Publications related to Systematic model reduction captures the dynamics of extrinsic noise in biochemical subnetworks

Altruism, reciprocity, and tokens to reward forwarding data: Is that fair?

Verónica del Carmen Estrada Galiñanes, Arman Babaei

Decentralized storage networks offer services with intriguing possibilities to reduce inequalities in an extremely centralized market. Fair distribution of rewards, however, is still a persistent problem in the current generation of decentralized applicati ...

2024

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Asli Sahin

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

Mechanisms and functions of protein S-acylation

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Francisco De Magalhães Sarmento R De Mesquita

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Nature Portfolio2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Fast and Future: Towards Efficient Forecasting in Video Semantic Segmentation

Evann Pierre Guy Courdier

Deep learning has revolutionized the field of computer vision, a success largely attributable to the growing size of models, datasets, and computational power. Simultaneously, a critical pain point arises as several computer vision applications are deploye ...

EPFL2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Global, Passive Detection of Connection Tampering

Louis-Henri Manuel Jakob Merino

In-network devices around the world monitor and tamper with connections for many reasons, including intrusion prevention, combating spam or phishing, and country-level censorship. Connection tampering seeks to block access to specific domain names or keywo ...

Assoc Computing Machinery2023

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

Equilibria in Network Constrained Energy Markets

Leonardo Massai

We study an energy market composed of producers who compete to supply energy to different markets and want to maximize their profits. The energy market is modeled by a graph representing a constrained power network where nodes represent the markets and lin ...

Elsevier2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Artificial Neural Network Training on an Optical Processor via Direct Feedback Alignment

Florent Gérard Krzakala, Julien Marcel Daniel Emmanuel Launay

Artificial Neural Networks (ANN) are habitually trained via the back-propagation (BP) algorithm. This approach has been extremely successful: Current models like GPT-3 have O(10 11 ) parameters, are trained on O(10 11 ) words and produce awe-inspiring resu ...

IEEE2023

Estimating pollution spread in water networks as a Schrödinger bridge problem with partial information

Isabel Haasler

Incidents where water networks are contaminated with microorganisms or pollutants can result in a large number of infected or ill persons, and it is therefore important to quickly detect, localize and estimate the spread and source of the contamination. In ...

Elsevier2023

Short-term dynamics of drainage density based on a combination of channel flow state surveys and water level measurements

Andrea Rinaldo, Izabela Bujak-Ozga, Jana Freiin von Freyberg

Headwater streams often experience intermittent flow. Consequently, the flowing drainage network expands and contracts and the flowing drainage density (DD) varies over time. Monitoring the DD dynamics is essential to understand the processes controlling i ...

Wiley2023

Caching and Neutrality

Aikaterini Argyraki, Pavlos Nikolopoulos, Muhammad Abdullah

We are used to defining network neutrality as absence of traffic differentiation, like policing or shaping. These mechanisms, however, are often not what determines end-users’ quality of experience (QoE). Most content today is accessed through edge caches, ...

ACM Association for Computing Machinery2023

Model Predictive Control for Multi-Agent Systems under Limited Communication and Time-Varying Network Topology

Melanie Nicole Zeilinger, Danilo Saccani

In control system networks, reconfiguration of the controller when agents are leaving or joining the network is still an open challenge, in particular when operation constraints that depend on each agent's behavior must be met. Drawing our motivation from ...

IEEE2023

Community-based reconstruction and simulation of a full-scale model of region CA1 of rat hippocampus

Henry Markram, Felix Schürmann, James Gonzalo King, Srikanth Ramaswamy, Juan Bautista Hernando Vieites, Alexis Arnaudon, Eilif Benjamin Muller, Michael Reimann, Huanxiang Lu, Ying Shi, Marwan Muhammad Ahmed Abdellah, Vishal Sood, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Lida Kanari, Juan Luis Riquelme Roman, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Liesbeth Maria L Vanherpe, Armando Romani, Cyrille Pierre Henri Favreau, Michele Migliore, Mohameth François Sy, Szabolcs Kali, Judit Planas Carbonell, Genrich Ivaska, Sàra Sàray, Carmen Alina Lupascu, Rosanna Migliore, Audrey Mercer, András Ecker, Alberto Antonietti, Cristina Colangelo, Anna-Kristin Kaufmann, Julian Martin Budd, Elisabetta Giacalone, Thomas Brice Delemontex, Davide Bella, Fabien Petitjean, , , , ,

Estimating the Topology of Preferential Attachment Graphs Under Partial Observability

Ali H. Sayed, Michele Cirillo

This work addresses the problem of learning the topology of a network from the signals emitted by the network nodes. These signals are generated over time through a linear diffusion process, where neighboring nodes exchange messages according to the underl ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2023

Fundamental Limits in Statistical Learning Problems: Block Models and Neural Networks

Elisabetta Cornacchia

This thesis focuses on two selected learning problems: 1) statistical inference on graphs models, and, 2) gradient descent on neural networks, with the common objective of defining and analysing the measures that characterize the fundamental limits. In th ...

EPFL2023

Predicting nonlinear optical scattering with physics-driven neural networks

Demetri Psaltis, Ahmed Ayoub, Carlo Gigli

Deep neural networks trained on physical losses are emerging as promising surrogates for nonlinear numerical solvers. These tools can predict solutions to Maxwell's equations and compute gradients of output fields with respect to the material and geometric ...

AIP Publishing2023