45 citations · 87 across the 12 of their papers we have counts for
12 papers
Modeling Protein Evolution with Generative Models: from Extant Sequence Data to Evolutionary Dynamics
Matteo Bisardi, Leonardo Di Bari, Saverio Rossi +3
Protein sequences carry a record of evolutionary history shaped by mutation, selection, drift, and epistasis. Recent generative models trained on homologous sequence families offer…
Towards coevolution-aware ancestral sequence reconstruction
Alya Zeinaty, Leonardo di Bari, Saverio Rossi +3
Ancestral sequence reconstruction (ASR) is a powerful approach for studying molecular evolution and the emergence of protein function. Yet most ASR methods assume that sites evolve…
Dreaming improves memorization in a Hopfield model with bounded synaptic strength
Enzo Marinari, Saverio Rossi, Francesco Zamponi
The Hopfield model provides a paradigmatic framework for associative memory. Its classical implementation, based on the Hebbian learning rule, suffers from catastrophic forgetting:…
Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics
Leonardo Di Bari, Thierry Mora, Andrea Pagnani +3
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics…
Yielding in dense active matter
Adil Ghaznavi, Saverio Rossi, Francesco Zamponi +1
High-density granular active matter is a useful model for dense animal collectives and could be useful for designing reconfigurable materials that can flow or solidify on command.…
Pseudo-likelihood produces associative memories able to generalize, even for asymmetric couplings
Francesco D'Amico, Dario Bocchi, Luca Maria Del Bono +2
Energy-based probabilistic models learned by maximizing the likelihood of the data are limited by the intractability of the partition function. A widely used workaround is to maxim…
Functional bottlenecks can emerge from non-epistatic underlying traits
Anna Ottavia Schulte, Samar Alqatari, Saverio Rossi +1
Protein fitness landscapes frequently exhibit epistasis, where the effect of a mutation depends on the genetic context in which it occurs, i.e., the rest of the protein sequence. E…
Fluctuations and the limit of predictability in protein evolution
Saverio Rossi, Leonardo Di Bari, Martin Weigt +1
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests…
Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions
Thibaut Divoux, Elisabeth Agoritsas, Stefano Aime +37
Soft amorphous materials are viscoelastic solids ubiquitously found around us, from clays and cementitious pastes to emulsions and physical gels encountered in food or biomedical e…
Far-from-equilibrium criticality in the Random Field Ising Model with Eshelby Interactions
Saverio Rossi, Giulio Biroli, Misaki Ozawa +1
We study a quasi-statically driven random field Ising model (RFIM) at zero temperature with interactions mediated by the long-range anisotropic Eshelby kernel. Analogously to amorp…
Finite-disorder critical point in the yielding transition of elasto-plastic models
Saverio Rossi, Giulio Biroli, Misaki Ozawa +2
Upon loading, amorphous solids can exhibit brittle yielding, with the abrupt formation of macroscopic shear bands leading to fracture, or ductile yielding, with a multitude of plas…
Emergence of a random field at the yielding transition of a mean-field Elasto-Plastic model
Saverio Rossi, Gilles Tarjus
We study the mean-field limit of an elasto-plastic model introduced to describe the yielding transition of athermally and quasi-statically sheared amorphous solids. We focus on the…