Data Science Commons^™

So What Are You Going To Do With That? The Promises And Pitfalls Of Massive Data Sets, Sigrid Anderson Cordell, Melissa Gomis

University of Nebraska-Lincoln Libraries: Faculty Publications

This article takes as its case study the challenge of data sets for text mining, sources that offer tremendous promise for digital humanities (DH) methodology but present specific challenges for humanities scholars. These text sets raise a range of issues: What skills do you train humanists to have? What is the library’s role in enabling and supporting use of those materials? How do you allocate staff? Who oversees sustainability and data management? By addressing these questions through a specific use case scenario, this article shows how these questions are central to mapping out future directions for a range of library …

Tools And Techniques For Computational Reproducibility, Stephen Piccolo, Michael B. Frampton

Faculty Publications

When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will …

The Global Rock-Art Database Project Towards Machine Learning: Building A Collaborative Open Source Platform For Heritage Management From Information Structure To Information Visualization Using Australian Heritage Examples, Robert Haubt

Staff Scholarship - Australia & Dubai

This guest talk, presented at Lava Lab at the University of Hawaiʻi, explores the intersection of collaboration, data ontology, and information visualization in advancing machine learning within the Global Rock Art Database project. Drawing on insights from the project’s first four years, the talk emphasizes the critical need for cultural heritage preservation by systematically recording and structuring global rock art data in accessible and sustainable ways. This effort not only supports public education on rock art but also facilitates scholarly research.

Key discussions include advancements in data ontology using the CIDOC Conceptual Reference Model (CIDOC CRM) for semantic data management …

Two Influential Primate Classifications Logically Aligned, Nico M. Franz, Naomi M. Pier, Deeann M. Reeder, Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Shaun Bowers, Bertram Ludäscher

Computer Science Faculty Scholarship

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence inways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications.We demonstrate that such alignments are feasible for …

Names Are Not Good Enough: Reasoning Over Taxonomic Change In The Andropogon Complex, Nico M. Franz, Mingmin Chen, Parisa Kianmajd, Shizhuo Yu, Shaun Bowers, Alan S. Weakley, Bertram Ludäscher

Computer Science Faculty Scholarship

We present a novel, logic-based solution to the challenge of reconciling the meanings of taxonomic names across multiple biological taxonomies. The challenge arises due to limitations inherent in using type-anchored taxonomic names as identifiers of granular semantic similarities and differences being expressed in original and revised taxonomic classifications. We address this challenge through: (1) the use of taxonomic concept labels – thereby individuating name usages according to particular sources and allowing each taxonomy to be recognized separately; (2) sets of user-provided Region Connection Calculus articulations among concepts (RCC-5: congruence, proper inclusion, inverse proper inclusion, overlap, exclusion); and (3) the use …

Mining Human Activity Using Dimensionality Reduction And Pattern Recognition, Ismail El Moudden, Mounir Ouzir, Badreddine Benyacoub, Souad El Bernoussi

Research and Infrastructure Service Enterprise (RISE) Faculty Publications

Human activity recognition (HAR) is an emerging research topic in pattern recognition, especially in computer vision. The main objective of human activity recognition is to automatically detect and analyze human activities from the information acquired from different sensors. Human activity prediction using big data remains a challengingly open problem. Several approaches have recently been developed in order to find practical ways to solve high dimensionality of data problems. The aim of this study is to attempt, using data mining techniques, to deal with HAR modeling involving a significant number of variables in order to identify relevant parameters from data and …

An Improved Smote Algorithm Based On Genetic Algorithm For Imbalanced Data Collection, Qiong Gu, Xian-Ming Wang, Zhao Wu, Bing Ning, Chun-Sheng Xin

Electrical & Computer Engineering Faculty Publications

Classification of imbalanced data has been recognized as a crucial problem in machine learning and data mining. In an imbalanced dataset, minority class instances are likely to be misclassified. When the synthetic minority over-sampling technique (SMOTE) is applied in imbalanced dataset classification, the same sampling rate is set for all samples of the minority class in the process of synthesizing new samples, this scenario involves blindness. To overcome this problem, an improved SMOTE algorithm based on genetic algorithm (GA), namely, GASMOTE was proposed. First, GASMOTE set different sampling rates for different minority class samples. A combination of the sampling rates …

Results And Challenges In Visualizing Analytic Provenance Of Text Analysis Tasks Using Interaction Logs, Rhema Linder, Alyssa M. Peña, Sampath Jayarathna, Eric D. Ragan

