Spatially-constrained clustering of ecological networks

Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g., populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar biological entities are firstly identified and the spatial information is used afterwards to improve the ecological interpretation. We develop an integrative approach to retrieve groups of nodes that are geographically close and ecologically similar. Our model-based spatially-constrained method embeds the geographical information within a regularization framework by adding some constraints to the maximum likelihood estimation of parameters. A simulation study and the analysis of real data demonstrate that our approach is able to detect complex spatial patterns that are ecologically meaningful. The model-based framework allows us to consider external information (e.g., geographic proximities, covariates) in the analysis of ecological networks and appears to be an appealing alternative to consider such data

Analysis and optimisation of the tuning of the twelfths for a clarinet resonator

Even if the tuning between the first and second register of a clarinet has been optimized by instrument makers, the lowest twelfths remain slightly too large (inharmonicity). In this article, we study the problem from two different points of view. First, we systematically review various physical reasons why this inharmonicity may take place, and the effect of different bore perturbations inserted in cylindrical instruments. Applications to a real clarinet resonator and comparisons with impedance measurements are then presented. A commonly accepted idea is that the register hole is the dominant cause for this inharmonicity: it is natural to expect that opening this hole will raise the resonance frequencies of the instrument, except for the note for which the hole is at the pressure node. We show that the real situation is actually more complicated because other effects, such as open holes or bore taper and bell, introduce resonance shifts that are comparable but with opposite sign, so that a relatively good overall compensation takes place. The origin of the observed inharmonicity in playing frequencies is therefore different. In a second part, we use an elementary model of the clarinet in order to isolate the effect of the register hole: a perfect cylindrical tube without closed holes. Optimization techniques are then used to calculate an optimum location for the register hole; the result turns out to be close to the location chosen by clarinet makers. Finally, attempts are made numerically to improve the situation by introducing small perturbations in the higher part of the cylindrical resonator, but no satisfactory improvement is obtained.Comment: 28 June 2004 (submitted to Applied Acoustics

Strategies for online inference of model-based clustering in large and growing networks

In this paper we adapt online estimation strategies to perform model-based clustering on large networks. Our work focuses on two algorithms, the first based on the SAEM algorithm, and the second on variational methods. These two strategies are compared with existing approaches on simulated and real data. We use the method to decipher the connexion structure of the political websphere during the US political campaign in 2008. We show that our online EM-based algorithms offer a good trade-off between precision and speed, when estimating parameters for mixture distributions in the context of random graphs.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS359 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A Comparative Study of Sparse Associative Memories

We study various models of associative memories with sparse information, i.e. a pattern to be stored is a random string of $0$s and $1$s with about $\log N$ $1$s, only. We compare different synaptic weights, architectures and retrieval mechanisms to shed light on the influence of the various parameters on the storage capacity.Comment: 28 pages, 2 figure

Influence of various redox conditions on the degradation of microalgal triacylglycerols and fatty acids in marine sediments

Sediment cakes, supplemented with microalgal cells (Nannochloropsis salina), were incubated for 35 days under permanently oxic, oscillating (5d:5d changeover oxic/anoxic) and strictly anoxic conditions of oxygenation in diffusively ‘‘open’’ sedimentary systems. Total lipids (TLip) and triacylglycerols (TG) concentrations were monitored by thin layer chromatography-flame ionisation detection, whereas the concentrations of the main extractable (free+ester-bound) individual fatty acids (C16:0, C16:1, C18:1) were followed using gas chromatography-mass spectrometry. Under the three conditions of oxygenation, TOC, TLip and TG showed a sharp decrease in concentration during the early days of incubation and seemed to stabilise thereafter, defining an apparent non degradable fraction (GNR). The GNR content was systematically higher in the anoxic incubation than under the oxic and oscillating conditions. The ratio of the main hydrolysis products of TG versus TG [(Free fatty acids+Monoacylglycerols+1,2-Diacylglycerols)/TG], used as an indicator of the hydrolysis of TG, showed that the presence of oxygen in the sediments (oxic and oscillating conditions) stimulates the hydrolysis of TG and the subsequent degradation of their metabolites. Unlike TOC, TLip and TG, individual fatty acids (FA) showed a continuous concentration decrease until the end of the experiment, which was fitted with a simple first order model [G(t)=G0e_kt] to yield apparent degradation rate constants. The values observed under oscillating conditions (kFA=0.019 +/- 0.001 d_1) were intermediate to those observed during oxic (kFA=0.029 +/- 0.003 d_1) and anoxic (kFA=0.011 +/- 0.001 d_1) incubations, and no significant difference between individual FA could be observed. The production of saturated and monounsaturated C16 (and to a lesser extent C18) alkanols under oscillating and anoxic redox conditions suggested that (a part of) the dominant FA were reduced to the corresponding alcohols under anoxic conditions, following their release from acylglycerols