Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iRMSD). Results: We introduce a novel algorithm, Bayesian Active Learning (BAL), for optimization and UQ of such black-box functions and flexible protein docking. BAL directly models the posterior distribution of the global optimum (or native structures for protein docking) with active sampling and posterior estimation iteratively feeding each other. Furthermore, we use complex normal modes to represent a homogeneous Euclidean conformation space suitable for high-dimension optimization and construct funnel-like energy models for encounter complexes. Over a protein docking benchmark set and a CAPRI set including homology docking, we establish that BAL significantly improve against both starting points by rigid docking and refinements by particle swarm optimization, providing for one third targets a top-3 near-native prediction. BAL also generates tight confidence intervals with half range around 25% of iRMSD and confidence level at 85%. Its estimated probability of a prediction being native or not achieves binary classification AUROC at 0.93 and AUPRC over 0.60 (compared to 0.14 by chance); and also found to help ranking predictions. To the best of our knowledge, this study represents the first uncertainty quantification solution for protein docking, with theoretical rigor and comprehensive assessment. Source codes are available at https://github.com/Shen-Lab/BAL.

A team of scientists has discovered the ideal wing shape for fast flight - opening up the possibility of harvesting more energy from water. The team, from New York University, conducted a series of tests on 3D-printed wings. Now, they claim their findings could offer improved methods for harvesting renewable energy from sources such as water. Leif Ristroph, an assistant professor at New York University's Courant Institute of Mathematical Sciences, explained how the wing shape was determined using a form of biological evolution. 'We can simulate evolution in the lab by generating a population of wings of different shapes,' he said.

A grand challenge in reinforcement learning is intelligent exploration, especially when rewards are sparse or deceptive. Two Atari games serve as benchmarks for such hard-exploration domains: Montezuma's Revenge and Pitfall. On both games, current RL algorithms perform poorly, even those with intrinsic motivation, which is the dominant method to improve performance on hard-exploration domains. To address this shortfall, we introduce a new algorithm called Go-Explore. It exploits the following principles: (1) remember previously visited states, (2) first return to a promising state (without exploration), then explore from it, and (3) solve simulated environments through any available means (including by introducing determinism), then robustify via imitation learning. The combined effect of these principles is a dramatic performance improvement on hard-exploration problems. On Montezuma's Revenge, Go-Explore scores a mean of over 43k points, almost 4 times the previous state of the art. Go-Explore can also harness human-provided domain knowledge and, when augmented with it, scores a mean of over 650k points on Montezuma's Revenge. Its max performance of nearly 18 million surpasses the human world record, meeting even the strictest definition of "superhuman" performance. On Pitfall, Go-Explore with domain knowledge is the first algorithm to score above zero. Its mean score of almost 60k points exceeds expert human performance. Because Go-Explore produces high-performing demonstrations automatically and cheaply, it also outperforms imitation learning work where humans provide solution demonstrations. Go-Explore opens up many new research directions into improving it and weaving its insights into current RL algorithms. It may also enable progress on previously unsolvable hard-exploration problems in many domains, especially those that harness a simulator during training (e.g. robotics).

In fact, the winner of the 2018 Human-Competitive Award at the ACM Genetic and Evolutionary Computation Conference in Kyoto, Japan (see http://www.human-competitive.org/awards)

We propose a new framework for constructing polar codes (i.e., selecting the frozen bit positions) for arbitrary channels, and tailored to a given decoding algorithm, rather than based on the (not necessarily optimal) assumption of successive cancellation (SC) decoding. The proposed framework is based on the Genetic Algorithm (GenAlg), where populations (i.e., collections) of information sets evolve successively via evolutionary transformations based on their individual error-rate performance. These populations converge towards an information set that fits both the decoding behavior and the defined channel. Using our proposed algorithm over the additive white Gaussian noise (AWGN) channel, we construct a polar code of length 2048 with code rate 0.5, without the CRC-aid, tailored to plain successive cancellation list (SCL) decoding, achieving the same error-rate performance as the CRC-aided SCL decoding, and leading to a coding gain of 1 dB at BER of $10^{-6}$. Further, a belief propagation (BP)-tailored construction approaches the SCL error-rate performance without any modifications in the decoding algorithm itself. The performance gains can be attributed to the significant reduction in the total number of low-weight codewords. To demonstrate the flexibility, coding gains for the Rayleigh channel are shown under SCL and BP decoding. Besides improvements in error-rate performance, we show that, when required, the GenAlg can be also set up to reduce the decoding complexity, e.g., the SCL list size or the number of BP iterations can be reduced, while maintaining the same error-rate performance.

