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

The type of algorithm addressed in this chapter is based on the following general idea. Given a valid solution to the tackled problem instance—henceforth called the incumbent solution—first, destroy selected parts of it, resulting in a partial solution. Then apply some other, possibly exact, technique to find the best valid solution on the basis of the given partial solution, that is, the best valid solution that contains the given partial solution. Thus, the destroy-step defines a large neighborhood, from which a best (or nearly best) solution is determined not by naive enumeration but by the application of a more effective alternative technique. In our examples here, we mainly consider a MIP solver for this purpose, which is applied to a MIP model for the original problem in which the variables corresponding to the given partial solution get respective fixed values preassigned. The motivating aspect for this concept is the same as that described in the context of hybrid algorithms based on instance reduction in Chapter 3: Even though it might be unfeasible to apply a MIP solver to the original problem instance, the solver might be particularly effective in solving the reduced ILP model in which a part of the variables has fixed values.

Hybridization Based on Large Neighborhood Search

In the minimum common string partition (MCSP) problem two related input strings are given. "Related" refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings. The MCSP seeks a minimum cardinality partitioning of one string into non-overlapping substrings that is also a valid partitioning for the second string. This problem has applications in bioinformatics e.g. in analyzing related DNA or protein sequences. For strings with lengths less than about 1000 letters, a previously published integer linear programming (ILP) formulation yields, when solved with a state-of-the-art solver such as CPLEX, satisfactory results. In this work, we propose a new, alternative ILP model that is compared to the former one. While a polyhedral study shows the linear programming relaxations of the two models to be equally strong, a comprehensive experimental comparison using real-world as well as artificially created benchmark instances indicates substantial computational advantages of the new formulation.

Computational Performance Evaluation of Two Integer Linear Programming Models for the Minimum Common String Partition Problem

Hybrid metaheuristics: 10th International Workshop, HM 2016, Plymouth, UK, June 8-10, 2016. Proceedings

A Probabilistic Beam Search Approach to the Shortest Common Supersequence Problem

In this paper we solve a variant of the multi-hop influence maximization problem in social networks by means of a hybrid algorithm that combines a biased random key genetic algorithm with a graph neural network. Hereby, the predictions of the graph neural network are used with the biased random key genetic algorithm for a more accurate translation of individuals into valid solutions to the tackled problem. The obtained results show that the hybrid algorithm is able to outperform both the biased random key genetic algorithm and the graph neural network when used as standalone techniques. In other words, we were able to show that an integration of both techniques leads to a better algorithm.

https://annals-csis.org/proceedings/2022/drp/pdf/78.pdf

Christian Blum

Papers

Hybridization Based on Large Neighborhood Search

Computational Performance Evaluation of Two Integer Linear Programming Models for the Minimum Common String Partition Problem

Hybrid metaheuristics: 10th International Workshop, HM 2016, Plymouth, UK, June 8-10, 2016. Proceedings

A Probabilistic Beam Search Approach to the Shortest Common Supersequence Problem

Boosting a Genetic Algorithm with Graph Neural Networks for Multi-Hop Influence Maximization in Social Networks