Physical Sciences and Mathematics Commons^™

A Genetic Algorithm For Multiobjective Hard Scheduling Optimization, Elías Niño, Carlos Ardila, Alfredo J. Perez, Yexid Donoso

Computer Science Faculty Publications

This paper proposes a genetic algorithm for multiobjective scheduling optimization based in the object oriented design with constrains on delivery times, process precedence and resource availability. Initially, the programming algorithm (PA) was designed and implemented, taking into account all constraints mentioned. This algorithm’s main objective is, given a sequence of production orders, products and processes, calculate its total programming cost and time.
Once the programming algorithm was defined, the genetic algorithm (GA) was developed for minimizing two objectives: delivery times and total programming cost. The stages defined for this algorithm were: selection, crossover and mutation. During the first stage, the …

3d Oceanographic Data Compression Using 3d-Odetlap, You Li, Tsz-Yam Lau, Christopher S. Stuetzle, Peter Fox, W. Randolph Franklin

Computer Science Faculty Publications

This paper describes a 3D environmental data compression technique for oceanographic datasets. With proper point selection, our method approximates uncompressed marine data using an over-determined system of linear equations based on, but essentially different from, the Laplacian partial differential equation. Then this approximation is refined via an error metric. These two steps work alternatively until a predefined satisfying approximation is found. Using several different datasets and metrics, we demonstrate that our method has an excellent compression ratio. To further evaluate our method, we compare it with 3D-SPIHT. 3D-ODETLAP averages 20% better compression than 3D-SPIHT on our eight test datasets, from …

Quantitative Analysis Of Simulated Erosion For Different Soils, Zhongxian Chen, Christopher S. Stuetzle, Barbara Cutler, Jared Gross, W. Randolph Franklin, Thomas F. Zimmie

Computer Science Faculty Publications

Levee overtopping can lead to failure and cause catastrophic damage, as was the case during Hurricane Katrina. We present a computer simulation of erosion to study the development of the rills and gullies that form along an earthen embankment during overtopping. We have coupled 3D Smoothed Particle Hydrodynamics with an erodibility model to produce our simulation. Through comparison between simulations and between simulation and analogous laboratory experiments, we provide quantitative and qualitative results, evaluating the accuracy of our simulation.

Mapsplice: Accurate Mapping Of Rna-Seq Reads For Splice Junction Discovery, Kai Wang, Darshan Singh, Zheng Zeng, Stephen J. Coleman, Yan Huang, Gleb L. Savich, Xiaping He, Piotr Mieczkowski, Sara A. Grimm, Charles M. Perou, James N. Macleod, Derek Y. Chiang, Jan F. Prins, Jinze Liu

Computer Science Faculty Publications

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.

Simulating Levee Erosion With Physical Modeling Validation, Jared Gross, Christopher S. Stuetzle, Zhongxian Chen, Barbara Cutler, W. Randolph Franklin, Thomas F. Zimmie

Computer Science Faculty Publications

This paper studies rill and gully initiation and propagation on levees, dams, and general earth embankments. It specifically studies where these erosion features occur, and how long a particular embankment can sustain overtopping before breaching and catastrophic failure. This contrasts to previous levee erosion analysis, which has primarily concerned the final effects of erosion, such as soil loss, depth of scour and breach width. This paper describes the construction of scaled-down physical models of levees composed of different homogeneous sands, as well as sand-clay mixtures, and their laboratory testing. A 3-D laser range scanner captured the surface features of the …

Program Transformations For Information Personalization, Saverio Perugini, Naren Ramakrishnan

Computer Science Faculty Publications

Personalization constitutes the mechanisms necessary to automatically customize information content, structure, and presentation to the end user to reduce information overload. Unlike traditional approaches to personalization, the central theme of our approach is to model a website as a program and conduct website transformation for personalization by program transformation (e.g., partial evaluation, program slicing). The goal of this paper is study personalization through a program transformation lens and develop a formal model, based on program transformations, for personalized interaction with hierarchical hypermedia. The specific research issues addressed involve identifying and developing program representations and transformations suitable for classes of hierarchical …

A Comparative Study Of Threshold-Based Feature Selection Techniques, Huanjing Wang, Taghi M. Khoshgoftaar, Jason Van Hulse

Computer Science Faculty Publications

Abstract Given high-dimensional software measurement data, researchers and practitioners often use feature (metric) selection techniques to improve the performance of software quality classification models. This paper presents our newly proposed threshold-based feature selection techniques, comparing the performance of these techniques by building classification models using five commonly used classifiers. In order to evaluate the effectiveness of different feature selection techniques, the models are evaluated using eight different performance metrics separately since a given performance metric usually captures only one aspect of the classification performance. All experiments are conducted on three Eclipse data sets with different levels of class imbalance. The …

A Comparative Study Of Filter-Based Feature Ranking Techniques, Huanjing Wang, Taghi M. Khoshgoftaar, Kehan Gao

Computer Science Faculty Publications

One factor that affects the success of machine learning is the presence of irrelevant or redundant information in the training data set. Filter-based feature ranking techniques (rankers) rank the features according to their relevance to the target attribute and we choose the most relevant features to build classification models subsequently. In order to evaluate the effectiveness of different feature ranking techniques, a commonly used method is to assess the classification performance of models built with the respective selected feature subsets in terms of a given performance metric (e.g., classification accuracy or misclassification rate). Since a given performance metric usually can …

G-Sense: A Scalable Architecture For Global Sensing And Monitoring, Alfredo J. Perez, Miguel A. Labrador, Sean J. Barbeau

Computer Science Faculty Publications

The pervasiveness of cellular phones combined with Internet connectivity, GPS embedded chips, location information, and integrated sensors provide an excellent platform to collect data about the individual and its surrounding environment. As a result, new applications have recently appeared to address large-scale societal problems as well as improve the quality of life of the individual. However, these new applications, recently called location-based services, participatory sensing, and human-centric sensing, bring many new challenges, one of them being the management of the huge amount of traffic (data) they generate. This article presents G-Sense, for Global-Sense, an architecture that integrates mobile and static …

A Location-Aware Framework For Intelligent Real-Time Mobile Applications, Sean J. Barbeau, Rafael A. Perez, Miguel A. Labrador, Alfredo J. Perez, Nevine Labib Georggi, Philip L. Winters

Computer Science Faculty Publications

The Location-Aware Information Systems Client (LAISYC) supports intelligent, real-time, mobile applications for GPS-enabled mobile phones by dynamically adjusting platform parameters for application performance while conserving device resources such as battery life.

Personalization By Website Transformation: Theory And Practice, Saverio Perugini

Computer Science Faculty Publications

We present an analysis of a progressive series of out-of-turn transformations on a hierarchical website to personalize a user’s interaction with the site. We formalize the transformation in graph-theoretic terms and describe a toolkit we built that enumerates all of the traversals enabled by every possible complete series of these transformations in any site and computes a variety of metrics while simulating each traversal therein to qualify the relationship between a site’s structure and the cumulative effect of support for the transformation in a site. We employed this toolkit in two websites. The results indicate that the transformation enables users …

Sat-Based Answer Set Programming, Yuliya Lierler

Computer Science Faculty Publications

Answer set programming (ASP) is a declarative programming paradigm oriented towards difficult combinatorial search problems. Syntactically, ASP programs look like Prolog programs, but solutions are represented in ASP by sets of atoms, and not by substitutions, as in Prolog. Answer set systems, such as SMODELS, SMODELSCC, and DLV, compute answer sets of a given program in the sense of the answer set (stable model) semantics. This is different from the functionality of Prolog systems, which determine when a given query is true relative to a given logic program. ASP has been applied to many areas of science and technology, from …

A Peer-Tree Based Location Lookup Service In Mobile Wireless Networks, Jun Liu

Computer Science Faculty Publications

We present a location look-up service for aiding location-based routing in wireless networks with mobile hosts. This location look up service is constructed based on a peer-tree indexing structure which represents the friendship relations among mobile hosts. The friendship is derived from the relations of sharing various-length common suffixes of host identifiers. A friendship relation determines the cooperation relation among mobile hosts. The Peer-Tree indexing structure provides a guideline for propagating location updates and queries in an organized manner. Each host periodically propagates its up-to-date location to a small number of its friends. Location queries are forwarded to and serviced …

Neuronbank: A Tool For Cataloging Neuronal Circuitry, Paul S. Katz, Robert Calin-Jageman, Akshaye Dhawan, Chad Frederick, Shuman Guo, Rasanjalee Dissanayaka, Naveen Hiremath, Wenjun Ma, Xiuyn Shen, Hsui C. Wang, Hong Yang, Sushil Prasad, Rajshekhar Sunderraman, Ying Zhu