Computer Science Faculty Publications

After data analysis, recalling and communicating the steps and rationale followed during the analysis can be difficult. This paper explores the use of interaction logs to generate summaries of an analyst's interest based on interactions with specific data items in a text analysis scenario. Our approach uses data-interaction events as a proxy for user interest in and experience of information. Logging can produce verbose logs that detail all available readable content, so the discussed approach uses topic modeling (LDA) over different time segments to summarize the verbose information and generate visualizations of the history of user interest. Our preliminary results …

Data Science In Statistics Curricula: Preparing Students To “Think With Data”, J. Hardin, R. Hoerl, Nicholas J. Horton, D. Nolan, B. Baumer, O. Hall-Holt, P. Murrell, R. Peng, P. Roback, D. Temple Lang, M. D. Ward

Statistical and Data Sciences: Faculty Publications

A growing number of students are completing undergraduate degrees in statistics and entering the workforce as data analysts. In these positions, they are expected to understand how to use databases and other data warehouses, scrape data from Internet sources, program solutions to complex problems in multiple languages, and think algorithmically as well as statistically. These data science topics have not traditionally been a major component of undergraduate programs in statistics. Consequently, a curricular shift is needed to address additional learning outcomes. The goal of this article is to motivate the importance of data science proficiency and to provide examples and …

Engineering Analytics: Research Into The Governance Structure Needed To Integrate The Dominant Design Methodologies, Teddy Steven Cotter

Engineering Management & Systems Engineering Faculty Publications

In the ASEM-IAC 2014, Cotter (2014) explored the current state of engineering design, identified the dominate approaches to engineering design, discussed potential contributions from the new field of data analytics to engineering design, and proposed an Engineering Analytics framework that integrates the dominate engineering design approaches and data analytics within a human-intelligence/machine-intelligence (HI-MI) design architecture. This paper reports research applying ontological engineering to integrate the dominate engineering design methodologies into a systemic engineering design decision governance architecture.

Reasoning Over Taxonomic Change: Exploring Alignments For The Perelleschus Use Case, Nico M. Franz, Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Shaun Bowers, Bertram Ludäscher

Computer Science Faculty Scholarship

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted …

Adaptive Graph Construction For Isomap Manifold Learning, Loc Tran, Zezhong Zheng, Guoquing Zhou, Jiang Li, Karen O. Egiazarian (Ed.), Sos S. Agaian (Ed.), Atanas P. Gotchev (Ed.)

Electrical & Computer Engineering Faculty Publications

Isomap is a classical manifold learning approach that preserves geodesic distance of nonlinear data sets. One of the main drawbacks of this method is that it is susceptible to leaking, where a shortcut appears between normally separated portions of a manifold. We propose an adaptive graph construction approach that is based upon the sparsity property of the ℓ₁ norm. The ℓ₁ enhanced graph construction method replaces k-nearest neighbors in the classical approach. The proposed algorithm is first tested on the data sets from the UCI data base repository which showed that the proposed approach performs better than …

Visualization Of Multidimensional Data With Collocated Paired Coordinates And General Line Coordinates, Boris Kovalerchuk

All Faculty Scholarship for the College of the Sciences

Often multidimensional data are visualized by splitting n-D data to a set of low dimensional data. While it is useful it destroys integrity of n-D data, and leads to a shallow understanding complex n-D data. To mitigate this challenge a difficult perceptual task of assembling low-dimensional visualized pieces to the whole n-D vectors must be solved. Another way is a lossy dimension reduction by mapping n-D vectors to 2-D vectors (e.g., Principal Component Analysis). Such 2-D vectors carry only a part of information from n-D vectors, without a way to restore n-D vectors exactly from it. An alternative way for …

Semantics In Support Of Biodiversity Knowledge Discovery: An Introduction To The Biological Collections Ontology And Related Ontologies, Ramona L. Walls, John Deck, Robert Guralnick, Steve Baskauf, Reed Beaman, Stanley Blum, Shaun Bowers

Computer Science Faculty Scholarship

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to …

Information In Biological Systems And The Fluctuation Theorem, Yaşar Demirel

Department of Chemical and Biomolecular Engineering: Faculty Publications

Some critical trends in information theory, its role in living systems and utilization in fluctuation theory are discussed. The mutual information of thermodynamic coupling is incorporated into the generalized fluctuation theorem by using information theory and nonequilibrium thermodynamics. Thermodynamically coupled dissipative structures in living systems are capable of degrading more energy, and processing complex information through developmental and environmental constraints. The generalized fluctuation theorem can quantify the hysteresis observed in the amount of the irreversible work in nonequilibrium regimes in the presence of information and thermodynamic coupling.

