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. Copyright © 2017, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved. Motivated by the fact that in several cases a matching in a graph is stable if and only if it is produced by a greedy algorithm, we study the problem of computing a maximum weight greedy matching on weighted graphs, termed GREEDY-MATCHING. In wide contrast to the maximum weight matching problem, for which many efficient algorithms are known, we prove that GREEDYMATCHING is strongly NP-hard and APX-complete, and thus it does not admit a PTAS unless P=NP, even on graphs with maximum degree at most 3 and with at most three different integer edge weights. Furthermore we prove that GREEDYMATCHING is strongly NP-hard if the input graph is in addition bipartite. Moreover we consider three natural parameters of the problem, for which we establish a sharp threshold behavior between NP-hardness and computational tractability. On the positive side, we present a randomized approximation algorithm (RGMA) for GREEDYMATCHING on a special class of weighted graphs, called bush graphs. We highlight an unexpected connection between RGMA and the approximation of maximum cardinality matching in unweighted graphs via randomized greedy algorithms. We show that, if the approximation ratio of RGMA is θ, then for every ϵ > 0 the randomized MRG algorithm of ( 1995) gives a (ρ - ϵ)-approximation for the maximum cardinality matching. We conjecture that a tight bound for ρ is 2 3; we prove our conjecture true for four subclasses of bush graphs. Proving a tight bound for the approximation ratio of MRG on unweighted graphs (and thus also proving a tight value for ρ) is a long-standing open problem (Poloczek and Szegedy 2012). This unexpected relation of our RGMA algorithm with the MRG algorithm may provide new insights for solving this problem. A new heuristic procedure for the transportation problem with exclusionary side constraints is developed and implemented. Tabu search, a meta-heuristic method, is used to guide the search to follow a path selectively to prevent from being trapped at local optimal solutions in order to find a global optimal or near global optimal solution. The simplex method on a graph is employed to lead the search from one solution to an adjacent solution in order to take advantage of the underlying network structure of the problem. In the procedure, net changes in cost and in infeasibility are used to measure the attractiveness of a move, and strategic oscillation is used to implement the intensification and diversification functions. A computational experiment was conducted to test the performance of the heuristic procedure and substantial computational results are reported. These results show that the new heuristic procedure finds very good quality solutions and outperforms an existing heuristic procedure in terms of both solution quality and CPU time. 1. Summary In Part I, four ostensibly different theoretical models of induction are presented, in which the problem dealt with is the extrapolation of a very long sequence of symbols—presumably containing all of the information to be used in the induction. Almost all, if not all problems in induction can be put in this form. Some strong heuristic arguments have been obtained for the equivalence of the last three models. One of these models is equivalent to a Bayes formulation, in which a priori probabilities are assigned to sequences of symbols on the basis of the lengths of inputs to a universal Turing machine that are required to produce the sequence of interest as output. Though it seems likely, it is not certain whether the first of the four models is equivalent to the other three. Few rigorous results are presented. Informal investigations are made of the properties of these models. There are discussions of their consistency and meaningfulness, of their degree of independence of the exact nature of the Turing machine used, and of the accuracy of their predictions in comparison to those of other induction methods. In Part II these models are applied to the solution of three problems—prediction of the Bernoulli sequence, extrapolation of a certain kind of Markov chain, and the use of phrase structure grammars for induction. Though some approximations are used, the first of these problems is treated most rigorously. The result is Laplace's rule of succession. The solution to the second problem uses less certain approximations, but the properties of the solution that are discussed, are fairly independent of these approximations. The third application, using phrase structure grammars, is least exact of the three. First a formal solution is presented. Though it appears to have certain deficiencies, it is hoped that presentation of this admittedly inadequate model will suggest acceptable improvements in it. This formal solution is then applied in an approximate way to the determination of the “optimum” phrase structure grammar for a given set of strings. The results that are obtained are plausible, but subject to the uncertainties of the approximation used. Display Omitted HHH is the first strategy that adopts the hyper-heuristic approach for t-way test suite generationHHH introduces new approach for the heuristic