Computer Sciences Commons^™

Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models.

Methods: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. …

Automated Identification Of Cell Type Specific Genes In The Mouse Brain By Image Computing Of Expression Patterns, Rongjian Li, Wenlu Zhang, Shuiwang Ji

Computer Science Faculty Publications

Background: Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are expressed only in specific cell-types. Analysis of cell-type-specific gene expression patterns can provide insights into the relationship between genes, connectivity, brain regions, and cell-types. However, automated methods for identifying cell-type-specific genes are lacking to date.

Results: Here, we describe a set of computational methods for identifying cell-type-specific genes in the mouse brain by automated image computing of in situ hybridization (ISH) expression patterns. We applied invariant image feature …

Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He

Computer Science Faculty Publications

Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM …

An Artificial Neural Network For Predicting Crops Yield In Nepal, Tirtha Ranjeet, Leisa Armstrong

Research outputs 2014 to 2021

This paper examines the application of artificial neural networks (ANNs) for predicting crop yields for an agricultural region in Nepal. The neural network algorithm has become an effective data mining tool and the outcome produced by this algorithm is considered to be less error prone than other computer science techniques. The backpropagation algorithm which iteratively finds a suitable weight value is considered for computing the error derivative. Agricultural data was collected from thirteen years from paddy field cultivation in the Siraha district, an eastern region in Nepal, and used for this investigation of neural networks. Additionally, climatic parameters including rainfall, …

A Genetic Algorithm-Based Feature Selection, Oluleye H. Babatunde, Leisa Armstrong, Jinsong Leng, Dean Diepeveen

Research outputs 2014 to 2021

This article details the exploration and application of Genetic Algorithm (GA) for feature selection. Particularly a binary GA was used for dimensionality reduction to enhance the performance of the concerned classifiers. In this work, hundred (100) features were extracted from set of images found in the Flavia dataset (a publicly available dataset). The extracted features are Zernike Moments (ZM), Fourier Descriptors (FD), Lengendre Moments (LM), Hu 7 Moments (Hu7M), Texture Properties (TP) and Geometrical Properties (GP). The main contributions of this article are (1) detailed documentation of the GA Toolbox in MATLAB and (2) the development of a GA-based feature …

Application Of Cellular Neural Networks And Naive Bayes Classifier In Agriculture, Oluleye H. Babatunde, Leisa Armstrong, Jinsong Leng, Dean Diepeveen

Research outputs 2014 to 2021

This article describes the use of Cellular Neural Networks (a class of Ordinary Differential Equation (ODE)), Fourier Descriptors (FD) and NaiveBayes Classifier (NBC) for automatic identification of images of plant leaves. The novelty of this article is seen in the use of CNN for image segmentation and a combination FDs with NBC. The main advantage of the segmentation method is the computation speed compared with other edge operators such as canny, sobel, Laplacian of Gaussian (LoG). The results herein show the potential of the methods in this paper for examining different agricultural images and distinguishing between different crops and weeds …

Mobile Applications For Indian Agriculture Sector: A Case Study, Pratik Shah, Niketa Gandhi, Leisa Armstrong

Research outputs 2014 to 2021

Government, private agencies and the general public are often interested in the decisions made by the Indian farmers as they have large influences beyond the farm boundary. Over many years, the process of adoption of new technologies and policies in the Indian agricultural sector has received considerable academic attention highlighting the role of many social, financial and other influences on their decision making. The Indian government and other development agencies promote income generating projects as a way of encouraging growth through increased agricultural production and the protection of the natural resource base. The impact of new technology to economic growth …

Geospatial Data Pre-Processing On Watershed Datasets: A Gis Approach, Sreedhar Nallan, Leisa Armstrong, Barry Croke, Amiya K. Tripathy

Research outputs 2014 to 2021

Spatial data mining helps to identify interesting patterns from the spatial data sets. However, geo spatial data requires substantial data pre-processing before data can be interrogated further using data mining techniques. Multi-dimensional spatial data has been used to explain the spatial analysis and SOLAP for pre-processing data. This paper examines some of the methods for pre-processing of the data using Arc GIS 10.2 and Spatial Analyst with a case study dataset of a watershed.

