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Classification of datasets with imbalanced sample distributions has always been a challenge. In general, a popular approach for enhancing classification performance is the construction of an ensemble of classifiers. However, the performance of an ensemble is dependent on the choice of constituent base classifiers. Therefore, we propose a genetic algorithm-based search method for finding the optimum combination from a pool of base classifiers to form a heterogeneous ensemble. The algorithm, called GA-EoC, utilises 10 fold-cross validation on training data for evaluating the quality of each candidate ensembles. In order to combine the base classifiers decision into ensemble's output, we used the simple and widely used majority voting approach. The proposed algorithm, along with the random sub-sampling approach to balance the class distribution, has been used for classifying class-imbalanced datasets. Additionally, if a feature set was not available, we used the (α, β) - k Feature Set method to select a better subset of features for classification. We have tested GA-EoC with three benchmarking datasets from the UCI-Machine Learning repository, one Alzheimer's disease dataset and a subset of the PubFig database of Columbia University. In general, the performance of the proposed method on the chosen datasets is robust and better than that of the constituent base classifiers and many other well-known ensembles. Based on our empirical study we claim that a genetic algorithm is a superior and reliable approach to heterogeneous ensemble construction and we expect that the proposed GA-EoC would perform consistently in other cases.

Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of 'parts' and 'devices'. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in synthetic biology. A recent study shows that Darwinian evolution can gradually develop higher topological robustness. Subsequently, this work presents an evolutionary algorithm that simulates natural evolution in silico, for identifying network topologies that are robust to perturbations. We present a Monte Carlo based method for quantifying topological robustness and designed a fitness approximation approach for efficient calculation of topological robustness which is computationally very intensive. The proposed framework was verified using two classic GRN behaviors: oscillation and bistability, although the framework is generalized for evolving other types of responses. The algorithm identified robust GRN architectures which were verified using different analysis and comparison. Analysis of the results also shed light on the relationship among robustness, cooperativity and complexity. This study also shows that nature has already evolved very robust architectures for its crucial systems; hence simulation of this natural process can be very valuable for designing robust biological systems.

Most of the existing in silico phosphorylation site prediction systems use machine learning approach that requires preparing a good set of classification data in order to build the classification knowledge. Furthermore, phosphorylation is catalyzed by kinase enzymes and hence the kinase information of the phosphorylated sites has been used as major classification data in most of the existing systems. Since the number of kinase annotations in protein sequences is far less than that of the proteins being sequenced to date, the prediction systems that use the information found from the small clique of kinase annotated proteins can not be considered as completely perfect for predicting outside the clique. Hence the systems are certainly not generalized. In this paper, a novel generalized prediction system, PPRED (Phosphorylation PREDictor) is proposed that ignores the kinase information and only uses the evolutionary information of proteins for classifying phosphorylation sites. Experimental results based on cross validations and an independent benchmark reveal the significance of using the evolutionary information alone to classify phosphorylation sites from protein sequences. The prediction performance of the proposed system is better than those of the existing prediction systems that also do not incorporate kinase information. The system is also comparable to systems that incorporate kinase information in predicting such sites. The approach presented in this paper provides an efficient way to identify phosphorylation sites in a given protein primary sequence that would be a valuable information for the molecular biologists working on protein phosphorylation sites and for bioinformaticians developing generalized prediction systems for the post translational modifications like phosphorylation or glycosylation. PPRED is publicly available at the URL http://www.cse.univdhaka.edu/~ashis/ppred/index.php.

