Computer Engineering Commons^™

Woodstocc: Extracting Latent Parallelism From A Dna Sequence Aligner On A Gpu, Stephen V. Cole, Jacob R. Gardner, Jeremy D. Buhler

All Computer Science and Engineering Research

An exponential increase in the speed of DNA sequencing over the past decade has driven demand for fast, space-efficient algorithms to process the resultant data. The first step in processing is alignment of many short DNA sequences, or reads, against a large reference sequence. This work presents WOODSTOCC, an implementation of short-read alignment designed for Graphics Processing Unit (GPU) architectures. WOODSTOCC translates a novel CPU implementation of gapped short-read alignment, which has guaranteed optimal and complete results, to the GPU. Our implementation combines an irregular trie search with dynamic programming to expose regularly structured parallelism. We first describe this implementation, …

Sandra Helps You Learn: The More You Walk, The More Battery Your Phone Drains, Chulhong Min, Chungkuk Yoo, Inseok Hwang, Seungwoo Kang, Youngki Lee, Seungchul Lee, Pillsoon Park, Changhun Lee, Seungpyo Choi Choi

Research Collection School Of Computing and Information Systems

Emerging continuous sensing apps introduce new major factors governing phones’ overall battery consumption behaviors: (1) added nontrivial persistent battery drain, and more importantly (2) different battery drain rate depending on the user’s different mobility condition. In this paper, we address the new battery impacting factors significant enough to outdate users’ existing battery model in real life. We explore an initial approach to help users understand the cause and effect between their physical activity and phones’ battery life. To this end, we present Sandra, a novel mobility-aware smartphone battery information advisor, and study its potential to help users redevelop their battery …

An Investigation Into Partitioning Algorithms For Automatic Heterogeneous Compilers, Antonio M. Leija

Master's Theses

Automatic Heterogeneous Compilers allows blended hardware-software solutions to be explored without the cost of a full-fledged design team, but limited research exists on current partitioning algorithms responsible for separating hardware and software. The purpose of this thesis is to implement various partitioning algorithms onto the same automatic heterogeneous compiler platform to create an apples to apples comparison for AHC partitioning algorithms. Both estimated outcomes and actual outcomes for the solutions generated are studied and scored. The platform used to implement the algorithms is Cal Poly’s own Twill compiler, created by Doug Gallatin last year. Twill’s original partitioning algorithm is chosen …

Error Probabilities For Optical Receivers That Employ Dynamically Biased Avalanche Photodiodes, Georges El-Howayek, Majeed M. Hayat

Electrical and Computer Engineering Faculty Research and Publications

A novel theory was recently reported for the avalanche multiplication process in avalanche photodiodes (APDs) under dynamic reverse-biasing conditions. It has been shown theoretically that the bit-synchronized, periodic modulation of the electric field in the multiplication region can offer improvements in the gain-bandwidth product by reducing intersymbol interference in optical receivers. This paper reports a rigorous formulation of the sensitivity of optical receivers that employ dynamically biased APDs. To enable the sensitivity analysis, a recurrence theory is developed to calculate the joint probability distribution function (PDF) of the stochastic gain and avalanche buildup time in APDs that are operated under …

Study Of The Research Status On E-Navigation, Qiwei Chen

Maritime Safety & Environment Management Dissertations (Dalian)

No abstract provided.

Software Metrics And Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, Nicholas J. Hayward

Computer Science: Faculty Publications and Other Works

Software metrics are a critical tool which provide continuous insight to products and processes and help build reliable software in mission critical environments. Using software metrics we can perform calculations that help assess the effectiveness of the underlying software or process. The two types of metrics relevant to our work is complexity metrics and in-process metrics. Complexity metrics tend to focus on intrinsic code properties like code complexity. In-process metrics focus on a higher-level view of software quality, measuring information that can provide insight into the underlying software development process.

Our aim is to develop and evaluate a metrics dashboard …

Api-Based Acquisition Of Evidence From Cloud Storage Providers, Andres E. Barreto

LSU New Orleans Theses and Dissertations

Cloud computing and cloud storage services, in particular, pose a new challenge to digital forensic investigations. Currently, evidence acquisition for such services still follows the traditional approach of collecting artifacts on a client device. In this work, we show that such an approach not only requires upfront substantial investment in reverse engineering each service, but is also inherently incomplete as it misses prior versions of the artifacts, as well as cloud-only artifacts that do not have standard serialized representations on the client.

