Publications related to Kinetic Euclidean Distance Matrices

Related publications (35)

Spectral Estimators for High-Dimensional Matrix Inference

A key challenge across many disciplines is to extract meaningful information from data which is often obscured by noise. These datasets are typically represented as large matrices. Given the current trend of ever-increasing data volumes, with datasets grow ...

EPFL2024

VDMNav: Software Architecture for Aerodynamically Constrained Navigation on Small Fixed-Wing Drones

Jan Skaloud, Aman Sharma, Gabriel François Laupré

Navigation of drones is predominantly based on sensor fusion algorithms. Most of these algorithms make use of some form of Bayesian filtering with a majority employing an Extended Kalman Filter (EKF), wherein inertial measurements are fused with a Global N ...

2024

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

RANDOMIZED JOINT DIAGONALIZATION OF SYMMETRIC

Daniel Kressner, Haoze He

Given a family of nearly commuting symmetric matrices, we consider the task of computing an orthogonal matrix that nearly diagonalizes every matrix in the family. In this paper, we propose and analyze randomized joint diagonalization (RJD) for performing t ...

Siam Publications2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

VDM-based navigation for Delta-wing UAVs: Models, calibration, implementation

Pasquale Longobardi

Autonomous navigation of small UAVs is typically based on the integration of inertial navigation systems (INS) together with global navigation satellite systems (GNSS). However, GNSS signals can face various forms of interference affecting their continuous ...

EPFL2024

The Power of Two Matrices in Spectral Algorithms for Community Recovery

Colin Peter Sandon

Spectral algorithms are some of the main tools in optimization and inference problems on graphs. Typically, the graph is encoded as a matrix and eigenvectors and eigenvalues of the matrix are then used to solve the given graph problem. Spectral algorithms ...

Ieee-Inst Electrical Electronics Engineers Inc2024

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

SPEEDING UP KRYLOV SUBSPACE METHODS FOR COMPUTING f(A)b VIA RANDOMIZATION

Daniel Kressner, Alice Cortinovis

This work is concerned with the computation of the action of a matrix function f(A), such as the matrix exponential or the matrix square root, on a vector b. For a general matrix A, this can be done by computing the compression of A onto a suitable Krylov ...

Siam Publications2024

Performance and accuracy of cross‐section tracking methods for hydromorphological habitat assessment in wadable rivers with sparse canopy conditions

Giovanni De Cesare, Paolo Perona, Robin Schroff

This article investigates the performance and accuracy of continuous Real-Time Kinematic (RTK) Global Navigation Satellite System (GNSS) position tracking for hydromorphological surveys, based on a comprehensive river restoration monitoring campaign. The a ...

2024

Accelerator-driven Data Arrangement to Minimize Transformers Run-time on Multi-core Architectures

David Atienza Alonso, Giovanni Ansaloni, Alireza Amirshahi

The increasing complexity of transformer models in artificial intelligence expands their computational costs, memory usage, and energy consumption. Hardware acceleration tackles the ensuing challenges by designing processors and accelerators tailored for t ...

2024

Aerodynamic modeling of a delta-wing UAV for model-based navigation

Jan Skaloud, Pasquale Longobardi

This study aims to identify an optimal, as well as practical, parametric structure for a delta-wing UAV aerodynamic model for the purpose of model-based navigation. We present a comprehensive procedure for characterizing the aerodynamics of this platform, ...

2024

RMAML: Riemannian meta-learning with orthogonality constraints

Soumava Kumar Roy

Meta-learning is the core capability that enables intelligent systems to rapidly generalize their prior ex-perience to learn new tasks. In general, the optimization-based methods formalize the meta-learning as a bi-level optimization problem, that is a nes ...

ELSEVIER SCI LTD2023

A mixed precision LOBPCG algorithm

Daniel Kressner, Meiyue Shao

The locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm is a popular approach for computing a few smallest eigenvalues and the corresponding eigenvectors of a large Hermitian positive definite matrix A. In this work, we propose a mix ...

SPRINGER2023

Duality and bicrystals on infinite binary matrices

Thomas Gerber

The set of finite binary matrices of a given size is known to carry a finite type AA bicrystal structure. We first review this classical construction, explain how it yields a short proof of the equality between Kostka polynomials and one-dimensional sums t ...

EMS Press2023

espm: A Python library for the simulation of STEM-EDXS datasets

Adrien Maxime Louis Teurtrie, Cécile Hébert, Duncan Thomas Lindsay Alexander, Nathanaël Perraudin, Hui Chen, Guillaume Romain Obozinski, Hui Chen

We present two open-source Python packages: "electron spectro-microscopy"(espm) and "electron microscopy tables"(emtables). The espm software enables the simulation of scanning transmission electron microscopy energy-dispersive X-ray spectroscopy datacubes ...

ELSEVIER2023

A new age in protein design empowered by deep learning

Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Casper Alexander Goverde, Arne Schneuing, Hamed Khakzad, Ilia Igashov

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Cell Press2023

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023