Engineering Commons^™

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, …

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, …

Improving Rolling Bearing Fault Diagnosis By Ds Evidence Theory Based Fusion Model, Xuemei Yao, Shaobo Li, Jianjun Hu

Faculty Publications

Rolling bearing plays an important role in rotating machinery and its working condition directly affects the equipment efficiency. While dozens of methods have been proposed for real-time bearing fault diagnosis and monitoring, the fault classification accuracy of existing algorithms is still not satisfactory. This work presents a novel algorithm fusion model based on principal component analysis and Dempster-Shafer evidence theory for rolling bearing fault diagnosis. It combines the advantages of the learning vector quantization (LVQ) neural network model and the decision tree model. Experiments under three different spinning bearing speeds and two different crack sizes show that our fusion model …

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 …

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 …

An Ensemble Deep Convolutional Neural Network Model With Improved D-S Evidence Fusion For Bearing Fault Diagnosis, Shaobo Li, Guokai 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 …

An Advanced Multi-Sensor Acousto-Ultrasonic Structural Health Monitoring System: Development And Aerospace Demonstration, Joel Smithard, Nik Rajic, Stephen Van Der Velden, Patrick Norman, Cedric Rosalie, Steve Galea, Hanfei Mei, Bin Lin, Victor Giurgiutiu

Faculty Publications

A key longstanding objective of the Structural Health Monitoring (SHM) research community is to enable the embedment of SHM systems in high value assets like aircraft to provide on-demand damage detection and evaluation. As against traditional non-destructive inspection hardware, embedded SHM systems must be compact, lightweight, low-power and sufficiently robust to survive exposure to severe in-flight operating conditions. Typical Commercial-Off-The-Shelf (COTS) systems can be bulky, costly and are often inflexible in their configuration and/or scalability, which militates against in-service deployment. Advances in electronics have resulted in ever smaller, cheaper and more reliable components that facilitate the development of compact and …

Analysis Of Co-Associated Transcription Factors Via Ordered Adjacency Differences On Motif Distribution, Gaofeng Pan, Jijun Tang, Fei Guo

Faculty Publications

Transcription factors (TFs) binding to specific DNA sequences or motifs, are elementary to the regulation of transcription. The gene is regulated by a combination of TFs in close proximity. Analysis of co-TFs is an important problem in understanding the mechanism of transcriptional regulation. Recently, ChIP-seq in mapping TF provides a large amount of experimental data to analyze co-TFs. Several studies show that if two TFs are co-associated, the relative distance between TFs exhibits a peak-like distribution. In order to analyze co-TFs, we develop a novel method to evaluate the associated situation between TFs. We design an adjacency score based on …