In this work, we introduce the concept of API-based evidence acquisition for cloud services, which addresses these concerns …

Gpu/Cpu Performance Of Image Processing Tasks For Use In The Cam 2 System, Jonathan Cottom, Yung-Hsiang Lu, Young-Sol Koh

The Summer Undergraduate Research Fellowship (SURF) Symposium

Over the past several years, graphics processing units (GPU) have increasingly been viewed as the future of image processing engines. Currently, the Continuous Analysis of Many CAMeras (CAM²) project performs its processing on CPUs, which will potentially be more costly as the system scales to service more users. This study seeks to analyze the performance gains of GPU processing and evaluate the advantage of supporting GPU-accelerated analysis for CAM² users. The platform for comparing the CPU and GPU performance has been the NVIDIA Jetson TK1. The target hardware implementation is an Amazon cloud instance, where final cost …

Demonstration Of A Platform Architecture That Enables Ultra-Low Power Iot Applications, Jacob Stevens, Hrishikesh Jayakumar, Vijay Raghunathan

The Summer Undergraduate Research Fellowship (SURF) Symposium

The coming years will see a surge of billions more devices connected in an “Internet of Things” (IoT) that aim to improve the day to day life of humans by sensing relevant physical phenomena and using the data to make intelligent decisions and predictions. But with current devices, this surge will result in billions more batteries needing to be used and changed regularly. The need for batteries—and its impact—can be mitigated through low power devices that harvest ambient energy (e.g. solar, vibrational, thermoelectric, radio wave), but energy harvesting devices require the ability to continue computations across power cycles, a paradigm …

Development Of A Web Application For Continuous Analysis Of Many Cameras (Cam2), Anurag Anjaria, Dr. Yung-Hsiang Lu, Young-Sol Koh, Charles Hansen

The Summer Undergraduate Research Fellowship (SURF) Symposium

There are tens of thousands of web cameras located around the world and publicly available on the Internet. The images captured by these cameras contain data relating to our living environment such as traffic patterns, weather and crowd movement. Researchers can capture this data using image analysis techniques on the video and image from these cameras. However, there is a lack of a single, unified repository of all the public cameras on the Internet; this, coupled with the computational demands of image analysis means there is a need for a tool to help researchers perform large-scale image analyis on many …

Optimization In The Simulation Of Jammed Polyhedral Particles, Joseph W. Mynhier, Ishan Srivastava, Timothy S. Fisher

The Summer Undergraduate Research Fellowship (SURF) Symposium

Energy loss due to poor transport properties in electrically and thermally conducting materials, such as battery electrodes and thermoelectric composites, contributes to the energy inefficiency of electronic devices. For conductive materials composed of granular materials, particle-particle contact topology strongly governs the efficiency of energy transfer. Although there is a large body of existing work on the arrangements made by granular materials comprised of spherical particles, less is known about the mechanically stable arrangements of granular materials made of convex polyhedra. This project seeks to create a computer simulation of the solidification of convex polyhedra from a diffuse state into a …

Visualization Of The Growth And Production Of Grapes Through Analysis Of Sensory Data, Sung Yeon Choi, Luke Neumann, Brian Olsen, Sungahn Ko, David Ebert Ph.D

The Summer Undergraduate Research Fellowship (SURF) Symposium

Grapes used in the wine industry have been one of the highest value crops in the United States. However, with unpredictable weather changes and recent drought in the Western United States, vineyard owners and grape growers have faced difficulties on producing good quality grapes suited for wine making. Therefore, a technology that would keep record of environmental data and incorporate the data to support agricultural decisions will help the growers to produce quality grapes even in extreme conditions. As such, this research focuses on developing an interactive system that uses sensory data and visual analytics to facilitate vineyard management and …

Implementation Of A Speech Recognition Algorithm To Facilitate Verbal Commands For Visual Analytics Law Enforcement Toolkit, Shubham S. Rastogi, David L. Wiszowaty, Hanye Xu, Abish Malik, David S. Ebert

