8,872 research outputs found

    Problem dependent metaheuristic performance in Bayesian network structure learning.

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    Bayesian network (BN) structure learning from data has been an active research area in the machine learning field in recent decades. Much of the research has considered BN structure learning as an optimization problem. However, the finding of optimal BN from data is NP-hard. This fact has driven the use of heuristic algorithms for solving this kind of problem. Amajor recent focus in BN structure learning is on search and score algorithms. In these algorithms, a scoring function is introduced and a heuristic search algorithm is used to evaluate each network with respect to the training data. The optimal network is produced according to the best score evaluated. This thesis investigates a range of search and score algorithms to understand the relationship between technique performance and structure features of the problems. The main contributions of this thesis include (a) Two novel Ant Colony Optimization based search and score algorithms for BN structure learning; (b) Node juxtaposition distribution for studying the relationship between the best node ordering and the optimal BN structure; (c) Fitness landscape analysis for investigating the di erent performances of both chain score function and the CH score function; (d) A classifier method is constructed by utilizing receiver operating characteristic curve with the results on fitness landscape analysis; and finally (e) a selective o -line hyperheuristic algorithm is built for unseen BN structure learning with search and score algorithms. In this thesis, we also construct a new algorithm for producing BN benchmark structures and apply our novel approaches to a range of benchmark problems and real world problem

    Machine learning-guided directed evolution for protein engineering

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    Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the underlying physics or biological pathways. To demonstrate ML-guided directed evolution, we introduce the steps required to build ML sequence-function models and use them to guide engineering, making recommendations at each stage. This review covers basic concepts relevant to using ML for protein engineering as well as the current literature and applications of this new engineering paradigm. ML methods accelerate directed evolution by learning from information contained in all measured variants and using that information to select sequences that are likely to be improved. We then provide two case studies that demonstrate the ML-guided directed evolution process. We also look to future opportunities where ML will enable discovery of new protein functions and uncover the relationship between protein sequence and function.Comment: Made significant revisions to focus on aspects most relevant to applying machine learning to speed up directed evolutio

    The IBMAP approach for Markov networks structure learning

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    In this work we consider the problem of learning the structure of Markov networks from data. We present an approach for tackling this problem called IBMAP, together with an efficient instantiation of the approach: the IBMAP-HC algorithm, designed for avoiding important limitations of existing independence-based algorithms. These algorithms proceed by performing statistical independence tests on data, trusting completely the outcome of each test. In practice tests may be incorrect, resulting in potential cascading errors and the consequent reduction in the quality of the structures learned. IBMAP contemplates this uncertainty in the outcome of the tests through a probabilistic maximum-a-posteriori approach. The approach is instantiated in the IBMAP-HC algorithm, a structure selection strategy that performs a polynomial heuristic local search in the space of possible structures. We present an extensive empirical evaluation on synthetic and real data, showing that our algorithm outperforms significantly the current independence-based algorithms, in terms of data efficiency and quality of learned structures, with equivalent computational complexities. We also show the performance of IBMAP-HC in a real-world application of knowledge discovery: EDAs, which are evolutionary algorithms that use structure learning on each generation for modeling the distribution of populations. The experiments show that when IBMAP-HC is used to learn the structure, EDAs improve the convergence to the optimum

    Denoising Autoencoders for fast Combinatorial Black Box Optimization

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    Estimation of Distribution Algorithms (EDAs) require flexible probability models that can be efficiently learned and sampled. Autoencoders (AE) are generative stochastic networks with these desired properties. We integrate a special type of AE, the Denoising Autoencoder (DAE), into an EDA and evaluate the performance of DAE-EDA on several combinatorial optimization problems with a single objective. We asses the number of fitness evaluations as well as the required CPU times. We compare the results to the performance to the Bayesian Optimization Algorithm (BOA) and RBM-EDA, another EDA which is based on a generative neural network which has proven competitive with BOA. For the considered problem instances, DAE-EDA is considerably faster than BOA and RBM-EDA, sometimes by orders of magnitude. The number of fitness evaluations is higher than for BOA, but competitive with RBM-EDA. These results show that DAEs can be useful tools for problems with low but non-negligible fitness evaluation costs.Comment: corrected typos and small inconsistencie

    Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1

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    With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods
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