Publications associées à Models and Algorithms in Biological Network Evolution with Modularity

Towards an Understanding of Hydraulic Sensitivity: Graph Theory Contributions to Water Distribution Analysis

Water distribution systems (WDSs) are complex networks with numerous interconnected junctions and pipes. The robustness and reliability of these systems are critically dependent on their network structure, necessitating detailed analysis for proactive leak ...

MDPI2024

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

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

GELEX: Generative AI-Hybrid System for Example-Based Learning

Tanja Christina Käser Jacober, Paola Mejia Domenzain, Aybars Yazici, Jibril Albachir Frej

Traditional example-based learning methods are often limited by static, expert-created content. Hence, they face challenges in scalability, engagement, and effectiveness, as some learners might struggle to relate to the examples or find them relevant. To a ...

Association for Computing Machinery2024

Network-based kinetic models: Emergence of a statistical description of the graph topology

Matteo Raviola

In this paper, we propose a novel approach that employs kinetic equations to describe the collective dynamics emerging from graph-mediated pairwise interactions in multi-agent systems. We formally show that for large graphs and specific classes of interact ...

Cambridge Univ Press2024

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Yimon Aye

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Wiley-V C H Verlag Gmbh2024

Driving and suppressing the human language network using large language models

Martin Schrimpf

Transformer models such as GPT generate human-like language and are predictive of human brain responses to language. Here, using functional-MRI-measured brain responses to 1,000 diverse sentences, we first show that a GPT-based encoding model can predict t ...

Nature Portfolio2024

Infusing structured knowledge priors in neural models for sample-efficient symbolic reasoning

Mattia Atzeni

The ability to reason, plan and solve highly abstract problems is a hallmark of human intelligence. Recent advancements in artificial intelligence, propelled by deep neural networks, have revolutionized disciplines like computer vision and natural language ...

EPFL2024

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

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

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

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Daria Korotkova

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

2023

Determining an optimum quantity of interleaved instruction streams of defined coroutines

Anastasia Ailamaki, Georgios Psaropoulos

A method for optimizing memory access for database operations is provided. The method may include performing a first database operation by at least executing a first instruction stream associated with the first database operation. The first database opera ...

2023

Network Alignment With Holistic Embeddings

Quoc Viet Hung Nguyen, Thành Tâm Nguyên, Chi Thang Duong, Thanh Trung Huynh

Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. It plays an important role in various applications ranging from social network analysis to bioinformatic network interactions. Howeve ...

IEEE COMPUTER SOC2023

Efficient Concurrent Analytical Query Processing using Data and Workload-conscious Sharing

Panagiotis Sioulas

Analytical workloads are evolving as the number of users surges and applications that submit queries in batches become popular. However, traditional analytical databases that optimize-then-execute each query individually struggle to provide timely response ...

EPFL2023

Robust Outlier Rejection for 3D Registration with Variational Bayes

Mathieu Salzmann, Zheng Dang, Zhen Wei, Jiancheng Yang, Haobo Jiang

Learning-based outlier (mismatched correspondence) rejection for robust 3D registration generally formulates the outlier removal as an inlier/outlier classification problem. The core for this to be successful is to learn the discriminative inlier/outlier f ...

Ieee Computer Soc2023

Multi-agent reinforcement learning with graph convolutional neural networks for optimal bidding strategies of generation units in electricity markets

Olga Fink, Mina Montazeri

Finding optimal bidding strategies for generation units in electricity markets would result in higher profit. However, it is a challenging problem due to the system uncertainty which is due to the lack of knowledge of the strategies of other generation uni ...

PERGAMON-ELSEVIER SCIENCE LTD2023

4M: Massively Multimodal Masked Modeling

Amir Roshan Zamir, Roman Christian Bachmann, Shuqing Teresa Yeo, David Mizrahi, Oguzhan Fatih Kar

Current machine learning models for vision are often highly specialized and limited to a single modality and task. In contrast, recent large language models exhibit a wide range of capabilities, hinting at a possibility for similarly versatile models in co ...

Neural Information Processing Systems (Nips)2023

Deep Learning Generalization with Limited and Noisy Labels

Mahsa Forouzesh

Deep neural networks have become ubiquitous in today's technological landscape, finding their way in a vast array of applications. Deep supervised learning, which relies on large labeled datasets, has been particularly successful in areas such as image cla ...

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