A Unifying Variational Perspective on Some Fundamental Information Theoretic Inequalities

This paper proposes a unifying variational approach for proving and extending some fundamental information theoretic inequalities. Fundamental information theory results such as maximization of differential entropy, minimization of Fisher information (Cram\'er-Rao inequality), worst additive noise lemma, entropy power inequality (EPI), and extremal entropy inequality (EEI) are interpreted as functional problems and proved within the framework of calculus of variations. Several applications and possible extensions of the proposed results are briefly mentioned

Time-varying Clock Offset Estimation in Two-way Timing Message Exchange in Wireless Sensor Networks Using Factor Graphs

The problem of clock offset estimation in a two-way timing exchange regime is considered when the likelihood function of the observation time stamps is exponentially distributed. In order to capture the imperfections in node oscillators, which render a time-varying nature to the clock offset, a novel Bayesian approach to the clock offset estimation is proposed using a factor graph representation of the posterior density. Message passing using the max-product algorithm yields a closed form expression for the Bayesian inference problem.Comment: 4 pages, 2 figures, ICASSP 201

Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge

Based on time series gene expressions, cyclic genes can be recognized via spectral analysis and statistical periodicity detection tests. These cyclic genes are usually associated with cyclic biological processes, for example, cell cycle and circadian rhythm. The power of a scheme is practically measured by comparing the detected periodically expressed genes with experimentally verified genes participating in a cyclic process. However, in the above mentioned procedure the valuable prior knowledge only serves as an evaluation benchmark, and it is not fully exploited in the implementation of the algorithm. In addition, partial data sets are also disregarded due to their nonstationarity. This paper proposes a novel algorithm to identify cyclic-process-involved genes by integrating the prior knowledge with the gene expression analysis. The proposed algorithm is applied on data sets corresponding to Saccharomyces cerevisiae and Drosophila melanogaster, respectively. Biological evidences are found to validate the roles of the discovered genes in cell cycle and circadian rhythm. Dendrograms are presented to cluster the identified genes and to reveal expression patterns. It is corroborated that the proposed novel identification scheme provides a valuable technique for unveiling pathways related to cyclic processes

Multi-hop Cooperative Relaying for Energy Efficient In Vivo Communications

This paper investigates cooperative relaying to support energy efficient in vivo communications. In such a network, the in vivo source nodes transmit their sensing information to an on-body destination node either via direct communications or by employing on-body cooperative relay nodes in order to promote energy efficiency. Two relay modes are investigated, namely single-hop and multi-hop (two-hop) relaying. In this context, the paper objective is to select the optimal transmission mode (direct, single-hop, or two-hop relaying) and relay assignment (if cooperative relaying is adopted) for each source node that results in the minimum per bit average energy consumption for the in vivo network. The problem is formulated as a binary program that can be efficiently solved using commercial optimization solvers. Numerical results demonstrate the significant improvement in energy consumption and quality-of-service (QoS) support when multi-hop communication is adopted

Optimal reference sequence selection for genome assembly using minimum description length principle

Reference assisted assembly requires the use of a reference sequence, as a model, to assist in the assembly of the novel genome. The standard method for identifying the best reference sequence for the assembly of a novel genome aims at counting the number of reads that align to the reference sequence, and then choosing the reference sequence which has the highest number of reads aligning to it. This article explores the use of minimum description length (MDL) principle and its two variants, the two-part MDL and Sophisticated MDL, in identifying the optimal reference sequence for genome assembly. The article compares the MDL based proposed scheme with the standard method coming to the conclusion that “counting the number of reads of the novel genome present in the reference sequence” is not a sufficient condition. Therefore, the proposed MDL scheme includes within itself the standard method of “counting the number of reads that align to the reference sequence” and also moves forward towards looking at the model, the reference sequence, as well, in identifying the optimal reference sequence. The proposed MDL based scheme not only becomes the sufficient criterion for identifying the optimal reference sequence for genome assembly but also improves the reference sequence so that it becomes more suitable for the assembly of the novel genome