Traveling Salesperson Problem

Some days ago, I wrote blog about knapsack problem. Next I tried to solve traveling salesperson problem(TSP). The problem is : “Given a list of cites and the distances between each pair of cities, what is the shortest possible route that visits each city exactly once and returns to the origin city ?”. It isContinue reading “Traveling Salesperson Problem”

Knapshack problem

Drug discovery project is multi objective optimization process. It’s difficult to solve you know. There are many approaches to solve the problem and one is genetic algorithm. Recently, deap is active library of GA for python. I used deap for knapsack problem. You know…. the knapsack problem or rucksack problem is a problem in combinatorialContinue reading “Knapshack problem”

select diverse molecules from dataset.

To select subset from compound library, I think about molecular diversity. So, I often use clustering . There are many clustering method in chemo-informatics area. But, today I used another approach. Use GA. My strategy is that, evaluate diversity of molecules is sum of dissimilarity. Let’s start. For convenience, I used rdkit first_prop_200.sdf as dataset.Continue reading “select diverse molecules from dataset.”