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Dynamic simulation of regulatory networks using SQUAD

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Generalizing Bulk-Synchronous Parallel Processing for Data Science: From Data to Threads and Agent-Based Simulations

Zilu Tian

Agent-based simulations have been widely applied in many disciplines, by scientists and engineers alike. Scientists use agent-based simulations to tackle global problems, including alleviating poverty, reducing violence, and predicting the impact of pandem ...

EPFL2023

Additive and geometric transversality of fractal sets in the integers

Florian Karl Richter

By juxtaposing ideas from fractal geometry and dynamical systems, Furstenberg proposed a series of conjectures in the late 1960's that explore the relationship between digit expansions with respect to multiplicatively independent bases. In this work, we in ...

2024

Mechanism of Chromatin Ubiquitination by PRC1 on the Single-Molecule Level

Alexandra Teslenko

Multicellular eukaryotic organisms contain identical genetic information within each cell, stored within the nucleus as chromatin fibers. The regulation of gene expression allows cell-type-specific temporal and spatial gene activation or repression despite ...

EPFL2024

Higher-order organization of multivariate time series

Enrico Amico, Andrea Santoro

Time series analysis has proven to be a powerful method to characterize several phenomena in biology, neuroscience and economics, and to understand some of their underlying dynamical features. Several methods have been proposed for the analysis of multivar ...

NATURE PORTFOLIO2023

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

PINION: physics-informed neural network for accelerating radiative transfer simulations for cosmic reionization

Jean-Paul Richard Kneib, Emma Elizabeth Tolley, Michele Bianco

With the advent of the Square Kilometre Array Observatory (SKAO), scientists will be able to directly observe the Epoch of Reionization by mapping the distribution of neutral hydrogen at different redshifts. While physically motivated results can be simula ...

OXFORD UNIV PRESS2023

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

Unlocking Hidden Potential: Exploring the Complexities of Signaling in Immune Cell Activation to Optimize CAR Therapy

Mathieu Girardin

Chimeric antigen receptors (CARs) are synthetic, transmembrane proteins that trigger immune cell signaling following their engagement. They have been first utilized in T cells and later in natural killer (NK) cells to redirect their cytotoxicity toward a s ...

EPFL2023

Violation-aware contextual Bayesian optimization for controller performance optimization with unmodeled constraints

Colin Neil Jones, Wenjie Xu

We study the problem of performance optimization of closed -loop control systems with unmodeled dynamics. Bayesian optimization (BO) has been demonstrated to be effective for improving closed -loop performance by automatically tuning controller gains or re ...

Elsevier Sci Ltd2024

Reciprocal inhibition of NOTCH and SOX2 shapes tumor cell plasticity and therapeutic escape in triple-negative breast cancer

Joaquim Roland Guy Bernard Javary, Freddy Radtke, Nadine Fournier, Morgane Fournier

Cancer cell plasticity contributes significantly to the failure of chemo- and targeted therapies in triple-negative breast cancer (TNBC). Molecular mechanisms of therapy-induced tumor cell plasticity and associated resistance are largely unknown. Using a g ...

2024

Traversing Time Dependent Light Fields for Daylight Glare Evaluation

Stephen William Wasilewski

To understand how daylight gives shape and life to architectural spaces, whether existing or imagined, requires quantifying its dynamism and energy. Maintaining these details presents a challenge to simulation and analysis methods that flatten data into di ...

EPFL2023

Digital Twin Generalization with Meta and Geometric Deep Learning

Olga Fink, Raffael Pascal Theiler

Deep digital twins (DDTs) are deep neural networks that encode the behavior of complex physical systems. DDTs are excellent system representations due to their ability to continuously adapt to operational changes and their capability to capture complex rel ...

Prognostics and Health Management Society2024

Motion Planning and Inertia Based Control for Impact Aware Manipulation

Aude Billard, Harshit Khurana

In this paper, we propose a metric called hitting flux which is used in the motion generation and controls for a robot manipulator to interact with the environment through a hitting or a striking motion. Given the task of placing a known object outside of ...

2023

Hybrid Quadratic Programming - Pullback Bundle Dynamical Systems Control

Aude Billard, Bernardo Fichera

Dynamical System (DS)-based closed-loop control is a simple and effective way to generate reactive motion policies that well generalize to the robotic workspace, while retaining stability guarantees. Lately the formalism has been expanded in order to handl ...

SPRINGER INTERNATIONAL PUBLISHING AG2023

Towards practical reinforcement learning for tokamak magnetic control

Federico Alberto Alfredo Felici, Jonas Buchli, Cristian Galperti

Reinforcement learning (RL) has shown promising results for real-time control systems, including the domain of plasma magnetic control. However, there are still significant drawbacks compared to traditional feedback control approaches for magnetic confinem ...

Elsevier Science Sa2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

Creating Trust by Abolishing Hierarchies

Mathias Josef Payer, Edouard Bugnion, Evangelos Marios Kogias, Adrien Ghosn, Charly Nicolas Lucien Castes, Yuchen Qian, Neelu Shivprakash Kalani

Software is going through a trust crisis. Privileged code is no longer trusted and processes insufficiently protect user code from unverified libraries. While usually treated separately, confidential computing and program compartmentalization are both symp ...

Association for Computing Machinery2023