selection and move acceptance mechanism based on three operators (i.e. improvement operator, diversify operator, and intensify operator) that are integrated into the Tabu search HLH.HHH outperforms existing strategies as far as optimality of test suite is concerned in many benchmarks. This paper proposes a novel hybrid t-way test generation strategy (where t indicates interaction strength), called High Level Hyper-Heuristic (HHH). HHH adopts Tabu Search as its high level meta-heuristic and leverages on the strength of four low level meta-heuristics, comprising of Teaching Learning based Optimization, Global Neighborhood Algorithm, Particle Swarm Optimization, and Cuckoo Search Algorithm. HHH is able to capitalize on the strengths and limit the deficiencies of each individual algorithm in a collective and synergistic manner. Unlike existing hyper-heuristics, HHH relies on three defined operators, based on improvement, intensification and diversification, to adaptively select the most suitable meta-heuristic at any particular time. Our results are promising as HHH manages to outperform existing t-way strategies on many of the benchmarks. We consider the problem of scheduling a number of jobs on a single machine against a restrictive common due date. The paper consists of two parts: firstly a new and appropriate problem representation is developed. As the restrictive common due date problem is known to be intractable we decided, secondly, to apply meta-heuristics, namely evolutionary strategies, simulated annealing and threshold accepting. We demonstrate that our application of these meta-heuristics is efficient in obtaining near-optimal solutions by solving 140 benchmark problems with up to 1000 jobs. Furthermore, we compare their solution quality and find that a new variant of threshold accepting is superior to the other approaches. Many biological processes are governed by large assemblies of protein molecules. However, it is often very difficult to determine the three-dimensional structures of these assemblies using experimental biophysical techniques. Hence there is a need to develop computational approaches to fill this gap. This article presents an ant colony optimization approach to predict the structure of large multi-component protein complexes. Starting from pair-wise docking predictions, a multi-graph consisting of vertices representing the component proteins and edges representing candidate interactions is constructed. This allows the assembly problem to be expressed in terms of searching for a minimum weight spanning tree. However, because the problem remains highly combinatorial, the search space cannot be enumerated exhaustively and therefore heuristic optimisation techniques must be used. The utility of the ant colony based approach is demonstrated by re-assembling known protein complexes from the Protein Data Bank. The algorithm is able to identify near-native solutions for five of the six cases tested. This demonstrates that the ant colony approach provides a useful way to deal with the highly combinatorial multi-component protein assembly problem. Recently, researchers have started to explore the use of Artificial Intelligence (AI)-based algorithms as t-way (where t indicates the interaction strength) testing strategies. Many AI-based strategies have been developed, such as Ant Colony, Simulated Annealing, Genetic Algorithm, and Tabu Search. Although useful, most existing AI-based t-way testing strategies adopt complex search processes and require heavy computations. For this reason, existing AI-based t-way testing strategies have been confined to small interaction strengths (i.e., t@?3) and small test configurations. Recent studies demonstrate the need to go up to t=6 in order to capture most faults. In this paper, we demonstrate the effectiveness of our proposed Particle Swarm-based t-way Test Generator (PSTG) for generating uniform and variable strength covering arrays. Unlike other existing AI-based t-way testing strategies, the lightweight computation of the particle swarm search process enables PSTG to support high interaction strengths of up to t=6. The performance of our proposed PSTG is evaluated using several sets of benchmark experiments. Comparatively, PSTG consistently outperforms its AI counterparts and other existing testing strategies as far as the size of the array is concerned. Furthermore, our case study demonstrates the usefulness of PSTG for facilitating fault detection owing to interactions of the input components. This paper presents a novel evolutionary optimization strategy based on the derandomized evolution strategy with covariance matrix adaptation (CMA-ES). This new approach is intended to reduce the number of generations required for convergence to the optimum. Reducing the number of generations, i.e., the time complexity of the algorithm, is important if a large population size is desired: (1) to reduce the effect of noise; (2) to improve global search properties; and (3) to implement the algorithm on (highly) parallel machines. Our method results in a highly parallel algorithm which scales favorably with large numbers of processors. This is accomplished by efficiently incorporating the available information from a large population, thus