Publications associées à Reconciling Utility with Privacy in Genomics

Optimization Algorithms for Decentralized, Distributed and Collaborative Machine Learning

Distributed learning is the key for enabling training of modern large-scale machine learning models, through parallelising the learning process. Collaborative learning is essential for learning from privacy-sensitive data that is distributed across various ...

EPFL2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Melanie Blokesch, Sandrine Stutzmann, Natalia Carolina Drebes Dorr, Alexandre Lemopoulos

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Differentially private multi-agent constraint optimization

Boi Faltings, Aleksei Triastcyn, Sujit Prakash Gujar, Sankarshan Damle

Distributed constraint optimization (DCOP) is a framework in which multiple agents with private constraints (or preferences) cooperate to achieve a common goal optimally. DCOPs are applicable in several multi-agent coordination/allocation problems, such as ...

Springer2024

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Hannes Markus Peter

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Massimo Bourquin

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Tamar Kohn, Xavier Fernandez Cassi

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

Philippe Schwaller, Jeff Guo

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

Amer Chemical Soc2024

A ride time-oriented scheduling algorithm for dial-a-ride problems

Nikolaos Geroliminis, Claudia Bongiovanni, Mor Kaspi

This paper offers a new algorithm to efficiently optimize scheduling decisions for dial-a-ride problems (DARPs), including problem variants considering electric and autonomous vehicles (e-ADARPs). The scheduling heuristic, based on linear programming theor ...

Pergamon-Elsevier Science Ltd2024

The Privacy Power of Correlated Noise in Decentralized Learning

Rachid Guerraoui, Martin Jaggi, Anastasiia Koloskova, Youssef Allouah, Aymane El Firdoussi

Decentralized learning is appealing as it enables the scalable usage of large amounts of distributed data and resources (without resorting to any central entity), while promoting privacy since every user minimizes the direct exposure of their data. Yet, wi ...

PMLR2024

A Privacy-Preserving Querying Mechanism with High Utility for Electric Vehicles

Sayan Biswas

Electric vehicles (EVs) are becoming more popular due to environmental consciousness. The limited availability of charging stations (CSs), compared to the number of EVs on the road, has led to increased range anxiety and a higher frequency of CS queries du ...

Ieee-Inst Electrical Electronics Engineers Inc2024

The effect of smooth parametrizations on nonconvex optimization landscapes

Nicolas Boumal

We develop new tools to study landscapes in nonconvex optimization. Given one optimization problem, we pair it with another by smoothly parametrizing the domain. This is either for practical purposes (e.g., to use smooth optimization algorithms with good g ...

Springer Heidelberg2024

Scalable constrained optimization

Maria-Luiza Vladarean

Modern optimization is tasked with handling applications of increasingly large scale, chiefly due to the massive amounts of widely available data and the ever-growing reach of Machine Learning. Consequently, this area of research is under steady pressure t ...

EPFL2024

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Evangelia Vagena

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

BENIGN LANDSCAPES OF LOW-DIMENSIONAL RELAXATIONS FOR ORTHOGONAL SYNCHRONIZATION ON GENERAL GRAPHS

Nicolas Boumal

Orthogonal group synchronization is the problem of estimating n elements Z(1),& mldr;,Z(n) from the rxr orthogonal group given some relative measurements R-ij approximate to Z(i)Z(j)(-1). The least-squares formulation is nonconvex. To avoid its local minim ...

Siam Publications2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Kristina Makasheva

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

Stochastic adaptive resampling for the estimation of discrete choice models

Michel Bierlaire, Nicola Marco Ortelli, Matthieu Marie Cochon de Lapparent

In the field of choice modeling, the availability of ever-larger datasets has the potential to significantly expand our understanding of human behavior, but this prospect is limited by the poor scalability of discrete choice models (DCMs): as sample sizes ...

2023