Recherche

Afficher tous les résultats pour

Accueil

Publication

Scaffolding protein functional sites using deep learning

À propos
Confidentialité
Mentions légales

Graph Chatbot

Publications associées (50)

Page 2 sur 3

A phase transition between positional and semantic learning in a solvable model of dot-product attention

Lenka Zdeborová, Florent Gérard Krzakala, Hugo Chao Cui, Freya Behrens

Many empirical studies have provided evidence for the emergence of algorithmic mechanisms (abilities) in the learning of language models, that lead to qualitative improvements in the model capabilities. Yet, a theoretical characterization of how such mecha ...

2025

Mechanisms and functions of protein S-acylation

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

Improving the accuracy and interpretability of neural networks for wind power forecasting

Fernando Porté Agel, Jiannong Fang, Wenlong Liao

Deep neural networks (DNNs) are receiving increasing attention in wind power forecasting due to their ability to effectively capture complex patterns in wind data. However, their forecast errors are severely limited by the local optimal weight issue in opt ...

2025

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical Soc2024

Context selectivity with dynamic availability enables lifelong continual learning

Wulfram Gerstner, Guillaume Emmanuel Fernand Bellec, Martin Louis Lucien Rémy Barry

“You never forget how to ride a bike”, – but how is that possible? The brain is able to learn complex skills, stop the practice for years, learn other skills in between, and still retrieve the original knowledge when necessary. The mechanisms of this capab ...

Elsevier BV2025

Benchmarking machine-readable vectors of chemical reactions on computed activation barriers

Anne-Clémence Corminboeuf, Puck Elisabeth van Gerwen, Ksenia Briling, Yannick Calvino Alonso

In recent years, there has been a surge of interest in predicting computed activation barriers, to enable the acceleration of the automated exploration of reaction networks. Consequently, various predictive approaches have emerged, ranging from graph-based ...

Royal Soc Chemistry2024

GraphFedAI framework for DDoS attack detection in IoT systems using federated learning and graph based artificial intelligence

Zaffar Ahmed Shaikh

The Internet of Things (IoT) consists of physical objects and devices embedded with network connectivity, software, and sensors to collect and transmit data. The development of the Internet of Things (IoT) has led to various security and privacy issues, in ...

2025

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

2024

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Henning Paul-Julius Stahlberg, Dongchun Ni

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Nature Portfolio2024

Machine-learning-empowered FDTD/FEM simulations for predictive solar energy absorption in plasmonic metamaterial nanocavity arrays

Amir Jafargholi

FDTD/FEM simulations, strengthened by machine learning, achieve 95.44% optical absorption efficiency in TiO 2 /TiN plasmonic nanocavities for solar energy harvesting. ...

Royal Society of Chemistry (RSC)2025

Using deep reinforcement learning to investigate stretch feedback during swimming of the lamprey

Auke Ijspeert, Astha Gupta

Animals have to navigate complex environments and perform intricate swimming maneuvers in the real world. To conquer these challenges, animals evolved a variety of motion control strategies. While it is known that many factors contribute to motion control, ...

IOP Publishing Ltd2025

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Publishing Group2024

Self-supervised and few-shot learning for robust bioaerosol monitoring

Sophie Catherine Erb

Real-time bioaerosol monitoring is improving the quality of life for people affected by allergies, but it often relies on deep learning models which pose challenges for widespread adoption. These models are typically trained in a supervised fashion and req ...

2025

Predicting the long-term collective behaviour of fish pairs with deep learning

Francesco Mondada, Alexandre Massoud Alahi, Vaios Papaspyros

Modern computing has enhanced our understanding of how social interactions shape collective behaviour in animal societies. Although analytical models dominate in studying collective behaviour, this study introduces a deep learning model to assess social in ...

2024

Integrating Physics and Topology in Neural Networks for Learning Rigid Body Dynamics

Amaury Pierre Jiezhi Wei, Olga Fink

Rigid body interactions are fundamental to numerous scientific disciplines, but remain challenging to simulate due to their abrupt nonlinear nature and sensitivity to complex, often unknown environmental factors. These challenges call for adaptable learnin ...

NATURE PORTFOLIO2025

Understanding generalization and robustness in modern deep learning

Maksym Andriushchenko

In this thesis, we study two closely related directions: robustness and generalization in modern deep learning. Deep learning models based on empirical risk minimization are known to be often non-robust to small, worst-case perturbations known as adversari ...

EPFL2024

Feature-based encoding of face identity by single neurons in the human amygdala and hippocampus

Emanuela De Falco

Neurons in the human amygdala and hippocampus are classically thought to encode a person’s identity invariant to visual features. However, it remains largely unknown how visual information from higher visual cortical areas is translated into such a semanti ...

2025

Boon and Bane of Local Solid State Chemistry on the Performance of LSM-Based Solid Oxide Electrolysis Cells

Hanna Christine Türk

Advanced Energy Materials published by Wiley-VCH GmbH.High-temperature solid oxide cells are highly efficient energy converters. However, their lifetime is limited by rapid deactivation. Little is known about the local, atomic scale transformation that dri ...

2025

Subtle variations in a client protein determine bacterial Hsp90 dependence

Mathieu Rebeaud

Chaperones ensure protein homeostasis and are conserved across species. The ATP-dependent chaperone Hsp90 is present from bacteria to eukaryotes, where it stabilizes and activates a wide range of substrate proteins called clients. However, what determines ...

Elsevier BV2025

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (2/6)

Jean-Philippe Thiran, Roser Vinals Terres

This dataset contains a collection of ultrafast ultrasound acquisitions from nine volunteers and the CIRS 054G phantom. For a comprehensive understanding of the dataset, please refer to the paper: Viñals, R.; Thiran, J.-P. A KL Divergence-Based Loss for In ...

EPFL Infoscience2024