Good Concatenated Code Ensembles for the Binary Erasure Channel

In this work, we give good concatenated code ensembles for the binary erasure channel (BEC). In particular, we consider repeat multiple-accumulate (RMA) code ensembles formed by the serial concatenation of a repetition code with multiple accumulators, and the hybrid concatenated code (HCC) ensembles recently introduced by Koller et al. (5th Int. Symp. on Turbo Codes & Rel. Topics, Lausanne, Switzerland) consisting of an outer multiple parallel concatenated code serially concatenated with an inner accumulator. We introduce stopping sets for iterative constituent code oriented decoding using maximum a posteriori erasure correction in the constituent codes. We then analyze the asymptotic stopping set distribution for RMA and HCC ensembles and show that their stopping distance hmin, defined as the size of the smallest nonempty stopping set, asymptotically grows linearly with the block length. Thus, these code ensembles are good for the BEC. It is shown that for RMA code ensembles, contrary to the asymptotic minimum distance dmin, whose growth rate coefficient increases with the number of accumulate codes, the hmin growth rate coefficient diminishes with the number of accumulators. We also consider random puncturing of RMA code ensembles and show that for sufficiently high code rates, the asymptotic hmin does not grow linearly with the block length, contrary to the asymptotic dmin, whose growth rate coefficient approaches the Gilbert-Varshamov bound as the rate increases. Finally, we give iterative decoding thresholds for the different code ensembles to compare the convergence properties.Comment: To appear in IEEE Journal on Selected Areas in Communications, special issue on Capacity Approaching Code

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking

Investigating the relation between the structure and behavior of complex biological networks often involves posing the following two questions: Is a hypothesized structure of a regulatory network consistent with the observed behavior? And can a proposed structure generate a desired behavior? Answering these questions presupposes that we are able to test the compatibility of network structure and behavior. We cast these questions into a parameter search problem for qualitative models of regulatory networks, in particular piecewise-affine differential equation models. We develop a method based on symbolic model checking that avoids enumerating all possible parametrizations, and show that this method performs well on real biological problems, using the IRMA synthetic network and benchmark experimental data sets. We test the consistency between the IRMA network structure and the time-series data, and search for parameter modifications that would improve the robustness of the external control of the system behavior

Generic algorithms for halting problem and optimal machines revisited

The halting problem is undecidable --- but can it be solved for "most" inputs? This natural question was considered in a number of papers, in different settings. We revisit their results and show that most of them can be easily proven in a natural framework of optimal machines (considered in algorithmic information theory) using the notion of Kolmogorov complexity. We also consider some related questions about this framework and about asymptotic properties of the halting problem. In particular, we show that the fraction of terminating programs cannot have a limit, and all limit points are Martin-L\"of random reals. We then consider mass problems of finding an approximate solution of halting problem and probabilistic algorithms for them, proving both positive and negative results. We consider the fraction of terminating programs that require a long time for termination, and describe this fraction using the busy beaver function. We also consider approximate versions of separation problems, and revisit Schnorr's results about optimal numberings showing how they can be generalized.Comment: a preliminary version was presented at the ICALP 2015 conferenc