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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

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

Maximum Independent Set: Self-Training through Dynamic Programming

Volkan Cevher, Grigorios Chrysos, Efstratios Panteleimon Skoulakis

This work presents a graph neural network (GNN) framework for solving the maximum independent set (MIS) problem, inspired by dynamic programming (DP). Specifically, given a graph, we propose a DP-like recursive algorithm based on GNNs that firstly construc ...

2023

A full characterization of invariant embeddability of unimodular planar graphs

Laszlo Marton Toth

When can a unimodular random planar graph be drawn in the Euclidean or the hyperbolic plane in a way that the distribution of the random drawing is isometry-invariant? This question was answered for one-ended unimodular graphs in Benjamini and Timar, using ...

WILEY2023

GAP: Differentially Private Graph Neural Networks with Aggregation Perturbation

Daniel Gatica-Perez, Sina Sajadmanesh

In this paper, we study the problem of learning Graph Neural Networks (GNNs) with Differential Privacy (DP). We propose a novel differentially private GNN based on Aggregation Perturbation (GAP), which adds stochastic noise to the GNN's aggregation functio ...

Usenix Assoc2023

Acceleration of graph pattern mining and applications to financial crime

Jovan Blanusa

Various forms of real-world data, such as social, financial, and biological networks, can be represented using graphs. An efficient method of analysing this type of data is to extract subgraph patterns, such as cliques, cycles, and motifs, from graphs. For ...

EPFL2023

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Anne-Florence Raphaëlle Bitbol, Alia Abbara

Natural microbial populations often have complex spatial structures. This can impact their evolution, in particular the ability of mutants to take over. While mutant fixation probabilities are known to be unaffected by sufficiently symmetric structures, ev ...

Oxford Univ Press2023

Graph neural networks for dynamic modeling of roller bearings

Olga Fink, Vinay Sharma

Machine learning has paved the way for the real-time monitoring of complex infrastructure and industrial systems. However, purely data-driven methods have not been able to learn the underlying dynamics and generalize them to operating conditions that have ...

PHM Society2023

Brain Fingerprinting Using Fmri Spectral Signatures On High-Resolution Cortical Graphs

Dimitri Nestor Alice Van De Ville, Maria Giulia Preti, Hamid Behjat, Stefano Moia, Carlo Ferritto

Resting-state fMRI has proven to entail subject-specific signatures that can serve as a fingerprint to identify individuals. Conventional methods are based on building a connectivity matrix based on correlation between the average time course of pairs of b ...

IEEE2023

Results on Sparse Integer Programming and Geometric Independent Sets

Jana Tabea Cslovjecsek

An integer linear program is a problem of the form max{c^T x : Ax=b, x >= 0, x integer}, where A is in Z^(n x m), b in Z^m, and c in Z^n. Solving an integer linear program is NP-hard in general, but there are several assumptions for which it becomes fixed ...

EPFL2023

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