arXiv subjects

Saverio Rossi

Publications and source records attributed to Saverio Rossi.

12 recordsLinked to original sources

arXiv2026

Modeling Protein Evolution with Generative Models: from Extant Sequence Data to Evolutionary Dynamics

Protein sequences carry a record of evolutionary history shaped by mutation, selection, drift, and epistasis. Recent generative models trained on homologous sequence families offer a new way to read this record: they define probabilistic landscapes that score sequences, generate viable variants, and capture constraints that are difficult to measure experimentally. In this review, we discuss how such landscapes can be used not only for protein design or mutation-effect prediction, but also for modeling evolutionary dynamics. We focus particularly on Direct Coupling Analysis as an interpretable and experimentally validated framework, while placing it in the broader context of generative sequence modeling. We first describe how generative sequence landscapes are inferred and assessed, then review how they can be coupled to population-genetic or substitution-model dynamics to simulate protein evolution across experimental and phylogenetic timescales. Applications include viral evolution, laboratory drift experiments, historical contingency, entrenchment, epistatic drift over time, and long-term sequence-space exploration. We conclude by discussing open challenges, including score-fitness calibration, phylogenetic structure, codon-level mutation biases, indels, and the integration of experimental data.

q-bio.PE↗

arXiv2026

Towards coevolution-aware ancestral sequence reconstruction

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 independently, neglecting the epistatic constraints that shape protein structure, stability, and function. This simplification affects both ancestral inference and its evaluation: maximum-a-posteriori reconstructions may over-concentrate probability into a single over-idealized sequence, whereas independent posterior sampling can generate implausible or poorly functional ancestors. Here, we introduce a coevolution-aware ASR framework that combines standard phylogenetic inference with Direct Coupling Analysis (DCA), thereby preserving site-wise ancestral uncertainty while enforcing residue-residue constraints learned from extant protein families. To benchmark the method, we develop a controlled forward-evolution framework based on a DCA evolutionary sampler, allowing reconstructed ancestors to be compared with known ground-truth sequences generated under realistic epistatic constraints. Applied to beta-lactamases and DNA-binding domains, the approach improves reconstruction when ancestral states are epistatically constrained, and yields ensembles of candidate ancestors that are both phylogenetically consistent and statistically compatible with natural protein families. This framework bridges the gap between single-sequence MAP reconstruction and unconstrained posterior sampling, providing a practical route toward ancestral reconstructions that better reflect the coupled nature of protein evolution.

q-bio.BM↗

arXiv2026

Dreaming improves memorization in a Hopfield model with bounded synaptic strength

The Hopfield model provides a paradigmatic framework for associative memory. Its classical implementation, based on the Hebbian learning rule, suffers from catastrophic forgetting: when one attempts storing too many patterns, the network fails to retrieve any of them. Yet, the Hebbian rule does not take into account that synaptic strength is bounded. Introducing this biologically plausible modification, known as "clipping", eliminates catastrophic forgetting; the model is now able to retrieve the most recently seen memories, eliminating older ones. Yet, its memorization capacity is much reduced with respect to the unclipped case. Here, we investigate the effects of adding a "dreaming" phase on the capacity of a clipped Hopfield model. Following a proposal by Hopfield, Feinstein and Palmer, we assume that during the dreaming phase, the model generates random patterns that are then "unlearned". We show that while clipping still removes catastrophic forgetting, alternating learning and dreaming phases improves the memorization capacity and makes the search for optimal performance more realistic from an evolutionary perspective.

cond-mat.dis-nn↗

arXiv2026

Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics

Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous comparative analysis of three simulation schemes, designed to mimic evolution in silico by local sampling of the probability distribution defined by a generative model. We compare standard independent Markov Chain Monte Carlo, Monte Carlo on a phylogenetic tree, and a population genetics dynamics, benchmarking their outputs against deep sequencing data from four distinct in vitro evolution experiments. We find that standard Monte Carlo fails to reproduce the correct phylogenetic structure and generates unrealistic, gradual mutational sweeps. Performing Monte Carlo on a tree inferred from data improves phylogenetic fidelity and historical accuracy. The population genetics scheme successfully captures phylogenetic correlations, mutational abundances, and selective sweeps as emergent properties, without the need to infer additional information from data. However, the latter choice come at the price of not sampling the proper generative model distribution at long times. Our findings highlight the crucial role of phylogenetic correlations and finite-population effects in shaping evolutionary trajectories on fitness landscapes. These models therefore provide powerful tools for predicting complex adaptive paths and for reliably extrapolating evolutionary dynamics beyond current experimental limitations.

q-bio.PE↗

arXiv2025

Yielding in dense active matter

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. Recent work has demonstrated key similarities and differences between the mechanical response of dense active matter and its sheared passive counterpart, yet a constitutive law that predicts precisely how dense active matter flows or fails remains elusive. Here we study the yielding transition in dense active matter in the limit of slow driving and large persistence times, across a wide range of material preparations. Under shear, materials prepared to be very low energy or ultrastable are brittle, and well-described by elastoplastic constitutive laws. We show that under random active forcing, however, ultrastable materials are always ductile. We develop a modified elastoplastic model that captures and explains these observations, where the key parameter is the correlation length of the input active driving field. We also observe large parameter regimes where the plastic flow is surprisingly well-predicted by the input active driving field and not highly dependent on the structural disorder, suggesting new strategies for control.

