27,498 research outputs found
Genetic algorithms with DNN-based trainable crossover as an example of partial specialization of general search
Universal induction relies on some general search procedure that is doomed to
be inefficient. One possibility to achieve both generality and efficiency is to
specialize this procedure w.r.t. any given narrow task. However, complete
specialization that implies direct mapping from the task parameters to
solutions (discriminative models) without search is not always possible. In
this paper, partial specialization of general search is considered in the form
of genetic algorithms (GAs) with a specialized crossover operator. We perform a
feasibility study of this idea implementing such an operator in the form of a
deep feedforward neural network. GAs with trainable crossover operators are
compared with the result of complete specialization, which is also represented
as a deep neural network. Experimental results show that specialized GAs can be
more efficient than both general GAs and discriminative models.Comment: AGI 2017 procedding, The final publication is available at
link.springer.co
Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum.
The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In fivefold cross-validation, prediction accuracies ranged from 0.46 (PBN) to 0.49 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.75 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4-52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits
Efficient Benchmarking of Algorithm Configuration Procedures via Model-Based Surrogates
The optimization of algorithm (hyper-)parameters is crucial for achieving
peak performance across a wide range of domains, ranging from deep neural
networks to solvers for hard combinatorial problems. The resulting algorithm
configuration (AC) problem has attracted much attention from the machine
learning community. However, the proper evaluation of new AC procedures is
hindered by two key hurdles. First, AC benchmarks are hard to set up. Second
and even more significantly, they are computationally expensive: a single run
of an AC procedure involves many costly runs of the target algorithm whose
performance is to be optimized in a given AC benchmark scenario. One common
workaround is to optimize cheap-to-evaluate artificial benchmark functions
(e.g., Branin) instead of actual algorithms; however, these have different
properties than realistic AC problems. Here, we propose an alternative
benchmarking approach that is similarly cheap to evaluate but much closer to
the original AC problem: replacing expensive benchmarks by surrogate benchmarks
constructed from AC benchmarks. These surrogate benchmarks approximate the
response surface corresponding to true target algorithm performance using a
regression model, and the original and surrogate benchmark share the same
(hyper-)parameter space. In our experiments, we construct and evaluate
surrogate benchmarks for hyperparameter optimization as well as for AC problems
that involve performance optimization of solvers for hard combinatorial
problems, drawing training data from the runs of existing AC procedures. We
show that our surrogate benchmarks capture overall important characteristics of
the AC scenarios, such as high- and low-performing regions, from which they
were derived, while being much easier to use and orders of magnitude cheaper to
evaluate
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