CellCycleTRACER accounts for cell cycle and volume in mass cytometry data.

Recent studies have shown that cell cycle and cell volume are confounding factors when studying biological phenomena in single cells. Here we present a combined experimental and computational method, CellCycleTRACER, to account for these factors in mass cytometry data. CellCycleTRACER is applied to mass cytometry data collected on three different cell types during a TNFα stimulation time-course. CellCycleTRACER reveals signaling relationships and cell heterogeneity that were otherwise masked.

Computing gap free Pareto front approximations with stochastic search algorithms.

Recently, a convergence proof of stochastic search algorithms toward finite size Pareto set approximations of continuous multi-objective optimization problems has been given. The focus was on obtaining a finite approximation that captures the entire solution set in some suitable sense, which was defined by the concept of epsilon-dominance. Though bounds on the quality of the limit approximation-which are entirely determined by the archiving strategy and the value of epsilon-have been obtained, the strategies do not guarantee to obtain a gap free approximation of the Pareto front. That is, such approximations A can reveal gaps in the sense that points f in the Pareto front can exist such that the distance of f to any image point F(a), a epsilon A, is "large." Since such gap free approximations are desirable in certain applications, and the related archiving strategies can be advantageous when memetic strategies are included in the search process, we are aiming in this work for such methods. We present two novel strategies that accomplish this task in the probabilistic sense and under mild assumptions on the stochastic search algorithm. In addition to the convergence proofs, we give some numerical results to visualize the behavior of the different archiving strategies. Finally, we demonstrate the potential for a possible hybridization of a given stochastic search algorithm with a particular local search strategy-multi-objective continuation methods-by showing that the concept of epsilon-dominance can be integrated into this approach in a suitable way.

Combining convergence and diversity in evolutionary multiobjective optimization.

Over the past few years, the research on evolutionary algorithms has demonstrated their niche in solving multiobjective optimization problems, where the goal is to find a number of Pareto-optimal solutions in a single simulation run. Many studies have depicted different ways evolutionary algorithms can progress towards the Pareto-optimal set with a widely spread distribution of solutions. However, none of the multiobjective evolutionary algorithms (MOEAs) has a proof of convergence to the true Pareto-optimal solutions with a wide diversity among the solutions. In this paper, we discuss why a number of earlier MOEAs do not have such properties. Based on the concept of epsilon-dominance, new archiving strategies are proposed that overcome this fundamental problem and provably lead to MOEAs that have both the desired convergence and distribution properties. A number of modifications to the baseline algorithm are also suggested. The concept of epsilon-dominance introduced in this paper is practical and should make the proposed algorithms useful to researchers and practitioners alike.