Showing results 1141 to 1160 on 1588 in total
Thèse de Yoann ANSELMETTI le mercredi 29 novembre 2017 à 15 h, amphithéâtre BU (La Doua)
-
Background. Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binary matrix, a maximum weight subset of rows that satisfies such a property. This problem is in general intractable, and in particular if the ancestral genome is expected to contain only linear chromosomes or a unique circular chromosome. In the present work, we consider a relaxation of this problem, which allows ancestral genomes that can contain several chromosomes, each either linear or circular.Result. We show that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem. This result holds in the more general case where columns have bounded multiplicity, which models possibly duplicated ancestral genes. We also prove that for matrices with rows of degrees 2 and 3, without multiplicity and without weights on the rows, the problem is NP-complete, thus tracing sharp tractability boundaries. I also give a preliminary result on a method for generating these binary matrices of degree 2, i.e., a method for inferring ancestral adjacencies, and how the Linearization Problem fits into this larger context.Conclusion. As it happened for the breakpoint median problem, also used in ancestral genome reconstruction, relaxing the definition of a genome turns an intractable problem into a tractable one. The relaxation is adapted to some biological contexts, such as bacterial genomes with several replicons, possibly partially assembled. Algorithms can also be used as heuristics for hard variants. More generally, this work opens a way to better understand linearization results for ancestral genome structure inference.
The 10th Congress of the International Symbiosis Society joint with the 3rd International Conference on Holobiont will be held from July 25th to 29th 2022 in Lyon (France).
Thèse d'Abdou Akkouche - Vendredi 13 avril 2012 - 14h30 - Amphithéâtre du CNRS
-
Odds ratio (OR) is a statistic commonly encountered in professional or scientific medical literature. Most readers perceive it as relative risk (RR), although most of them do not know why that would be true. But since such perception is mostly correct, there is nothing (or almost nothing) wrong with that. It is nevertheless useful to be reminded now and then what is the relation between the relative risk and the odds ratio, and when by equating the two statistics we are sometimes forcing OR to be something it is not. Another statistic which is often also perceived as a relative risk is the hazard ratio (HR). We encounter it, for example, when we fit the Cox model to survival data. Under proportional hazards it is probably "natural" to think in the following way: if the probability of death in one group is at every time point k-times as high as the probability of death in another group, then the relative risk must be k, regardless of where in time we are. Well, we shall see if this is true