Related papers: Auto-WHATMD : Automated Wasserstein-based High-dim…

We introduce LOT Wassmap, a computationally feasible algorithm to uncover low-dimensional structures in the Wasserstein space. The algorithm is motivated by the observation that many datasets are naturally interpreted as probability…

Wasserstein Discriminant Analysis (WDA) is a new supervised method that can improve classification of high-dimensional data by computing a suitable linear map onto a lower dimensional subspace. Following the blueprint of classical Linear…

Finding meaningful distances between high-dimensional data samples is an important scientific task. To this end, we propose a new tree-Wasserstein distance (TWD) for high-dimensional data with two key aspects. First, our TWD is specifically…

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…

In this work, the application of the multi-dimensional higher order dynamic mode decomposition (HODMD) is proposed for the first time to analyse combustion databases. In particular, HODMD has been adapted and combined with other…

Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…

Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…

Finding process pathways in molecular simulations such as the unbinding paths of small molecule ligands from their binding sites at protein targets in a set of trajectories via unsupervised learning approaches requires the definition of a…

Dataset Distillation (DD) aims to generate a compact synthetic dataset that enables models to achieve performance comparable to training on the full large dataset, significantly reducing computational costs. Drawing from optimal transport…

In this work, a new algorithm based on the application of higher-order dynamic mode decomposition (HODMD) is proposed for feature selection and variables clustering in reacting flow simulations. The hierarchical HODMD (h-HODMD) performs a…

The Wasserstein metric or earth mover's distance (EMD) is a useful tool in statistics, machine learning and computer science with many applications to biological or medical imaging, among others. Especially in the light of increasingly…

We propose a new architecture for the learning of predictive spatio-temporal motion models from data alone. Our approach, dubbed the Dropout Autoencoder LSTM, is capable of synthesizing natural looking motion sequences over long time…

Protein sequence alignment is a cornerstone of bioinformatics, traditionally approached using dynamic programming (DP) algorithms that find an optimal sequential path. This paper introduces UniOTalign, a novel framework that recasts…

High-dimensional data often exhibit hierarchical structures in both modes: samples and features. Yet, most existing approaches for hierarchical representation learning consider only one mode at a time. In this work, we propose an…

Practical large-scale recommender systems usually contain thousands of feature fields from users, items, contextual information, and their interactions. Most of them empirically allocate a unified dimension to all feature fields, which is…

The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…

Measuring the semantic similarity between two sentences is still an important task. The word mover's distance (WMD) computes the similarity via the optimal alignment between the sets of word embeddings. However, WMD does not utilize word…

Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is…

Studying the pathways of ligand-receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein-ligand complexes can be computed using molecular dynamics…

Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…