A Network That Really Works - The Application Of Artificial Neural Networks To Improve Yield Predictions And Nitrogen Management In Western Australia, Jinsong Leng, Andreas Neuhaus, Leisa Armstrong

Research outputs 2014 to 2021

Yield predictions are notorious for being difficult due to many interdependent factors such as rainfall, soil properties, plant health, plant density etc. This study is based upon the author’s previously published work and extends its findings by further investigating the best mathematical solution to this dilemma. Artificial intelligence (AI) techniques have been applied to a large set of soil, plant, rainfall, and yield data from CSBP’s field research trial program. Here we further differentiate by investigate two ANN techniques, a genetic algorithm with back propagation neural networks (GA-BP-NN) and a particle swarm optimization with back propagation neural networks (PSO-BP-NN). Results …

A Survey Of Image Processing Techniques For Agriculture, Lalit Saxena, Leisa Armstrong

Research outputs 2014 to 2021

Computer technologies have been shown to improve agricultural productivity in a number of ways. One technique which is emerging as a useful tool is image processing. This paper presents a short survey on using image processing techniques to assist researchers and farmers to improve agricultural practices. Image processing has been used to assist with precision agriculture practices, weed and herbicide technologies, monitoring plant growth and plant nutrition management. This paper highlights the future potential for image processing for different agricultural industry contexts.

Decision Support System Data For Farmer Decision Making, Pornchai Taechatanasat, Leisa Armstrong

Research outputs 2014 to 2021

The capacity of farmers and agricultural scientists to be able to make in-season decisions is dependent on accurate climate, soil and plant data. This paper will provide a review of the types of environmental and crop data that can be collected by sensors which can used for decision support systems (DSS) or be further interrogated for real time data mining and analysis. This paper also presents a review of the data requirements for agricultural decision making by firstly reviewing decision support frameworks and agricultural DSSs, data acquisition, sensors for data acquisition and examples of data incorporation for agricultural DSSs.

Genetic Algorithm With Logistic Regression For Prediction Of Progression To Alzheimer's Disease, Piers Johnson, Luke Vandewater, William Wilson, Paul Maruff, Greg Savage, Petra Graham, Lance S. Macaulay, Kathryn A. Ellis, Cassandra Szoeke, Ralph N. Martins, Christopher Rowe, Colin L. Masters, David Ames, Ping Zhang

Research outputs 2014 to 2021

Assessment of risk and early diagnosis of Alzheimer's disease (AD) is a key to its prevention or slowing the progression of the disease. Previous research on risk factors for AD typically utilizes statistical comparison tests or stepwise selection with regression models. Outcomes of these methods tend to emphasize single risk factors rather than a combination of risk factors. However, a combination of factors, rather than any one alone, is likely to affect disease development. Genetic algorithms (GA) can be useful and efficient for searching a combination of variables for the best achievement (eg. accuracy of diagnosis), especially when the search …

Grayscale-Image Encryption Using Random Hill Cipher Over Sln(F) Associated With Discrete Wavelet Transformation, D. C. Mishra, R. K. R. K. Sharma

Applications and Applied Mathematics: An International Journal (AAM)

Image data are highly sensitive and prone to incidental decoding by intruders. The security of image data in an insecure network is therefore a major issue. In this paper, we have presented a novel approach for grayscale-image encryption and decryption using Random Hill cipher over SLn(F) associated with discrete wavelet transformation. Earlier techniques for encryption and decryption of image data discussed missing the keys, but in this approach, both the keys and the arrangement of RHC are emphasized. Additionally, keys multiplication side (pre or post) over a grayscale-image data matrix also inevitable to know, to correctly decrypt the encrypted image …

Clustering And Classification Of Multi-Domain Proteins, Neethu Shah

School of Computing: Dissertations, Theses, and Student Research

Rapid development of next-generation sequencing technology has led to an unprecedented growth in protein sequence data repositories over the last decade. Majority of these proteins lack structural and functional characterization. This necessitates design and development of fast, efficient, and sensitive computational tools and algorithms that can classify these proteins into functionally coherent groups.