The Summer Undergraduate Research Fellowship (SURF) Symposium

The VALET (Visual Analytics Law Enforcement Toolkit) system allows the user to visualize and predict crime hotspots and analyze crime data. Police officers have difficulty in using VALET in a mobile situation, since the system allows only conventional input interfaces (keyboard and mouse). This research focuses on introducing a new input interface to VALET in the form of speech recognition, which allows the user to interact with the software without losing functionality. First an Application Program Interface (API) that was compatible with the VALET system was found and initial code scripts to test its functionality were written. Next, the code …

Network Structure, Network Flows And The Phenomenon Of Influence In Online Social Networks: An Exploratory Empirical Study Of Twitter Conversations About Youtube Product Categories, Nitin Venkat Mayande

Dissertations and Theses

Traditional marketing models are swiftly being upended by the advent of online social networks. Yet, practicing firms that are engaging with online social networks neither have a reliable theory nor sufficient practical experience to make sense of the phenomenon. Extant theory in particular is based on observations of the real world, and may thus not apply to online social networks. Practicing firms may consequently be misallocating a large amount of resources, simply because they do not know how the online social networks with which they interact are organized.

The purpose of this dissertation is to investigate how online social networks …

Decrypting Financial Markets Through E-Joint Attention Efforts: On-Line Adaptive Networks Of Investors In Periods Of Market Uncertainty, Niccolò Casnici, Pierpaolo Dondio, Roberto Casarin, Flaminio Squazzoni

Articles

No abstract provided.

Application Of Fiscal Incentives For Development Of East Natuna Gas Field For Long-Term National Natural Gas Demand, Marwan Batubara, Widodo Wahyu Purwanto, Akhmad Fauzi

Makara Journal of Technology

East Natuna gas field, which has proven reserves of 46 trillion cubic feet, is projected to meet long-term natural gas needs. However, CO2-content of the gas reserves reaches 71%, leading to expensive development costs. This research investigates the feasibility of the field based on several fiscal incentives. Firstly, gas supply-demand until year 2040 was analyzed. Then, based on the analysis, the field was developed using high CO2 gas separation technology to produce gas of 1300 MMSCFD in 2023, 2600 MMSCFD in 2031, and 3900 MMSCFD in 2039. Finally, the economic feasibility was assessed using cash flow analysis in accordance with …

Transmission Electron Microscopy Characterization Of High-Temperatur Oxidation Of Fe-20cr-5al Alloy Prepared By Focused Ion Beam Technique, Mohammad Dani, Pudji Untoro, Teguh Yulius Surya Panca Putra, Parikin Parikin, Joachim Mayer, Arbi Dimyati

Makara Journal of Technology

The Focused Ion Beam (FIB) technique was applied for cross section preparation of the oxidized alloy for Transmission Electron Microscopy (TEM) study. Prior to preparation, the specimens of Fe-20Cr-5Al alloy sheet were oxidized in air at 1200 oC for 2 minutes, 10 minutes, 2 hours, and 100 hours. The microstructure and elemental composition of the samples were characterized using TEM equipped with an Energy Dispersive X-Ray Spectroscopy (EDX). The Electron Energy Loss Spectroscopy (EELS) was used to determine of the light elements. The TEM investigation reveals remarkable microstructure evolution of the specimens during oxidation which generally exhibit a typical multi-layer …

High Temperature Corrosion Of Aluminized Aisi 4130 Steel With The Different Composition Of Nacl/Na2so4 Deposits, Mohammad Badaruddin, Chaur Jeng Wang, Yudhistyra Saputra, Abu Khalid Rivai

Makara Journal of Technology

The high temperature corrosion of AISI 4130 steel can be increased by hot-dip aluminizing coating. The aluminized steel specimens with the deposit composition of 100/0, 30/70, 50/50, 70/30, and 0/100 (wt.%) NaCl/Na2SO4 were oxidized at 750 °C for 1-49 h periods. According to a parabolic rate constant (kp) value, the aluminized steel with deposit composition of 70/30 NaCl/Na2SO4 shows the highest kp value (3.71 × 10-11 g2cm- 4s-1), later followed by the kp value of 3.35 × 10-11 g2cm-4s-1 for 100/0 and the lowest kp value is 7.731 × 10-12 g2cm-4s-1 for 0/100. Whereas, the kp value for the aluminized …

