Related papers: Path Similarity Analysis: a Method for Quantifying…

Enzymes and proteins are live driven biochemicals, which has a dramatic impact over the environment, in which it is active. So, therefore, it is highly looked-for to build such a robust and highly accurate automatic and computational model…

With recent advances in sensing and tracking technology, trajectory data is becoming increasingly pervasive and analysis of trajectory data is becoming exceedingly important. A fundamental problem in analyzing trajectory data is that of…

We propose a novel algorithm for supervised dimensionality reduction named Manifold Partition Discriminant Analysis (MPDA). It aims to find a linear embedding space where the within-class similarity is achieved along the direction that is…

Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…

In many real-world applications data exhibits non-stationarity, i.e., its distribution changes over time. One approach to handling non-stationarity is to remove or minimize it before attempting to analyze the data. In the context of brain…

High-resolution stellar spectra offer valuable insights into atmospheric parameters and chemical compositions. However, their inherent complexity and high-dimensionality present challenges in fully utilizing the information they contain. In…

Sensitivity analysis plays an important role in searching for constitutive parameters (e.g. permeability) subsurface flow simulations. The mathematics behind is to solve a dynamic constrained optimization problem. Traditional methods like…

The Phase-Space approach (PSA), which was originally introduced in [Lacroix et al., Phys. Rev. D 106, 123006 (2022)] to describe neutrino flavor oscillations for interacting neutrinos emitted from stellar objects is extended to describe…

Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…

Principal component analysis (PCA) is a well-known linear dimension-reduction method that has been widely used in data analysis and modeling. It is an unsupervised learning technique that identifies a suitable linear subspace for the input…

Topological Data Analysis (TDA) is an approach to handle with big data by studying its shape. A main tool of TDA is the persistence diagram, and one can use it to compare data sets. One approach to learn on the similarity between two…

Different parallel frameworks for implementing data analysis applications have been proposed by the HPC and Big Data communities. In this paper, we investigate three task-parallel frameworks: Spark, Dask and RADICAL-Pilot with respect to…

We introduce Pairwise Distance-Diffusion Analysis (PDDA), a geometric framework for estimating the Hurst exponent from distance plots of long-memory stochastic processes. A single construction yields two complementary routes: R/S-PDDA, a…

Acquiring plausible pathways on high-dimensional structural distributions is beneficial in several domains. For example, in the drug discovery field, a protein conformational pathway, i.e. a highly probable sequence of protein structural…

Quadratic discriminant analysis (QDA) is a standard tool for classification due to its simplicity and flexibility. Because the number of its parameters scales quadratically with the number of the variables, QDA is not practical, however,…

Principal Subspace Analysis (PSA) -- and its sibling, Principal Component Analysis (PCA) -- is one of the most popular approaches for dimensionality reduction in signal processing and machine learning. But centralized PSA/PCA solutions are…

Understanding disease progression at the molecular pathway level usually requires capturing both structural dependencies between pathways and the temporal dynamics of disease evolution. In this work, we solve the former challenge by…

The adsorption or adhesion of large particles (proteins, colloids, cells, >...) at the liquid-solid interface plays an important role in many diverse applications. Despite the apparent complexity of the process, two features are…

Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly equivalent, are standard models for interprocedural analysis. Yet RSMs are more convenient as they (a) explicitly model function calls and returns, and (b)…

Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…