Domains are fundamental units of protein structure and function. Multi-domain proteins are extremely complex as opposed to proteins that have single or no domains. They exhibit network-like complex evolutionary events such as domain shuffling, domain loss, and domain gain. These events therefore, cannot be represented in the …

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 …

Automatic Domain Identification For Linked Open Data, Sarasi Lalithsena, Pascal Hitzler, Amit P. Sheth, Prateek Jain

Kno.e.sis Publications

Linked Open Data (LOD) has emerged as one of the largest collections of interlinked structured datasets on the Web. Although the adoption of such datasets for applications is increasing, identifying relevant datasets for a specific task or topic is still challenging. As an initial step to make such identification easier, we provide an approach to automatically identify the topic domains of given datasets. Our method utilizes existing knowledge sources, more specifically Freebase, and we present an evaluation which validates the topic domains we can identify with our system. Furthermore, we evaluate the effectiveness of identified topic domains for the purpose …

Semantics-Empowered Big Data Processing With Applications, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

We discuss the nature of Big Data and address the role of semantics in analyzing and processing Big Data that arises in the context of Physical-Cyber-Social Systems. We organize our research around the Five Vs of Big Data, where four of the Vs are harnessed to produce the fifth V - value. To handle the challenge of Volume, we advocate semantic perception that can convert low-level observational data to higher-level abstractions more suitable for decision-making. To handle the challenge of Variety, we resort to the use of semantic models and annotations of data so that much of the intelligent processing …

Pcaanalyser: A 2d-Image Analysis Based Module For Effective Determination Of Prostate Cancer Progression In 3d Culture, Md Tamjidul Hoque, Louisa C. E. Windus, Carrie J. Lovitt, Vicky M. Avery

Computer Science Faculty Publications

Three-dimensional (3D) in vitro cell based assays for Prostate Cancer (PCa) research are rapidly becoming the preferred alternative to that of conventional 2D monolayer cultures. 3D assays more precisely mimic the microenvironment found in vivo, and thus are ideally suited to evaluate compounds and their suitability for progression in the drug discovery pipeline. To achieve the desired high throughput needed for most screening programs, automated quantification of 3D cultures is required. Towards this end, this paper reports on the development of a prototype analysis module for an automated high-content-analysis (HCA) system, which allows for accurate and fast investigation of …

City Notifications As A Data Source For Traffic Management, Pramod Anantharam, Biplav Srivastava

Kno.e.sis Publications

A common problem for cities of developing countries like India in managing traffic is the lack of basic automated instrumentation to track road conditions or vehicle locations. Still, to help their citizens make informed travel decisions based on changing city dynamics; many cities have an authorized, city-initiated, notification service in place to alert subscribing commuters about road conditions. Here, alternative means may be used to create informal textual notifications e.g., inputs from field personnel, citizen updates, and pre-authorized events from city calendar. In this paper, we show that collections of such notifications, when processed with information extraction techniques, can turn …

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 …

Reasoning Across Language And Vision In Machines And Humans, Andrei Barbu

Open Access Dissertations

Humans not only outperform AI and computer-vision systems, but use an unknown computational mechanism to perform tasks for which no suitable approaches exist. I present work investigating both novel tasks and how humans approach them in the context of computer vision and linguistics. I demonstrate a system which, like children, acquires high-level linguistic knowledge about the world. Robots learn to play physically-instantiated board games and use that knowledge to engage in physical play. To further integrate language and vision I develop an approach which produces rich sentential descriptions of events depicted in videos. I then show how to simultaneously detect …

A Statistical And Schema Independent Approach To Identify Equivalent Properties On Linked Data, Kalpa Gunaratna, Krishnaprasad Thirunarayan, Prateek Jain, Amit P. Sheth, Sanjaya Wijeratne

Kno.e.sis Publications

Linked Open Data (LOD) cloud has gained significant attention in the Semantic Web community recently. Currently it consists of approximately 295 interlinked datasets with over 50 billion triples including 500 million links, and continues to expand in size. This vast source of structured information has the potential to have a significant impact on knowledge-based applications. However, a key impediment to the use of LOD cloud is limited support for data integration tasks over concepts, instances, and properties. Efforts to address this limitation over properties have focused on matching data-type properties across datasets; however, matching of object-type properties has not received …

Mining Effective Multi-Segment Sliding Window For Pathogen Incidence Rate Prediction, Lei Duan, Changjie Tang, Xiasong Li, Guozhu Dong, Xianming Wang, Jie Zuo, Min Jiang, Zhongqi Li, Yongqing Zhang

