Protein-Ligand Binding Affinity Directed Multi-Objective Drug Design Based on Fragment Representation Methods

Drug discovery is a challenging process with a vast molecular space to be explored and numerous pharmacological properties to be appropriately considered. Among various drug design protocols, fragment-based drug design is an effective way of constraining the search space and better utilizing biologically active compounds. Motivated by fragment-based drug search for a given protein target and the emergence of artificial intelligence (AI) approaches in this field, this work advances the field of in silico drug design by (1) integrating a graph fragmentation-based deep generative model with a deep evolutionary learning process for large-scale multi-objective molecular optimization, and (2) applying protein-ligand binding affinity scores together with other desired physicochemical properties as objectives. Our experiments show that the proposed method can generate novel molecules with improved property values and binding affinities

State-of-the-art in aerodynamic shape optimisation methods

Aerodynamic optimisation has become an indispensable component for any aerodynamic design over the past 60 years, with applications to aircraft, cars, trains, bridges, wind turbines, internal pipe flows, and cavities, among others, and is thus relevant in many facets of technology. With advancements in computational power, automated design optimisation procedures have become more competent, however, there is an ambiguity and bias throughout the literature with regards to relative performance of optimisation architectures and employed algorithms. This paper provides a well-balanced critical review of the dominant optimisation approaches that have been integrated with aerodynamic theory for the purpose of shape optimisation. A total of 229 papers, published in more than 120 journals and conference proceedings, have been classified into 6 different optimisation algorithm approaches. The material cited includes some of the most well-established authors and publications in the field of aerodynamic optimisation. This paper aims to eliminate bias toward certain algorithms by analysing the limitations, drawbacks, and the benefits of the most utilised optimisation approaches. This review provides comprehensive but straightforward insight for non-specialists and reference detailing the current state for specialist practitioners

A Survey of Methods for Converting Unstructured Data to CSG Models

The goal of this document is to survey existing methods for recovering CSG representations from unstructured data such as 3D point-clouds or polygon meshes. We review and discuss related topics such as the segmentation and fitting of the input data. We cover techniques from solid modeling and CAD for polyhedron to CSG and B-rep to CSG conversion. We look at approaches coming from program synthesis, evolutionary techniques (such as genetic programming or genetic algorithm), and deep learning methods. Finally, we conclude with a discussion of techniques for the generation of computer programs representing solids (not just CSG models) and higher-level representations (such as, for example, the ones based on sketch and extrusion or feature based operations).Comment: 29 page

Metaheuristic design of feedforward neural networks: a review of two decades of research

Over the past two decades, the feedforward neural network (FNN) optimization has been a key interest among the researchers and practitioners of multiple disciplines. The FNN optimization is often viewed from the various perspectives: the optimization of weights, network architecture, activation nodes, learning parameters, learning environment, etc. Researchers adopted such different viewpoints mainly to improve the FNN's generalization ability. The gradient-descent algorithm such as backpropagation has been widely applied to optimize the FNNs. Its success is evident from the FNN's application to numerous real-world problems. However, due to the limitations of the gradient-based optimization methods, the metaheuristic algorithms including the evolutionary algorithms, swarm intelligence, etc., are still being widely explored by the researchers aiming to obtain generalized FNN for a given problem. This article attempts to summarize a broad spectrum of FNN optimization methodologies including conventional and metaheuristic approaches. This article also tries to connect various research directions emerged out of the FNN optimization practices, such as evolving neural network (NN), cooperative coevolution NN, complex-valued NN, deep learning, extreme learning machine, quantum NN, etc. Additionally, it provides interesting research challenges for future research to cope-up with the present information processing era

Machine learning into metaheuristics: A survey and taxonomy of data-driven metaheuristics

