Engineering Commons^™

Reconstructing Yeasts Phylogenies And Ancestors From Whole Genome Data, Bing Feng, Yu Ling, Lingxi Zhou, Roufan Xia, Fei Hu, Chao Liu

Faculty Publications

Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, …

Reconstructing Yeasts Phylogenies And Ancestors From Whole Genome Data, Bing Feng, Yu Lin, Lingxi Zhou, Yan Guo, Robert Friedman, Roufan Xia, Chao Liu, Jijun Tang

Faculty Publications

Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, …

Formal Performance Guarantees For An Approach To Human In The Loop Robot Missions, Damian Lyons, Ron Arkin, Shu Jiang, Matt O'Brien, Feng Tang, Peng Tang

Faculty Publications

Abstract— A key challenge in the automatic verification of robot mission software, especially critical mission software, is to be able to effectively model the performance of a human operator and factor that into the formal performance guarantees for the mission. We present a novel approach to modelling the skill level of the operator and integrating it into automatic verification using a linear Gaussians model parameterized by experimental calibration. Our approach allows us to model different skill levels directly in terms of the behavior of the lumped, robot plus operator, system.

Using MissionLab and VIPARS (a behavior-based robot mission verification …

A Framework For Recommendation Of Highly Popular News Lacking Social Feedback, Nuno Moniz, Luís Torgo, Magdalini Eirinaki, Paula Branco

Faculty Publications

Social media is rapidly becoming the main source of news consumption for users, raising significant challenges to news aggregation and recommendation tasks. One of these challenges concerns the recommendation of very recent news. To tackle this problem, approaches to the prediction of news popularity have been proposed. In this paper, we study the task of predicting news popularity upon their publication, when social feedback is unavailable or scarce, and to use such predictions to produce news rankings. Unlike previous work, we focus on accurately predicting highly popular news. Such cases are rare, causing known issues for standard prediction models and …

Use Of A Novel Infrared Wavelength-Tunable Laser Mueller-Matrix Polarimetric Scatterometer To Measure Nanostructured Optical Materials, Jason C. Vap, Stephen E. Nauyoks, Michael R. Benson, Michael A. Marciniak

Faculty Publications

Nanostructured optical materials, for example, metamaterials, have unique spectral, directional, and polarimetric properties. Samples designed and fabricated for infrared (IR) wavelengths have been characterized using broadband instruments to measure specular polarimetric transmittance or reflectance as in ellipsometry or integrated hemisphere transmittance or reflectance. We have developed a wavelength-tunable IR Mueller-matrix (Mm) polarimetric scatterometer which uses tunable external-cavity quantum-cascade lasers (EC-QCLs) to tune onto and off of the narrowband spectral resonances of nanostructured optical materials and performed full polarimeteric and directional evaluation to more fully characterize their behavior. Using a series of EC-QCLs, the instrument is tunable over 4.37-6.54 μm wavelengths …

Spin-Imbalance In A 2d Fermi-Hubbard System, Peter Brown, Debayan Mitra, Elmer Guardado-Sanchez, Peter Schauß, Stanimir Kondov, Ehsan Khatami, Thereza Paiva, Nandini Trivedi, David Huse, Waseem Bakr

Faculty Publications

The interplay of strong interactions and magnetic fields gives rise to unusual forms of superconductivity and magnetism in quantum many-body systems. Here, we present an experimental study of the two-dimensional Fermi-Hubbard model—a paradigm for strongly correlated fermions on a lattice—in the presence of a Zeeman field and varying doping. Using site-resolved measurements, we revealed anisotropic antiferromagnetic correlations, a precursor to long-range canted order. We observed nonmonotonic behavior of the local polarization with doping for strong interactions, which we attribute to the evolution from an antiferromagnetic insulator to a metallic phase. Our results pave the way to experimentally mapping the low-temperature …

Improvement Of Phylogenetic Method To Analyze Compositional Heterogeneity, Zehua Zhang, Kecheng Guo, Gaofeng Pan, Jijun Tang, Fei Guo

Faculty Publications

Background: Phylogenetic analysis is a key way to understand current research in the biological processes and detect theory in evolution of natural selection. The evolutionary relationship between species is generally reflected in the form of phylogenetic trees. Many methods for constructing phylogenetic trees, are based on the optimization criteria. We extract the biological data via modeling features, and then compare these characteristics to study the biological evolution between species.

