Publications related to A metric for phylogenetic trees based on matching

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

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

Interpret3C: Interpretable Student Clustering Through Individualized Feature Selection

Julian Thomas Blackwell, Tanja Christina Käser Jacober, Paola Mejia Domenzain, Vinitra Swamy, Isadora Alves de Salles

Clustering in education, particularly in large-scale online environments like MOOCs, is essential for understanding and adapting to diverse student needs. However, the effectiveness of clustering depends on its interpretability, which becomes challenging w ...

2024

Planning urban proximities: An empirical analysis of how residential preferences conflict with the urban morphologies and residential practices

Vincent Kaufmann, Luca Giovanni Pattaroni, Marc-Edouard Baptiste Grégoire Schultheiss

Urban proximity planning is foreseen as a solution to foster a “sustainable” city, including economic viability, environmental soundness and social inclusivity. This paper focuses on the inclusivity aspects by questioning the adoption of urban proximities: ...

2024

Reliable data-driven decision-making through optimal transport

Bahar Taskesen

Decision-making permeates every aspect of human and societal development, from individuals' daily choices to the complex decisions made by communities and institutions. Central to effective decision-making is the discipline of optimization, which seeks th ...

EPFL2024

Transportation-based functional ANOVA and PCA for covariance operators

Victor Panaretos, Yoav Zemel, Valentina Masarotto

We consider the problem of comparing several samples of stochastic processes with respect to their second-order structure, and describing the main modes of variation in this second order structure, if present. These tasks can be seen as an Analysis of Vari ...

Inst Mathematical Statistics-Ims2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

Jacques Fellay, Zhi Ming Xu

The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aim ...

Nature Portfolio2024

On Speed and Advantage : Results in Information Velocity and Monitoring Problems

Reka Inovan

Information theory has allowed us to determine the fundamental limit of various communication and algorithmic problems, e.g., the channel coding problem, the compression problem, and the hypothesis testing problem. In this work, we revisit the assumptions ...

EPFL2024

Tree diversity reduces variability in sapling survival under drought

Charlotte Grossiord, Xiaojuan Liu, Jingjing Liang

Enhancing tree diversity may be important to fostering resilience to drought-related climate extremes. So far, little attention has been given to whether tree diversity can increase the survival of trees and reduce its variability in young forest plantatio ...

Wiley2024

Extensions of Peer Prediction Incentive Mechanisms

Adam Julian Richardson

As large, data-driven artificial intelligence models become ubiquitous, guaranteeing high data quality is imperative for constructing models. Crowdsourcing, community sensing, and data filtering have long been the standard approaches to guaranteeing or imp ...

EPFL2024

Impact of phylogeny on structural contact inference from protein sequence data

Nicola Dietler, Umberto Lupo, Anne-Florence Raphaëlle Bitbol

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

Qiang Liu, Feng Yu, Yichen Xu

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

Chunmin Zhang, Mathias Josef Payer, Zhiyao Feng, 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