Kno.e.sis Publications

Pathogen incidence rate prediction, which can be considered as time series modeling, is an important task for infectious disease incidence rate prediction and for public health. This paper investigates the application of a genetic computation technique, namely GEP, for pathogen incidence rate prediction. To overcome the shortcomings of traditional sliding windows in GEP-based time series modeling, the paper introduces the problem of mining effective sliding window, for discovering optimal sliding windows for building accurate prediction models. To utilize the periodical characteristic of pathogen incidence rates, a multi-segment sliding window consisting of several segments from different periodical intervals is proposed and …

Types Of Property Pairs And Alignment On Linked Datasets - A Preliminary Analysis, Kalpa Gunaratna, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Dataset publication on the Web has been greatly influenced by the Linked Open Data (LOD) project. Many interlinked datasets have become freely available on the Web creating a structured and distributed knowledge representation. Analysis and aligning of concepts and instances in these interconnected datasets have received a lot of attention in the recent past compared to properties. We identify three different categories of property pairs found in the alignment process and study their relative distribution among well known LOD datasets. We also provide comparative analysis of state-of-the-art techniques with regard to different categories, highlighting their capabilities. This could lead to …

Utilizing A Modular Approach To Gamification To Improve Nutrition And Fitness In Children, Chad Richards

Graduate Theses and Dissertations

Obesity is a worldwide epidemic that affects adults and children, impacts over 30% of the population in several states of the U.S., damages national economies, and is a factor in four out of the six of the leading causes of death, including diabetes and heart disease. Obesity is preventable: solution approaches include better education, more exercise, better nutrition, and changing eating habits. Still, it is difficult for many people to remain interested enough to educate themselves and to learn new behaviors to change their eating and exercise habits.

Gamification is a relatively new research area that involves using video game …

From Questions To Effective Answers: On The Utility Of Knowledge-Driven Querying Systems For Life Sciences Data, Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya S. Sahoo, Priti Parikh, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and provides intuitive form-based interfaces to facilitate querying of the data, commonly used by the life science researchers that we study. The second approach utilizes a large OWL ontology and the same datasets associated as RDF instances of the ontology. Both approaches are being used in parallel by a team of cell biologists in their daily research activities, with the objective of gradually replacing the conventional approach with the knowledge-driven one. We describe several benefits …

Crisis Response Coordination In Online Communities, Hemant Purohit

Kno.e.sis Publications

During recent crises, citizens (sensors) are increasingly using social media to share variety of information- situation on the ground, emerging needs, donation offers, damage, etc. In such an evolving ad-hoc community, how can we extract actionable nuggets from the social media streams to aid relief efforts? This doctoral consortium presentation summarizes a framework to analyze social data and manage information to assist coordination by focusing on three important questions to answer: Whom to coordinate with, Why to coordinate and How to coordinate, with exemplary insights for needs and availability from the recent disaster events.

Demo: Approximate Semantic Matching In The Collider Event Processing Engine, Souleiman Hasan, Kalpa Gunaratna, Yongrui Qin, Edward Curry

Kno.e.sis Publications

This demo presents a use case from the energy management domain. It builds upon previous work on approximate semantic matching of heterogeneous events and compares two semantic matching scenarios: exact and approximate. It illustrates how a large number of exact matching event subscriptions are needed to match heterogeneous power consumption events. It then demonstrates how a small number of approximate semantic matching subscriptions are needed but possibly with a lower true positives/negatives performance. The demo is delivered via the COLLIDER approximate event processing engine currently under development in DERI.

Dynamics Of The Fitzhugh-Nagumo Neuron Model, Zechariah Thurman

Physics

In this paper, the dynamical behavior of the Fitzhugh-Nagumo model is examined. The relationship between neuron input current and the firing frequency of the neuron is characterized. Various coupling schemes are also examined, and their effects on the dynamics of the system is discussed. The phenomenon of stochastic resonance is studied for a single uncoupled Fitzhugh-Nagumo neuron.

Genome Wide Search For Pseudo Knotted Non-Coding Rnas, Meghana S. Vasavada

Theses

Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To annotate an individual genome for a specific family of ncRNAs, a computational tool is interpreted to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a …