surrogate-model-development-for-digital-experiments-in-welding

Surrogate Model Development for Digital Experiments in Welding

The manufacturing industry heavily relies on welding processes to join materials, forming integral components across various sectors. Many aspects will ...

University of Manchester

The self-organising map (SOM) is finding more and more applications in a wide range of fields, such as clustering, pattern recognition and visualisation. It has also been employed in knowledge management and information retrieval. We propose an alternative to existing 2-dimensional SOM based methods for document analysis. The method, termed Adaptive Topological Tree Structure (ATTS), generates a taxonomy of underlying topics from a set of unclassified, unstructured documents. The ATTS consists of a hierarchy of adaptive self-organising chains, each of which is validated independently using a proposed entropy-based Bayesian information criterion. A node meeting the expansion criterion spans a child chain, with reduced vocabulary and increased specialisation. The ATTS creates a topological tree of topics, which can be browsed like a content hierarchy and reflects the connections between related topics at each level. A review is also given on the existing neural network based methods for document clustering and organisation. Experimental results on real-world datasets using the proposed ATTS method are presented and compared with other approaches. The results demonstrate the advantages of the proposed validation criteria and the efficiency of the ATTS approach for document organisation, visualisation and search. It shows that the proposed methods not only improve the clustering results but also boost the retrieval.

Adaptive topological tree structure for document organisation and visualisation.

In this paper a novel approach is introduced for modeling and clustering gene expression time-series. The radial basis function neural networks have been used to produce a generalized and smooth characterization of the expression time-series. A co-expression coefficient is defined to evaluate the similarities of the models based on their temporal shapes and the distribution of the time points. The profiles are grouped using a fuzzy clustering algorithm incorporated with the proposed co-expression coefficient metric. The results on artificial and real data are presented to illustrate the advantages of the metric and method in grouping temporal profiles. The proposed metric has also been compared with the commonly used correlation coefficient under the same procedures and the results show that the proposed method produces better biologically relevant clusters.

Modeling and analysis of gene expression time-series based on co-expression.

We present a new method for content management and knowledge discovery using a topology-preserving neural network. The method, termed topological organization of content (TOC), can generate a taxonomy of topics from a set of unannotated, unstructured documents. The TOC consists of a hierarchy of self-organizing growing chains (GCs), each of which can develop independently in terms of size and topics. The dynamic development process is validated continuously using a proposed entropy-based Bayesian information criterion (BIC). Each chain meeting the criterion spans child chains, with reduced vocabularies and increased specializations. This results in a topological tree hierarchy, which can be browsed like a table of contents directory or web portal. A brief review is given on existing methods for document clustering and organization, and clustering validation measures. The proposed approach has been tested and compared with several existing methods on real world web page datasets. The results have clearly demonstrated the advantages and efficiency in content organization of the proposed method in terms of computational cost and representation. The TOC can be easily adapted for large-scale applications. The topology provides a unique, additional feature for retrieving related topics and confining the search space.

Web content management by self-organization.

Proteome science relies on bioinformatics tools to characterize proteins via their proteolytic peptides which are identified via characteristic mass spectra generated after their ions undergo fragmentation in the gas phase within the mass spectrometer. The resulting secondary ion mass spectra are compared with protein sequence databases in order to identify the amino acid sequence. Although these search tools (e.g. SEQUEST, Mascot, X!Tandem, Phenyx) are frequently successful, much is still not understood about the amino acid sequence patterns which promote/protect particular fragmentation pathways, and hence lead to the presence/absence of particular ions from different ion series. In order to advance this area, we have developed a database, PepSeeker (http://nwsr.smith.man.ac.uk/pepseeker), which captures this peptide identification and ion information from proteome experiments. The database currently contains >185,000 peptides and associated database search information. Users may query this resource to retrieve peptide, protein and spectral information based on protein or peptide information, including the amino acid sequence itself represented by regular expressions coupled with ion series information. We believe this database will be useful to proteome researchers wishing to understand gas phase peptide ion chemistry in order to improve peptide identification strategies. Questions can be addressed to j.selley@manchester.ac.uk.

PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns.

The kernel method has become a useful trick and has been widely applied to various learning models to extend their nonlinear approximation and classification capabilities. Such extensions have also recently occurred to the Self-Organising Map (SOM). In this paper, two recently proposed kernel SOMs are reviewed, together with their link to an energy function. The Self-Organising Mixture Network is an extension of the SOM for mixture density modelling. This paper shows that with an isotropic, density-type kernel function, the kernel SOM is equivalent to a homoscedastic Self-Organising Mixture Network, an entropy-based density estimator. This revelation on the one hand explains that kernelising SOM can improve classification performance by acquiring better probability models of the data; but on the other hand it also explains that the SOM already naturally approximates the kernel method.

On the equivalence between kernel self-organising maps and self-organising mixture density networks.

The self-organising map (SOM) and its variant, visualisation induced SOM (ViSOM), have been known to yield similar results to multidimensional scaling (MDS). However, the exact connection has not been established. In this paper, a review on the SOM and its cost function and topological measures is provided first. We then examine the exact scaling effect of the SOM and ViSOM from their objective functions. The SOM is shown to produce a qualitative, nonmetric scaling, while the local distance-preserving ViSOM produces a quantitative or metric scaling. Their relationship with the principal manifold is also discussed. The SOM-based methods not only produce topological or metric scaling but also provide a principal manifold. Furthermore a growing ViSOM is proposed to aid the adaptive embedding of highly nonlinear manifolds. Examples and comparisons with other embedding methods such as Isomap and local linear embedding are also presented.

