47 research outputs found
Cooperative Coevolution for Non-Separable Large-Scale Black-Box Optimization: Convergence Analyses and Distributed Accelerations
Given the ubiquity of non-separable optimization problems in real worlds, in
this paper we analyze and extend the large-scale version of the well-known
cooperative coevolution (CC), a divide-and-conquer optimization framework, on
non-separable functions. First, we reveal empirical reasons of why
decomposition-based methods are preferred or not in practice on some
non-separable large-scale problems, which have not been clearly pointed out in
many previous CC papers. Then, we formalize CC to a continuous game model via
simplification, but without losing its essential property. Different from
previous evolutionary game theory for CC, our new model provides a much simpler
but useful viewpoint to analyze its convergence, since only the pure Nash
equilibrium concept is needed and more general fitness landscapes can be
explicitly considered. Based on convergence analyses, we propose a hierarchical
decomposition strategy for better generalization, as for any decomposition
there is a risk of getting trapped into a suboptimal Nash equilibrium. Finally,
we use powerful distributed computing to accelerate it under the multi-level
learning framework, which combines the fine-tuning ability from decomposition
with the invariance property of CMA-ES. Experiments on a set of
high-dimensional functions validate both its search performance and scalability
(w.r.t. CPU cores) on a clustering computing platform with 400 CPU cores
PyPop7: A Pure-Python Library for Population-Based Black-Box Optimization
In this paper, we present a pure-Python open-source library, called PyPop7,
for black-box optimization (BBO). It provides a unified and modular interface
for more than 60 versions and variants of different black-box optimization
algorithms, particularly population-based optimizers, which can be classified
into 12 popular families: Evolution Strategies (ES), Natural Evolution
Strategies (NES), Estimation of Distribution Algorithms (EDA), Cross-Entropy
Method (CEM), Differential Evolution (DE), Particle Swarm Optimizer (PSO),
Cooperative Coevolution (CC), Simulated Annealing (SA), Genetic Algorithms
(GA), Evolutionary Programming (EP), Pattern Search (PS), and Random Search
(RS). It also provides many examples, interesting tutorials, and full-fledged
API documentations. Through this new library, we expect to provide a
well-designed platform for benchmarking of optimizers and promote their
real-world applications, especially for large-scale BBO. Its source code and
documentations are available at
https://github.com/Evolutionary-Intelligence/pypop and
https://pypop.readthedocs.io/en/latest, respectively.Comment: 5 page
Design, synthesis, and protein methyltransferase activity of a unique set of constrained amine containing compounds
Epigenetic alterations relate to various human diseases, and developing inhibitors of Kme regulatory proteins is considered to be a new frontier for drug discovery. We were inspired by the known multicyclic ligands, UNC669 and UNC926, which are the first reported small molecule ligands for a methyl-lysine binding domain. We hypothesized that reducing the conformational flexibility of the key amine moiety of UNC669 would result in a unique set of ligands. Twenty-five novel compounds containing a fused bi- or tricyclic amine or a spirocyclic amine were designed and synthesized. To gauge the potential of these amine-containing compounds to interact with Kme regulatory proteins, the compounds were screened against a panel of 24 protein methyltransferases. Compound 13 was discovered as a novel scaffold that interacts with SETD8 and could serve as a starting point for the future development of PKMT inhibitors
Syntaxin of plants71 plays essential roles in plant development and stress response via regulating pH homeostasis
SYP71, a plant-specific Qc-SNARE with multiple subcellular localization, is essential for symbiotic nitrogen fixation in nodules in Lotus, and is implicated in plant resistance to pathogenesis in rice, wheat and soybean. Arabidopsis SYP71 is proposed to participate in multiple membrane fusion steps during secretion. To date, the molecular mechanism underlying SYP71 regulation on plant development remains elusive. In this study, we clarified that AtSYP71 is essential for plant development and stress response, using techniques of cell biology, molecular biology, biochemistry, genetics, and transcriptomics. AtSYP71-knockout mutant atsyp71-1 was lethal at early development stage due to the failure of root elongation and albinism of the leaves. AtSYP71-knockdown mutants, atsyp71-2 and atsyp71-3, had short roots, delayed early development, and altered stress response. The cell wall structure and components changed significantly in atsyp71-2 due to disrupted cell wall biosynthesis and dynamics. Reactive oxygen species homeostasis and pH homeostasis were also collapsed in atsyp71-2. All these defects were likely resulted from blocked secretion pathway in the mutants. Strikingly, change of pH value significantly affected ROS homeostasis in atsyp71-2, suggesting interconnection between ROS and pH homeostasis. Furthermore, we identified AtSYP71 partners and propose that AtSYP71 forms distinct SNARE complexes to mediate multiple membrane fusion steps in secretory pathway. Our findings suggest that AtSYP71 plays an essential role in plant development and stress response via regulating pH homeostasis through secretory pathway
Osmium-mediated hexamerization of phenylacetylene
(Chemical Equation Presented) A larger oligomer: Although transition-metal-mediated reactions of alkynes to give dimers, trimers, tetramers, and polymers are well-known, reactions of alkynes to give well-defined oligomers of medium molecular weight (e.g. pentamers, hexamers) are very scarce. The selective hexamerization of HC≡CPh in the reaction with [OsCl(PCP)(PPh<sub>3</sub>)] (PCP = 2,6-(Ph<sub>2</sub>PCH<sub>2</sub>) <sub>2</sub>C<sub>6</sub>H<sub>3</sub>; see scheme) is a rare example thereof. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA