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ORCIDAlessandro Laio
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2020 – today
- 2024
[j20]Tobias Grafke
, Alessandro Laio:
Metadynamics for Transition Paths in Irreversible Dynamics. Multiscale Model. Simul. 22(1): 125-141 (2024)- [i19]Antonio Di Noia, Iuri Macocco, Aldo Glielmo, Alessandro Laio, Antonietta Mira:
Beyond the noise: intrinsic dimension estimation with optimal neighbourhood identification. CoRR abs/2405.15132 (2024) - [i18]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 abs/2405.15471 (2024) - [i17]Matteo Carli, Alex Rodriguez, Alessandro Laio, Aldo Glielmo:
Density Estimation via Binless Multidimensional Integration. CoRR abs/2407.08094 (2024) - [i16]Riccardo Rende, Federica Gerace, Alessandro Laio, Sebastian Goldt:
A distributional simplicity bias in the learning dynamics of transformers. CoRR abs/2410.19637 (2024) - [i15]Romina Wild, Vittorio Del Tatto, Felix Wodaczek, Bingqing Cheng, Alessandro Laio:
Automatic feature selection and weighting using Differentiable Information Imbalance. CoRR abs/2411.00851 (2024) - [i14]Santiago Acevedo, Alex Rodriguez, Alessandro Laio:
Unsupervised detection of semantic correlations in big data. CoRR abs/2411.02126 (2024) - 2023
- [c5]Lucrezia Valeriani, Diego Doimo, Francesca Cuturello, Alessandro Laio, Alessio Ansuini, Alberto Cazzaniga:
The geometry of hidden representations of large transformer models. NeurIPS 2023 - [i13]Lucrezia Valeriani, Diego Doimo, Francesca Cuturello, Alessandro Laio, Alessio Ansuini, Alberto Cazzaniga:
The geometry of hidden representations of large transformer models. CoRR abs/2302.00294 (2023) - [i12]Federica Gerace, Diego Doimo, Stefano Sarao Mannelli, Luca Saglietti, Alessandro Laio:
Optimal transfer protocol by incremental layer defrosting. CoRR abs/2303.01429 (2023) - [i11]Riccardo Rende, Federica Gerace, Alessandro Laio, Sebastian Goldt:
Optimal inference of a generalised Potts model by single-layer transformers with factored attention. CoRR abs/2304.07235 (2023) - 2022
- [j19]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): 100589 (2022) - [j18]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): 1010610 (2022) - [c4]Diego Doimo, Aldo Glielmo, Sebastian Goldt, Alessandro Laio:
Redundant representations help generalization in wide neural networks. NeurIPS 2022 - [c3]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 - [i10]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 abs/2205.03373 (2022) - [i9]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 abs/2205.13816 (2022) - [i8]Iuri Macocco, Aldo Glielmo, Jacopo Grilli, Alessandro Laio:
Intrinsic dimension estimation for discrete metrics. CoRR abs/2207.09688 (2022) - 2021
- [j17]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): 121 (2021) - [j16]Rodrigo Ochoa, Miguel A. Soler, Alessandro Laio, Pilar Cossio:
PARCE: Protocol for Amino acid Refinement through Computational Evolution. Comput. Phys. Commun. 260: 107716 (2021) - [j15]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: 476-492 (2021) - [i7]Aldo Glielmo, Claudio Zeni, Bingqing Cheng, Gábor Csányi, Alessandro Laio:
Ranking the information content of distance measures. CoRR abs/2104.15079 (2021) - [i6]Diego Doimo, Aldo Glielmo, Sebastian Goldt, Alessandro Laio:
Representation mitosis in wide neural networks. CoRR abs/2106.03485 (2021) - 2020
- [j14]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): 5014-5020 (2020) - [j13]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: 116854 (2020) - [c2]Diego Doimo, Aldo Glielmo, Alessio Ansuini, Alessandro Laio:
Hierarchical nucleation in deep neural networks. NeurIPS 2020 - [i5]Diego Doimo, Aldo Glielmo, Alessio Ansuini, Alessandro Laio:
Hierarchical nucleation in deep neural networks. CoRR abs/2007.03506 (2020)
2010 – 2019
- 2019
- [j12]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): 3464-3473 (2019) - [j11]Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio:
The intrinsic dimension of protein sequence evolution. PLoS Comput. Biol. 15(4) (2019) - [c1]Alessio Ansuini, Alessandro Laio, Jakob H. Macke, Davide Zoccolan:
Intrinsic dimension of data representations in deep neural networks. NeurIPS 2019: 6109-6119 - [i4]Michele Allegra, Elena Facco, Alessandro Laio, Antonietta Mira:
Clustering by the local intrinsic dimension: the hidden structure of real-world data. CoRR abs/1902.10459 (2019) - [i3]Alessio Ansuini, Alessandro Laio, Jakob H. Macke, Davide Zoccolan:
Intrinsic dimension of data representations in deep neural networks. CoRR abs/1905.12784 (2019) - 2018
- [j10]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) - [i2]Maria d'Errico, Elena Facco, Alessandro Laio, Alex Rodriguez:
Automatic topography of high-dimensional data sets by non-parametric Density Peak clustering. CoRR abs/1802.10549 (2018) - [i1]Elena Facco, Maria d'Errico, Alex Rodriguez, Alessandro Laio:
Estimating the intrinsic dimension of datasets by a minimal neighborhood information. CoRR abs/1803.06992 (2018) - 2017
- [j9]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: 204-209 (2017) - 2016
- [j8]Francesca Rizzato, Alex Rodriguez, Alessandro Laio:
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates. BMC Bioinform. 17: 258 (2016) - 2015
- [j7]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: 191-198 (2015) - 2014
- [j6]Ina Bisha, Alex Rodriguez, Alessandro Laio, Alessandra Magistrato:
Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT. PLoS Comput. Biol. 10(12) (2014) - 2013
- [j5]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): 2860-2865 (2013) - 2012
- [j4]Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio:
METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. Comput. Phys. Commun. 183(1): 203-211 (2012) - 2010
- [j3]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)
2000 – 2009
- 2009
- [j2]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) - 2006
- [j1]Håkan W. Hugosson, Alessandro Laio, Patrick Maurer, Ursula Rothlisberger:
A comparative theoretical study of dipeptide solvation in water. J. Comput. Chem. 27(5): 672-684 (2006)
Coauthor Index
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