Results: Here, we use maximum likelihood and Bayesian inference method to establish phylogenetic trees; multi-chain Markov chain Monte Carlo sampling method can be used to select optimal phylogenetic tree, resolving local …

Synthesis Of Non-Uniformly Correlated Partially Coherent Sources Using A Deformable Mirror, Milo W. Hyde Iv, Santasri Bose-Pillai, Ryan A. Wood

Faculty Publications

The near real-time synthesis of a non-uniformly correlated partially coherent source using a low-actuator-count deformable mirror is demonstrated. The statistical optics theory underpinning the synthesis method is reviewed. The experimental results of a non-uniformly correlated source are presented and compared to theoretical predictions. A discussion on how deformable mirror characteristics such as actuator count and pitch affect source generation is also included.

On-Chip, High-Sensitivity Temperature Sensors Based On Dye-Doped Solid-State Polymer Microring Lasers, Lei Wan, Hengky Chandrahalim, Cong Chen, Qiushu Chen, Ting Mei, Yuji Oki, Naoya Nishimura, Lingjie Jay Guo, Xudong Fan

Faculty Publications

We developed a chip-scale temperature sensor with a high sensitivity of 228.6 pm/°C based on a rhodamine 6G (R6G)-doped SU-8 whispering-gallery mode microring laser. The optical mode was largely distributed in a polymer core layer with a 30 μm height that provided detection sensitivity, and the chemically robust fused-silica microring resonator host platform guaranteed its versatility for investigating different functional polymer materials with different refractive indices. As a proof of concept, a dye-doped hyperbranched polymer (TZ-001) microring laser-based temperature sensor was simultaneously developed on the same host wafer and characterized using a free-space optics measurement setup. Compared to TZ-001, the …

Electron Paramagnetic Resonance Study Of Neutral Mg Acceptors In Β-Ga2O3 Crystals, Brant E. Kananen, Larry E. Halliburton, Elizabeth M. Scherrer, K. T. Stevens, G. K. Foundos, K. B. Chang, Nancy C. Giles

Faculty Publications

Electron paramagnetic resonance (EPR) is used to directly observe and characterize neutral Mg acceptors (Mg⁰_Ga) in a β-Ga₂O₃ crystal. These acceptors, best considered as small polarons, are produced when the Mg-doped crystal is irradiated at or near 77 K with x rays. During the irradiation, neutral acceptors are formed when holes are trapped at singly ionized Mg acceptors (Mg−Ga). Unintentionally present Fe³⁺ (3d⁵) and Cr³⁺ (3d³) transition-metal ions serve as the corresponding electron traps. The hole is localized in a nonbonding p orbital on a threefold-coordinated oxygen ion …

An Ameliorated Prediction Of Drug–Target Interactions Based On Multi-Scale Discrete Wavelet Transform And Network Features, Cong Shen, Yijie Ding, Jijun Tang, Xinying Xu, Fei Guo

Faculty Publications

The prediction of drug–target interactions (DTIs) via computational technology plays a crucial role in reducing the experimental cost. A variety of state-of-the-art methods have been proposed to improve the accuracy of DTI predictions. In this paper, we propose a kind of drug–target interactions predictor adopting multi-scale discrete wavelet transform and network features (named as DAWN) in order to solve the DTIs prediction problem. We encode the drug molecule by a substructure fingerprint with a dictionary of substructure patterns. Simultaneously, we apply the discrete wavelet transform (DWT) to extract features from target sequences. Then, we concatenate and normalize the target, drug, …

An Ensemble Deep Convolutional Neural Network Model With Improved D-S Evidence Fusion For Bearing Fault Diagnosis, Shaobo Li, Guoka Liu, Xianghong Tang, Jianguang Lu, Jianjun Hu

Faculty Publications

Intelligent machine health monitoring and fault diagnosis are becoming increasingly important for modern manufacturing industries. Current fault diagnosis approaches mostly depend on expert-designed features for building prediction models. In this paper, we proposed IDSCNN, a novel bearing fault diagnosis algorithm based on ensemble deep convolutional neural networks and an improved Dempster–Shafer theory based evidence fusion. The convolutional neural networks take the root mean square (RMS) maps from the FFT (Fast Fourier Transformation) features of the vibration signals from two sensors as inputs. The improved D-S evidence theory is implemented via distance matrix from evidences and modified Gini Index. Extensive evaluations …

Measuring The Reflection Matrix Of A Rough Surface, Kenneth W. Burgi, Michael A. Marciniak, Mark E. Oxley, Stephen E. Nauyoks

Faculty Publications

Phase modulation methods for imaging around corners with reflectively scattered light required illumination of the occluded scene with a light source either in the scene or with direct line of sight to the scene. The RM (reflection matrix) allows control and refocusing of light after reflection, which could provide a means of illuminating an occluded scene without access or line of sight. Two optical arrangements, one focal-plane, the other an imaging system, were used to measure the RM of five different rough-surface reflectors. Intensity enhancement values of up to 24 were achieved. Surface roughness, correlation length, and slope were examined …

