Alessandro Laio

According to our database, Alessandro Laio authored at least 32 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Metadynamics for Transition Paths in Irreversible Dynamics.

Tobias Grafke, Alessandro Laio

Multiscale Model. Simul., March, 2024

2023

Optimal inference of a generalised Potts model by single-layer transformers with factored attention.

Riccardo Rende, Federica Gerace, Alessandro Laio, Sebastian Goldt

CoRR, 2023

Optimal transfer protocol by incremental layer defrosting.

Federica Gerace, Diego Doimo, Stefano Sarao Mannelli, Luca Saglietti, Alessandro Laio

CoRR, 2023

The geometry of hidden representations of large transformer models.

Lucrezia Valeriani, Diego Doimo, Francesca Cuturello, Alessandro Laio, Alessio Ansuini, Alberto Cazzaniga

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022

DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets.

Elena Tea Russo, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio

PLoS Comput. Biol., October, 2022

DADApy: Distance-based analysis of data-manifolds in Python.

Aldo Glielmo, Iuri Macocco, Diego Doimo, Matteo Carli, Claudio Zeni, Romina Wild, Maria d'Errico, Alex Rodriguez, Alessandro Laio

Patterns, 2022

Intrinsic dimension estimation for discrete metrics.

Iuri Macocco, Aldo Glielmo, Jacopo Grilli, Alessandro Laio

CoRR, 2022

Prune and distill: similar reformatting of image information along rat visual cortex and deep neural networks.

Paolo Muratore, Sina Tafazoli, Eugenio Piasini, Alessandro Laio, Davide Zoccolan

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Redundant representations help generalization in wide neural networks.

Diego Doimo, Aldo Glielmo, Sebastian Goldt, Alessandro Laio

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

2021

Automatic topography of high-dimensional data sets by non-parametric density peak clustering.

Maria d'Errico, Elena Facco, Alessandro Laio, Alex Rodriguez

Inf. Sci., 2021

PARCE: Protocol for Amino acid Refinement through Computational Evolution.

Rodrigo Ochoa, Miguel A. Soler, Alessandro Laio, Pilar Cossio

Comput. Phys. Commun., 2021

Representation mitosis in wide neural networks.

Diego Doimo, Aldo Glielmo, Sebastian Goldt, Alessandro Laio

CoRR, 2021

Ranking the information content of distance measures.

Aldo Glielmo, Claudio Zeni, Bingqing Cheng, Gábor Csányi, Alessandro Laio

CoRR, 2021

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation.

Elena Tea Russo, Alessandro Laio, Marco Punta

BMC Bioinform., 2021

2020

Brain network dynamics during spontaneous strategy shifts and incremental task optimization.

Michele Allegra, Shima Seyed-Allaei, Nicolas W. Schuck, Daniele Amati, Alessandro Laio, Carlo Reverberi

NeuroImage, 2020

Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples.

Nina I Ilieva, Nicola Galvanetto, Michele Allegra, Marco Brucale, Alessandro Laio

Bioinform., 2020

Hierarchical nucleation in deep neural networks.

Diego Doimo, Aldo Glielmo, Alessio Ansuini, Alessandro Laio

Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020

2019

The intrinsic dimension of protein sequence evolution.

Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio

PLoS Comput. Biol., 2019

Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations.

Rodrigo Ochoa, Alessandro Laio, Pilar Cossio

J. Chem. Inf. Model., 2019

Clustering by the local intrinsic dimension: the hidden structure of real-world data.

Michele Allegra, Elena Facco, Alessandro Laio, Antonietta Mira

CoRR, 2019

Intrinsic dimension of data representations in deep neural networks.

Alessio Ansuini, Alessandro Laio, Jakob H. Macke, Davide Zoccolan

Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

2018

The permeation mechanism of organic cations through a CNG mimic channel.

Luisa M. R. Napolitano, Arin Marchesi, Alex Rodriguez, Matteo De March, Silvia Onesti, Alessandro Laio, Vincent Torre

PLoS Comput. Biol., 2018

Estimating the intrinsic dimension of datasets by a minimal neighborhood information.

Elena Facco, Maria d'Errico, Alex Rodriguez, Alessandro Laio

CoRR, 2018

2017

METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations.

Toni Giorgino, Alessandro Laio, Alex Rodriguez

Comput. Phys. Commun., 2017

2016

Non-Markovian effects on protein sequence evolution due to site dependent substitution rates.

Francesca Rizzato, Alex Rodriguez, Alessandro Laio

BMC Bioinform., 2016

2015

QMMMW: A wrapper for QM/MM simulations with Quantum ESPRESSO and LAMMPS.

Changru Ma, Layla Martin-Samos, Stefano Fabris, Alessandro Laio, Simone Piccinin

Comput. Phys. Commun., 2015

2014

Metadynamics Simulations Reveal a Na⁺ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT.

Ina Bisha, Alex Rodriguez, Alessandro Laio, Alessandra Magistrato

PLoS Comput. Biol., 2014

2013

BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures.

Edoardo Sarti, Stefano Zamuner, Pilar Cossio, Alessandro Laio, Flavio Seno, Antonio Trovato

Comput. Phys. Commun., 2013

2012

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations.

Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio

Comput. Phys. Commun., 2012

2010

Exploring the Universe of Protein Structures beyond the Protein Data Bank.

Pilar Cossio, Antonio Trovato, Fabio Pietrucci, Flavio Seno, Amos Maritan, Alessandro Laio

PLoS Comput. Biol., 2010

2009

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations.

Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana

PLoS Comput. Biol., 2009

2006

A comparative theoretical study of dipeptide solvation in water.

Håkan W. Hugosson, Alessandro Laio, Patrick Maurer, Ursula Rothlisberger

J. Comput. Chem., 2006