Visual exploration of high-dimensional real-valued datasets is a fundamental task in exploratory data analysis (EDA). Existing methods use predefined criteria to choose the representation of data. There is a lack of methods that (i) elicit from the user what she has learned from the data and (ii) show patterns that she does not know yet. We construct a theoretical model where identified patterns can be input as knowledge to the system. The knowledge syntax here is intuitive, such as "this set of points forms a cluster", and requires no knowledge of maths. This background knowledge is used to find a Maximum Entropy distribution of the data, after which the system provides the user data projections in which the data and the Maximum Entropy distribution differ the most, hence showing the user aspects of the data that are maximally informative given the user's current knowledge. We provide an open source EDA system with tailored interactive visualizations to demonstrate these concepts. We study the performance of the system and present use cases on both synthetic and real data. We find that the model and the prototype system allow the user to learn information efficiently from various data sources and the system works sufficiently fast in practice. We conclude that the information theoretic approach to exploratory data analysis where patterns observed by a user are formalized as constraints provides a principled, intuitive, and efficient basis for constructing an EDA system.
Dimensionality reduction for EDA has been studied for decades starting with multidimensional scaling (MDS) @cite_9 @cite_22 and projection pursuit @cite_33 @cite_31 . Recent research on this topic (referred to as manifold learning) is still inspired by MDS: find a low-dimensional embedding of points representing well the the distances in the high-dimensional space. In contrast to PCA @cite_23 , the idea is to preserve small distances, and large distances are irrelevant, as long as they remain large, e.g., Local Linear and (t-)Stochastic Neighbor Embedding @cite_14 @cite_16 @cite_30 . This is typically not possible to achieve perfectly, and a trade-off between precision and recall arises @cite_4 .
@cite_30 @cite_14 @cite_4 @cite_22 @cite_33 @cite_9 @cite_23 @cite_31 @cite_16
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Scientists working with large volumes of high-dimensional data, such as global climate patterns, stellar spectra, or human gene distributions, regularly confront the problem of dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. The human brain confronts the same problem in everyday perception, extracting from its high-dimensional sensory inputs—30,000 auditory nerve fibers or 106 optic nerve fibers—a manageably small number of perceptually relevant features. Here we describe an approach to solving dimensionality reduction problems that uses easily measured local metric information to learn the underlying global geometry of a data set. Unlike classical techniques such as principal component analysis (PCA) and multidimensional scaling (MDS), our approach is capable of discovering the nonlinear degrees of freedom that underlie complex natural observations, such as human handwriting or images of a face under different viewing conditions. In contrast to previous algorithms for nonlinear dimensionality reduction, ours efficiently computes a globally optimal solution, and, for an important class of data manifolds, is guaranteed to converge asymptotically to the true structure. Reducing the dimensionality of data without losing intrinsic information is an important preprocessing step in high-dimensional data analysis. Fisher discriminant analysis (FDA) is a traditional technique for supervised dimensionality reduction, but it tends to give undesired results if samples in a class are multimodal. An unsupervised dimensionality reduction method called locality-preserving projection (LPP) can work well with multimodal data due to its locality preserving property. However, since LPP does not take the label information into account, it is not necessarily useful in supervised learning scenarios. In this paper, we propose a new linear supervised dimensionality reduction method called local Fisher discriminant analysis (LFDA), which effectively combines the ideas of FDA and LPP. LFDA has an analytic form of the embedding transformation and the solution can be easily computed just by solving a generalized eigenvalue problem. We demonstrate the practical usefulness and high scalability of the LFDA method in data visualization and classification tasks through extensive simulation studies. We also show that LFDA can be extended to non-linear dimensionality reduction scenarios by applying the kernel trick. The paper addresses large scale image retrieval with short vector representations. We study dimensionality reduction by Principal Component Analysis (PCA) and propose improvements to its different phases. We show and explicitly exploit relations between i) mean subtraction and the negative evidence, i.e., a visual word that is mutually missing in two descriptions being compared, and ii) the axis de-correlation and the co-occurrences phenomenon. Finally, we propose an effective way to alleviate the quantization artifacts through a joint dimensionality reduction of multiple vocabularies. The proposed techniques are simple, yet significantly and consistently improve over the state of the art on compact image representations. Complementary experiments in image classification show that the methods are generally applicable. We derive a least-squares formulation for MDDMp technique.A novel multi-label feature extraction algorithm is proposed.Our algorithm maximizes both feature variance and feature-label dependence.Experiments show that our algorithm is a competitive candidate. Dimensionality reduction is an important pre-processing procedure for multi-label classification to mitigate the possible effect of dimensionality curse, which is divided into feature extraction and selection. Principal component analysis (PCA) and multi-label dimensionality reduction via dependence maximization (MDDM) represent two mainstream feature extraction techniques for unsupervised and supervised paradigms. They produce many small and a few large positive eigenvalues respectively, which could deteriorate the classification performance due to an improper number of projection directions. It has been proved that PCA proposed primarily via maximizing feature variance is associated with a least-squares formulation. In this paper, we prove that MDDM with orthonormal projection directions also falls into the least-squares framework, which originally maximizes Hilbert-Schmidt independence criterion (HSIC). Then we propose a novel multi-label feature extraction method to integrate two least-squares formulae through a linear combination, which maximizes both feature variance and feature-label dependence simultaneously and thus results in a proper number of positive eigenvalues. Experimental results on eight data sets show that our proposed method can achieve a better performance, compared with other seven state-of-the-art multi-label feature extraction algorithms.