An essential task in comparative genomics is usually to decompose two or more genomes into synteny blocks, that is, segments of chromosomes with similar contents. In this paper, we study the Maximal Strip Recovery problem (MSR) [Zheng et al. 07], which aims at finding an optimal decomposition of a set of genomes into synteny blocks, amidst possible noise and ambiguities. We present a panel of n...

Climate prediction experiences various input uncertainties such as initial condition errors (predictability of the first kind), boundary condition (or model parameter) errors (predictability of the second kind), and combined errors (predictability of the third kind). Quantification of model predictability due to input uncertainties is a key issue leading to successful climate prediction. The fi...

Parameterized complexity studies a generalization of the notion of polynomial time where, in addition to the overall input size n, one also considers the effects on computational complexity of a secondary measurement, the parameter. The central notion of the field is fixed-parameter tractability (FPT), which refers to solvability in time f(k)n, where f is some function (usually exponential) of ...

It has long been appreciated that the transport properties of molecules can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target-the first-passage time (FPT). Determining the FPT distribution in realistic confined geometries has until now, however, seemed intractable. Here, we calculate this FPT distribution analytically and sho...

We introduce a framework in parameterized algorithms whose purpose is to solve resiliency versions of decision problems. In resiliency problems, the goal is to decide whether an instance remains positive after any (appropriately defined) perturbation has been applied to it. To tackle these kinds of problems, some of which might be of practical interest, we introduce a notion of resiliency for I...

The association between serum IgG concentration and preweaning health performance in Holstein calves were evaluated in a prospective cohort study design framework. Post colostral blood samples were collected from 561 calves and serum IgG concentrations were quantitated using a single radial immunodiffusion assay. Preweaning treatments for diarrhea, pneumonia, omphalitis and frequency of antibio...

Motivated by the dynamics of resonant neurons we discuss the properties of the first passage time (FPT) densities for non-Markovian differentiable random processes. We start from an exact expression for the FPT density in terms of an infinite series of integrals over joint densities of level crossings, and consider different approximations based on truncation or on approximate summation of this...

Given a digraph D, the Minimum Leaf Out-Branching problem (MinLOB) is the problem of finding in D an out-branching with the minimum possible number of leaves, i.e., vertices of out-degree 0. We prove that MinLOB is polynomial-time solvable for acyclic digraphs. In general, MinLOB is NP-hard and we consider three parameterizations of MinLOB. We prove that two of them are NP-complete for every va...

Given two k-independent sets I and J of a graph G, one can ask if it is possible to transform the one into the other in such a way that, at any step, we replace one vertex of the current independent set by another while keeping the property of being independent. Deciding this problem, known as the Token Jumping (TJ) reconfiguration problem, is PSPACE-complete even on planar graphs. Ito et al. p...