Psychophysical identity and free energy

An approach to implementing variational Bayesian inference in biological systems is considered, under which the thermodynamic free energy of a system directly encodes its variational free energy. In the case of the brain, this assumption places constraints on the neuronal encoding of generative and recognition densities, in particular requiring a stochastic population code. The resulting relationship between thermodynamic and variational free energies is prefigured in mind-brain identity theses in philosophy and in the Gestalt hypothesis of psychophysical isomorphism.Comment: 22 pages; published as a research article on 8/5/2020 in Journal of the Royal Society Interfac

A PBIL for load balancing in network coding based multicasting

One of the most important issues in multicast is how to achieve a balanced traffic load within a communications network. This paper formulates a load balancing optimization problem in the context of multicast with network coding and proposes a modified population based incremental learning (PBIL) algorithm for tackling it. A novel probability vector update scheme is developed to enhance the global exploration of the stochastic search by introducing extra flexibility when guiding the search towards promising areas in the search space. Experimental results demonstrate that the proposed PBIL outperforms a number of the state-of-the-art evolutionary algorithms in terms of the quality of the best solution obtained

A quantum inspired evolutionary algorithm for dynamic multicast routing with network coding

This paper studies and models the multicast routing problem with network coding in dynamic network environment, where computational and bandwidth resources are to be jointly optimized. A quantum inspired evolutionary algorithm (QEA) is developed to address the problem above, where a restart scheme is devised for well adapting QEA for tracing the ever-changing optima in dynamic environment. Experimental results show that the proposed QEA outperforms a number of existing evolutionary algorithms in terms of the best solution obtained

A path-oriented encoding evolutionary algorithm for network coding resource minimization

Network coding is an emerging telecommunication technique, where any intermediate node is allowed to recombine incoming data if necessary. This technique helps to increase the throughput, however, very likely at the cost of huge amount of computational overhead, due to the packet recombination performed (ie coding operations). Hence, it is of practical importance to reduce coding operations while retaining the benefits that network coding brings to us. In this paper, we propose a novel evolutionary algorithm (EA) to minimize the amount of coding operations involved. Different from the state-of-the-art EAs which all use binary encodings for the problem, our EA is based on path-oriented encoding. In this new encoding scheme, each chromosome is represented by a union of paths originating from the source and terminating at one of the receivers. Employing path-oriented encoding leads to a search space where all solutions are feasible, which fundamentally facilitates more efficient search of EAs. Based on the new encoding, we develop three basic operators, that is, initialization, crossover and mutation. In addition, we design a local search operator to improve the solution quality and hence the performance of our EA. The simulation results demonstrate that our EA significantly outperforms the state-of-the-art algorithms in terms of global exploration and computational time

A nondominated sorting genetic algorithm for bi-objective network coding based multicast routing problems

Network coding is a new communication technique that generalizes routing, where, instead of simply forwarding the packets they receive, intermediate nodes are allowed to recombine (code) together some of the data packets received from different incoming links if necessary. By doing so, the maximum information flow in a network can always be achieved. However, performing coding operations (i.e. recombining data packets) incur computational overhead and delay of data processing at the corresponding nodes. In this paper, we investigate the optimization of the network coding based multicast routing problem with respect to two widely considered objectives, i.e. the cost and the delay. In general, reducing cost can result into a cheaper multicast solution for network service providers, while decreasing delay improves the service quality for users. Hence we model the problem as a bi-objective optimization problem to minimize the total cost and the maximum transmission delay of a multicast. This bi-objective optimization problem has not been considered in the literature. We adapt the Elitist Nondominated Sorting Genetic Algorithm (NSGA-II) for the new problem by introducing two adjustments. As there are many infeasible solutions in the search space, the first adjustment is an initialization scheme to generate a population of feasible and diversified solutions. These initial solutions help to guide the search towards the Pareto-optimal front. In addition, the original NSGA-II is very likely to produce a number of solutions with identical objective values at each generation, which may seriously deteriorate the level of diversity and the optimization performance. The second adjustment is an individual delegate scheme where, among those solutions with identical objective values, only one of them is retained in the population while the others are deleted. Experimental results reveal that each adopted adjustment contributes to the adaptation of NSGA-II for the problem concerned. Moreover, the adjusted NSGA-II outperforms a number of state-of-the-art multiobjective evolutionary algorithms with respect to the quality of the obtained nondominated solutions in the conducted experiments

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

A modified ant colony optimization algorithm for network coding resource minimization

The paper presents a modified ant colony optimization approach for the network coding resource minimization problem. It is featured with several attractive mechanisms specially devised for solving the network coding resource minimization problem: 1) a multi-dimensional pheromone maintenance mechanism is put forward to address the issue of pheromone overlapping; 2) problem-specific heuristic information is employed to enhance the heuristic search (neighboring area search) capability; 3) a tabu-table based path construction method is devised to facilitate the construction of feasible (link-disjoint) paths from the source to each receiver; 4) a local pheromone updating rule is developed to guide ants to construct appropriate promising paths; 5) a solution reconstruction method is presented, with the aim of avoiding prematurity and improving the global search efficiency of proposed algorithm. Due to the way it works, the ant colony optimization can well exploit the global and local information of routing related problems during the solution construction phase. The simulation results on benchmark instances demonstrate that with the five extended mechanisms integrated, our algorithm outperforms a number of existing algorithms with respect to the best solutions obtained and the computational time