Alessandro Laio

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 34

Top Topics

Data Representations

Molecular Dynamics Simulations

Major Histocompatibility Complex

Top Venues

PLoS Comput. Biol.

Comput. Phys. Commun.

Publications

Tobias Grafke, Alessandro Laio
Metadynamics for Transition Paths in Irreversible Dynamics. Multiscale Model. Simul. 22 (1) (2024)
Antonio Di Noia, Iuri Macocco, Aldo Glielmo, Alessandro Laio, Antonietta Mira
Beyond the noise: intrinsic dimension estimation with optimal neighbourhood identification. CoRR (2024)
Emily Cheng, Diego Doimo, Corentin Kervadec, Iuri Macocco, Jade Yu, Alessandro Laio, Marco Baroni
Emergence of a High-Dimensional Abstraction Phase in Language Transformers. CoRR (2024)
Matteo Carli, Alex Rodriguez, Alessandro Laio, Aldo Glielmo
Density Estimation via Binless Multidimensional Integration. CoRR (2024)
Lucrezia Valeriani, Diego Doimo, Francesca Cuturello, Alessandro Laio, Alessio Ansuini, Alberto Cazzaniga
The geometry of hidden representations of large transformer models. NeurIPS (2023)
Lucrezia Valeriani, Diego Doimo, Francesca Cuturello, Alessandro Laio, Alessio Ansuini, Alberto Cazzaniga
The geometry of hidden representations of large transformer models. CoRR (2023)
Federica Gerace, Diego Doimo, Stefano Sarao Mannelli, Luca Saglietti, Alessandro Laio
Optimal transfer protocol by incremental layer defrosting. CoRR (2023)
Riccardo Rende, Federica Gerace, Alessandro Laio, Sebastian Goldt
Optimal inference of a generalised Potts model by single-layer transformers with factored attention. CoRR (2023)
Diego Doimo, Aldo Glielmo, Sebastian Goldt, Alessandro Laio
Redundant representations help generalization in wide neural networks. NeurIPS (2022)
Elena Tea Russo, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio
DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets. PLoS Comput. Biol. 18 (10) (2022)
Iuri Macocco, Aldo Glielmo, Jacopo Grilli, Alessandro Laio
Intrinsic dimension estimation for discrete metrics. CoRR (2022)
Aldo Glielmo, Iuri Macocco, Diego Doimo, Matteo Carli, Claudio Zeni, Romina Wild, Maria d'Errico, Alex Rodriguez, Alessandro Laio
DADApy: Distance-based Analysis of DAta-manifolds in Python. CoRR (2022)
Aldo Glielmo, Iuri Macocco, Diego Doimo, Matteo Carli, Claudio Zeni, Romina Wild, Maria d'Errico, Alex Rodriguez, Alessandro Laio
DADApy: Distance-based analysis of data-manifolds in Python. Patterns 3 (10) (2022)
Paolo Muratore, Sina Tafazoli, Eugenio Piasini, Alessandro Laio, Davide Zoccolan
Prune and distill: similar reformatting of image information along rat visual cortex and deep neural networks. NeurIPS (2022)
Paolo Muratore, Sina Tafazoli, Eugenio Piasini, Alessandro Laio, Davide Zoccolan
Prune and distill: similar reformatting of image information along rat visual cortex and deep neural networks. CoRR (2022)
Elena Tea Russo, Alessandro Laio, Marco Punta
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. BMC Bioinform. 22 (1) (2021)
Maria d'Errico, Elena Facco, Alessandro Laio, Alex Rodriguez
Automatic topography of high-dimensional data sets by non-parametric density peak clustering. Inf. Sci. 560 (2021)
Aldo Glielmo, Claudio Zeni, Bingqing Cheng, Gábor Csányi, Alessandro Laio
Ranking the information content of distance measures. CoRR (2021)
Rodrigo Ochoa, Miguel A. Soler, Alessandro Laio, Pilar Cossio
PARCE: Protocol for Amino acid Refinement through Computational Evolution. Comput. Phys. Commun. 260 (2021)
