45 citations · 87 across the 12 of their papers we have counts for
4 papers · 1 filter
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…