Publication

Benchmarking machine-readable vectors of chemical reactions on computed activation barriers

Related publications (31)

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

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

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

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

Molecular hypergraph neural networks

Philippe Schwaller, Junwu Chen

Graph neural networks (GNNs) have demonstrated promising performance across various chemistry-related tasks. However, conventional graphs only model the pairwise connectivity in molecules, failing to adequately represent higher order connections, such as m ...

Aip Publishing2024

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

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

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

Self-catalysed frontal polymerisation enables fast and low-energy processing of fibre reinforced polymer composites

Véronique Michaud, Jacobus Gerardus Rudolph Staal, Baris Çaglar

Frontal polymerisation has the potential to bring unprecedented reductions in energy demand and process time to produce fibre reinforced polymer composites. Production of epoxy-based fibre reinforced polymer parts with high fibre volume content, commonly e ...

2024

A tutorial on graph models for scheduling round-robin sports tournaments

Dominique de Werra

Many sports leagues organize their competitions as round-robin tournaments. This tournament design has a rich mathematical structure that has been studied in the literature over the years. We review some of the main properties and fundamental scheduling me ...

WILEY2023

Bayesian Optimization for Chemical Reactions

Philippe Schwaller, Jeff Guo, Bojana Rankovic

Reaction optimization is challenging and traditionally delegated to domain experts who iteratively pro-pose increasingly optimal experiments. Problematically, the reaction landscape is complex and often requires hundreds of experiments to reach convergence ...

Swiss Chemical Soc2023

Equivariant Neural Architectures for Representing and Generating Graphs

Clément Arthur Yvon Vignac

Graph machine learning offers a powerful framework with natural applications in scientific fields such as chemistry, biology and material sciences. By representing data as a graph, we encode the prior knowledge that the data is composed of a set of entiti ...

EPFL2023