An Approach To Robust Homing With Stereovision, Fuqiang Fu, Damian Lyons

Faculty Publications

Visual Homing is a bioinspired approach to robot navigation which can be fast and uses few assumptions. However, visual homing in a cluttered and unstructured outdoor environment offers several challenges to homing methods that have been developed for primarily indoor environments. One issue is that any current image during homing may be tilted with respect to the home image. The second is that moving through a cluttered scene during homing may cause obstacles to interfere between the home scene and location and the current scene and location. In this paper, we introduce a robust method to improve a previous developed …

Multi-Valued Sequences Generated By Power Residue Symbols Over Odd Characteristic Fields, Begum Nasima, Yasuyuki Nogami, Satoshi Uehara, Robert Morelos-Zaragoza

Faculty Publications

This paper proposes a new approach for generating pseudo random multi-valued (including binary-valued) sequences. The approach uses a primitive polynomial over an odd characteristic prime field $\f{p}$, where p is an odd prime number. Then, for the maximum length sequence of vectors generated by the primitive polynomial, the trace function is used for mapping these vectors to scalars as elements in the prime field. Power residue symbol (Legendre symbol in binary case) is applied to translate the scalars to k-value scalars, where k is a prime factor of p-1. Finally, a pseudo random k-value sequence is obtained. Some important properties …

Performance Verification For Robot Missions In Uncertain Environments, Damian Lyons, Ron Arkin, Shu Jiang, Matt O'Brien, Feng Tang, Peng Tang

Faculty Publications

Abstract—Certain robot missions need to perform predictably in a physical environment that may have significant uncertainty. One approach is to leverage automatic software verification techniques to establish a performance guarantee. The addition of an environment model and uncertainty in both program and environment, however, means the state-space of a model-checking solution to the problem can be prohibitively large. An approach based on behavior-based controllers in a process-algebra framework that avoids state-space combinatorics is presented here. In this approach, verification of the robot program in the uncertain environment is reduced to a filtering problem for a Bayesian Network. Validation results …

A Summer Camp In Engineering Physics For Incoming Freshman To Improve Retention And Student Success, Hector A. Ochoa, Christopher J. Aul, Dan Bruton, Collin J. Timmons

Faculty Publications

Summer camps have proven to be a valuable tool to attract and recruit students interested in pursuing a career in the STEM field. They have been also used to spark their curiosity in areas like mathematics. However, these camps do not help with issues that appear after the student has been admitted at the university. It is well known that many students are shocked when they transition from high-school to college. Many of them do not know how to handle their academic freedom; they start without any friends, and they do not know the campus and the resources available. By …

Robust And Agile System Against Fault And Anomaly Traffic In Software Defined Networks, Mihui Kim, Younghee Park, Rohit Kotalwar

Faculty Publications

The main advantage of software defined networking (SDN) is that it allows intelligent control and management of networking though programmability in real time. It enables efficient utilization of network resources through traffic engineering, and offers potential attack defense methods when abnormalities arise. However, previous studies have only identified individual solutions for respective problems, instead of finding a more global solution in real time that is capable of addressing multiple situations in network status. To cover diverse network conditions, this paper presents a comprehensive reactive system for simultaneously monitoring failures, anomalies, and attacks for high availability and reliability. We design three …

Impact Of Reviewer Social Interaction On Online Consumer Review Fraud Detection, Kunal Goswami, Younghee Park, Chungsik Song

Faculty Publications

Background Online consumer reviews have become a baseline for new consumers to try out a business or a new product. The reviews provide a quick look into the application and experience of the business/product and market it to new customers. However, some businesses or reviewers use these reviews to spread fake information about the business/product. The fake information can be used to promote a relatively average product/business or can be used to malign their competition. This activity is known as reviewer fraud or opinion spam. The paper proposes a feature set, capturing the user social interaction behavior to identify fraud. …

Establishing A-Priori Performance Guarantees For Robot Missions That Include Localization Software, Damian Lyons, Ron Arkin, Shu Jiang, Matt O'Brien, Feng Tang, Peng Tang

Faculty Publications

One approach to determining whether an automated system is performing correctly is to monitor its performance, signaling when the performance is not acceptable; another approach is to automatically analyze the possible behaviors of the system a-priori and determine performance guarantees. Thea authors have applied this second approach to automatically derive performance guarantees for behaviorbased, multi-robot critical mission software using an innovative approach to formal verification for robotic software. Localization and mapping algorithms can allow a robot to navigate well in an unknown environment. However, whether such algorithms enhance any specific robot mission is currently a matter for empirical validation. Several …