Description of GADEL

This article describes the first implementation of the GADEL system : a Genetic Algorithm for Default Logic. The goal of GADEL is to compute extensions in Reiter's default logic. It accepts every kind of finite propositional default theories and is based on evolutionary principles of Genetic Algorithms. Its first experimental results on certain instances of the problem show that this new approach of the problem can be successful.Comment: System Descriptions and Demonstrations at Nonmonotonic Reasoning Workshop, 2000 6 pages, 2 figures, 5 table

Error Correcting Coding for a Non-symmetric Ternary Channel

Ternary channels can be used to model the behavior of some memory devices, where information is stored in three different levels. In this paper, error correcting coding for a ternary channel where some of the error transitions are not allowed, is considered. The resulting channel is non-symmetric, therefore classical linear codes are not optimal for this channel. We define the maximum-likelihood (ML) decoding rule for ternary codes over this channel and show that it is complex to compute, since it depends on the channel error probability. A simpler alternative decoding rule which depends only on code properties, called \da-decoding, is then proposed. It is shown that \da-decoding and ML decoding are equivalent, i.e., \da-decoding is optimal, under certain conditions. Assuming \da-decoding, we characterize the error correcting capabilities of ternary codes over the non-symmetric ternary channel. We also derive an upper bound and a constructive lower bound on the size of codes, given the code length and the minimum distance. The results arising from the constructive lower bound are then compared, for short sizes, to optimal codes (in terms of code size) found by a clique-based search. It is shown that the proposed construction method gives good codes, and that in some cases the codes are optimal.Comment: Submitted to IEEE Transactions on Information Theory. Part of this work was presented at the Information Theory and Applications Workshop 200

Using Short Synchronous WOM Codes to Make WOM Codes Decodable

In the framework of write-once memory (WOM) codes, it is important to distinguish between codes that can be decoded directly and those that require that the decoder knows the current generation to successfully decode the state of the memory. A widely used approach to construct WOM codes is to design first nondecodable codes that approach the boundaries of the capacity region, and then make them decodable by appending additional cells that store the current generation, at an expense of a rate loss. In this paper, we propose an alternative method to make nondecodable WOM codes decodable by appending cells that also store some additional data. The key idea is to append to the original (nondecodable) code a short synchronous WOM code and write generations of the original code and of the synchronous code simultaneously. We consider both the binary and the nonbinary case. Furthermore, we propose a construction of synchronous WOM codes, which are then used to make nondecodable codes decodable. For short-to-moderate block lengths, the proposed method significantly reduces the rate loss as compared to the standard method.Comment: To appear in IEEE Transactions on Communications. The material in this paper was presented in part at the 2012 IEEE International Symposium on Information Theory, Cambridge, MA, July 201

Detection boundary in sparse regression

We study the problem of detection of a p-dimensional sparse vector of parameters in the linear regression model with Gaussian noise. We establish the detection boundary, i.e., the necessary and sufficient conditions for the possibility of successful detection as both the sample size n and the dimension p tend to the infinity. Testing procedures that achieve this boundary are also exhibited. Our results encompass the high-dimensional setting (p>> n). The main message is that, under some conditions, the detection boundary phenomenon that has been proved for the Gaussian sequence model, extends to high-dimensional linear regression. Finally, we establish the detection boundaries when the variance of the noise is unknown. Interestingly, the detection boundaries sometimes depend on the knowledge of the variance in a high-dimensional setting

Further Criteria for the Existence of Steady Line-Driven Winds

In Paper I, we showed that steady line-driven disk wind solutions can exist by using "simple" models that mimic the disk environment. Here I extend the concepts introduced in Paper I and discuss many details of the analysis of the steady/unsteady nature of 1D line-driven winds. This work confirms the results and conclusions of Paper I, and is thus consistent with the steady nature of the 1D streamline line-driven disk wind models of Murray and collaborators and the 2.5D line-driven disk wind models of Pereyra and collaborators. When including gas pressures effects, as is routinely done in time-dependent numerical models, I find that the spatial dependence of the nozzle function continues to play a key role in determining the steady/unsteady nature of supersonic line-driven wind solutions. I show here that the existence/nonexistence of local wind solutions can be proved through the nozzle function without integrating the equation of motion. This work sets a detailed framework with which we will analyze, in a following paper, more realistic models than the "simple" models of Paper I.Comment: 30 pages, 5 figures, accepted for publication by The Astrophysical Journa

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII

Activation of CaMKII by calmodulin and the subsequent maintenance of constitutive activity through autophosphorylation at threonine residue 286 (Thr286) are thought to play a major role in synaptic plasticity. One of the effects of autophosphorylation at Thr286 is to increase the apparent affinity of CaMKII for calmodulin, a phenomenon known as “calmodulin trapping”. It has previously been suggested that two binding sites for calmodulin exist on CaMKII, with high and low affinities, respectively. We built structural models of calmodulin bound to both of these sites. Molecular dynamics simulation showed that while binding of calmodulin to the supposed low-affinity binding site on CaMKII is compatible with closing (and hence, inactivation) of the kinase, and could even favour it, binding to the high-affinity site is not. Stochastic simulations of a biochemical model showed that the existence of two such binding sites, one of them accessible only in the active, open conformation, would be sufficient to explain calmodulin trapping by CaMKII. We can explain the effect of CaMKII autophosphorylation at Thr286 on calmodulin trapping: It stabilises the active state and therefore makes the high-affinity binding site accessible. Crucially, a model with only one binding site where calmodulin binding and CaMKII inactivation are strictly mutually exclusive cannot reproduce calmodulin trapping. One of the predictions of our study is that calmodulin binding in itself is not sufficient for CaMKII activation, although high-affinity binding of calmodulin is