Computer Science Faculty Publications

The basic unit of any nervous system is the neuron. Therefore, understanding the operation of nervous systems ultimately requires an inventory of their constituent neurons and synaptic connectivity, which form neural circuits. The presence of uniquely identifi able neurons or classes of neurons in many invertebrates has facilitated the construction of cellular-level connectivity diagrams that can be generalized across individuals within a species. Homologous neurons can also be recognized across species. Here we describe NeuronBank.org, a web-based tool that we are developing for cataloging, searching, and analyzing neuronal circuitry within and across species. Information from a single species is represented …

Admission Control Mechanisms For Continuous Queries In The Cloud, Christine Chung, Lory Al Moakar, Panos Chrysanthis, Shenoda Guirguis, Alexandros Labrinidis, Panayiotis (Panickos) Neophytou, Kirk Pruhs

Computer Science Faculty Publications

No abstract provided.

A Metric For Routing In Delay-Sensitive Wireless Sensor Networks, Zhen Jiang, Jie Wu, Risa Ito

Computer Science Faculty Publications

No abstract provided.

Cr: Capability Information For Routing Of Wireless Ad Hoc Networks In The Real Environment, Zhen Jiang, Zhigang Li, Nong Xiao, Jie Wu

Computer Science Faculty Publications

No abstract provided.

Srpt Is 1.86-Competitive For Completion Time Scheduling, Christine Chung, Tim Nonner, Alexander Souza

Computer Science Faculty Publications

No abstract provided.

Practical Play Of The Dice Game Pig, Todd W. Neller, Clifton G.M. Presser

Computer Science Faculty Publications

The object of the jeopardy dice game Pig is to be the first player to reach 100 points. Each turn, a player repeatedly rolls a die until either a 1 is rolled or the player holds and scores the sum of the rolls (i.e., the turn total). At any time during a player’s turn, the player is faced with two choices: roll or hold. If the player rolls a 1, the player scores nothing and it becomes the opponent’s turn. If the player rolls a number other than 1, the number is added to the player’s turn total …

Applying Hessian Curves In Parallel To Improve Elliptic Curve Scalar Multiplication Hardware, F. B. Muhaya, Q. A. Al-Haijá, Lo'ai A. Tawalbeh

Computer Science Faculty Publications

As a public key cryptography, Elliptic Curve Cryptography (ECC) is well known to be the most secure algorithms that can be used to protect information during the transmission. ECC in its arithmetic computations suffers from modular inversion operation. Modular Inversion is a main arithmetic and very long-time operation that performed by the ECC crypto-processor. The use of projective coordinates to define the Elliptic Curves (EC) instead of affine coordinates replaced the inversion operations by several multiplication operations. Many types of projective coordinates have been proposed for the elliptic curve E: y2 = x3 + ax + b which is defined …

Challenges Of Utilizing E-Learning Systems In Public Universities In Jordan, M. Al-Shboul, Izzat M. Alsmadi

Computer Science Faculty Publications

This research paper lists and discusses major challenges and barriers that may face faculty members at the public universities in Jordan in employing e-Learning systems authoring tools in their instructions. It also proposes several suggestions for the administrators in public universities in Jordan for what they could do to improve the utilization of e-Learning authoring tools at their campuses. E-Learning systems authoring tools allow instructors to easily create and deliver their e-contents and e-lectures. Furthermore, online course materials which uploaded by using such authoring tools could be viewed by any popular web browser system.

Identifying Protein Complexes From Interaction Networks Based On Clique Percolation And Distance Restriction, Jianxin Wang, Binbin Liu, Min Li, Yi Pan

Computer Science Faculty Publications

Background: Identification of protein complexes in large interaction networks is crucial to understand principles of cellular organization and predict protein functions, which is one of the most important issues in the post-genomic era. Each protein might be subordinate multiple protein complexes in the real protein-protein interaction networks.Identifying overlapping protein complexes from protein-protein interaction networks is a considerable research topic.