significantly reducing the number of generations needed to adapt the covariance matrix. The original version of the CMA-ES was designed to reliably adapt the covariance matrix in small populations but it cannot exploit large populations efficiently. Our modifications scale up the efficiency to population sizes of up to 10n, where n is the problem dimension. This method has been applied to a large number of test problems, demonstrating that in many cases the CMA-ES can be advanced from quadratic to linear time complexity. This paper presents the results of our investigation of code positioning techniques using execution profile data as input into the compilation process. The primary objective of the positioning is to reduce the overhead of the instruction memory hierarchy. After initial investigation in the literature, we decided to implement two prototypes for the Hewlett-Packard Precision Architecture (PA-RISC). The first, built on top of the linker, positions code based on whole procedures. This prototype has the ability to move procedures into an order that is determined by a “closest is best” strategy. The second prototype, built on top of an existing optimizer package, positions code based on basic blocks within procedures. Groups of basic blocks that would be better as straight-line sequences are identified as chains . These chains are then ordered according to branch heuristics. Code that is never executed during the data collection runs can be physically separated from the primary code of a procedure by a technique we devised called procedure splitting . The algorithms we implemented are described through examples in this paper. The performance improvements from our work are also summarized in various tables and charts. List of Algorithms Preface 1. Introduction. Brief Overview of the State of the Art Notation Review of Relevant Linear Algebra Part I. Krylov Subspace Approximations. 2. Some Iteration Methods. Simple Iteration Orthomin(1) and Steepest Descent Orthomin(2) and CG Orthodir, MINRES, and GMRES Derivation of MINRES and CG from the Lanczos Algorithm 3. Error Bounds for CG, MINRES, and GMRES. Hermitian Problems-CG and MINRES Non-Hermitian Problems-GMRES 4. Effects of Finite Precision Arithmetic. Some Numerical Examples The Lanczos Algorithm A Hypothetical MINRES CG Implementation A Matrix Completion Problem Orthogonal Polynomials 5. BiCG and Related Methods. The Two-Sided Lanczos Algorithm The Biconjugate Gradient Algorithm The Quasi-Minimal Residual Algorithm Relation Between BiCG and QMR The Conjugate Gradient Squared Algorithm The BiCGSTAB Algorithm Which Method Should I Use? 6. Is There A Short Recurrence for a Near-Optimal Approximation? The Faber and Manteuffel Result Implications 7. Miscellaneous Issues. Symmetrizing the Problem Error Estimation and Stopping Criteria Attainable Accuracy Multiple Right-Hand Sides and Block Methods Computer Implementation Part II. Preconditioners. 8. Overview and Preconditioned Algorithms. 9. Two Example Problems. The Diffusion Equation The Transport Equation 10. Comparison of Preconditioners. Jacobi, Gauss--Seidel, SOR The Perron--Frobenius Theorem Comparison of Regular Splittings Regular Splittings Used with the CG Algorithm Optimal Diagonal and Block Diagonal Preconditioners 11. Incomplete Decompositions. Incomplete Cholesky Decomposition Modified Incomplete Cholesky Decomposition 12. Multigrid and Domain Decomposition Methods. Multigrid Methods Basic Ideas of Domain Decomposition Methods. In this paper we introduce an Ant Colony Optimisation (ACO) algorithm for the Shortest Common Supersequence (SCS) problem, which has applications in production system planning, mechanical engineering and molecular biology. The ACO algorithm is used to find good parameters for a heuristic for the SCS problem. An island model with several populations of ants is used for the ACO algorithm. Besides we introduce a lookahead function which makes the decisions of the ants dependent on the state arrived after the decision. This paper presents a new algorithm based on integrating genetic algorithms, tabu search and simulated annealing methods to solve the unit commitment problem. The core of the proposed algorithm is based on genetic algorithms. Tabu search is used to generate new population members in the reproduction phase of the genetic algorithm. A simulated annealing method is used to accelerate the convergence of the genetic algorithm by applying the simulated annealing test for all the population members. A new implementation of the genetic algorithm is introduced. The genetic algorithm solution is coded as a mix between binary and decimal representation. The fitness function is constructed from the total operating cost of the generating units without penalty terms. In the tabu search part of the proposed algorithm, a simple short-term memory procedure is used to counter the danger of entrapment at a local optimum, and the premature convergence of the genetic algorithm. A simple cooling schedule has been implemented to apply the simulated annealing test in the algorithm. Numerical results showed the superiority of the solutions obtained compared to genetic algorithms, tabu search and simulated annealing methods, and to two exact algorithms.