De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables thorough investigation of protein structure formation and evolution. Although HP model discretizes the conformational space and simplifies the folding energy function, it has been proven to be an NP-complete problem. In this paper, we propose a novel protein folding framework FoldingZero, self-folding a de novo protein 2D HP structure from scratch based on deep reinforcement learning. FoldingZero features the coupled approach of a two-head (policy and value heads) deep convolutional neural network (HPNet) and a regularized Upper Confidence Bounds for Trees (R-UCT). It is trained solely by a reinforcement learning algorithm, which improves HPNet and R-UCT iteratively through iterative policy optimization. Without any supervision and domain knowledge, FoldingZero not only achieves comparable results, but also learns the latent folding knowledge to stabilize the structure. Without exponential computation, FoldingZero shows promising potential to be adopted for real-world protein properties prediction.
Heuristic algorithms cannot guarantee the optimal solution, but they usually obtain an approximation solution in a reasonable time frame. Beutler and Dill introduced a Core-directed chain Growth method (CG) using a heuristic bias function to help assemble a hydrophobic core @cite_27 . Ant colony optimization based algorithms were developed by Shmygelska @cite_25 and Thalheim @cite_3 . proposed a new Monte Carlo method, fragment regrowth via energy-guided sequential sampling @cite_19 . Other techniques, such as simulated annealing @cite_26 , quantum annealing @cite_9 , genetic algorithms @cite_22 and reinforcement learning @cite_5 , were also applied to the HP model with limited success and scalability.
@cite_26 @cite_22 @cite_9 @cite_3 @cite_19 @cite_27 @cite_5 @cite_25
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Recently, many meta-heuristic algorithms have been proposed to serve as the basis of a t-way test generation strategy (where t indicates the interaction strength) including Genetic Algorithms (GA), Ant Colony Optimization (ACO), Simulated Annealing (SA), Cuckoo Search (CS), Particle Swarm Optimization (PSO), and Harmony Search (HS). Although useful, meta-heuristic algorithms that make up these strategies often require specific domain knowledge in order to allow effective tuning before good quality solutions can be obtained. Hyper-heuristics provide an alternative methodology to meta-heuristics which permit adaptive selection and or generation of meta-heuristics automatically during the search process. This paper describes our experience with four hyper-heuristic selection and acceptance mechanisms namely Exponential Monte Carlo with counter (EMCQ), Choice Function (CF), Improvement Selection Rules (ISR), and newly developed Fuzzy Inference Selection (FIS), using the t-way test generation problem as a case study. Based on the experimental results, we offer insights on why each strategy differs in terms of its performance. Minimum dominating set, which is an NP-hard problem, finds many practical uses in diverse domains. A greedy algorithm to compute the minimum dominating set is proven to be the optimal approximate algorithm unless P=NP. Meta-heuristics, generally, find solutions better than simple greedy approximate algorithms as they explore the search space better without incurring the cost of an exponential algorithm. However, there are hardly any studies of application of meta-heuristic techniques for this problem. In some applications it is important to minimize the dominating set as much as possible to reduce cost and or time to perform other operations based on the dominating set. In this paper, we propose a hybrid genetic algorithm and an ant-colony optimization (ACO) algorithm enhanced with local search. We compare the performance of these two hybrid algorithms against the solutions obtained using the greedy heuristic and another hybrid genetic algorithm proposed in literature. We find that the ACO algorithm enhanced with a minimization heuristic performs better than all other algorithms in almost all instances. In this paper we present an application of ant colony optimization (ACO) to the Minimum Weighted Dominating Set Problem. We introduce a heuristic for this problem that takes into account the weights of vertexes being covered and show that it is more efficient than the greedy algorithm using the standard heuristic. Further we give implementation details of ACO applied to this problem. We tested our algorithm on graphs with different sizes, edge densities, and weight distribution functions and shown that it gives greatly improved results over these acquired by the greedy algorithms. Recently, a number of algorithms inspired by the foraging behavior of ant colonies have been applied to the solution of difficult discrete optimization problems. We put these algorithms in a common framework by defining the Ant Colony Optimization (ACO) meta-heuristic. A couple of paradigmatic examples of applications of these novel meta-heuristic are given, as well as a brief overview of existing applications.