An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes

Background In the comparative genomics field, one of the goals is to estimate a sequence of genetic changes capable of transforming a genome into another. Genome rearrangement events are mutations that can alter the genetic content or the arrangement of elements from the genome. Reversal and transposition are two of the most studied genome rearrangement events. A reversal inverts a segment of a genome while a transposition swaps two consecutive segments. Initial studies in the area considered only the order of the genes. Recent works have incorporated other genetic information in the model. In particular, the information regarding the size of intergenic regions, which are structures between each pair of genes and in the extremities of a linear genome. Results and conclusions In this work, we investigate the sorting by intergenic reversals and transpositions problem on genomes sharing the same set of genes, considering the cases where the orientation of genes is known and unknown. Besides, we explored a variant of the problem, which generalizes the transposition event. As a result, we present an approximation algorithm that guarantees an approximation factor of 4 for both cases considering the reversal and transposition (classic definition) events, an improvement from the 4.5-approximation previously known for the scenario where the orientation of the genes is unknown. We also present a 3-approximation algorithm by incorporating the generalized transposition event, and we propose a greedy strategy to improve the performance of the algorithms. We performed practical tests adopting simulated data which indicated that the algorithms, in both cases, tend to perform better when compared with the best-known algorithms for the problem. Lastly, we conducted experiments using real genomes to demonstrate the applicability of the algorithms.

Deadline-Constrained Cost-Effective Load-Balanced Improved Genetic Algorithm for Workflow Scheduling

Resource scheduling in a cloud computing environment is noteworthy for scientific workflow execution under a cost-effective deadline constraint. Although various researchers have proposed to resolve this critical issue by applying various meta-heuristic and heuristic approaches, no one is able to meet the strict deadline conditions with load-balanced among machines. This article has proposed an improved genetic algorithm that initializes the population with a greedy strategy. Greedy strategy assigns the task to a virtual machine that is under loaded instead of assigning the tasks randomly to a machine. In general workflow scheduling, task dependency is tested after each crossover and mutation operators of genetic algorithm, but here the authors perform after the mutation operation only which yield better results. The proposed model also considered booting time and performance variation of virtual machines. The authors compared the algorithm with previously developed heuristics and metaheuristics both and found it increases hit rate and load balance. It also reduces execution time and cost.

A Self-Adaptive Reinforcement-Exploration Q-Learning Algorithm

Directing at various problems of the traditional Q-Learning algorithm, such as heavy repetition and disequilibrium of explorations, the reinforcement-exploration strategy was used to replace the decayed ε-greedy strategy in the traditional Q-Learning algorithm, and thus a novel self-adaptive reinforcement-exploration Q-Learning (SARE-Q) algorithm was proposed. First, the concept of behavior utility trace was introduced in the proposed algorithm, and the probability for each action to be chosen was adjusted according to the behavior utility trace, so as to improve the efficiency of exploration. Second, the attenuation process of exploration factor ε was designed into two phases, where the first phase centered on the exploration and the second one transited the focus from the exploration into utilization, and the exploration rate was dynamically adjusted according to the success rate. Finally, by establishing a list of state access times, the exploration factor of the current state is adaptively adjusted according to the number of times the state is accessed. The symmetric grid map environment was established via OpenAI Gym platform to carry out the symmetrical simulation experiments on the Q-Learning algorithm, self-adaptive Q-Learning (SA-Q) algorithm and SARE-Q algorithm. The experimental results show that the proposed algorithm has obvious advantages over the first two algorithms in the average number of turning times, average inside success rate, and number of times with the shortest planned route.

Extracting an Optimal Set of Linguistic Summaries using Genetic Algorithm Combined with Greedy Strategy

The goal of extracting linguistic data summaries is to produce summary sentences expressed in natural language which represent knowledge hidden in numerical dataset. At the most general level, human users can get a very large number of linguistic summaries. In this paper, we propose a model of genetic algorithm combined with greedy strategy to extract an optimal set of linguistic summaries based on the evaluation measures of goodness and diversity of the set of linguistic summaries. The experimental results on creep dataset have demonstrated the outperformance of the proposed model of genetic algorithm combined with greedy strategy in comparison with the existing genetic algorithm models in extracting linguistic summaries from data.