on strategies such as fine-tuning a pre-trained neural networks or the use of domain-specific hand-engineered features. Here we take the approach of treating network layers, or entire networks, as modules and combine pre-trained modules with untrained modules, to learn the shift in distributions between data sets. The central impact of using a modular approach comes from adding new representations to a network, as opposed to replacing representations via fine-tuning. Using this technique, we are able surpass results using standard fine-tuning transfer learning approaches, and we are also able to significantly increase performance over such approaches when using smaller amounts of data.

data science↗

Studying Military Community Health, Well-being, and Discourse through the Social Media Lens

Social media can provide a resource for characterizing communities and targeted populations through activities and content shared online. For instance, studying the armed forces’ use of social media may provide insights into their health and wellbeing. In this paper, we address three broad research questions: (1) How do military populations use social media? (2) What topics do military users discuss in social media? (3) Do military users talk about health and well-being differently than civilians? Military Twitter users were identified through keywords in the profile description of users who posted geotagged tweets at military installations. These military tweets were compared with the tweets from remaining population. Our analysis indicate that military users talk more about military related responsibilities and events, whereas non-military users talk more about school, work, and leisure activities. A significant difference in online content generated by both populations was identified, involving sentiment, health, language, and social media features.

healthcare analytics↗

Uncovering the relationships between military community health and affects expressed in social media

Military populations present a small, unique community whose mental and physical health impacts the security of the nation. Recent literature has explored social media's ability to enhance disease surveillance and characterize distinct communities with encouraging results. We present a novel analysis of the relationships between influenza-like illnesses (ILI) clinical data and affects (i.e., emotions and sentiments) extracted from social media around military facilities. Our analyses examine (1) differences in affects expressed by military and control populations, (2) affect changes over time by users, (3) differences in affects expressed during high and low ILI seasons, and (4) correlations and cross-correlations between ILI clinical visits and affects from an unprecedented scale –171M geo-tagged tweets across 31 global geolocations. Key findings include: Military and control populations dier in the way they express affects in social media over space and time. Control populations express more positive and less negative sentiments and less sadness, fear, disgust, and anger emotions than military. However, affects expressed in social media by both populations within the same area correlate similarly with ILI visits to military health facilities. We have identified potential responsible co-factors leading to location variability, e.g., region or state locale, military service type and/or the ratio of military to civilian populations. For most locations, ILI proportions positively correlate with sadness and neutral sentiment, which are the affects most often expressed during high ILI season. The ILI proportions negatively correlate with fear, disgust, surprise, and positive sentiment. These results are similar to the low ILI season where anger, surprise, and positive sentiment are highest. Finally, cross-correlation analysis shows that most affects lead ILI clinical visits, i.e. are predictive of ILI data, with affect-ILI leading intervals dependent on geo-location and affect type. Altogether, information gained in this study exemplifies a usage of social media data to understand the correlation between psychological behavior and health in the military population and the potential for use of social media affects for prediction of ILI cases.

60 APPLIED LIFE SCIENCES↗

Soda Pop: A Time-Series Clustering, Alarming and Disease Forecasting Application

To introduce Soda Pop, an R/Shiny application designed to be a disease agnostic time-series clustering, alarming, and forecasting tool to assist in disease surveillance “triage, analysis and reporting” workflows within the Biosurveillance Ecosystem (BSVE). In this poster, we highlight the new capabilities that are brought to the BSVE by Soda Pop with an emphasis on the impact of methodological decisions. The Biosurveillance Ecosystem (BSVE) is a biological and chemical threat surveillance system sponsored by the Defense Threat Reduction Agency (DTRA). BSVE is intended to be user-friendly, multi-agency, cooperative, modular and threat agnostic platform for biosurveillance. In BSVE, a web-based workbench presents the analyst with applications (apps) developed by various DTRA funded researchers, which are deployed on-demand in the cloud(e.g., Amazon Web Services). These apps aim to address emerging needs and refine capabilities to enable early warning of chemical and biological threats for multiple users across local, state, and federal agencies. Soda Pop is an app developed by Pacific Northwest National Laboratory (PNNL) to meet the current needs of the BSVE for early warning and detection of disease outbreaks. Aimed for use bya diverse set of analysts, the application is agnostic to data source and spatial scale enabling it to be generalizable across many diseases and locations. To achieve this, we placed a particular emphasis on clustering and alerting of disease signals within Soda Pop without strong prior assumptions on the nature of observed diseased counts. Although designed to be agnostic to the data source, Soda Pop was initially developed and tested on data summarizing Influenza-Like Illness in military hospitals from collaboration with the Armed Forces Health Surveillance Branch. Currently, the data incorporated also includes the CDC’s National Notifiable Diseases Surveillance System(NNDSS) tables and the WHO’s Influenza A/B Influenza Data(Flunet). These data sources are now present in BSVE’s Postgres data storage for direct access. Soda Pop is designed to automate time-series tasks of data summarization, exploration, clustering, alarming and forecasting. Built as an R/Shiny application, Soda Pop is founded on the powerful statistical tool R.. Where applicable, Soda Pop facilitates nonparametric seasonal decomposition of time-series; hierarchical agglomerative clustering across reporting areas and between diseases within reporting areas; and a variety of alarming techniques including Exponential Weighted Moving Average alarms and Early Aberration Detection. Soda Pop embeds these techniques within a user-interface designed to enhance an analyst’s understanding of emerging trends in their data and enables the inclusion of its graphical elements into their dossier for further tracking and reporting. The ultimate goal of this software is to facilitate the discovery of unknown disease signals along with increasing the speed of detection of unusual patterns within these signals. Soda Pop organizes common statistical disease surveillance tasks in a manner integrated with BSVE data source inputs and outputs. The app analyzes time-series disease data and supports a robust set of clustering and alarming routines that avoid strong assumptions on the nature of observed disease counts. This attribute allows for flexibility in the data source, spatial scale, and disease types making it useful to a wide range of analysts.

97 MATHEMATICS AND COMPUTING↗

Novel Analysis and Visualization of Chemical Events for Public Health Surveillance

Pacific Northwest National Laboratory hosted an intern-based web application development contest in the summer of 2016 centered around developing novel chemical surveillance applications to aid in health situational awareness. Making up the three teams were three graduate students (n=9) from various US schools majoring in non-public health domains, such as computer science and user design. The interns successfully developed three applications that demonstrated a value-add to chemical surveillance—ChemAnalyzer (text analytics), RetroSpect (retrospective analysis of chemical events),and ToxicBusters (geo-based trend analytics). These applications will be the basis for the first chemical surveillance application to be incorporated into the DTRA Biosurveillance Ecosystem (BSVE).Pacific Northwest National Laboratory (PNNL), on behalf the Defense Threat Reduction Agency (DTRA; project number CB10190), hosts an annual intern- based web app development contest. Previous competitions have focused on mobile biosurveillance. The 2016 competition pivoted away from biosurveillance to focus on addressing challenges within the field of chemical surveillance and increasing public health chemical situational awareness. The result of the app will be integrated within the DTRA BSVE. PNNL hosted nine graduate interns for a 10-week period in the summer of 2016 as participants in a summer web application development contest. Students were drawn from such fields as software engineering and user experience and design and placed into three teams of three students. The challenge presented to the interns was to design and develop a fully-functional web application that would address a critical need within the chemical surveillance community. The interns developed their own ideas (vetted by PNNL and DTRA), discovered and integrated their own data sources, and produced their own visualizations and analytics, independent of any assistance outside of that provided in an advisory capacity. The competition end with a judging event with a panel of subject matter experts and cash awards were distributed to the teams. Each team produced a unique application. Although there was mild overlap between some of the ideas, the applications were developed independently and each reflected the unique contributions of the teams. ChemAnalyzer is a text-analytics platform designed to facilitate more data-driven decision, given a corpus of text data about a chemical event. Their platform provided the ability to automatically identify and highlight key words in documents related to chemical events. The keywords are drawn from an ontology installed with the system, as well as any user-identified keywords. The ChemAnalyzer team finished in third place. The RetroSpect team developed a visual analytic tool for performing retrospective analysis and monitoring of chemical events. Their app provided the ability to search and analyze past events, as well as visualization of state and county information for the recorded chemical events. The RetroSpect team finished in second place. The Toxic busters team - the winners of the competition - created a geo-based situational awareness tool for tracking chemical events. Their app featured an updateable map overlay, search functionality for finding specific or related events, incident and city/state/national-level statistics and trends, as well as news and social media integration based on keywords related to chemical surveillance. Each of the apps developed by the teams provides value to an analyst tasked with monitoring chemical events. The apps integrated unique data sources to provides a full picture of a chemical event, and its effects upon the surrounding population. This integrated analytics provides a valuable benefit over existing workflows, where analysts must monitor news, social, and other information sources manually for real-time information. The apps developed by these interns are designed to enable identification and analysis of the incident as quickly as possible, allowing for more timely assessments of the incident and its impacts. The web app development contest provided a unique opportunity for students to learn about the emerging needs in chemical surveillance as it relates to health situational awareness. Students were drawn from a variety of fields and were tasked with developing novel web apps addressing some of the most pressing challenges in the field of chemical surveillance. The ideas generated by the students will help form the basis for future chemical surveillance application development to be integrated with the DTRABSVE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ChemAnalyzer: A Text Analytics Platform for Chemical Surveillance

