Relay Selection with Network Coding in Two-Way Relay Channels

In this paper, we consider the design of joint network coding (NC)and relay selection (RS) in two-way relay channels. In the proposed schemes, two users first sequentially broadcast their respective information to all the relays. We propose two RS schemes, a single relay selection with NC and a dual relay selection with NC. For both schemes, the selected relay(s) perform NC on the received signals sent from the two users and forward them to both users. The proposed schemes are analyzed and the exact bit error rate (BER) expressions are derived and verified through Monte Carlo simulations. It is shown that the dual relay selection with NC outperforms other considered relay selection schemes in two-way relay channels. The results also reveal that the proposed NC relay selection schemes provide a selection gain compared to a NC scheme with no relay selection, and a network coding gain relative to a conventional relay selection scheme with no NC.Comment: 11 pages, 5 figure

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets

Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate identification of lncRNAs in RNA-seq datasets is crucial for exploring their characteristic functions in the genome as most coding potential computation (CPC) tools fail to accurately identify them in transcriptomic data. Well-known CPC tools such as CPC2, lncScore, CPAT are primarily designed for prediction of lncRNAs based on the GENCODE, NONCODE and CANTATAdb databases. The prediction accuracy of these tools often drops when tested on transcriptomic datasets. This leads to higher false positive results and inaccuracy in the function annotation process. In this study, we present a novel tool, PLIT, for the identification of lncRNAs in plants RNA-seq datasets. PLIT implements a feature selection method based on L1 regularization and iterative Random Forests (iRF) classification for selection of optimal features. Based on sequence and codon-bias features, it classifies the RNA-seq derived FASTA sequences into coding or long non-coding transcripts. Using L1 regularization, 31 optimal features were obtained based on lncRNA and protein-coding transcripts from 8 plant species. The performance of the tool was evaluated on 7 plant RNA-seq datasets using 10-fold cross-validation. The analysis exhibited superior accuracy when evaluated against currently available state-of-the-art CPC tools

Coding of details in very low bit-rate video systems

In this paper, the importance of including small image features at the initial levels of a progressive second generation video coding scheme is presented. It is shown that a number of meaningful small features called details should be coded, even at very low data bit-rates, in order to match their perceptual significance to the human visual system. We propose a method for extracting, perceptually selecting and coding of visual details in a video sequence using morphological techniques. Its application in the framework of a multiresolution segmentation-based coding algorithm yields better results than pure segmentation techniques at higher compression ratios, if the selection step fits some main subjective requirements. Details are extracted and coded separately from the region structure and included in the reconstructed images in a later stage. The bet of considering the local background of a given detail for its perceptual selection breaks the concept ofPeer ReviewedPostprint (published version

Source coding by efficient selection of ground states clusters

In this letter, we show how the Survey Propagation algorithm can be generalized to include external forcing messages, and used to address selectively an exponential number of glassy ground states. These capabilities can be used to explore efficiently the space of solutions of random NP-complete constraint satisfaction problems, providing a direct experimental evidence of replica symmetry breaking in large-size instances. Finally, a new lossy data compression protocol is introduced, exploiting as a computational resource the clustered nature of the space of addressable states.Comment: 4 pages, 4 figure

A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease

Transmit Antenna Selection for Physical-Layer Network Coding Based on Euclidean Distance

Physical-layer network coding (PNC) is now well-known as a potential candidate for delay-sensitive and spectrally efficient communication applications, especially in two-way relay channels (TWRCs). In this paper, we present the error performance analysis of a multiple-input single-output (MISO) fixed network coding (FNC) system with two different transmit antenna selection (TAS) schemes. For the first scheme, where the antenna selection is performed based on the strongest channel, we derive a tight closed-form upper bound on the average symbol error rate (SER) with $M$-ary modulation and show that the system achieves a diversity order of 1 for $M > 2$. Next, we propose a Euclidean distance (ED) based antenna selection scheme which outperforms the first scheme in terms of error performance and is shown to achieve a diversity order lower bounded by the minimum of the number of antennas at the two users.Comment: 15 pages, 4 figures, Globecom 2017 (Wireless Communications Symposium

Fountain Codes with Nonuniform Selection Distributions through Feedback

One key requirement for fountain (rateless) coding schemes is to achieve a high intermediate symbol recovery rate. Recent coding schemes have incorporated the use of a feedback channel to improve intermediate performance of traditional rateless codes; however, these codes with feedback are designed based on uniformly at random selection of input symbols. In this paper, on the other hand, we develop feedback-based fountain codes with dynamically-adjusted nonuniform symbol selection distributions, and show that this characteristic can enhance the intermediate decoding rate. We provide an analysis of our codes, including bounds on computational complexity and failure probability for a maximum likelihood decoder; the latter are tighter than bounds known for classical rateless codes. Through numerical simulations, we also show that feedback information paired with a nonuniform selection distribution can highly improve the symbol recovery rate, and that the amount of feedback sent can be tuned to the specific transmission properties of a given feedback channel.Comment: Submitted to the IEEE Transactions on Information Theor