On multidimensional scaling and the embedding of self-organising maps.

The empirical mode decomposition (EMD) method can adaptively decompose a non-stationary time series into a number of amplitude or frequency modulated functions known as intrinsic mode functions. This paper combines the EMD method with information analysis and presents a framework of information-preserving EMD. The enhanced EMD method has been exploited in the analysis of neural recordings. It decomposes a signal and extracts only the most informative oscillations contained in the non-stationary signal. Information analysis has shown that the extracted components retain the information content of the signal. More importantly, a limited number of components reveal the main oscillations presented in the signal and their instantaneous frequencies, which are not often obvious from the original signal. This information-coupled EMD method has been tested on several field potential datasets for the analysis of stimulus coding in visual cortex, from single and multiple channels, and for finding information connectivity among channels. The results demonstrate the usefulness of the method in extracting relevant responses from the recorded signals. An investigation is also conducted on utilizing the Hilbert phase for cases where phase information can further improve information analysis and stimulus discrimination. The components of the proposed method have been integrated into a toolbox and the initial implementation is also described.

Information quantification of empirical mode decomposition and applications to field potentials.

Many real-world problems require modeling and forecasting of time series, such as weather temperature, electricity demand, stock prices and foreign exchange (FX) rates. Often, the tasks involve predicting over a long-term period, e.g. several weeks or months. Most existing time series models are inheritably for one-step prediction, that is, predicting one time point ahead. Multi-step or long-term prediction is difficult and challenging due to the lack of information and uncertainty or error accumulation. The main existing approaches, iterative and independent, either use one-step model recursively or treat the multi-step task as an independent model. They generally perform poorly in practical applications. In this paper, as an extension of the self-organizing mixture autoregressive (AR) model, the varied length mixture (VLM) models are proposed to model and forecast time series over multi-steps. The key idea is to preserve the dependencies between the time points within the prediction horizon. Training data are segmented to various lengths corresponding to various forecasting horizons, and the VLM models are trained in a self-organizing fashion on these segments to capture these dependencies in its component AR models of various predicting horizons. The VLM models form a probabilistic mixture of these varied length models. A combination of short and long VLM models and an ensemble of them are proposed to further enhance the prediction performance. The effectiveness of the proposed methods and their marked improvements over the existing methods are demonstrated through a number of experiments on synthetic data, real-world FX rates and weather temperatures.

Multi-Step Time Series Forecasting with an Ensemble of Varied Length Mixture Models.

The use of spectral imaging within the plant phenotyping and breeding community has been increasing due its utility as a non-invasive diagnostic tool. However, there is a lack of imaging systems targeted specifically at plant science duties, resulting in low precision for canopy-scale measurements. This study trials a prototype multispectral system designed specifically for plant studies and looks at its use as an early detection system for visually asymptomatic disease phases, in this case  in . The analysis takes advantage of machine learning in the form of feature selection and novelty detection to facilitate the classification. An initial study into recording the morphology of the samples is also included to allow for further improvement to the system performance.

Multispectral imaging for presymptomatic analysis of light leaf spot in oilseed rape.

Cassava brown streak disease (CBSD) is an emerging viral disease that can greatly reduce cassava productivity, while causing only mild aerial symptoms that develop late in infection. Early detection of CBSD enables better crop management and intervention. Current techniques require laboratory equipment and are labour intensive and often inaccurate. We have developed a handheld active multispectral imaging (A-MSI) device combined with machine learning for early detection of CBSD in real-time. The principal benefits of A-MSI over passive MSI and conventional camera systems are improved spectral signal-to-noise ratio and temporal repeatability. Information fusion techniques further combine spectral and spatial information to reliably identify features that distinguish healthy cassava from plants with CBSD as early as 28 days post inoculation on a susceptible and a tolerant cultivar. Application of the device has the potential to increase farmers' access to healthy planting materials and reduce losses due to CBSD in Africa. It can also be adapted for sensing other biotic and abiotic stresses in real-world situations where plants are exposed to multiple pest, pathogen and environmental stresses.

Article	Year
Adaptive topological tree structure for document organisation and visualisation. Neural networks : the official journal of the International Neural Network Society\| PubMed ID: 15555865	2004
Modeling and analysis of gene expression time-series based on co-expression. International journal of neural systems\| PubMed ID: 16187406	2005
Web content management by self-organization. IEEE transactions on neural networks\| PubMed ID: 16252831	2005
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. Nucleic acids research\| PubMed ID: 16381951	2006
On the equivalence between kernel self-organising maps and self-organising mixture density networks. Neural networks : the official journal of the International Neural Network Society\| PubMed ID: 16759835	2006
On multidimensional scaling and the embedding of self-organising maps. Neural networks : the official journal of the International Neural Network Society\| PubMed ID: 18255262	2008
Information quantification of empirical mode decomposition and applications to field potentials. International journal of neural systems\| PubMed ID: 21243730	2011
Multi-Step Time Series Forecasting with an Ensemble of Varied Length Mixture Models. International journal of neural systems\| PubMed ID: 29297261	2018
Multispectral imaging for presymptomatic analysis of light leaf spot in oilseed rape. Plant methods\| PubMed ID: 30697329	2019
Early detection of plant virus infection using multispectral imaging and spatial-spectral machine learning. Scientific reports\| PubMed ID: 35210452	2022

Hujun Yin

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