Abstract

Abstract
Recent advances in high-throughput technologies have given rise to collecting large amounts of multidimensional heterogeneous data that provide diverse information on the same biological samples. Integrative analysis of such multisource datasets may reveal new biological insights into complex biological mechanisms and therefore remains an important research field in systems biology. Most of the modern integrative clustering approaches rely on independent analysis of each dataset and consensus clustering, probabilistic or statistical modeling, while flexible distance-based integrative clustering techniques are sparsely covered. We propose two distance-based integrative clustering frameworks based on bi-level and bi-objective extensions of the p-median problem. A hybrid branch-and-cut method is developed to find global optimal solutions to the bi-level p-median model. As to the bi-objective problem, an epsilon-constraint algorithm is proposed to generate an approximation to the Pareto optimal set. Every solution found by any of the frameworks corresponds to an integrative clustering. We present an application of our approaches to integrative analysis of NCI-60 human tumor cell lines characterized by gene expression and drug activity profiles. We demonstrate that the proposed mathematical optimization-based approaches outperform some state-of-the-art and traditional distance-based integrative and non-integrative clustering techniques.

Abstract
The growing economic importance of the biomass-for-bioenergy in Europe motivates research on biomass supply chain design and planning. The temporally and geographically fragmented availability of woody biomass makes it particularly relevant to find cost-effective solutions for biomass production, storage and transportation up to the consumption facility. This paper addresses tactical decisions related with optimal allocation of wood chips from forest residues at forest sites to terminals and power plants. The emphasis is on a "hot-system" with synchronized chipping and chips transportation at the roadside. Thus, decisions related with the assignment of chippers to forest sites are also considered. We extend existing studies by considering the impact of the wood chips energy content variation in the logistics planning. This is a key issue in biomass-for-bioenergy supply chains. The higher the moisture content of wood chips, the lower its net caloric value and therefore, a larger amount of chips is needed to meet the contracted demand. We propose a Mixed Integer Programming (MIP) model to solve this problem to optimality. Results of applying the model in a biomass supply chain case in Finland are presented. Results suggest that a 20% improvement in the supplier profit can be obtained with the proposed approach when compared with a baseline situation that relies on empirical estimates for a fixed and known moisture content in the end of an obliged storage age.

Abstract
Multi-compartment vehicles (MCVs) can deliver several product segments jointly. Separate compartments are necessary as each product segment has its own specific characteristics and segments cannot be mixed during transportation. The size and position of the compartments can be adjusted for each tour with the use of flexible compartments. However, this requires that the compartments can be accessed for loading/unloading. The layout of the compartments is defined by the customer and segment sequence, and it needs to be organized in a way that no blocking occurs during loading/unloading processes. Routing and loading layouts are interdependent for MCVs. This paper addresses such loading/unloading issues raised in the distribution planning when using MCVs with flexible compartments, loading from the rear, and standardized transportation units. The problem can therefore be described as a two-dimensional loading and multi-compartment vehicle routing problem (2L-MCVRP). We address the problem of obtaining feasible MCV loading with minimal routing, loading and unloading costs. We define the loading problem that configures the compartment setup. Consequently, we develop a branch-and-cut (B&C) algorithm as an exact approach and extend a large neighborhood search (LNS) as a heuristic approach. In both cases, we use the loading model in order to verify the feasibility of the tours and to assess the problem as a routing and loading problem. The loading model dictates the cuts to be performed in the B&C, and it is used as a repair mechanism in the LNS. Numerical studies show that the heuristic reaches the optimal solution for small instances and can be applied efficiently to larger problems. Additionally, further tests on large instances enable us to derive general rules regarding the influence of loading constraints. Our results were validated in a case study with a European retailer. We identified that loading constraints matter even for small instances. Feasible loading can often be achieved only through minor changes to the routing solution and therefore with limited additional costs. Further, the importance to integrate loading constraints grows as the problem size increases, especially when a heterogeneous mix of segments is ordered.

Abstract

Abstract