Publication

A metric for phylogenetic trees based on matching

Publications associées (31)

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Fairness and Explainability in Clustering Problems

Xinrui Jia

In this thesis we present and analyze approximation algorithms for three different clustering problems. The formulations of these problems are motivated by fairness and explainability considerations, two issues that have recently received attention in the ...

EPFL2023

Unsupervised Graph Representation Learning with Cluster-aware Self-training and Refining

Yichen Xu, Qiang Liu, Feng Yu

Unsupervised graph representation learning aims to learn low-dimensional node embeddings without supervision while preserving graph topological structures and node attributive features. Previous Graph Neural Networks (GNN) require a large number of labeled ...

Assoc Computing Machinery2023

Augmented Lagrangian Methods for Provable and Scalable Machine Learning

Mehmet Fatih Sahin

Non-convex constrained optimization problems have become a powerful framework for modeling a wide range of machine learning problems, with applications in k-means clustering, large- scale semidefinite programs (SDPs), and various other tasks. As the perfor ...

EPFL2023

AIFORE: Smart Fuzzing Based on Automatic Input Format Reverse Engineering

Mathias Josef Payer, Zhiyao Feng, Chunmin Zhang, Ji Shi

Knowledge of a program's input format is essential for effective input generation in fuzzing. Automated input format reverse engineering represents an attractive but challenging approach to learning the format. In this paper, we address several challenges ...

Usenix Assoc2023

The Impact of Data Persistence Bias on Social Media Studies

Tugrulcan Elmas

Social media studies often collect data retrospectively to analyze public opinion. Social media data may decay over time and such decay may prevent the collection of the complete dataset. As a result, the collected dataset may differ from the complete data ...

Assoc Computing Machinery2023

Multiplicative chaos of the Brownian loop soup

Antoine Pierre François Jego, Titus Lupu

We construct a measure on the thick points of a Brownian loop soup in a bounded domain D

D

of the plane with given intensity theta>0

\theta >0

, which is formally obtained by exponentiating the square root of its occupation field. The measure is construct ...

WILEY2023

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

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

Analysis of a Class of Multilevel Markov Chain Monte Carlo Algorithms Based on Independent Metropolis–Hastings

Fabio Nobile, Juan Pablo Madrigal Cianci

In this work, we present, analyze, and implement a class of multilevel Markov chain Monte Carlo(ML-MCMC) algorithms based on independent Metropolis--Hastings proposals for Bayesian inverse problems. In this context, the likelihood function involves solving ...

2023

Multiplicative chaos of the Brownian loop soup

Antoine Pierre François Jego, Titus Lupu

We construct a measure on the thick points of a Brownian loop soup in a bounded domain D

D

of the plane with given intensity theta>0

\theta >0

, which is formally obtained by exponentiating the square root of its occupation field. The measure is construct ...

WILEY2023