Abstract
Methods for dimensionality reduction are showing significant contributions to knowledge generation in high-dimensional modeling scenarios throughout many disciplines. By achieving a lower dimensional representation (also called embedding), fewer computing resources are needed in downstream machine learning tasks, thus leading to a faster training time, lower complexity, and statistical flexibility. In this work, we investigate the utility of three prominent unsupervised embedding techniques (principal component analysis—PCA, uniform manifold approximation and projection—UMAP, and variational autoencoders—VAEs) for solving classification tasks in the domain of toxicology. To this end, we compare these embedding techniques against a set of molecular fingerprint-based models that do not utilize additional pre-preprocessing of features. Inspired by the success of transfer learning in several fields, we further study the performance of embedders when trained on an external dataset of chemical compounds. To gain a better understanding of their characteristics, we evaluate the embedders with different embedding dimensionalities, and with different sizes of the external dataset. Our findings show that the recently popularized UMAP approach can be utilized alongside known techniques such as PCA and VAE as a pre-compression technique in the toxicology domain. Nevertheless, the generative model of VAE shows an advantage in pre-compressing the data with respect to classification accuracy.
Highlights
Chemical representation is an important topic in cheminformatics [1]and quantitative structure–activity relationships (QSARs), as QSAR model quality depends largely on the predictive features defined by the task at hand, i.e., mapping a feature space (X) onto a target chemical or biological activity (y)
Pharmaceuticals 2021, 14, 758 utilized [16]. Another difficulty in machine learning is the so-called curse of dimensionality, a term coined by Richard Bellman [17], which refers to various problems that arise when working with high-dimensional data including increased chances of overfitting and spurious results
The linearity of principal component analysis (PCA) is what makes the method mathematically more concise than some nonlinear methods, but at the price of variance maximization as well as the inability to capture nonlinear phenomena in single dimensions. When it comes to nonlinear methods for dimensionality reduction, there are a number of noteworthy approaches, such as locally linear embedding [26], Laplacian eigenmaps [27], or t-SNE [26]
Summary
Chemical (or molecular) representation is an important topic in cheminformatics [1]and quantitative structure–activity relationships (QSARs), as QSAR model quality depends largely on the predictive features defined by the task at hand, i.e., mapping a feature space (X) onto a target chemical or biological activity (y). A well-established strategy, besides feature selection, to cope with this issue is dimensionality reduction, i.e., transforming the data into a low-dimensional space such that the resulting low-dimensional representation preserves certain properties of the original data Such an approach has proven to be highly useful for numerous downstream machine learning tasks like classification [19], anomaly detection [20], and recommender systems [21]. It is a nonlinear method that works by utilizing local manifold approximations and combining their local fuzzy simplicial set representations in order to create a topological representation of the high-dimensional data. It minimizes the cross-entropy between topological representations, optimizing the layout of the data representation. As they were originally proposed, there has been a number of adaptations of the original autoencoder with variational autoencoders or VAEs [34] as one of the latest state-of-the-art methods
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