A comparative theoretical study of dipeptide solvation in water. - Håkan W. Hugosson; Alessandro Laio; Patrick Maurer; Ursula Rothlisberger (J. Comput. Chem., 2006)

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations. - Fabrizio Marinelli 002; Fabio Pietrucci; Alessandro Laio; Stefano Piana (PLoS Comput. Biol., 2009)

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)

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. - Xevi Biarnés; Fabio Pietrucci; Fabrizio Marinelli 002; Alessandro Laio (Comput. Phys. Commun., 2012)

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)

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)

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)

Non-Markovian effects on protein sequence evolution due to site dependent substitution rates. - Francesca Rizzato; Alex Rodriguez; Alessandro Laio (BMC Bioinform., 2016)

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)

Estimating the intrinsic dimension of datasets by a minimal neighborhood information. - Elena Facco; Maria d'Errico; Alex Rodriguez; Alessandro Laio (CoRR, 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)

Intrinsic dimension of data representations in deep neural networks. - Alessio Ansuini; Alessandro Laio; Jakob H. Macke; Davide Zoccolan (NeurIPS, 2019)

Clustering by the local intrinsic dimension: the hidden structure of real-world data. - Michele Allegra; Elena Facco; Alessandro Laio; Antonietta Mira (CoRR, 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)

The intrinsic dimension of protein sequence evolution. - Elena Facco; Andrea Pagnani; Elena Tea Russo; Alessandro Laio (PLoS Comput. Biol., 2019)

Hierarchical nucleation in deep neural networks. - Diego Doimo; Aldo Glielmo; Alessio Ansuini; Alessandro Laio (NeurIPS, 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)

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)

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)

Ranking the information content of distance measures. - Aldo Glielmo; Claudio Zeni; Bingqing Cheng; Gábor Csányi; Alessandro Laio (CoRR, 2021)

Representation mitosis in wide neural networks. - Diego Doimo; Aldo Glielmo; Sebastian Goldt; Alessandro Laio (CoRR, 2021)

PARCE: Protocol for Amino acid Refinement through Computational Evolution. - Rodrigo Ochoa; Miguel A. Soler; Alessandro Laio; Pilar Cossio (Comput. Phys. Commun., 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)

Redundant representations help generalization in wide neural networks. - Diego Doimo; Aldo Glielmo; Sebastian Goldt; Alessandro Laio (NeurIPS, 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 (NeurIPS, 2022)

Intrinsic dimension estimation for discrete metrics. - Iuri Macocco; Aldo Glielmo; Jacopo Grilli; Alessandro Laio (CoRR, 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)

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., 2022)

The geometry of hidden representations of large transformer models. - Lucrezia Valeriani; Diego Doimo; Francesca Cuturello; Alessandro Laio; Alessio Ansuini; Alberto Cazzaniga (NeurIPS, 2023)

Optimal transfer protocol by incremental layer defrosting. - Federica Gerace; Diego Doimo; Stefano Sarao Mannelli; Luca Saglietti; Alessandro Laio (CoRR, 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)

A distributional simplicity bias in the learning dynamics of transformers. - Riccardo Rende; Federica Gerace; Alessandro Laio; Sebastian Goldt (NeurIPS, 2024)

Beyond the noise: intrinsic dimension estimation with optimal neighbourhood identification. - Antonio Di Noia; Iuri Macocco; Aldo Glielmo; Alessandro Laio; Antonietta Mira (CoRR, 2024)

Emergence of a High-Dimensional Abstraction Phase in Language Transformers. - Emily Cheng; Diego Doimo; Corentin Kervadec; Iuri Macocco; Jade Yu; Alessandro Laio; Marco Baroni (CoRR, 2024)

Density Estimation via Binless Multidimensional Integration. - Matteo Carli; Alex Rodriguez; Alessandro Laio; Aldo Glielmo (CoRR, 2024)

Automatic feature selection and weighting using Differentiable Information Imbalance. - Romina Wild; Vittorio Del Tatto; Felix Wodaczek; Bingqing Cheng; Alessandro Laio (CoRR, 2024)

Unsupervised detection of semantic correlations in big data. - Santiago Acevedo; Alex Rodriguez; Alessandro Laio (CoRR, 2024)

How to choose the right transfer learning protocol? A qualitative analysis in a controlled set-up. - Federica Gerace; Diego Doimo; Stefano Sarao Mannelli; Luca Saglietti; Alessandro Laio (Trans. Mach. Learn. Res., 2024)

Metadynamics for Transition Paths in Irreversible Dynamics. - Tobias Grafke; Alessandro Laio (Multiscale Model. Simul., 2024)

Emergence of a High-Dimensional Abstraction Phase in Language Transformers. - Emily Cheng; Diego Doimo; Corentin Kervadec; Iuri Macocco; Lei Yu; Alessandro Laio; Marco Baroni (ICLR, 2025)

Detecting Localized Density Anomalies in Multivariate Data via Coin-Flip Statistics. - Sebastian Springer; Andre Scaffidi; Maximilian Autenrieth; Gabriella Contardo; Alessandro Laio; Roberto Trotta; Heikki Haario (CoRR, 2025)

An approach to identify the most semantically informative deep representations of text and images. - Santiago Acevedo; Andrea Mascaretti; Riccardo Rende; Matéo Mahaut; Marco Baroni; Alessandro Laio (CoRR, 2025)