Bayesian optimization of the PC algorithm for learning Gaussian Bayesian networks

The PC algorithm is a popular method for learning the structure of Gaussian Bayesian networks. It carries out statistical tests to determine absent edges in the network. It is hence governed by two parameters: (i) The type of test, and (ii) its significance level. These parameters are usually set to values recommended by an expert. Nevertheless, such an approach can suffer from human bias, leading to suboptimal reconstruction results. In this paper we consider a more principled approach for choosing these parameters in an automatic way. For this we optimize a reconstruction score evaluated on a set of different Gaussian Bayesian networks. This objective is expensive to evaluate and lacks a closed-form expression, which means that Bayesian optimization (BO) is a natural choice. BO methods use a model to guide the search and are hence able to exploit smoothness properties of the objective surface. We show that the parameters found by a BO method outperform those found by a random search strategy and the expert recommendation. Importantly, we have found that an often overlooked statistical test provides the best over-all reconstruction results

Architectural Engineering Approach to Developing a Matrix for Planning in Extreme Environments

Extreme environments on Earth share similar facilities and operations, design and planning challenges. Each environment presents special lessons regarding housing design, crew/staff operations and training, and equipment and logistical requirements for human activities. The paper discusses these challenges and lessons. Recurrent and specific to environment and conditions events are outlined and categorized based on case studies reviews and literature summary. Understanding of relationships and influences between different facets of human society and architecture can help to find a design approach which would optimize needs and requirements for various types of people living in different environments, societies and cultures. Environmental conditions affecting architectural requirements include form developing factors, site orientation and circulation, and budget considerations. They have to be addressed at the programming design stage in order to avoid costly adjustments at later development stages. It is even more critical in case of designing for challenging environments

Lengthscales and Cooperativity in DNA Bubble Formation

It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in specific regions with lengths which at physiological temperatures are of the order of (but not equal to) the size of the bubble. The analysis is based on the Peyrard- Bishop-Dauxois model, whose equilibrium statistical properties have been accurately calculated here with a transfer integral approach

Structurally specific thermal fluctuations identify functional sites for DNA transcription

We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that the most probable opening occurs at the transcription start site. Minor openings appear to be related to other regulatory sites. Our results suggest that coherent thermal fluctuations play an important role in the initiation of transcription. Essential elements of the dynamics, in addition to sequence specificity, are nonlinearity and entropy, provided by local base-pair constraints

Gender-related differences in the formation of skatole metabolites by specific CYP450 in porcine hepatic S9 fractions

Higher accumulation of skatole in the fat of male pigs compared with female pigs might be due to gender-related differences in the rate of skatole degradation. In the present study, skatole metabolites and cytochrome P450 (CYP450) isoforms involved in skatole metabolism were for the first time investigated in hepatic S9 fractions from six male and four female pigs (crossbred Landrace× Yorkshire dams and Duroc boar). Surprisingly, the rates of production of major skatole metabolites were similar in male and female pigs. The most abundant metabolite of skatole was 3-hydroxy-3-methyloxindole (HMOI) followed by 3-methyloxindole and indole-3-carbinol in both male and female S9 fractions. Concentrations of formed HMOI and 3-methyloxindole did not differ between the genders (P = 0.124 for HMOI, and P = 0.575 for 3-methyloxindole). Indole-3-carbinol formation was higher in S9 fractions from the females compared with male pigs (P = 0.0001). Enzyme kinetic parameters were similar for both genders (P> 0.05). In both male and female pigs, ellipticine, diallyl sulphide (DAS) and quercetin inhibited HMOI formation, confirming the involvement of CYP1A1 and CYP2E1. The formation of 3-methyloxindole was reduced in the presence of the CYP2E1 inhibitor DAS, and formation of indole-3-carbinol was reduced in the presence of CYP1A1 and CYP2A19 inhibitors. We found only minor differences in skatole metabolism between male and female pigs, particularly the involvement of CYP2C and CYP3A in indole-3-carbinol formation in female but not in male pigs. This is a very essential finding, suggesting the involvement of larger number of CYP450 isoforms in female pigs. On the other hand, indole-3-carbinol is a minor skatole metabolite, and the physiological significance of CYP2C and CYP3A involvement in its formation in female pigs, but not in male pigs, needs to be elucidated. Our results, however, should be interpreted with caution because of the low number of animals and possibility of breed and age effects on skatole metabolism.info:eu-repo/semantics/publishedVersio

Khovanov homology is an unknot-detector

We prove that a knot is the unknot if and only if its reduced Khovanov cohomology has rank 1. The proof has two steps. We show first that there is a spectral sequence beginning with the reduced Khovanov cohomology and abutting to a knot homology defined using singular instantons. We then show that the latter homology is isomorphic to the instanton Floer homology of the sutured knot complement: an invariant that is already known to detect the unknot.Comment: 124 pages, 13 figure

Superconductivity-enhanced bias spectroscopy in carbon nanotube quantum dots

We study low-temperature transport through carbon nanotube quantum dots in the Coulomb blockade regime coupled to niobium-based superconducting leads. We observe pronounced conductance peaks at finite source-drain bias, which we ascribe to elastic and inelastic cotunneling processes enhanced by the coherence peaks in the density of states of the superconducting leads. The inelastic cotunneling lines display a marked dependence on the applied gate voltage which we relate to different tunneling-renormalizations of the two subbands in the nanotube. Finally, we discuss the origin of an especially pronounced sub-gap structure observed in every fourth Coulomb diamond