1 code implementation • 6 Feb 2024 • Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol
Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the probability that a mutant will fix.
no code implementations • 18 Sep 2023 • Alix Moawad, Alia Abbara, Anne-Florence Bitbol
Models of spatially structured populations with one individual per node of a graph have shown that cooperation, modeled via the prisoner's dilemma, can be favored by natural selection.
1 code implementation • 14 Aug 2023 • Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context.
1 code implementation • 19 Jun 2023 • Alia Abbara, Anne-Florence Bitbol
Natural microbial populations often have complex spatial structures.
no code implementations • 26 Sep 2022 • Nicola Dietler, Umberto Lupo, Anne-Florence Bitbol
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins.
no code implementations • 24 Aug 2022 • Carlos A. Gandarilla-Perez, Sergio Pinilla, Anne-Florence Bitbol, Martin Weigt
We show that these two signals can be combined to improve the performance of the inference of interaction partners among paralogs.
no code implementations • 11 Aug 2022 • Richard Servajean, Anne-Florence Bitbol
Due to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size.
1 code implementation • 14 Apr 2022 • Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol
Moreover, for small protein families, our generation method based on MSA Transformer outperforms Potts models.
1 code implementation • 29 Mar 2022 • Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Simple combinations of MSA Transformer's row attentions have led to state-of-the-art unsupervised structural contact prediction.
1 code implementation • 22 Nov 2021 • Andonis Gerardos, Nicola Dietler, Anne-Florence Bitbol
We show that correlations from these two sources combine constructively to increase the performance of partner inference by DCA or MI.
no code implementations • 12 Dec 2020 • Loïc Marrec, Irene Lamberti, Anne-Florence Bitbol
We demonstrate that by tuning migration asymmetry, the star graph transitions from amplifying to suppressing natural selection.