Publications associées à A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

Publications associées (31)

The role of LRRK2 in lung adenocarcinoma

Lung cancer is the leading cause of cancer-related deaths worldwide and the most common lung cancer subtype is lung adenocarcinoma (LUAD). Frequently mutated genes involve activating mutations in KRAS and loss of function mutations in TP53. LUADs primarily ...

EPFL2024

Seebeck Coefficient of Ionic Conductors from Bayesian Regression Analysis

Paolo Pegolo

We propose a novel approach to evaluating the ionic Seebeck coefficient in electrolytes from relatively short equilibrium molecular dynamics simulations, based on the Green-Kubo theory of linear response and Bayesian regression analysis. By exploiting the ...

Amer Chemical Soc2024

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

Beyond fine-tuning: LoRA modules boost near-OOD detection and LLM security

Pierre Vandergheynst, Milos Vasic, Renata Khasanova, Francesco Craighero

Under resource constraints, LLMs are usually fine- tuned with additional knowledge using Parameter Efficient Fine-Tuning (PEFT), using Low-Rank Adaptation (LoRA) modules. In fact, LoRA injects a new set of small trainable matrices to adapt an LLM to a new ...

2024

Beyond fine-tuning: LoRA modules boost near-OOD detection and LLM security

Pierre Vandergheynst, Milos Vasic, Renata Khasanova, Francesco Craighero

Under resource constraints, LLMs are usually fine-tuned with additional knowledge using Parameter Efficient Fine-Tuning (PEFT), using Low-Rank Adaptation (LoRA) modules. In fact, LoRA injects a new set of small trainable matrices to adapt an LLM to a new t ...

2024

The Two Times Problem: Where Is the Problem?

Michael Herzog

Gruber et al. (2022) offered a framework how to explain "Physical time within human time", solving the 'two times problem: Here, I am asking whether such a problem exists at all. To question the question, I will appeal to neurobiological, evolutionary, and ...

Brill2024

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Ana Marija Jaksic

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

BMC2024

Regressive Tomography and Direct Regressive Reconstruction: A Research Note

Henri Weisen

Two related methods for inverting line-integrated measurements are presented in this research paper in the context of the recent deuterium-tritium experiments in the JET tokamak. Unlike traditional methods of tomography, these methods rely on making use of ...

2023

Price Discrimination with Robust Beliefs

Thomas Alois Weber, Jun Han

This paper considers the problem of second-degree price discrimination when the type distribution is unknown or imperfectly specified by means of an ambiguity set. As robustness measure we use a performance index, equivalent to relative regret, which quant ...

Elsevier2023

Robust discrete choice models with t-distributed kernel errors

Michel Bierlaire

Outliers in discrete choice response data may result from misclassification and misreporting of the response variable and from choice behaviour that is inconsistent with modelling assumptions (e.g. random utility maximisation). In the presence of outliers, ...

2023

Beyond the ultradeep frontier fields and legacy observations (BUFFALO): a high-resolution strong plus weak-lensing view of Abell 370

David Richard Harvey

The HST treasury programme BUFFALO provides extended wide-field imaging of the six Hubble Frontier Fields galaxy clusters. Here we present the combined strong and weak-lensing analysis of Abell 370, a massive cluster at z = 0.375. From the reconstructed to ...

OXFORD UNIV PRESS2023

Euclid preparation: XXVIII. Forecasts for ten different higher-order weak lensing statistics

Maurizio Martinelli, Frédéric Courbin, Gianluca Castignani, Austin Chandler Peel

Recent cosmic shear studies have shown that higher-order statistics (HOS) developed by independent teams now outperform standard two-point estimators in terms of statistical precision thanks to their sensitivity to the non-Gaussian features of large-scale ...

EDP SCIENCES S A2023

Learning Robust and Adaptive Representations: from Interactions, for Interactions

Yuejiang Liu

Interactions are ubiquitous in our world, spanning from social interactions between human individuals to physical interactions between robots and objects to mechanistic interactions among different components of an intelligent system. Despite their prevale ...

EPFL2023

Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Sebastian Martin Waszak

Background: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatri ...

2023

Two antagonistic response regulators control Pseudomonas aeruginosa polarization during mechanotaxis

Alexandre Louis André Persat, Lorenzo Anton-Louis Talà, Xavier Jean-Yves Pierrat, Zaïnebe Dhirani, Marco Julian Kühn

The opportunistic pathogen Pseudomonas aeruginosa adapts to solid surfaces to enhance virulence and infect its host. Type IV pili (T4P), long and thin filaments that power surface-specific twitching motility, allow single cells to sense surfaces and contro ...

WILEY2023

Regularization for distributionally robust state estimation and prediction

Giancarlo Ferrari Trecate, Jean-Sébastien Hubert Brouillon

The increasing availability of sensing techniques provides a great opportunity for engineers to design state estimation methods, which are optimal for the system under observation and the observed noise patterns. However, these patterns often do not fulfil ...

2023

Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range

Didier Trono, Henning Paul-Julius Stahlberg, Priscilla Turelli, Florence Pojer, Dongchun Ni, Kelvin Ka Ching Lau, Sergey Nazarov, Alexander Myasnikov, Bertrand Dominique Beckert, Emiko Uchikawa

nvestigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported to be transmitted from humans to various animals after req ...

2023

The role of the NF-kappaB pathway in Amyotrophic lateral sclerosis pathogenesis

Emma Charlotta Källstig

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative motor disorder, which results in death within a few years of diagnosis. While the cause of most cases of ALS is unknown, 10% of cases are familial (fALS), and associated with mutations in one of ov ...

EPFL2023

Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E

Jacques Fellay, Ali Saadat Varnosfaderanii

Background and Aims:The clinical spectrum of human infection by HEV ranges from asymptomatic to severe acute hepatitis. Furthermore, HEV can cause diverse neurological manifestations, especially Parsonage-Turner syndrome. Here, we used a large-scale human ...

Lippincott Williams & Wilkins2023

Engineering random spin models with atoms in a high-finesse cavity

Jean-Philippe Brantut, Nick Jacob Sauerwein, Tigrane Arthur Cantat Moltrecht, Francesca Orsi

Random spin models play a key role in our understanding of disorder and complex many-body systems. Two all-to-all interacting, disordered models have now been realized using a cavity quantum electrodynamics platform. ...

NATURE PORTFOLIO2023