SMILE

Stochastic Models for the Inference of Life Evolution

Presentation

SMILE is an interdisciplinary research group gathering probabilists, statisticians, bio-informaticians and biologists.
SMILE is affiliated to the Stochastics and Biology group of LPSM (Lab of Probability, Statistics and Modeling) at Sorbonne Université (ex Université Pierre et Marie Curie Paris 06).
SMILE is hosted within the CIRB (Center for Interdisciplinary Research in Biology) at Collège de France.
SMILE is supported by Collège de France and CNRS.
Visit also our homepage at CIRB.

Recent contributions of the SMILE group related to SARS-Cov2 and COVID-19.

Directions

SMILE is hosted at Collège de France in the Latin Quarter of Paris. To reach us, go to 11 place Marcelin Berthelot (stations Luxembourg or Saint-Michel on RER B).
Our working spaces are rooms 107, 121 and 122 on first floor of building B1 (ask us for the code). Building B1 is facing you upon exiting the traversing hall behind Champollion's statue.

Contact

You can reach us by email (amaury.lambert - at - upmc.fr) or (smile - at - listes.upmc.fr).

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Publication

2016

Renewal Structure of the Brownian Taut String

In a recent paper, M. Lifshits and E. Setterqvist introduced the taut string of a Brownian motion w, defined as the function of minimal quadratic energy on [0,T] staying in a tube of fixed width h>0 around w. The authors showed a Law of Large Number (L.L.N.) for the quadratic energy spent by the string for a large time T. In this note, we exhibit a natural renewal structure for the Brownian taut string, which is directly related to the time decomposition of the Brownian motion in terms of its h-extrema (as first introduced by Neveu and Pitman). Using this renewal structure, we derive an expression for the constant in the L.L.N. given by M. Lifshits and E. Setterqvist. In addition, we provide a Central Limit Theorem (C.L.T.) for the fluctuations of the energy spent by the Brownian taut string.

Publication

2018

Exchangeable coalescents, ultrametric spaces, nested interval-partitions: A unifying approach

Kingman's representation theorem (Kingman 1978) states that any exchangeable partition of \$$\mathbb{N}\$$ can be represented as a paintbox based on a random mass-partition. Similarly, any exchangeable composition (i.e.\ ordered partition of \$$\mathbb{N}\$$) can be represented as a paintbox based on an interval-partition (Gnedin 1997. Our first main result is that any exchangeable coalescent process (not necessarily Markovian) can be represented as a paintbox based on a random non-decreasing process valued in interval-partitions, called nested interval-partition, generalizing the notion of comb metric space introduced by Lambert & Uribe Bravo (2017) to represent compact ultrametric spaces. As a special case, we show that any \$$\Lambda\$$-coalescent can be obtained from a paintbox based on a unique random nested interval partition called \$$\Lambda\$$-comb, which is Markovian with explicit semi-group. This nested interval-partition directly relates to the flow of bridges of Bertoin & Le~Gall (2003). We also display a particularly simple description of the so-called evolving coalescent by a comb-valued Markov process. Next, we prove that any measured ultrametric space \$$U\$$, under mild measure-theoretic assumptions on \$$U\$$, is the leaf set of a tree composed of a separable subtree called the backbone, on which are grafted additional subtrees, which act as star-trees from the standpoint of sampling. Displaying this so-called weak isometry requires us to extend the Gromov-weak topology, that was initially designed for separable metric spaces, to non-separable ultrametric spaces. It allows us to show that for any such ultrametric space \$$U\$$, there is a nested interval-partition which is 1) indistinguishable from \$$U\$$ in the Gromov-weak topology; 2) weakly isometric to \$$U\$$ if \$$U\$$ has complete backbone; 3) isometric to \$$U\$$ if \$$U\$$ is complete and separable.

Publication

2017

The genealogical decomposition of a matrix population model with applications to the aggregation of stages

Matrix projection models are a central tool in many areas of population biology. In most applications, one starts from the projection matrix to quantify the asymptotic growth rate of the population (the dominant eigenvalue), the stable stage distribution, and the reproductive values (the dominant right and left eigenvectors, respectively). Any primitive projection matrix also has an associated ergodic Markov chain that contains information about the genealogy of the population. In this paper, we show that these facts can be used to specify any matrix population model as a triple consisting of the ergodic Markov matrix, the dominant eigenvalue and one of the corresponding eigenvectors. This decomposition of the projection matrix separates properties associated with lineages from those associated with individuals. It also clarifies the relationships between many quantities commonly used to describe such models, including the relationship between eigenvalue sensitivities and elasticities. We illustrate the utility of such a decomposition by introducing a new method for aggregating classes in a matrix population models to produce a simpler model with a smaller number of classes. Unlike the standard method, our method has the advantage of preserving reproductive values and elasticities. It also has conceptually satisfying properties such as commuting with changes of units.

Publication

2017

Renewal Sequences and Record Chains Related to Multiple Zeta Sums

For the random interval partition of \([0,1]\) generated by the uniform stick-breaking scheme known as GEM\((1)\), let \(u_k\) be the probability that the first \(k\) intervals created by the stick-breaking scheme are also the first \(k\) intervals to be discovered in a process of uniform random sampling of points from \([0,1]\). Then \(u_k\) is a renewal sequence. We prove that \(u_k\) is a rational linear combination of the real numbers \(1, \zeta(2), \ldots, \zeta(k)\) where \(\zeta\) is the Riemann zeta function, and show that \(u_k\) has limit \(1/3\) as \(k \to \infty\). Related results provide probabilistic interpretations of some multiple zeta values in terms of a Markov chain derived from the interval partition. This Markov chain has the structure of a weak record chain. Similar results are given for the GEM\((\theta)\) model, with beta\((1,\theta)\) instead of uniform stick-breaking factors, and for another more algebraic derivation of renewal sequences from the Riemann zeta function.

Publication

2019

Invasion and Extinction Dynamics of Mating Types Under Facultative Sexual Reproduction

In sexually reproducing isogamous species, syngamy between gametes is generally not indiscriminate, but rather restricted to occurring between complementary self-incompatible mating types. A longstanding question regards the evolutionary pressures that control the number of mating types observed in natural populations, which ranges from two to many thousands. Here, we describe a population genetic null model of this reproductive system and derive expressions for the stationary probability distribution of the number of mating types, the establishment probability of a newly arising mating type and the mean time to extinction of a resident type. Our results yield that the average rate of sexual reproduction in a population correlates positively with the expected number of mating types observed. We further show that the low number of mating types predicted in the rare-sex regime is primarily driven by low invasion probabilities of new mating type alleles, with established resident alleles being very stable over long evolutionary periods. Moreover, our model naturally exhibits varying selection strength dependent on the number of present mating types. This results in higher extinction and lower invasion rates for an increasing number of residents.

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April 19, 2015

Amaury at the Ernest

(Movie in French) Amaury Lambert explique les grands principes qui guident les travaux actuels dans le domaine de la modélisation mathématique de l'évolution du vivant.

Upcoming seminars

Resources

Planning des salles du Collège de France.
Intranet du Collège de France.