Result: As an effective algorithm in identifying overlapping module structures, clique percolation method (CPM) has a wide range of application in social networks and biological networks. However, the recognition accuracy of algorithm CPM is lowly. Furthermore, algorithm CPM is unfit to …

Recent Advances In Clustering Methods For Protein Interaction Networks, Jianxin Wang, Min Li, Youping Deng, Yi Pan

Computer Science Faculty Publications

The increasing availability of large-scale protein-protein interaction data has made it possible to understand the basic components and organization of cell machinery from the network level. The arising challenge is how to analyze such complex interacting data to reveal the principles of cellular organization, processes and functions. Many studies have shown that clustering protein interaction network is an effective approach for identifying protein complexes or functional modules, which has become a major research topic in systems biology. In this review, recent advances in clustering methods for protein interaction networks will be presented in detail. The predictions of protein functions and …

Representation Invariant Genetic Operators, Jonathan E. Rowe, Michael D. Vose, Alden H. Wright

Computer Science Faculty Publications

A genetic algorithm is invariant with respect to a set of representations if it runs the same no matter which of the representations is used. We formalize this concept mathematically, showing that the representations generate a group that acts upon the search space. Invariant genetic operators are those that commute with this group action. We then consider the problem of characterizing crossover and mutation operators that have such invariance properties. In the case where the corresponding group action acts transitively on the search space, we provide a complete characterization, including high-level representation-independent algorithms implementing these operators.

Results From The Ice-Sheet Model Intercomparison Project-Heinrich Event Intercomparison (Ismip Heino), Reinhard Calov, Ralf Greve, Ayako Abe-Ouchi, Ed Bueler, Philippe Huybrechts, Jesse V. Johnson, Rank Pattyn, David Pollard, Catherine Ritz, Fuyuki Saito, Lev Tarasov

Computer Science Faculty Publications

Results from the Heinrich Event INtercOmparison (HEINO) topic of the Ice-Sheet Model Intercomparison Project (ISMIP) are presented. ISMIP HEINO was designed to explore internal largescale ice-sheet instabilities in different contemporary ice-sheet models. These instabilities are of interest because they are a possible cause of Heinrich events. A simplified geometry experiment reproduces the main characteristics of the Laurentide ice sheet, including the sedimented region over Hudson Bay and Hudson Strait. The model experiments include a standard run plus seven variations. Nine dynamic/thermodynamic ice-sheet models were investigated; one of these models contains a combination of the shallow-shelf (SSA) and shallow-ice approximation (SIA), …

Supporting Multiple Paths To Objects In Information Hierarchies: Faceted Classification, Faceted Search, And Symbolic Links, Saverio Perugini

Computer Science Faculty Publications

We present three fundamental, interrelated approaches to support multiple access paths to each terminal object in information hierarchies: faceted classification, faceted search, and web directories with embedded symbolic links. This survey aims to demonstrate how each approach supports users who seek information from multiple perspectives. We achieve this by exploring each approach, the relationships between these approaches, including tradeoffs, and how they can be used in concert, while focusing on a core set of hypermedia elements common to all. This approach provides a foundation from which to study, understand, and synthesize applications which employ these techniques. This survey does not …

Fully Generalized Two-Dimensional Constrained Delaunay Mesh Refinement, Panagiotis A. Foteinos, Andrey N. Chernikov, Nikos P. Chrisochoides

Computer Science Faculty Publications

Traditional refinement algorithms insert a Steiner point from a few possible choices at each step. Our algorithm, on the contrary, defines regions from where a Steiner point can be selected and thus inserts a Steiner point among an infinite number of choices. Our algorithm significantly extends existing generalized algorithms by increasing the number and the size of these regions. The lower bound for newly created angles can be arbitrarily close to $30^{\circ}$. Both termination and good grading are guaranteed. It is the first Delaunay refinement algorithm with a $30^{\circ}$ angle bound and with grading guarantees. Experimental evaluation of our algorithm …

Structure Prediction For The Helical Skeletons Detected From The Low Resolution Protein Density Map, Kamal Al Nasr, Weitao Sun, Jing He

Computer Science Faculty Publications

Background: The current advances in electron cryo-microscopy technique have made it possible to obtain protein density maps at about 6-10 Å resolution. Although it is hard to derive the protein chain directly from such a low resolution map, the location of the secondary structures such as helices and strands can be computationally detected. It has been demonstrated that such low-resolution map can be used during the protein structure prediction process to enhance the structure prediction.

Results: We have developed an approach to predict the 3-dimensional structure for the helical skeletons that can be detected from the low resolution protein density …

Improving Predicted Protein Loop Structure Ranking Using A Pareto-Optimality Consensus Method, Yaohang Li, Ionel Rata, See-Wing Chiu, Erik Jakobsson

Computer Science Faculty Publications

Background

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction.

Results

We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy …