We develop and analyze low-complexity cooperative diversity protocols that combat fading induced by multipath propagation in wireless networks. The underlying techniques exploit space diversity available through cooperating terminals' relaying signals for one another. We outline several strategies employed by the cooperating radios, including fixed relaying schemes such as amplify-and-forward and decode-and-forward, selection relaying schemes that adapt based upon channel measurements between the cooperating terminals, and incremental relaying schemes that adapt based upon limited feedback from the destination terminal. We develop performance characterizations in terms of outage events and associated outage probabilities, which measure robustness of the transmissions to fading, focusing on the high signal-to-noise ratio (SNR) regime. Except for fixed decode-and-forward, all of our cooperative diversity protocols are efficient in the sense that they achieve full diversity (i.e., second-order diversity in the case of two terminals), and, moreover, are close to optimum (within 1.5 dB) in certain regimes. Thus, using distributed antennas, we can provide the powerful benefits of space diversity without need for physical arrays, though at a loss of spectral efficiency due to half-duplex operation and possibly at the cost of additional receive hardware. Applicable to any wireless setting, including cellular or ad hoc networks-wherever space constraints preclude the use of physical arrays-the performance characterizations reveal that large power or energy savings result from the use of these protocols.

Cooperative diversity in wireless networks: Efficient protocols and outage behavior

Cognitive radio is viewed as a novel approach for improving the utilization of a precious natural resource: the radio electromagnetic spectrum. The cognitive radio, built on a software-defined radio, is defined as an intelligent wireless communication system that is aware of its environment and uses the methodology of understanding-by-building to learn from the environment and adapt to statistical variations in the input stimuli, with two primary objectives in mind: /spl middot/ highly reliable communication whenever and wherever needed; /spl middot/ efficient utilization of the radio spectrum. Following the discussion of interference temperature as a new metric for the quantification and management of interference, the paper addresses three fundamental cognitive tasks. 1) Radio-scene analysis. 2) Channel-state estimation and predictive modeling. 3) Transmit-power control and dynamic spectrum management. This work also discusses the emergent behavior of cognitive radio.

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Cognitive radio: brain-empowered wireless communications

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Wireless Communications

We show that the diversity-multiplexing tradeoff of a half-duplex single-relay channel with identically distributed Rayleigh fading channel gains meets the 2 by 1 MISO bound. We generalize the result to the case when there are N non-interfering relays and show that the diversity-multiplexing tradeoff is equal to the N + 1 by 1 MISO bound.

Diversity-multiplexing tradeoff of the half-duplex relay channel

De novo assembly of short RNA-Seq reads into transcripts is challenging due to sequence similarities in transcriptomes arising from gene duplications and alternative splicing of transcripts. We present Shannon, an RNA-Seq assembler with an optimality guarantee derived from principles of information theory: Shannon reconstructs nearly all information-theoretically reconstructable transcripts. Shannon is based on a theory we develop for de novo RNA-Seq assembly that reveals differing abundances among transcripts to be the key, rather than the barrier, to effective assembly. The assembly problem is formulated as a sparsest-flow problem on a transcript graph, and the heart of Shannon is a novel iterative flow-decomposition algorithm. This algorithm provably solves the information-theoretically reconstructable instances in linear-time even though the general sparsest-flow problem is NP-hard. Shannon also incorporates several additional new algorithmic advances: a new error-correction algorithm based on successive cancelation, a multi-bridging algorithm that carefully utilizes read information in the k-mer de Bruijn graph, and an approximate graph partitioning algorithm to split the transcriptome de Bruijn graph into smaller components. In tests on large RNA-Seq datasets, Shannon obtains significant increases in sensitivity along with improvements in specificity in comparison to state-of-the-art assemblers.

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Shannon: An Information-Optimal de Novo RNA-Seq Assembler

We consider two-way interference channels (ICs) where forward and backward channels are ICs but not necessarily the same. We first consider a scenario where there are only two forward messages and feedback is offered through the backward IC for aiding forward-message transmission. For a linear deterministic model of this channel, we develop inner and outer bounds that match for a wide range of channel parameters. We find that the backward IC can be more efficiently used for feedback rather than if it were used for independent backward-message transmission. As a consequence, we show that feedback can provide a net increase in capacity even if feedback cost is taken into consideration. Moreover we extend this to a more general scenario with two additional independent backward messages, from which we find that interaction can provide an arbitrarily large gain in capacity.

Two-way interference channels

In this paper we characterize, in the context of vector space precoding strategies, the degrees of freedom of the parallel three-user interference channel as a function of the channel diversity L. A channel diversity of L is modeled by L independently fading real-valued parallel channels. Our results also apply to the case of parallel complex-valued channels, where the channel matrices H ij ∊ Cl×l are still diagonal but have complex entries. Here L = 2l is twice the number of parallel channels, and the resulting formulas (as a function of L) for the degrees of freedom are the same as in the real-valued case.

3 User interference channel: Degrees of freedom as a function of channel diversity

We characterize the sum capacity of the multiple transmit antenna Gaussian broadcast channel by showing that the existing inner bound of Marton (1979) and the existing upper bound of Sato (1978) are tight for this channel.

David Tse

Papers

Diversity-multiplexing tradeoff of the half-duplex relay channel

Shannon: An Information-Optimal de Novo RNA-Seq Assembler

Two-way interference channels

3 User interference channel: Degrees of freedom as a function of channel diversity

Sum capacity of the multiple antenna Gaussian broadcast channel