A robust cellular counter could enable synthetic biologists to design complex circuits with diverse behaviors. The existing synthetic-biological counters, responsive to the beginning of the pulse, are sensitive to the pulse duration. Here we present a pulse detecting circuit that responds only at the falling edge of a pulse-analogous to negative edge triggered electric circuits. As biological events do not follow precise timing, use of such a pulse detector would enable the design of robust asynchronous counters which can count the completion of events. This transcription-based pulse detecting circuit depends on the interaction of two co-expressed lambdoid phage-derived proteins: the first is unstable and inhibits the regulatory activity of the second, stable protein. At the end of the pulse the unstable inhibitor protein disappears from the cell and the second protein triggers the recording of the event completion. Using stochastic simulation we showed that the proposed design can detect the completion of the pulse irrespective to the pulse duration. In our simulation we also showed that fusing the pulse detector with a phage lambda memory element we can construct a counter which can be extended to count larger numbers. The proposed design principle is a new control mechanism for synthetic biology which can be integrated in different circuits for identifying the completion of an event.

Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well- known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.

Actor-critic (AC) algorithms are a class of model-free deep reinforcement learning algorithms, which have proven their efficacy in diverse domains, especially in solving continuous control problems. Improvement of exploration (action entropy) and exploitation (expected return) using more efficient samples is a critical issue in AC algorithms. A basic strategy of a learning algorithm is to facilitate indiscriminately exploring all of the environment state space, as well as to encourage exploring rarely visited states rather than frequently visited one. Under this strategy, we propose a new method to boost exploration through an intrinsic reward, based on measurement of a state's novelty and the associated benefit of exploring the state (with regards to policy optimization), altogether called plausible novelty. With incentivized exploration of plausible novel states, an AC algorithm is able to improve its sample efficiency and hence training performance. The new method is verified by extensive simulations of continuous control tasks of MuJoCo environments on a variety of prominent off-policy AC algorithms.

Internet of things (IoT) has significantly altered the traditional lifestyle to a highly technologically advanced society. Some of the significant transformations that have been achieved through IoT are smart homes, smart transportation, smart city, and control of pollution. A considerable number of studies have been conducted and continue to be done to increase the use of technology through IoT. Furthermore, the research about IoT has not been done fully in improving the application of technology through IoT. Besides, IoT experiences several problems that need to be considered in order to get the full capability of IoT in changing society. This research paper addresses the key applications of IoT, the architecture of IoT, and the key issues affecting IoT. In addition, the paper highlights how big data analytics is essential in improving the effectiveness of IoT in various applications within society.

Actor-critic (AC) algorithms are known for their efficacy and high performance in solving reinforcement learning problems, but they also suffer from low sampling efficiency. An AC based policy optimization process is iterative and needs to frequently access the agent-environment system to evaluate and update the policy by rolling out the policy, collecting rewards and states (i.e. samples), and learning from them. It ultimately requires a huge number of samples to learn an optimal policy. To improve sampling efficiency, we propose a strategy to optimize the training dataset that contains significantly less samples collected from the AC process. The dataset optimization is made of a best episode only operation, a policy parameter-fitness model, and a genetic algorithm module. The optimal policy network trained by the optimized training dataset exhibits superior performance compared to many contemporary AC algorithms in controlling autonomous dynamical systems. Evaluation on standard benchmarks show that the method improves sampling efficiency, ensures faster convergence to optima, and is more data-efficient than its counterparts.

Soft Actor-Critic (SAC) is an off-policy actor-critic reinforcement learning algorithm, essentially based on entropy regularization. SAC trains a policy by maximizing the trade-off between expected return and entropy (randomness in the policy). It has achieved state-of-the-art performance on a range of continuous-control benchmark tasks, outperforming prior on-policy and off-policy methods. SAC works in an off-policy fashion where data are sampled uniformly from past experiences (stored in a buffer) using which parameters of the policy and value function networks are updated. We propose certain crucial modifications for boosting the performance of SAC and make it more sample efficient. In our proposed improved SAC, we firstly introduce a new prioritization scheme for selecting better samples from the experience replay buffer. Secondly we use a mixture of the prioritized off-policy data with the latest on-policy data for training the policy and the value function networks. We compare our approach with the vanilla SAC and some recent variants of SAC and show that our approach outperforms the said algorithmic benchmarks. It is comparatively more stable and sample efficient when tested on a number of continuous control tasks in MuJoCo environments.