AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Swarm intelligence is a relatively new approach to problem solving that takes inspiration from the social behaviors of insects and of other animals In particular, ants have inspired a number of methods and techniques among which the most studied and the most successful is the general purpose optimization technique known as ant colony optimization Ant colony optimization (ACO) takes inspiration from the foraging behavior of some ant species These ants deposit pheromone on the ground in order to mark some favorable path that should be followed by other members of the colony Ant colony optimization exploits a similar mechanism for solving optimization problems From the early nineties, when the first ant colony optimization algorithm was proposed, ACO attracted the attention of increasing numbers of researchers and many successful applications are now available Moreover, a substantial corpus of theoretical results is becoming available that provides useful guidelines to researchers and practitioners in further applications of ACO The goal of this article is to introduce ant colony optimization and to survey its most notable applications

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Ant Colony Optimization

In this paper, we intend to formulate a new meta-heuristic algorithm, called Cuckoo Search (CS), for solving optimization problems. This algorithm is based on the obligate brood parasitic behaviour of some cuckoo species in combination with the Levy flight behaviour of some birds and fruit flies. We validate the proposed algorithm against test functions and then compare its performance with those of genetic algorithms and particle swarm optimization. Finally, we discuss the implication of the results and suggestion for further research.

Cuckoo Search via Lévy flights

Optimization problems are of great importance in many fields. They can be tackled, for example, by approximate algorithms such as metaheuristics. Examples of metaheuristics are simulated annealing, tabu search, evolutionary computation, iterated local search, variable neighborhood search, and ant colony optimization. In recent years it has become evident that a skilled combination of a metaheuristic with other optimization techniques, a so called hybrid metaheuristic, can provide a more efficient behavior and a higher flexibility. This is because hybrid metaheuristics combine their advantages with the complementary strengths of, for example, more classical optimization techniques such as branch and bound or dynamic programming. The authors involved in this book are among the top researchers in their domain. The book is intended both to provide an overview of hybrid metaheuristics to novices of the field, and to provide researchers from the field with a collection of some of the most interesting recent developments.

Hybrid Metaheuristics: An Emerging Approach to Optimization

We deal with the application of ant colony optimization to group shop scheduling, which is a general shop scheduling problem that includes, among others, the open shop scheduling problem and the job shop scheduling problem as special cases. The contributions of this paper are twofold. First, we propose a neighborhood structure for this problem by extending the well-known neighborhood structure derived by Nowicki and Smutnicki for the job shop scheduling problem. Then, we develop an ant colony optimization approach, which uses a strong non-delay guidance for constructing solutions and which employs black-box local search procedures to improve the constructed solutions. We compare this algorithm to an adaptation of the tabu search by Nowicki and Smutnicki to group shop scheduling. Despite its general nature, our algorithm works particularly well when applied to open shop scheduling instances, where it improves the best known solutions for 15 of the 28 tested instances. Moreover, our algorithm is the first competitive ant colony optimization approach for job shop scheduling instances.

An Ant Colony Optimization Algorithm for Shop Scheduling Problems

Ant colony optimization (ACO) is an optimization technique that was inspired by the foraging behaviour of real ant colonies. Originally, the method was introduced for the application to discrete optimization problems. Research efforts led to the development of algorithms for the application to continuous optimization problems. In this paper we extend and apply one of the most successful variants for the training of feed-forward neural networks. For evaluating our algorithm we apply it to pattern classification problems from the medical field. The results show that our algorithm is comparable to specialized algorithms for neural network training, and that it has advantages over other general purpose optimizers.

Training feed-forward neural networks with ant colony optimization: an application to pattern classification

We present a novel probabilistic approach to fully automated delineation of tree structures in noisy 2D images and 3D image stacks Unlike earlier methods that rely mostly on local evidence, ours builds a set of candidate trees over many different subsets of points likely to belong to the optimal tree and then chooses the best one according to a global objective function that combines image evidence with geometric priors Since the best tree does not necessarily span all the points, the algorithm is able to eliminate false detections while retaining the correct tree topology Manually annotated brightfield micrographs, retinal scans and the DIADEM challenge datasets are used to evaluate the performance of our method We used the DIADEM metric to quantitatively evaluate the topological accuracy of the reconstructions and showed that the use of the geometric regularization yields a substantial improvement

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Christian Blum

Papers

Hybrid Metaheuristics: An Emerging Approach to Optimization

An Ant Colony Optimization Algorithm for Shop Scheduling Problems

Training feed-forward neural networks with ant colony optimization: an application to pattern classification

Automated Reconstruction of Dendritic and Axonal Trees by Global Optimization with Geometric Priors

Hybrid Metaheuristics: An Introduction