cond-mat.soft↗

arXiv2025

Pseudo-likelihood produces associative memories able to generalize, even for asymmetric couplings

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 maximize the pseudo-likelihood, which replaces the global normalization with tractable local normalizations. Here we show that, in the zero-temperature limit, a network trained to maximize pseudo-likelihood naturally implements an associative memory: if the training set is small, patterns become fixed-point attractors whose basins of attraction exceed those of any classical Hopfield rule. We explain quantitatively this effect on uncorrelated random patterns. Moreover, we show that, for different structured datasets coming from computer science (random feature model, MNIST), physics (spin glasses) and biology (proteins), as the number of training examples increases the learned network goes beyond memorization, developing meaningful attractors with non-trivial correlations with test examples, thus showing the ability to generalize. Our results therefore reveal pseudo-likelihood works both as an efficient inference tool and as a principled mechanism for memory and generalization.

cond-mat.stat-mech↗

arXiv2025

Functional bottlenecks can emerge from non-epistatic underlying traits

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. Epistasis increases landscape complexity, often resulting in multiple fitness peaks. In its simplest form, known as global epistasis, fitness is modeled as a non-linear function of an underlying additive trait. In contrast, more complex epistasis arises from a network of (pairwise or many-body) interactions between residues, which cannot be removed by a single non-linear transformation. Recent studies have explored how global and network epistasis contribute to the emergence of functional bottlenecks - fitness landscape topologies where two broad high-fitness basins, representing distinct phenotypes, are separated by a bottleneck that can only be crossed via one or a few mutational paths. Here, we introduce and analyze a stylized model of global epistasis with an additive underlying trait. We demonstrate that functional bottlenecks arise with high probability if the model is properly calibrated. Furthermore, our results underscore that a proper balance between neutral and non-neutral mutations is needed for the emergence of functional bottlenecks.

q-bio.PE↗

arXiv2024

Fluctuations and the limit of predictability in protein evolution

Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct sites and times. To quantify these correlations, we examine the role of various fluctuation sources in protein evolution, simulated using a data-driven energy landscape as a proxy for protein fitness. By applying spatio-temporal correlation functions developed in the context of disordered physical systems, we disentangle fluctuations originating from the initial condition, i.e. the ancestral sequence from which the evolutionary process originated, from those driven by stochastic mutations along independent evolutionary paths. Our analysis shows that, in diverse protein families, fluctuations from the ancestral sequence predominate at shorter time scales. This allows us to identify a time scale over which ancestral sequence information persists, enabling its reconstruction. We link this persistence to the strength of epistatic interactions: ancestral sequences with stronger epistatic signatures impact evolutionary trajectories over extended periods. At longer time scales, however, ancestral influence fades as epistatically constrained sites evolve collectively. To confirm this idea, we apply a standard ancestral sequence reconstruction algorithm and verify that the time-dependent recovery error is influenced by the properties of the ancestor itself. Overall, our results reveal that the properties of ancestral sequences - particularly their epistatic constraints - influence the initial evolutionary dynamics and the performance of standard ancestral sequence reconstruction algorithms.

q-bio.BM↗

arXiv2023

Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions

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 engineering. Under an external deformation, these materials undergo a noteworthy transition from a solid to a liquid state that reshapes the material microstructure. This yielding transition was the main theme of a workshop held from January 9 to 13, 2023 at the Lorentz Center in Leiden. The manuscript presented here offers a critical perspective on the subject, synthesizing insights from the various brainstorming sessions and informal discussions that unfolded during this week of vibrant exchange of ideas. The result of these exchanges takes the form of a series of open questions that represent outstanding experimental, numerical, and theoretical challenges to be tackled in the near future.

cond-mat.soft↗

arXiv2023

Far-from-equilibrium criticality in the Random Field Ising Model with Eshelby Interactions

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 amorphous solids at their yielding transition, and differently from ferromagnetic and dipolar RFIMs, the model shows a discontinuous magnetization jump associated with the appearance of a band-like structure for weak disorder and a continuous magnetization growth, yet punctuated by avalanches, for strong disorder. Through a finite-size scaling analysis in 2 and 3 dimensions we find that the two regimes are separated by a finite-disorder critical point which we characterize. We discuss similarities and differences between the present model and models of sheared amorphous solids.

cond-mat.dis-nn↗

arXiv2022

Finite-disorder critical point in the yielding transition of elasto-plastic models

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 plastic events leading to homogeneous flow. It has been recently proposed, and subsequently questioned, that the two regimes are separated by a sharp critical point, as a function of some control parameter characterizing the intrinsic disorder strength and the degree of stability of the solid. In order to resolve this issue, we have performed extensive numerical simulations of athermally driven elasto-plastic models with long-range and anisotropic realistic interaction kernels in two and three dimensions. Our results provide clear evidence for a finite-disorder critical point separating brittle and ductile yielding, and we provide an estimate of the critical exponents in 2D and 3D.

cond-mat.soft↗

arXiv2022

Emergence of a random field at the yielding transition of a mean-field Elasto-Plastic model

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 sample-to-sample fluctuations, which we characterize analytically, and investigate in detail the analogy with the athermally driven random-field Ising model. We stress that the random field at the yielding transition is an emerging disorder and we investigate the various factors that determine its strength.

cond-mat.dis-nn↗