no code implementations • 14 Mar 2024 • Leonardo Di Bari, Matteo Bisardi, Sabrina Cotogno, Martin Weigt, Francesco Zamponi
Our model uncovers a highly collective nature of epistasis, gradually changing the fitness effect of mutations in a diverging sequence context, rather than acting via strong interactions between individual mutations.
1 code implementation • 19 Oct 2023 • Francesco Calvanese, Camille N. Lambert, Philippe Nghe, Francesco Zamponi, Martin Weigt
Generative probabilistic models emerge as a new paradigm in data-driven, evolution-informed design of biomolecular sequences.
no code implementations • 2 Jun 2023 • Max Sina Knicker, Karl Naumann-Woleske, Jean-Philippe Bouchaud, Francesco Zamponi
We include a mechanism through which trust of economic agents in the Central Bank can de-anchor.
1 code implementation • 9 Sep 2021 • Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi
Boltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families.
no code implementations • 4 Jun 2021 • Matteo Bisardi, Juan Rodriguez-Rivas, Francesco Zamponi, Martin Weigt
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection.
no code implementations • 4 Mar 2021 • Jeanne Trinquier, Guido Uguzzoni, Andrea Pagnani, Francesco Zamponi, Martin Weigt
Generative models emerge as promising candidates for novel sequence-data driven approaches to protein design, and for the extraction of structural and functional information about proteins deeply hidden in rapidly growing sequence databases.
no code implementations • 21 Dec 2020 • Eran Bouchbinder, Edan Lerner, Corrado Rainone, Pierfrancesco Urbani, Francesco Zamponi
We study a recently introduced and exactly solvable mean-field model for the density of vibrational states $\mathcal{D}(\omega)$ of a structurally disordered system.
Disordered Systems and Neural Networks Soft Condensed Matter Statistical Mechanics
no code implementations • 23 Nov 2020 • Pierre Barrat-Charlaix, Anna Paola Muntoni, Kai Shimagaki, Martin Weigt, Francesco Zamponi
For example, pairwise Potts models (PM), which are instances of the BM class, provide accurate statistical models of families of evolutionarily related protein sequences.
1 code implementation • 15 Jun 2020 • Dhruv Sharma, Jean-Philippe Bouchaud, Stanislao Gualdi, Marco Tarzia, Francesco Zamponi
We discuss the impact of a Covid-19--like shock on a simple model economy, described by the previously developed Mark-0 Agent-Based Model.
General Economics Physics and Society Economics
no code implementations • 24 May 2020 • Dhruv Sharma, Jean-Philippe Bouchaud, Marco Tarzia, Francesco Zamponi
More generally, our model shows that constraints at the individual scale can generate highly complex patterns at the aggregate level.
no code implementations • 18 May 2020 • Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi
Here, we present DCAlign, an efficient alignment algorithm based on an approximate message-passing strategy, which is able to overcome the limitations of profile models, to include coevolution among positions in a general way, and to be therefore universally applicable to protein- and RNA-sequence alignment without the need of using complementary structural information.