ZOOpt: Toolbox for Derivative-Free Optimization

Recent advances of derivative-free optimization allow efficient approximating the global optimal solutions of sophisticated functions, such as functions with many local optima, non-differentiable and non-continuous functions. This article describes the ZOOpt (https://github.com/eyounx/ZOOpt) toolbox that provides efficient derivative-free solvers and are designed easy to use. ZOOpt provides a Python package for single-thread optimization, and a light-weighted distributed version with the help of the Julia language for Python described functions. ZOOpt toolbox particularly focuses on optimization problems in machine learning, addressing high-dimensional, noisy, and large-scale problems. The toolbox is being maintained toward ready-to-use tool in real-world machine learning tasks

High functional coherence in k-partite protein cliques of protein interaction networks

We introduce a new topological concept called k-partite protein cliques to study protein interaction (PPI) networks. In particular, we examine functional coherence of proteins in k-partite protein cliques. A k-partite protein clique is a k-partite maximal clique comprising two or more nonoverlapping protein subsets between any two of which full interactions are exhibited. In the detection of PPI&rsquo;s k-partite maximal cliques, we propose to transform PPI networks into induced K-partite graphs with proteins as vertices where edges only exist among the graph&rsquo;s partites. Then, we present a k-partite maximal clique mining (MaCMik) algorithm to enumerate k-partite maximal cliques from K-partite graphs. Our MaCMik algorithm is applied to a yeast PPI network. We observe that there does exist interesting and unusually high functional coherence in k-partite protein cliques&mdash;most proteins in k-partite protein cliques, especially those in the same partites, share the same functions. Therefore, the idea of k-partite protein cliques suggests a novel approach to characterizing PPI networks, and may help function prediction for unknown proteins.<br /

Association of the Resistin Gene Promoter Region Polymorphism with Kawasaki Disease in Chinese Children

Objectives. The −420 C > G polymorphism located in the resistin gene (RETN) promoter has recently been suggested to play a potential role in proinflammatory conditions and cardiovascular disease. This study investigated the association of the RETN promoter polymorphism with Kawasaki disease (KD) and its clinical parameters in Chinese children. Methods. We compared patients with complete KD to incomplete KD children. Genotyping of the RETN promoter polymorphism was performed using MassARRAY system, and serum resistin levels were estimated using the sandwich enzyme immunoassay method. Results. There was no significant difference in RETN (−420 C > G) genotypes between KD and control groups. However, the frequency of the G allele was higher in iKD patients than in cKD children due to a significantly increased frequency of the GG genotypes. Serum levels of resistin were significantly higher in KD patients than in controls regardless of the presence of coronary artery lesions (CALs). Conclusion. The present findings suggest that while resistin may play a role in the pathogenesis of KD, there is no apparent association between CAL and the RETN (−420 C > G) gene polymorphism in KD children. However, the diagnosis of iKD is challenging but can be supported by the presence of the G allele and the GG genotypes

Sub-MHz spectral dip in a resonator-free twisted gain medium

Ultra-narrow optical spectral features resulting from highly dispersive light-matter interactions are essential for a broad range of applications such as spectroscopy, slow-light, and high-precision sensing. Features approaching sub-MHz, or equivalently, Q-factors approaching ~1 billion and beyond, are challenging to obtain in solid-state systems, ultimately limited by loss. We present a novel approach to achieve tunable sub-MHz spectral features, at room temperature, without resonators. We exploit gain-enhanced polarization pulling in a twisted birefringent medium where polarization eigenmodes are frequency-dependent. Using Brillouin gain in a commercial spun fiber, we experimentally achieve a 0.72 MHz spectral dip, the narrowest backward Brillouin scattering feature ever reported. Further optimization can potentially reduce the linewidth to <0.1 MHz. Our approach is simple and broadly applicable, offering on-demand tunability and high sensitivity, with a wide range of applications such as microwave photonic filters, slow and fast light, and optical sensing.Comment: 19 pages, 6 figures, Journal articl