Effects Of Supplier-Manufacturer Relationships On Supply-Chain Performance Of Manufacturing Industries In Indonesia, Rachmad Hidayat, Khisbullah Hudha, Sabarudin Akhmad

Makara Journal of Technology

The present study describes the relationships between commitment, communication, satisfaction, trust, relationship quality with suppliers, and supply-chain performance. The population of the study was manufacturing companies in Indonesia. Respondents were the chief executive officers or corporate secretaries or the designated managers involved in strategic decision making. Samples were taken by using a proportional area random sampling technique. Structural Equation Modeling (SEM) was used for analysis. Results of both direct and indirect testing of hypothesis indicated two hypotheses of positive and significant effects and nine hypotheses of positive but insignificant effects. Those hypotheses of positive and significant effects were the direct …

A New Method For Simulating Power Flow Density Focused By A Silicon Lens Antenna Irradiated With Linearly Polarized Thz Wave, Catur Apriono, Eko Tjipto Rahardjo, Norihisa Hiromoto

Makara Journal of Technology

A terahertz system uses dielectric lens antennas for focusing and collimating beams of terahertz wave radiation. Linearly polarized terahertz wave radiation has been widely applied in the terahertz system. Therefore, an accurate method for analyzing the power flow density in the dielectric lens antenna irradiated with the linearly polarized terahertz wave radiation is important to design the terahertz systems. In optics, ray-tracing method has been used to calculate the power flow density by a number density of rays. In this study, we propose a method of ray-tracing combined with Fresnel’s transmission, including transmittance and polarization of the terahertz wave radiation …

Stochastic Optimization Of Supply Chain Risk Measures –A Methodology For Improving Supply Security Of Subsidized Fuel Oil In Indonesia, Adinda Yuanita, Andi Noorsaman Sommeng, Anondho Wijonarko

Makara Journal of Technology

Monte Carlo simulation-based methods for stochastic optimization of risk measures is required to solve complex problems in supply security of subsidized fuel oil in Indonesia. In order to overcome constraints in distribution of subsidized fuel in Indonesia, which has the fourth largest population in the world—more than 250,000,000 people with 66.5% of productive population, and has more than 17,000 islands with its population centered around the nation's capital only—it is necessary to have a measurable and integrated risk analysis with monitoring system for the purpose of supply security of subsidized fuel. In consideration of this complex issue, uncertainty and probability …

Thermodynamic Analysis Of Irreversible Heat-Transformers, Niccolo` Giannetti, Arnas Arnas, Andrea Rocchetti, Kiyoshi Saito

Makara Journal of Technology

Absorption heat transformers extend the possibilities for efficient and environment-friendly energy conversion processes. Based on a general thermodynamic model of three-thermal cycles with finite thermal capacity of the heat sources, this paper is intent upon analyzing and optimizing the performance of absorption heat transformers, by including the influence of irreversibility in the analytical expression of the system efficiency. Dimensionless parameters for an overall optimization are defined and a first screening is performed to clarify their influence. Dependence on the main factors is highlighted to suggest how to change them in order to enhance the whole system performance. Under this point …

Creation Of Carbon Nanotube Based Biosensors Through Dielectrophoretic Assembly, Nilan S. Mani, Steve Kim, Kaushik Annam, Danielle Bane, Guru Subramanyam

Electrical and Computer Engineering Faculty Publications

Due to their excellent electrical, optical, and mechanical properties, nanosized single wall carbon nanotubes (SWNTs) have attracted significant attention as a transducing element in nano-bio sensor research. Controlled assembly, device fabrication, and bio-functionalization of the SWNTs are crucial in creating the sensors. In this study, working biosensor platforms were created using dielectrophoretic assembly of single wall carbon nanotubes (SWNTs) as a bridge between two gold electrodes. SWNTs in a commercial SDS surfactant solution were dispensed in the gap between the two gold electrodes, followed by applying an ac voltage across the two electrodes. The dielectrophoresis aligns the CNTs and forms …