ChemAnalyzer is designed to highlight and summarize important information in chemical incident reportings and other textual sources to reduce the burden on a chemical analyst. By reducing time spent identifying relevant information and summarizing important characteristics, the application (app) enables expedient and thorough surveillance of multiple sources to identify a potential chemical incident.

Gaurav, Sanket↗

Biosurveillance Using Clinical Diagnoses and Social Media Indicators in Military Populations

U.S. military influenza surveillance uses electronic reporting of clinical diagnoses to monitor health of military personnel and detect naturally occurring and bioterrorism-related epidemics. While accurate, these systems lack in timeliness. More recently, researchers have used novel data sources to detect influenza in real time and capture nontraditional populations. With data-mining techniques, military social media users are identified and influenza-related discourse is integrated along with medical data into a comprehensive disease model. By leveraging heterogeneous data streams and developing dashboard biosurveillance analytics, the researchers hope to increase the speed at which outbreaks are detected and provide accurate disease forecasting among military personnel.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Using Social Media to Measure Student Wellbeing: A Large-Scale Study of Emotional Response in Academic Discourse

Student resilience and emotional well-being are essential for both academic and social development. Earlier studies on tracking students' happiness in academia showed that many of them struggle with mental health issues. For example, a 2015 study at the University of California Berkeley found that 47% of graduate students suffer from depression, following a 2005 study that showed 10% had considered suicide. This is the first large-scale study that uses signals from social media to evaluate students' emotional well-being in academia. This work presents fine-grained emotion and opinion analysis of 79,329 tweets produced by students from 44 universities. The goal of this study is to qualitatively evaluate and compare emotions and sentiments emanating from students' communications across different academic discourse types and across universities in the U.S. We first build novel predictive models to categorize academic discourse types generated by students into personal, social, and general categories. We then apply emotion and sentiment classification models to annotate each tweet with six Ekman's emotions -- joy, fear, sadness, disgust, anger, and surprise and three opinion types -- positive, negative, and neutral. We found that emotions and opinions expressed by students vary across discourse types and universities, and correlate with survey-based data on student satisfaction, happiness and stress. Moreover, our results provide novel insights on how students use social media to share academic information, emotions, and opinions that would pertain to students academic performance and emotional well-being.

academic discourse↗

Understanding Roles of Social Media in Academic Engagement and Satisfaction for Graduate Students

Research indicates positive effects of social media in academia and education. However its main populations have been faculty, teachers, high school or college students, and its primary contexts have been course or classroom settings. We realized there exists a lack of studies on how Ph.D. (broadly graduate) students use social media for academic purposes and how its use is associated with academic motivation, engagement, and satisfaction, which are salient factors for the success of their graduate degrees and life. Based on the survey responses from 91 current Ph.D. students, our study results highlight that (1) students mainly use social media for broadcasting and keeping up with up-to-date academic and research information; yet, making connections and developing professional networks is one of the primary reasons, and (2) social media use is positively associated with their academic engagement and satisfaction. We discuss implications and future work of our study.

social media↗

Discourse, Health and Well-being of Military Populations through the Social Media Lens

