A two-phase approach for the Radiotherapy Scheduling Problem.

The Radiotherapy Scheduling Problem (RTSP) focuses on optimizing the planning of radiotherapy treatment sessions for cancer patients. In this paper, we propose a two-phase approach for the RTSP. In the first phase, radiotherapy sessions are assigned to specific linear accelerators (linacs) and days. The second phase then decides the sequence of patients on each day/linac and the specific appointment times. For the first phase, an Integer Linear Programming (IP) model is proposed and solved using CPLEX. For the second phase, a Mixed Integer Linear Programming (MIP) and a Constraint Programming (CP) model are proposed. The test data is generated based on real data from CHUM, a large cancer center in Montréal, Canada, with an average of 3,500 new patients and 40,000 radiotherapy treatments per year. The results show that in the second phase, CP is better at finding good solutions quickly while MIP is better at closing optimality gaps with more run time. Lastly, a simulation is conducted to evaluate the impact of different scheduling strategies on the outcome of the scheduling. Preliminary results show that batch scheduling reduces patients' waiting time and overdue time.

An unbiased evaluation of gene prioritization tools.

MOTIVATION: Gene prioritization aims at identifying the most promising candidate genes among a large pool of candidates-so as to maximize the yield and biological relevance of further downstream validation experiments and functional studies. During the past few years, several gene prioritization tools have been defined, and some of them have been implemented and made available through freely available web tools. In this study, we aim at comparing the predictive performance of eight publicly available prioritization tools on novel data. We have performed an analysis in which 42 recently reported disease-gene associations from literature are used to benchmark these tools before the underlying databases are updated. RESULTS: Cross-validation on retrospective data provides performance estimate likely to be overoptimistic because some of the data sources are contaminated with knowledge from disease-gene association. Our approach mimics a novel discovery more closely and thus provides more realistic performance estimates. There are, however, marked differences, and tools that rely on more advanced data integration schemes appear more powerful. CONTACT: yves.moreau@esat.kuleuven.be SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A guide to web tools to prioritize candidate genes.

Finding the most promising genes among large lists of candidate genes has been defined as the gene prioritization problem. It is a recurrent problem in genetics in which genetic conditions are reported to be associated with chromosomal regions. In the last decade, several different computational approaches have been developed to tackle this challenging task. In this study, we review 19 computational solutions for human gene prioritization that are freely accessible as web tools and illustrate their differences. We summarize the various biological problems to which they have been successfully applied. Ultimately, we describe several research directions that could increase the quality and applicability of the tools. In addition we developed a website (http://www.esat.kuleuven.be/gpp) containing detailed information about these and other tools, which is regularly updated. This review and the associated website constitute together a guide to help users select a gene prioritization strategy that suits best their needs.

A hybrid tabu search algorithm for automatically assigning patients to beds.

OBJECTIVE: We describe a patient admission scheduling algorithm that supports the operational decisions in a hospital. It involves efficiently assigning patients to beds in the appropriate departments, taking into account the medical needs of the patients as well as their preferences, while keeping the number of patients in the different departments balanced. METHODS: Due to the combinatorial complexity of the admission scheduling problem, there is a need for an algorithm that intelligently assists the admission scheduler in taking decisions fast. To this end a hybridized tabu search algorithm is developed to tackle the admission scheduling problem. For testing, we use a randomly generated data set. The performance of the algorithm is compared with an integer programming approach. RESULTS AND CONCLUSION: The metaheuristic allows flexible modelling and presents feasible solutions even when disrupted by the user at an early stage in the calculation. The integer programming approach is not able to find a solution in 1h of calculation time.