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Principal Component Analysis (PCA) is the workhorse tool for dimensionality reduction in this era of big data. While often overlooked, the purpose of PCA is not only to reduce data dimensionality, but also to yield features that are…
Kernel Principal Component Analysis (KPCA) is a popular dimensionality reduction technique with a wide range of applications. However, it suffers from the problem of poor scalability. Various approximation methods have been proposed in the…
Data compression can be achieved by reducing the dimensionality of high-dimensional but approximately low-rank datasets, which may in fact be described by the variation of a much smaller number of parameters. It often serves as a…
Dimensionality reduction algorithms are standard tools in a researcher's toolbox. Dimensionality reduction algorithms are frequently used to augment downstream tasks such as machine learning, data science, and also are exploratory methods…
Validity of fluid models breaks down for non-thermal or weakly collisional plasmas which often occur e.g. in the solar wind. In these regimes one has to resort to modelling through the first-principle Vlasov-Maxwell system, but its…
Constructing reduced representations of high-dimensional systems is a fundamental problem in physical chemistry. Many unsupervised machine learning methods can automatically find such low-dimensional representations. However, an often…
Dimensionality reduction is a main step in the learning process which plays an essential role in many applications. The most popular methods in this field like SVD, PCA, and LDA, only can be applied to data with vector format. This means…
High dimensional data has introduced challenges that are difficult to address when attempting to implement classical approaches of statistical process control. This has made it a topic of interest for research due in recent years. However,…
Because of high dimensionality, correlation among covariates, and noise contained in data, dimension reduction (DR) techniques are often employed to the application of machine learning algorithms. Principal Component Analysis (PCA), Linear…
This chapter discusses the way in which dimensionality reduction algorithms such as diffusion maps and sketch-map can be used to analyze molecular dynamics trajectories. The first part discusses how these various algorithms function, as…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Autoencoders (AE) provide a useful method for nonlinear dimensionality reduction but are ill-suited for low data regimes. Conversely, Principal Component Analysis (PCA) is data-efficient but is limited to linear dimensionality reduction,…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
Chemical space which encompasses all stable compounds is unfathomably large and its dimension scales linearly with the number of atoms considered. The success of machine learning methods suggests that many physical quantities exhibit…
The scalability of statistical estimators is of increasing importance in modern applications. One approach to implementing scalable algorithms is to compress data into a low dimensional latent space using dimension reduction methods. In…
Principal Component Analysis (PCA) is a fundamental data preprocessing tool in the world of machine learning. While PCA is often thought of as a dimensionality reduction method, the purpose of PCA is actually two-fold: dimension reduction…
Quantum computers could potentially simulate the dynamics of systems such as polyatomic molecules on a much larger scale than classical computers. We investigate a general quantum computational algorithm that simulates the time evolution of…
While humans effortlessly discern intrinsic dynamics and adapt to new scenarios, modern AI systems often struggle. Current methods for visual grounding of dynamics either use pure neural-network-based simulators (black box), which may…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…