Related papers: PepCompass: Navigating peptide embedding spaces us…

Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions.…

Despite the recent success of Bayesian optimization (BO) in a variety of applications where sample efficiency is imperative, its performance may be seriously compromised in settings characterized by high-dimensional parameter spaces. A…

Peptide self-assembly prediction offers a powerful bottom-up strategy for designing biocompatible, low-toxicity materials for large-scale synthesis in a broad range of biomedical and energy applications. However, screening the vast sequence…

What is the shortest path between two data points lying in a high-dimensional space? While the answer is trivial in Euclidean geometry, it becomes significantly more complex when the data lies on a curved manifold -- requiring a Riemannian…

In many robot motion planning problems, task objectives and physical constraints induce non-Euclidean geometry on the configuration space, yet many planners operate using Euclidean distances that ignore this structure. We address the…

We present Geodesic Semantic Search (GSS), a retrieval system that learns node-specific Riemannian metrics on citation graphs to enable geometry-aware semantic search. Unlike standard embedding-based retrieval that relies on fixed Euclidean…

Generating peptides with desired properties is crucial for drug discovery and biotechnology. Traditional sequence-based and structure-based methods often require extensive datasets, which limits their effectiveness. In this study, we…

Riemannian geometry provides the fundamental framework for optimization on nonlinear spaces such as matrix manifolds, which arise in machine learning, signal processing, and robotics. While the underlying theory is classical, existing…

Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…

Graph convolutional networks (GCNs) are powerful frameworks for learning embeddings of graph-structured data. GCNs are traditionally studied through the lens of Euclidean geometry. Recent works find that non-Euclidean Riemannian manifolds…

This study investigates the application of Riemannian geometry-based methods for brain decoding using invasive electrophysiological recordings. Although previously employed in non-invasive, the utility of Riemannian geometry for invasive…

Bayesian optimization is a data-efficient technique which can be used for control parameter tuning, parametric policy adaptation, and structure design in robotics. Many of these problems require optimization of functions defined on…

Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…

Machine learning holds tremendous promise for transforming the fundamental practice of scientific discovery by virtue of its data-driven nature. With the ever-increasing stream of research data collection, it would be appealing to…

The real symplectic Stiefel manifold is the manifold of symplectic bases of symplectic subspaces of a fixed dimension. It features in a large variety of applications in physics and engineering. In this work, we study this manifold with the…

In this paper, we propose a general procedure for establishing the geometric landscape connections of a Riemannian optimization problem under the embedded and quotient geometries. By applying the general procedure to the fixed-rank positive…

In this work, we investigate Riemannian geometry based dimensionality reduction methods that respect the underlying manifold structure of the data. In particular, we focus on Principal Geodesic Analysis (PGA) as a nonlinear generalization…

Manifold learning methods are an invaluable tool in today's world of increasingly huge datasets. Manifold learning algorithms can discover a much lower-dimensional representation (embedding) of a high-dimensional dataset through non-linear…

Rapid growth of high-dimensional datasets in fields such as single-cell RNA sequencing and spatial genomics has led to unprecedented opportunities for scientific discovery, but it also presents unique computational and statistical…

Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the…