Classification With Hidden Markov Model, Badreddine Benyacoub, Souad Elbernoussi, Abdelhak Zoglat, Ismail El Moudden

Research and Infrastructure Service Enterprise (RISE) Faculty Publications

Classification and statistical learning by hidden markov model has achieved remarkable progress in the past decade. They have been applied in many areas like speech recognition and handwriting recognition. However, learning by Hidden Markov Model (HMM) is still restricted to supervised problems. In this paper, we propose a new learning method based on HMM techniques estimations, to built a model for classification. The approach consists of evaluation of the probability to belonging in one group, given the observations by a linear classifier. Our developed algorithm is based on discrete states and discrete observations cases of HMM. Experimental results show that …

Short-Term Inflation Forecasting Models For Nigeria, Sani I. Doguwa, Sarah O. Alade

CBN Journal of Applied Statistics (JAS)

Short-term inflation forecasting is an essential component of the monetary policy projections at the Central Bank of Nigeria. This paper proposes four short-term headline inflation forecasting models using the SARIMA and SARIMAX processes and compares their performance using the pseudo-out-of-sample forecasting procedure over July 2011 to September 2013. According to the results the best forecasting performance is demonstrated by the model based on the all items CPI estimated using the SARIMAX model. This model is, therefore, recommended for use in short-term forecasting of headline inflation in Nigeria. The forecasting performance up to eight months ahead, of the models based on …

An Efficient Two Sample Capture-Recapture Model With High Recaptures, Danjuma Jibasen, Yusuf J. Adams

CBN Journal of Applied Statistics (JAS)

This paper proposed an efficient two sample capture-recapture model (Ma) with high recaptures and compared it with the existing models like the model of no factor effect (Mo), behavioral response model (Mb) and the Petersen model (Ms), using simulated data. We found that the Petersen model provides a better estimate of the population size when the observations follow a hypergeometric distribution and the population is overestimated when recapture is high. It was also found that the proposed model provides a better estimator of the population size than the existing ones when the recapture is high. This model is particularly useful …

Causal Relationship Between Stock Market Index And Exchange Rate: Evidence From Nigeria, Abdulrasheed Zubair

CBN Journal of Applied Statistics (JAS)

This paper uses Johansen’s cointegration to test for the possibility of cointegration and Granger-causality to estimate the causal relationship between stock market index and monetary indicators (exchange rate and M2) before and during the global financial crisis for Nigeria, using monthly data for the period 2001–2011. Results suggest absence of long-run relationship before and during the crisis. The Granger-causality tests show a uni-directional causality running from M2 to ASI before the crisis while during the period of the crisis there is absence of causality between the variables. This suggests that ASI show responsiveness to M2. Thus, absence of the direct …

Investigating Chaos In The Nigerian Asset And Resource Management (Arm) Discovery Fund, Ibiyinka A. Fuwape, Samuel T. Ogunjo

CBN Journal of Applied Statistics (JAS)

This paper investigates chaos in a Nigerian mutual fund, Asset and Resource Management Company Limited (ARM) for a period of eleven years. The existence of chaotic signals in the data was identified by the reconstruction of the phase space of the daily closing price of the fund and the delay time was quantified using mutual information function and the embedding dimension by the false nearest neighbours, where the values were identified to be 15 and 20 respectively. The presence of chaotic signals in the ARM data was further confirmed by the correlation dimension method which yielded a dimension of 2.2 …

Modeling The Nigerian Inflation Rates Using Periodogram And Fourier Series Analysis, Chukwuemeka O. Omekara,, Emmanuel J. Ekpenyong, Micheal P. Ekerete

CBN Journal of Applied Statistics (JAS)

This work considers the application of Periodogram and Fourier Series Analysis to model all-items monthly inflation rates in Nigeria from 2003 to 2011. The main objectives are to identify inflation cycles, fit a suitable model to the data and make forecasts of future values. To achieve these objectives, monthly all-items inflation rates for the period were obtained from the Central Bank of Nigeria (CBN) website. Periodogram and Fourier series methods of analysis are used to analyze the data. Based on the analysis, it was found that inflation cycle within the period was fifty one (51) months, which coincides with the …

Nigerian Stock Index: A Search For Optimal Garch Model Using High Frequency Data, Olaoluwa Simon Yaya

CBN Journal of Applied Statistics (JAS)