During the last years, research in applying machine learning (ML) to design efficient, effective and robust metaheuristics became increasingly popular. Many of those data driven metaheuristics have generated high quality results and represent state-of-the-art optimization algorithms. Although various appproaches have been proposed, there is a lack of a comprehensive survey and taxonomy on this research topic. In this paper we will investigate different opportunities for using ML into metaheuristics. We define uniformly the various ways synergies which might be achieved. A detailed taxonomy is proposed according to the concerned search component: target optimization problem, low-level and high-level components of metaheuristics. Our goal is also to motivate researchers in optimization to include ideas from ML into metaheuristics. We identify some open research issues in this topic which needs further in-depth investigations

Proceedings of the XIII Global Optimization Workshop: GOW'16

[Excerpt] Preface: Past Global Optimization Workshop shave been held in Sopron (1985 and 1990), Szeged (WGO, 1995), Florence (GO’99, 1999), Hanmer Springs (Let’s GO, 2001), Santorini (Frontiers in GO, 2003), San José (Go’05, 2005), Mykonos (AGO’07, 2007), Skukuza (SAGO’08, 2008), Toulouse (TOGO’10, 2010), Natal (NAGO’12, 2012) and Málaga (MAGO’14, 2014) with the aim of stimulating discussion between senior and junior researchers on the topic of Global Optimization. In 2016, the XIII Global Optimization Workshop (GOW’16) takes place in Braga and is organized by three researchers from the University of Minho. Two of them belong to the Systems Engineering and Operational Research Group from the Algoritmi Research Centre and the other to the Statistics, Applied Probability and Operational Research Group from the Centre of Mathematics. The event received more than 50 submissions from 15 countries from Europe, South America and North America. We want to express our gratitude to the invited speaker Panos Pardalos for accepting the invitation and sharing his expertise, helping us to meet the workshop objectives. GOW’16 would not have been possible without the valuable contribution from the authors and the International Scientific Committee members. We thank you all. This proceedings book intends to present an overview of the topics that will be addressed in the workshop with the goal of contributing to interesting and fruitful discussions between the authors and participants. After the event, high quality papers can be submitted to a special issue of the Journal of Global Optimization dedicated to the workshop. [...

An Improved Bees Algorithm for Training Deep Recurrent Networks for Sentiment Classification

Recurrent neural networks (RNNs) are powerful tools for learning information from temporal sequences. Designing an optimum deep RNN is difficult due to configuration and training issues, such as vanishing and exploding gradients. In this paper, a novel metaheuristic optimisation approach is proposed for training deep RNNs for the sentiment classification task. The approach employs an enhanced Ternary Bees Algorithm (BA-3+), which operates for large dataset classification problems by considering only three individual solutions in each iteration. BA-3+ combines the collaborative search of three bees to find the optimal set of trainable parameters of the proposed deep recurrent learning architecture. Local learning with exploitative search utilises the greedy selection strategy. Stochastic gradient descent (SGD) learning with singular value decomposition (SVD) aims to handle vanishing and exploding gradients of the decision parameters with the stabilisation strategy of SVD. Global learning with explorative search achieves faster convergence without getting trapped at local optima to find the optimal set of trainable parameters of the proposed deep recurrent learning architecture. BA-3+ has been tested on the sentiment classification task to classify symmetric and asymmetric distribution of the datasets from different domains, including Twitter, product reviews, and movie reviews. Comparative results have been obtained for advanced deep language models and Differential Evolution (DE) and Particle Swarm Optimization (PSO) algorithms. BA-3+ converged to the global minimum faster than the DE and PSO algorithms, and it outperformed the SGD, DE, and PSO algorithms for the Turkish and English datasets. The accuracy value and F1 measure have improved at least with a 30–40% improvement than the standard SGD algorithm for all classification datasets. Accuracy rates in the RNN model trained with BA-3+ ranged from 80% to 90%, while the RNN trained with SGD was able to achieve between 50% and 60% for most datasets. The performance of the RNN model with BA-3+ has as good as for Tree-LSTMs and Recursive Neural Tensor Networks (RNTNs) language models, which achieved accuracy results of up to 90% for some datasets. The improved accuracy and convergence results show that BA-3+ is an efficient, stable algorithm for the complex classification task, and it can handle the vanishing and exploding gradients problem of deep RNNs