Web Service Composition (WSC) is a particularly promising application of Web services, where multiple individual services with specific functionalities are composed to accomplish a more complex task, which must fulfil functional requirements and optimise Quality of Service (QoS) attributes, simultaneously. Additionally, large quantities of data, produced by technological advances, need to be exchanged between services. Data-intensive Web services, which manipulate and deal with those data, are of great interest to implement data-intensive processes, such as distributed Data-intensive Web Service Composition (DWSC). Researchers have proposed Evolutionary Computing (EC) fully-automated WSC techniques that meet all the above factors. Some of these works employed Memetic Algorithms (MAs) to enhance the performance of EC through increasing its exploitation ability of in searching neighbourhood area of a solution. However, those works are not efficient or effective. This paper proposes an MA-based approach to solving the problem of distributed DWSC in an effective and efficient manner. In particular, we develop an MA that hybridises EC with a flexible local search technique incorporating distance of services. An evaluation using benchmark datasets is carried out, comparing existing state-of-the-art methods. Results show that our proposed method has the highest quality and an acceptable execution time overall.

Neural Architecture Search has recently shown potential to automate the design of Neural Networks. The use of Neural Network agents trained with Reinforcement Learning can offer the possibility to learn complex architectural patterns, as well as the ability to explore a vast and compositional search space. On the other hand, evolutionary algorithms offer the sample efficiency needed for such a resource intensive application. We propose a class of Evolutionary-Neural hybrid agents (Evo-NAS), that retain the qualities of the two approaches. We show that the Evo-NAS agent outperforms both Neural and Evolutionary agents when applied to architecture search for a suite of text classification and image classification benchmarks. On a high-complexity architecture search space for image classification, the Evo-NAS agent surpasses the performance of commonly used agents with only 1/3 of the trials.

The current state-of-the-art Scrabble agents are not learning-based but depend on truncated Monte Carlo simulations and the quality of such agents is contingent upon the time available for running the simulations. This thesis takes steps towards building a learning-based Scrabble agent using self-play. Specifically, we try to find a better function approximation for the static evaluation function used in Scrabble which determines the move goodness at a given board configuration. In this work, we experimented with evolutionary algorithms and Bayesian Optimization to learn the weights for an approximate feature-based evaluation function. However, these optimization methods were not quite effective, which lead us to explore the given problem from an Imitation Learning point of view. We also tried to imitate the ranking of moves produced by the Quackle simulation agent using supervised learning with a neural network function approximator which takes the raw representation of the Scrabble board as the input instead of using only a fixed number of handcrafted features.

An important open problem in robotic planning is the autonomous generation of 3D inspection paths -- that is, planning the best path to move a robot along in order to inspect a target structure. We recently suggested a new method for planning paths allowing the inspection of complex 3D structures, given a triangular mesh model of the structure. The method differs from previous approaches in its emphasis on generating and considering also plans that result in imperfect coverage of the inspection target. In many practical tasks, one would accept imperfections in coverage if this results in a substantially more energy efficient inspection path. The key idea is using a multiobjective evolutionary algorithm to optimize the energy usage and coverage of inspection plans simultaneously - and the result is a set of plans exploring the different ways to balance the two objectives. We here test our method on a set of inspection targets with large variation in size and complexity, and compare its performance with two state-of-the-art methods for complete coverage path planning. The results strengthen our confidence in the ability of our method to generate good inspection plans for different types of targets. The method's advantage is most clearly seen for real-world inspection targets, since traditional complete coverage methods have no good way of generating plans for structures with hidden parts. Multiobjective evolution, by optimizing energy usage and coverage together ensures a good balance between the two - both when 100% coverage is feasible, and when large parts of the object are hidden.

Totally self-checking (TSC) circuits are synthesised with a grid of computers running a distributed population based stochastic optimisation algorithm. The presented method is the first to automatically synthesise TSC circuits from arbitrary logic as all previous methods fail to guarantee the checker is self-testing (ST) for circuits with limited output codespaces. The circuits synthesised by the presented method have significantly lower overhead than the previously reported best for every one of a set of 11 frequently used benchmarks. Average overhead across the entire set is 23% of duplication and comparison overhead, compared with an average of 69% for the previous best reported values across the set. The methodology presented represents a breakthrough in concurrent error detection (CED). The highly efficient, novel designs produced are tailored to each circuit's function, rather than being constrained by a particular modular CED design methodology. Results are synthesised using two-input gates and are TSC with respect to all gate input and output stuck-at faults. The method can be used to add CED with or without modifications to the original logic, and can be generalised to any implementation technology and fault model. An example circuit is analysed and rigorously proven to be TSC.