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. An efficient exploration of the configuration space of a biopolymer is essential for its structure modeling and prediction. In this study, the authors propose a new Monte Carlo method, fragment regrowth via energy-guided sequential sampling (FRESS), which incorporates the idea of multigrid Monte Carlo into the framework of configurational-bias Monte Carlo and is suitable for chain polymer simulations. As a by-product, the authors also found a novel extension of the Metropolis Monte Carlo framework applicable to all Monte Carlo computations. They tested FRESS on hydrophobic-hydrophilic (HP) protein folding models in both two and three dimensions. For the benchmark sequences, FRESS not only found all the minimum energies obtained by previous studies with substantially less computation time but also found new lower energies for all the three-dimensional HP models with sequence length longer than 80 residues. We describe two Go programs, Olga and Oleg, developed by a Monte-Carlo approach that is simpler than Bruegmann’s (1993) approach. Our method is based on Abramson (1990). We performed experiments, to assess ideas on (1) progressive pruning, (2) all moves as first heuristic, (3) temperature, (4) simulated annealing, and (5) depth-two tree search within the Monte-Carlo framework. Progressive pruning and the all moves as first heuristic are good speed-up enhancements that do not deteriorate the level of the program too much. Then, using a constant temperature is an adequate and simple heuristic that is about as good as simulated annealing. The depth-two heuristic gives deceptive results at the moment. The results of our Monte-Carlo programs against knowledge-based programs on 9x9 boards are promising. Finally, the ever-increasing power of computers lead us to think that Monte-Carlo approaches are worth considering for computer Go in the future. This paper presents a pseudo parallel ant colony optimization (ACO) algorithm in continuous domain. The variables of a solution are optimized by two parallel cooperative ACO-based processes, either of which attacks a relatively-independent sub-component of the original problem. Both processes contain tunable and untunable solution vectors. The best tunable vector migrates into the other process as an untunable vector through a migration controller, in which the migration strategy is synchronously sprung or adaptively controlled according to the temporal stagnation situation. Implementation of this mechanism is suitable for hardware which supports parallel computation, resulting in decline of unit computational cost and improvement of training speed. Optimization to a set of benchmark functions is carried out to prove the feasibility and efficiency of this parallel ACO algorithm. An analogy with the way ant colonies function has suggested the definition of a new computational paradigm, which we call ant system (AS). We propose it as a viable new approach to stochastic combinatorial optimization. The main characteristics of this model are positive feedback, distributed computation, and the use of a constructive greedy heuristic. Positive feedback accounts for rapid discovery of good solutions, distributed computation avoids premature convergence, and the greedy heuristic helps find acceptable solutions in the early stages of the search process. We apply the proposed methodology to the classical traveling salesman problem (TSP), and report simulation results. We also discuss parameter selection and the early setups of the model, and compare it with tabu search and simulated annealing using TSP. To demonstrate the robustness of the approach, we show how the ant system (AS) can be applied to other optimization problems like the asymmetric traveling salesman, the quadratic assignment and the job-shop scheduling. Finally we discuss the salient characteristics-global data structure revision, distributed communication and probabilistic transitions of the AS.