This paper attempts to fit the best Generalized Autoregressive Conditional Heteroscedastic (GARCH) model for All Share Index (ASI) of Nigerian Stock Exchange (NSE) returns. A search is made on various GARCH variants specified on the assumptions of stationarity and asymmetry. Fractionally integrated types are also considered to capture the possibility of return series having property of long range dependency. The parameter estimations are carried out on the assumptions of normality and non-normality of GARCH innovations, with models and forecasts evaluated using information criteria and loss functions respectively. Under normality assumption, Hyperbolic GARCH (HYGARCH(1,d,1)) model is selected and Integrated GARCH (IGARCH(1,1)) …

Time Series Modeling Of Nigeria External Reserves, Iheanyichukwu S. Iwueze, Eleazar C. Nwogu, Valentine U. Nlebedim

CBN Journal of Applied Statistics (JAS)

This paper discusses the levels and trend of external reserves in Nigeria. The relevance of this lies in the fact that it could help to monitor the reserves and throw early warning signal about any economic crisis. Monthly data on Nigeria external reserves for the period January 1999 to December, 2008 derived from the 2008 CBN Statistical Bulletin was analyzed using ARIMA model. Results of the analyses show that (i) the data requires logarithmic transformation to stabilize the variance and make the distribution normal (ii) the appropriate model that best describes the pattern in the transformed data is the Autoregressive- …

A Markov Decision Process Approach To Optimal Control Of A Multi-Level Hierarchical Manpower System, Akaninyene U. Udom

CBN Journal of Applied Statistics (JAS)

A recurrent problem in manpower control is how to attain the desired structural configuration in an optimal way, since it is possible to reach a desired structural configuration using different control inputs. The major aim of this paper is to develop a Markov Decision Process for optimal control of a Multi-level Hierarchical Manpower System (MHMS) by promotion and interdepartmental transfers. This is examined under control by intervention and contraction cost Markov Decision Process.

Mapping The Invisible: A Framework For Tracking Covid-19 Spread Among College Students With Google Location Data, Prajindra Sankar Krishnan, Chai Phing Chen, Gamal Alkawsi, Sieh Kiong Tiong, Luiz Fernando Capretz

Electrical and Computer Engineering Publications

The COVID-19 pandemic and the implementation of social distancing policies have rapidly changed people's visiting patterns, as reflected in mobility data that tracks mobility traffic using location trackers on cell phones. However, the frequency and duration of concurrent occupancy at specific locations govern the transmission rather than the number of customers visiting. Therefore, understanding how people interact in different locations is crucial to target policies, inform contact tracing, and prevention strategies. This study proposes an efficient way to reduce the spread of the virus among on-campus university students by developing a self-developed Google History Location Extractor and Indicator software based …

Estimating Loop Length From Cryoem Images At Medium Resolutions, Andrew Mcknight, Dong Si, Kamal Al Nasr, Andrey Chernikov, Nikos Chrisochoides, Jing He

Computer Science Faculty Research

Background

De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results

We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method …

Rigidity Analysis Of Protein Biological Assemblies And Periodic Crystal Structures, Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu

All Faculty Scholarship for the College of the Sciences

Background

We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu.

Results

We provide two types of results: on biological assemblies and on crystals. We found that when only isolated …

As Strong As The Weakest Link: Mining Diverse Cliques In Weighted Graphs, Petko Bogdanov, Ben Baumer, Prithwish Basu, Amotz Bar-Noy, Ambuj K. Singh

Statistical and Data Sciences: Faculty Publications

Mining for cliques in networks provides an essential tool for the discovery of strong associations among entities. Applications vary, from extracting core subgroups in team performance data arising in sports, entertainment, research and business; to the discovery of functional complexes in high-throughput gene interaction data. A challenge in all of these scenarios is the large size of real-world networks and the computational complexity associated with clique enumeration. Furthermore, when mining for multiple cliques within the same network, the results need to be diversified in order to extract meaningful information that is both comprehensive and representative of the whole dataset. We …

A Conservation And Rigidity Based Method For Detecting Critical Protein Residues, Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel

All Faculty Scholarship for the College of the Sciences

Background

Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine …

Detecting Student Dropouts Using Fuzzy Inferencing, Shahriar Husainy

Theses and Dissertations

Fuzzy logic provides a methodology for reasoning using imprecise rules and assertions. Fuzzy inference is the process of formulating the mapping from a given input to an output using fuzzy logic. The mapping then provides a basis from which decisions can be made, or patterns discerned. This study concerns the development of a Fuzzy Inference System (FIS) for identifying likely student dropouts at Columbus State University (CSU). The fuzzy inference based model uses a hybrid knowledge extraction process to predict how likely each freshman student will be to drop their program of study at the end of their first semester. …