Engineering Commons^™

Comparison Of Four Chip-Seq Analytical Algorithms Using Rice Endosperm H3k27 Trimethylation Profiling Data., Brandon M. Malone, Feng Tan, Susan M. Bridges, Zhaohua Peng

Bagley College of Engineering Publications and Scholarship

Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology laboratories.Here we profile H3K27me3 enrichment sites in rice young endosperm using the ChIP-Seq approach and analyze the data using four peak calling algorithms (FindPeaks, PeakSeq, USeq, and MACS). Comparison …

Towards Fast And Accurate Algorithms For Processing Fuzzy Data: Interval Computations Revisited, Gang Xiang, Vladik Kreinovich

Departmental Technical Reports (CS)

Adaptive Decision Support For Structured Organizations: A Case For Orgpomdps, Pradeep Reddy Varakantham, Nathan Schurr, Alan Carlin, Christopher Amato

Research Collection School Of Computing and Information Systems

In today's world, organizations are faced with increasingly large and complex problems that require decision-making under uncertainty. Current methods for optimizing such decisions fall short of handling the problem scale and time constraints. We argue that this is due to existing methods not exploiting the inherent structure of the organizations which solve these problems. We propose a new model called the OrgPOMDP (Organizational POMDP), which is based on the partially observable Markov decision process (POMDP). This new model combines two powerful representations for modeling large scale problems: hierarchical modeling and factored representations. In this paper we make three key contributions: …

Automatic Detection Of Aircraft Emergency Landing Sites, Yu-Fei Shen, Zia-Ur Rahman, Dean Krusienski, Jiang Li, Zia-Ur Rahman (Ed.), Stephen E. Reichenbach (Ed.), Mark Allen Neifeld (Ed.)

Electrical & Computer Engineering Faculty Publications

An automatic landing site detection algorithm is proposed for aircraft emergency landing. Emergency landing is an unplanned event in response to emergency situations. If, as is unfortunately usually the case, there is no airstrip or airfield that can be reached by the un-powered aircraft, a crash landing or ditching has to be carried out. Identifying a safe landing site is critical to the survival of passengers and crew. Conventionally, the pilot chooses the landing site visually by looking at the terrain through the cockpit. The success of this vital decision greatly depends on the external environmental factors that can impair …

Parallel-Sparse Symmetrical/Unsymmetrical Finite Element Domain Decomposition Solver With Multi-Point Constraints For Structural/Acoustic Analysis, Siroj Tungkahotara, Willie R. Watson, Duc T. Nguyen, Subramaniam D. Rajan

Civil & Environmental Engineering Faculty Publications

Details of parallel-sparse Domain Decomposition (DD) with multi-point constraints (MPC) formulation are explained. Major computational components of the DD formulation are identified. Critical roles of parallel (direct) sparse and iterative solvers with MPC are discussed within the framework of DD formulation. Both symmetrical and unsymmetrical system of simultaneous linear equations (SLE) can be handled by the developed DD formulation. For symmetrical SLE, option for imposing MPC equations is also provided.

Large-scale (up to 25 million unknowns involving complex numbers) structural and acoustic Finite Element (FE) analysis are used to evaluate the parallel computational performance of the proposed DD implementation using …

Self-Shape Optimisation Of Cold-Formed Steel Closed Profiles Using Genetic Algorithms, Benoit Gilbert, Lip H. Teh, Hong Guan

Faculty of Engineering and Information Sciences - Papers: Part A

For economical benefits, optimisation of mass-produced structural steel products is widely researched. The objective is to minimise the quantity of material used without sacrificing the strength and practicality of the structural members. Current research focuses on optimising the dimensions of conventional cross-sectional shapes but rarely considers discovering new optimum shapes. This report introduces the concepts of a new optimisation method which enables the crosssection to self-shape to an optimum by using the evolution and adaptation benefits of Genetic Algorithm. The feasibility and accuracy of the method are verified by implementing it to find optimum thin-walled profiles against simple parameters for …

Enhancement Technique For Aerial Images, Sertan Erkanli, Ahmet Gungor Pakfiliz, Jiang Li

Electrical & Computer Engineering Faculty Publications

Recently, we proposed an enhancement technique for uniformly and non-uniformly illuminated dark images that provides high color accuracy and better balance between the luminance and the contrast in images to improve the visual representations of digital images. In this paper we define an improved version of the proposed algorithm to enhance aerial images in order to reduce the gap between direct observation of a scene and its recorded image.

Histogram Analysis Of Adc In Brain Tumor Patients, Debrup Banerjee, Jihong Wang, Jiang Li, Norbert J. Pelc (Ed.), Ehsan Samei (Ed.), Robert M. Nishikawa (Ed.)

Electrical & Computer Engineering Faculty Publications

At various stage of progression, most brain tumors are not homogenous. In this presentation, we retrospectively studied the distribution of ADC values inside tumor volume during the course of tumor treatment and progression for a selective group of patients who underwent an anti-VEGF trial. Complete MRI studies were obtained for this selected group of patients including pre- and multiple follow-up, post-treatment imaging studies. In each MRI imaging study, multiple scan series were obtained as a standard protocol which includes T1, T2, T1-post contrast, FLAIR and DTI derived images (ADC, FA etc.) for each visit. All scan series (T1, T2, FLAIR, …