Diego Doimo, Aldo Glielmo, Sebastian Goldt, Alessandro Laio
Representation mitosis in wide neural networks. CoRR (2021)
Diego Doimo, Aldo Glielmo, Alessio Ansuini, Alessandro Laio
Hierarchical nucleation in deep neural networks. NeurIPS (2020)
Diego Doimo, Aldo Glielmo, Alessio Ansuini, Alessandro Laio
Hierarchical nucleation in deep neural networks. CoRR (2020)
Nina I Ilieva, Nicola Galvanetto, Michele Allegra, Marco Brucale, Alessandro Laio
Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples. Bioinform. 36 (20) (2020)
Michele Allegra, Shima Seyed-Allaei, Nicolas W. Schuck, Daniele Amati, Alessandro Laio, Carlo Reverberi
Brain network dynamics during spontaneous strategy shifts and incremental task optimization. NeuroImage 217 (2020)
Michele Allegra, Elena Facco, Alessandro Laio, Antonietta Mira
Clustering by the local intrinsic dimension: the hidden structure of real-world data. CoRR (2019)
Rodrigo Ochoa, Alessandro Laio, Pilar Cossio
Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. J. Chem. Inf. Model. 59 (8) (2019)
Alessio Ansuini, Alessandro Laio, Jakob H. Macke, Davide Zoccolan
Intrinsic dimension of data representations in deep neural networks. CoRR (2019)
Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
The intrinsic dimension of protein sequence evolution. PLoS Comput. Biol. 15 (4) (2019)
Alessio Ansuini, Alessandro Laio, Jakob H. Macke, Davide Zoccolan
Intrinsic dimension of data representations in deep neural networks. NeurIPS (2019)
Maria d'Errico, Elena Facco, Alessandro Laio, Alex Rodriguez
Automatic topography of high-dimensional data sets by non-parametric Density Peak clustering. CoRR (2018)
Luisa M. R. Napolitano, Arin Marchesi, Alex Rodriguez, Matteo De March, Silvia Onesti, Alessandro Laio, Vincent Torre
The permeation mechanism of organic cations through a CNG mimic channel. PLoS Comput. Biol. 14 (8) (2018)
Elena Facco, Maria d'Errico, Alex Rodriguez, Alessandro Laio
Estimating the intrinsic dimension of datasets by a minimal neighborhood information. CoRR (2018)
Toni Giorgino, Alessandro Laio, Alex Rodriguez
METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations. Comput. Phys. Commun. 217 (2017)
Francesca Rizzato, Alex Rodriguez, Alessandro Laio
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates. BMC Bioinform. 17 (2016)
Changru Ma, Layla Martin-Samos, Stefano Fabris, Alessandro Laio, Simone Piccinin
QMMMW: A wrapper for QM/MM simulations with Quantum ESPRESSO and LAMMPS. Comput. Phys. Commun. 195 (2015)
Ina Bisha, Alex Rodriguez, Alessandro Laio, Alessandra Magistrato
Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT. PLoS Comput. Biol. 10 (12) (2014)
Edoardo Sarti, Stefano Zamuner, Pilar Cossio, Alessandro Laio, Flavio Seno, Antonio Trovato
BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures. Comput. Phys. Commun. 184 (12) (2013)
Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio
METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. Comput. Phys. Commun. 183 (1) (2012)
Pilar Cossio, Antonio Trovato, Fabio Pietrucci, Flavio Seno, Amos Maritan, Alessandro Laio
Exploring the Universe of Protein Structures beyond the Protein Data Bank. PLoS Comput. Biol. 6 (11) (2010)
Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana
A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations. PLoS Comput. Biol. 5 (8) (2009)
Håkan W. Hugosson, Alessandro Laio, Patrick Maurer, Ursula Rothlisberger
A comparative theoretical study of dipeptide solvation in water. J. Comput. Chem. 27 (5) (2006)