Functional Dimension Reduction for Chemometrics

Functional Dimension Reduction for Chemometrics

Tuomas Kärnä (Helsinki University of Technology, Finland) and Amaury Lendasse (Helsinki University of Technology, Finland)
Copyright: © 2009 |Pages: 6
DOI: 10.4018/978-1-59904-849-9.ch100
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High dimensional data are becoming more and more common in data analysis. This is especially true in fields that are related to spectrometric data, such as chemometrics. Due to development of more accurate spectrometers one can obtain spectra of thousands of data points. Such a high dimensional data are problematic in machine learning due to increased computational time and the curse of dimensionality (Haykin, 1999; Verleysen & François, 2005; Bengio, Delalleau, & Le Roux, 2006). It is therefore advisable to reduce the dimensionality of the data. In the case of chemometrics, the spectra are usually rather smooth and low on noise, so function fitting is a convenient tool for dimensionality reduction. The fitting is obtained by fixing a set of basis functions and computing the fitting weights according to the least squares error criterion. This article describes a unsupervised method for finding a good function basis that is specifically built to suit the data set at hand. The basis consists of a set of Gaussian functions that are optimized for an accurate fitting. The obtained weights are further scaled using a Delta Test (DT) to improve the prediction performance. Least Squares Support Vector Machine (LS-SVM) model is used for estimation.
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The approach where multivariate data are treated as functions instead of traditional discrete vectors is called Functional Data Analysis (FDA) (Ramsay & Silverman, 1997). A crucial part of FDA is the choice of basis functions which allows the functional representation. Commonly used bases are B-splines (Alsberg & Kvalheim, 1993), Fourier series or wavelets (Shao, Leung, & Chau, 2003). However, it is appealing to build a problem-specific basis that employs the statistical properties of the data at hand.

In literature, there are examples of finding the optimal set of basis functions that minimize the fitting error, such as Functional Principal Component Analysis (Ramsay et al., 1997). The basis functions obtained by Functional PCA usually have global support (i.e. they are non-zero throughout the data interval). Thus these functions are not good for encoding spatial information of the data. The spatial information, however, may play a major role in many fields, such as spectroscopy. For example, often the measured spectra contain spikes at certain wavelengths that correspond to certain substances in the sample. Therefore these areas are bound to be relevant for estimating the quantity of these substances.

We propose that locally supported functions, such as Gaussian functions, can be used to encode this sort of spatial information. In addition, variable selection can be used to select the relevant functions from the irrelevant ones. Selecting important variables directly on the raw data is often difficult due to high dimensionality of data; computational cost of variable selection methods, such as Forward-Backward Selection (Benoudjit, Cools, Meurens, & Verleysen, 2004; Rossi, Lendasse, François, Wertz, & Verleysen, 2006), grows exponentially with the number of variables. Therefore, wisely placed Gaussian functions are proposed as a tool for encoding spatial information while reducing data dimensionality so that other more powerful information processing tools become feasible. Delta Test (DT) (Jones, 2004) based scaling of variables is suggested for improving the prediction performance.

A typical problem in chemometrics deals with predicting some chemical quantity directly from measured spectrum. Due to additivity of absorption spectra, the problem is assumed to be linear and therefore linear models, such as Partial Least Squares (Härdle, Liang, & Gao, 2000) have been widely used for the prediction task. However, it has been shown that the additivity assumption is not always true and environmental conditions may further introduce more non-linearity to the data (Wülfert, Kok, & Smilde, 1998). We therefore propose that in order to address a general prediction problem, a non-linear method should be used. LS-SVM is a relatively fast and reliable non-linear model which has been applied to chemometrics as well (Chauchard, Cogdill, Roussel, Roger, & Bellon-Maurel, 2004).

Key Terms in this Chapter

Chemometrics: Application of mathematical or statistical methods to chemical data. Closely related to monitoring of chemical processes and instrument design.

Over-Fitting: A common problem in Machine Learning where the training data can be explained well but the model is unable to generalize to new inputs. Over-fitting is related to the complexity of the model: any data set can be modelled perfectly with a model complex enough, but the risk of learning random features instead of meaningful causal features increases.

Support Vector Machine: A kernel based supervised learning method used for classification and regression. The data points are projected into a higher dimensional space where they are linearly separable. The projection is determined by the kernel function and a set of specifically selected support vectors. Training process involves solving a Quadratic Programming problem.

Delta Test: A Non-parametric Noise Estimation method. Estimates the amount of noise within a data set, i.e. the amount of information that cannot be explained by any model. Therefore Delta Test can be used to obtain a lower bound of learning error which can be achieved without risk of over-fitting.

Functional Data Analysis: A statistical approach where multivariate data are treated as functions instead of discrete vectors.

Machine Learning: An area of Artificial Intelligence dealing with adaptive computational methods such as Artificial Neural Networks and Genetic Algorithms.

Curse of Dimensionality: A theoretical result in machine learning that states that the lower bound of error that an adaptive machine can achieve increases with data dimension. Thus performance will degrade as data dimension grows.

Least Squares Support Vector Machine: A least squares modification of the Support Vector Machine which leads into solving a linear set of equations. Also bears close resemblance to Gaussian Processes.

Variable Selection: Process where unrelated input variables are discarded from the data set. Variable selection is usually based on correlation or noise estimators of the input-output pairs and can lead into significant improvement in performance.

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