11,373 research outputs found
Essential guidelines for computational method benchmarking
In computational biology and other sciences, researchers are frequently faced
with a choice between several computational methods for performing data
analyses. Benchmarking studies aim to rigorously compare the performance of
different methods using well-characterized benchmark datasets, to determine the
strengths of each method or to provide recommendations regarding suitable
choices of methods for an analysis. However, benchmarking studies must be
carefully designed and implemented to provide accurate, unbiased, and
informative results. Here, we summarize key practical guidelines and
recommendations for performing high-quality benchmarking analyses, based on our
experiences in computational biology.Comment: Minor update
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
‘The Action of the Brain’. Machine Models and Adaptive Functions in Turing and Ashby
Given the personal acquaintance between Alan M. Turing and W. Ross Ashby and the partial proximity of their research fields, a comparative view of Turing’s and Ashby’s work on modelling “the action of the brain” (letter from Turing to Ashby, 1946) will help to shed light on the seemingly strict symbolic/embodied dichotomy: While it is clear that Turing was committed to formal, computational and Ashby to material, analogue methods of modelling, there is no straightforward mapping of these approaches onto symbol-based AI and embodiment-centered views respectively. Instead, it will be demonstrated that both approaches, starting from a formal core, were at least partly concerned with biological and embodied phenomena, albeit in revealingly distinct ways
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