Social media can provide a resource for characterizing communities and small populations through activities and content shared online. For instance, studying the language use in social media within military populations may provide insights into their health and wellbeing. In this paper, we address three research questions: (1) How do military populations use social media? (2) What do military users discuss in social media? And (3) Do military users talk about health and well-being differently than civilians? Military Twitter users were identified through keywords in the profile description of users who posted geo-tagged tweets at military installations. The data was anonymized for the analysis. User profiles that belong to military population were compared to the nonmilitary population. Our results indicate that military users talk more about events in their military life, whereas nonmilitary users talk more about school, work, and leisure activities. We also found that the online content generated by both populations is significantly different, including health-related language and communication behavior.

analytics↗

Using social media for actionable disease surveillance and outbreak management. A systematic literature review

Here, research studies show that social media may be valuable tools in the disease surveillance toolkit used for improving public health professionals’ ability to detect disease outbreaks faster than traditional methods and to enhance outbreak response. A social media work group, consisting of surveillance practitioners, academic researchers, and other subject matter experts convened by the International Society for Disease Surveillance, conducted a systematic primary literature review using the PRISMA framework to identify research, published through February 2013, answering either of the following questions: 1) Can social media be integrated into disease surveillance practice and outbreak management to support and improve public health? 2) Can social media be used to effectively target populations, specifically vulnerable populations, to test an intervention and interact with a community to improve health outcomes? Examples of social media included are Facebook, MySpace, microblogs (e.g., Twitter), blogs, and discussion forums. For Question 1, 33 manuscripts were identified, starting in 2009 with topics on Influenza-like Illnesses (n=15), Infectious Diseases (n = 6), Non-infectious Diseases (n=4), Medication and Vaccines (n=3), and Other (n=5). For Question 2, 32 manuscripts were identified, the first in 2000 with topics on Health Risk Behaviors (n=10), Infectious Diseases (n = 3), Non-infectious Diseases (n=9), and Other (n=10). The literature on the use of social media to support public health practice has identified many gaps and biases in current knowledge. Despite the potential for success identified in exploratory studies, there are limited studies on interventions and little use of social media in practice. However, information gleaned from the articles demonstrates the effectiveness of social media in supporting and improving public health and in identifying target populations for intervention. A primary recommendation resulting from the review is to identify opportunities that enable public health professionals to integrate social media analytics into disease surveillance and outbreak management practice.

59 BASIC BIOLOGICAL SCIENCES↗

Social Sensor Analytics: Making Sense of Network Models in Social Media

Social networks can be thought of as noisy sensor networks mapping real world information to the web. Owing to the extensive body of literature in sensor network analysis, this work sought to apply several novel and traditional methods in sensor network analysis for the purposes of efficiently interrogating social media data streams from raw data. We carefully revisit our definition of a social media signal from previous work both in terms of time-varying features within the data and the networked nature of the medium. Further, we detail our analysis of global patterns in Twitter over the months of November 2013 and June 2014, detect and categorize events, and illustrate how these analyses can be used to inform graph-based models of Twitter, namely using a recent network influence model called PhySense: similar to PageRank but tuned to behavioral analysis by leveraging a sociologically inspired probabilistic model. We ultimately identify forms of information dissemination via analysis of time series and dynamic graph spectra and corroborate these findings through manual investigation of the data as a requisite step in modeling the diffusion process with PhySense. We hope to sufficiently characterize global behavior in a medium such as Twitter as a means of learning global model parameters one may use to predict or simulate behavior on a large scale. We have made our time series and dynamic graph analytical code available via a GitHub repository https://github.com/cpatdowling/salsa and our data are available upon request.

event detection↗

Disentangling the Lexicons of Disaster Response in Twitter

Abstract: People around the world use social media platforms such as Twitter heavily to express their opinion about various as- pects of daily life. In the same way social media changes communication in daily life, it also is transforming the way individuals communicate during disasters and emergencies. Emergency officials have come to rely on social media to communicate alerts and updates. How do users communi- cate risk on social media? We used a novel information- theoretic unsupervised learning tool, CorEx, to extract and classify highly relevant words used by the public on Twit- ter during known emergencies, such as fires, explosions, and hurricanes. By utilizing the resulting classification strategy, authorities can use the derived language to craft more rel- evant risk communication to maximize the effectiveness of short-message broadcasts such as the Wireless Emergency Alerts (WEA) service.

clustering↗