Exact Learning Augmented Naive Bayes Classifier

Earlier studies have shown that classification accuracies of Bayesian networks (BNs) obtained by maximizing the conditional log likelihood (CLL) of a class variable, given the feature variables, were higher than those obtained by maximizing the marginal likelihood (ML). However, differences between the performances of the two scores in the earlier studies may be attributed to the fact that they used approximate learning algorithms, not exact ones. This paper compares the classification accuracies of BNs with approximate learning using CLL to those with exact learning using ML. The results demonstrate that the classification accuracies of BNs obtained by maximizing the ML are higher than those obtained by maximizing the CLL for large data. However, the results also demonstrate that the classification accuracies of exact learning BNs using the ML are much worse than those of other methods when the sample size is small and the class variable has numerous parents. To resolve the problem, we propose an exact learning augmented naive Bayes classifier (ANB), which ensures a class variable with no parents. The proposed method is guaranteed to asymptotically estimate the identical class posterior to that of the exactly learned BN. Comparison experiments demonstrated the superior performance of the proposed method.Comment: 29 page

Vector–axial-vector mixing from a chiral effective field theory at finite temperature

We study the vector–axial-vector mixing in a hot medium and its evolution toward the chiral phase transition using different symmetry restoration scenarios based on the generalized hidden local symmetry framework. We show that the presence of the a_1 meson reduces the vector spectral function around the p meson mass and enhances it around the a_1 meson mass. The coupling strength of a_1 to p and πvanishes at the critical temperature due to the degenerate p-a_1 masses. This feature holds rigorously in the chiral limit and still stays intact to good approximation for the physical pion mass.journal articl

Exact Learning Augmented Naive Bayes Classifier

Earlier studies have shown that classification accuracies of Bayesian networks (BNs) obtained by maximizing the conditional log likelihood (CLL) of a class variable, given the feature variables, were higher than those obtained by maximizing the marginal likelihood (ML). However, differences between the performances of the two scores in the earlier studies may be attributed to the fact that they used approximate learning algorithms, not exact ones. This paper compares the classification accuracies of BNs with approximate learning using CLL to those with exact learning using ML. The results demonstrate that the classification accuracies of BNs obtained by maximizing the ML are higher than those obtained by maximizing the CLL for large data. However, the results also demonstrate that the classification accuracies of exact learning BNs using the ML are much worse than those of other methods when the sample size is small and the class variable has numerous parents. To resolve the problem, we propose an exact learning augmented naive Bayes classifier (ANB), which ensures a class variable with no parents. The proposed method is guaranteed to asymptotically estimate the identical class posterior to that of the exactly learned BN. Comparison experiments demonstrated the superior performance of the proposed method.journal articl

InN/InGaN系結晶の基礎物性解明および結晶成長のための基板探索

textapplication/pdfdepartmental bulletin pape

Observation of B+→ΛΛ̅K+

journal articl

藤沢市大庭城山地区保全のための植物社会学的研究

application/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfboo

Structural formulas and MS/MS fragmentation of AHLs.

(A) Structural formulas of AHLs produced by P. aurantiaca PB-St2. (B) Fragmentation of AHLs into the [M+H]+ ion of the lactone moiety in the collision cell.</p

AGOS: A Plug-and-Play Method for the Assembly of Artificial Gene Operons into Functional Biosynthetic Gene Clusters

The generation of novel secondary metabolites by reengineering or refactoring biochemical pathways is a rewarding but also challenging goal of synthetic biology. For this, the development of tools for the reconstruction of secondary metabolite gene clusters as well as the challenge of understanding the obstacles in this process is of great interest. The artificial gene operon assembly system (AGOS) is a plug-and-play method developed as a tool to consecutively assemble artificial gene operons into a destination vector and subsequently express them under the control of a de-repressed promoter in a <i>Streptomyces</i> host strain. AGOS was designed as a set of entry plasmids for the construction of artificial gene operons and a SuperCos1 based destination vector, into which the constructed operons can be assembled by Red/ET-mediated recombination. To provide a proof-of-concept of this method, we disassembled the well-known novobiocin biosynthetic gene cluster into four gene operons, encoding for the different moieties of novobiocin. We then genetically reorganized these gene operons with the help of AGOS to finally obtain the complete novobiocin gene cluster again. The production of novobiocin precursors and of novobiocin could successfully be detected by LC–MS and LC–MS/MS. Furthermore, we demonstrated that the omission of terminator sequences only had a minor impact on product formation in our system

Identification of Novel α‑Pyrones from <i>Conexibacter woesei</i> Serving as Sulfate Shuttles

Pyrones comprise a structurally diverse class of compounds. Although they are widespread in nature, their specific physiological functions remain unknown in most cases. We recently described that triketide pyrones mediate the sulfotransfer in caprazamycin biosynthesis. Herein, we report the identification of conexipyrones A–C, three previously unrecognized tetra-substituted α-pyrones, from the soil actinobacterium Conexibacter woesei. Insights into their biosynthesis via a type III polyketide synthase were obtained by feeding studies using isotope-enriched precursors. In vitro assays employing the genetically associated 3′-phosphoadenosine-5′-phosphosulfate (PAPS)-dependent sulfotransferase CwoeST revealed conexipyrones as the enzymes’ genuine sulfate acceptor substrates. Furthermore, conexipyrones were determined to function as sulfate shuttles in a two-enzyme assay, because their sulfated derivatives were accepted as donor molecules by the PAPS-independent arylsulfate sulfotransferase (ASST) Cpz4 to yield sulfated caprazamycin intermediates

Production of AHLs in PB-St2; quantified using LC-MS/MS precursor ion scans and calibration curves.

<p>(A) 3-OH-C6-HSL (red, quantification was possible between 5 and 42 h) and 3-oxo-C6-HSL (blue, quantification was possible between 5 and 42 h). (B) C4-HSL (black, quantification was possible between 5 and 42 h), C6-HSL (pink, quantification was possible between 9 and 42 h), and 3-OH-C8-HSL (green, quantification was possible between 11 and 42 h). (C) C8-HSL (purple, quantification was possible between 11 and 42 h), 3-oxo-C8-HSL (cyan, quantification was possible between 9 and 27 h), and 3-OH-C10-HSL (orange, quantification was possible between 11 and 42 h). Data represent means with corresponding standard deviation of three independent replicates. When the amount was lower than the limit of quantification (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167002#pone.0167002.s010" target="_blank">S2 Table</a>) the production was considered as zero.</p