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Graph Representation Learning with Optimal Transport: Analysis and Applications

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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 dwell times ...

2024

This article proposes an exploration technique for multiagent reinforcement learning (MARL) with graph-based communication among agents. We assume that the individual rewards received by the agents are independent of the actions by the other agents, while ...

Ieee-Inst Electrical Electronics Engineers Inc2024

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 entitie ...

EPFL2023

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 ...

Berkeley2023

Graph Neural Networks (GNNs) have emerged as a powerful tool for learning on graphs, demonstrating exceptional performance in various domains. However, as GNNs become increasingly popular, new challenges arise. One of the most pressing is the need to ensur ...

EPFL2023

Enforcing Privacy in Distributed Learning With Performance Guarantees

Ali H. Sayed, Stefan Vlaski, Elsa Rizk

We study the privatization of distributed learning and optimization strategies. We focus on differential privacy schemes and study their effect on performance. We show that the popular additive random perturbation scheme degrades performance because it is ...

Piscataway2023

Scalable Computation of Dynamic Flow Problems via Multimarginal Graph-Structured Optimal Transport

Isabel Haasler, Axel Ringh, Yiqiang Chen

In this work, we develop a new framework for dynamic network flow pro-blems based on optimal transport theory. We show that the dynamic multicommodity minimum-cost network flow problem can be formulated as a multimarginal optimal transport problem, where t ...

2023

A graph H is a minor of a second graph G if G can be transformed into H by two operations: 1) deleting nodes and/or edges, or 2) contracting edges. Coarse-grained reconfigurable array (CGRA) application mapping is closely related to the graph minor problem ...

2023

Beyond Spectral Gap: The Role of the Topology in Decentralized Learning

Martin Jaggi, Thijs Vogels, Hadrien Hendrikx

In data-parallel optimization of machine learning models, workers collaborate to improve their estimates of the model: more accurate gradients allow them to use larger learning rates and optimize faster. In the decentralized setting, in which workers commu ...

Brookline2023

DiGress: Discrete Denoising diffusion for graph generation

Pascal Frossard, Volkan Cevher, Igor Krawczuk, Bohan Wang, Clément Arthur Yvon Vignac

This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model utilizes a discrete diffusion process that progressively edits graphs with noise, through the process of adding or ...

2023