Automatic Registration Of Optical Aerial Imagery To A Lidar Point Cloud For Generation Of City Models, Bernard Olushola Abayowa, Alper Yilmaz, Russell C. Hardie

Electrical and Computer Engineering Faculty Publications

This paper presents a framework for automatic registration of both the optical and 3D structural information extracted from oblique aerial imagery to a Light Detection and Ranging (LiDAR) point cloud without prior knowledge of an initial alignment. The framework employs a coarse to fine strategy in the estimation of the registration parameters. First, a dense 3D point cloud and the associated relative camera parameters are extracted from the optical aerial imagery using a state-of-the-art 3D reconstruction algorithm. Next, a digital surface model (DSM) is generated from both the LiDAR and the optical imagery-derived point clouds. Coarse registration parameters are then …

A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results show …

In Need Of A Domain-Specific Language Modeling Notation For Smartphone Applications With Portable Capability, Hamza Ghandorh, Luiz Fernando Capretz Dr., Ali Bou Nassif Dr.

Electrical and Computer Engineering Publications

The rapid growth of the smartphone market and its increasing revenue has motivated developers to target multiple platforms. Market leaders, such as Apple, Google, and Microsoft, develop their smartphone applications complying with their platform specifications. The specification of each platform makes a platform-dedicated application incompatible with other platforms due to the diversity of operating systems, programming languages, and design patterns. Conventional development methodologies are applied to smartphone applications, yet they perform less well. Smartphone applications have unique hardware and software requirements. All previous factors push smartphone developers to build less sophisticated and low-quality products when targeting multiple smartphone platforms. Model-driven …

A Scaffolded, Metamorphic Ctf For Reverse Engineering, Wu-Chang Feng

Computer Science Faculty Publications and Presentations

Hands-on Capture-the-Flag (CTF) challenges tap into and cultivate the intrinsic motivation within people to solve puzzles, much in the same way Sudoku and crossword puzzles do. While the format has been successful in security competitions, there have been a limited number of attempts to integrate them into a classroom environment. This paper describes MetaCTF, a metamorphic set of CTF challenges for teaching reverse code engineering. MetaCTF is 1) scaffolded in a way that allows students to make incremental progress, 2) integrated with the course material so that students can immediately apply knowledge gained in class, 3) polymorphic and metamorphic so …

Mobile Cloud Computing Based Non Rigid Registration For Image Guided Surgery, Arun Brahmavar Vishwanatha

Computer Science Theses & Dissertations

In this thesis we present the design and implementation of a Mobile Cloud computing platform for non-rigid registration required in Image Guided Surgery (MCIGS). MCIGS contributes in flexible, portable and accurate alignment of pre-operative brain data with intra-operative MRI, for image guided diagnosis and therapy and endoscopic skull base surgery. Improved precision of image guided therapy and specifically neurosurgery procedures is known to result in the improved prognosis for brain tumor patients. MCI GS system is tested with Physics Based Non-Rigid Registration method form ITK. Our preliminary results for brain images indicate that the proposed system over Wi-Fi can be …

The Edge Group Coloring Problem With Applications To Multicast Switching, Jonathan Turner

All Computer Science and Engineering Research

This paper introduces a natural generalization of the classical edge coloring problem in graphs that provides a useful abstraction for two well-known problems in multicast switching. We show that the problem is NP-hard and evaluate the performance of several approximation algorithms, both analytically and experimentally. We find that for random χ-colorable graphs, the number of colors used by the best algorithms falls within a small constant factor of χ, where the constant factor is mainly a function of the ratio of the number of outputs to inputs. When this ratio is less than 10, the best algorithms produces solutions that …

Formal Specification Driven Development, Titus Fofung

Dissertations, Theses and Capstone Projects

This paper researches a quantitative metric of investigating Formal Specification-Driven Development (FSDD). Formal specification is needed at the beginning of the development process to prevent ambiguity and to improve the quality through corrections of errors found in the late phases of a traditional design process, Software Development Life Cycle (SDLC). The research is conducted with capstone students using both the FSDD and the SDLC (traditional) models and a quantitative analysis is presented to evaluate the internal quality of the software. The tool used to measure the internal quality is the .NET 2013 analysis tool. Formal Specification-Driven Development (FSDD) is a …