DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.

Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of function. A powerful predictive model for the function of non-coding DNA can have enormous benefit for both basic science and translational research because over 98% of the human genome is non-coding and 93% of disease-associated variants lie in these regions. To address this need, we propose DanQ, a novel hybrid convolutional and bi-directional long short-term memory recurrent neural network framework for predicting non-coding function de novo from sequence. In the DanQ model, the convolution layer captures regulatory motifs, while the recurrent layer captures long-term dependencies between the motifs in order to learn a regulatory 'grammar' to improve predictions. DanQ improves considerably upon other models across several metrics. For some regulatory markers, DanQ can achieve over a 50% relative improvement in the area under the precision-recall curve metric compared to related models. We have made the source code available at the github repository http://github.com/uci-cbcl/DanQ

A Novel Uplink Data Transmission Scheme For Small Packets In Massive MIMO System

Intelligent terminals often produce a large number of data packets of small lengths. For these packets, it is inefficient to follow the conventional medium access control (MAC) protocols because they lead to poor utilization of service resources. We propose a novel multiple access scheme that targets massive multiple-input multiple-output (MIMO) systems based on compressive sensing (CS). We employ block precoding in the time domain to enable the simultaneous transmissions of many users, which could be even more than the number of receive antennas at the base station. We develop a block-sparse system model and adopt the block orthogonal matching pursuit (BOMP) algorithm to recover the transmitted signals. Conditions for data recovery guarantees are identified and numerical results demonstrate that our scheme is efficient for uplink small packet transmission.Comment: IEEE/CIC ICCC 2014 Symposium on Signal Processing for Communication

Multiple Access for Small Packets Based on Precoding and Sparsity-Aware Detection

Modern mobile terminals often produce a large number of small data packets. For these packets, it is inefficient to follow the conventional medium access control protocols because of poor utilization of service resources. We propose a novel multiple access scheme that employs block-spreading based precoding at the transmitters and sparsity-aware detection schemes at the base station. The proposed scheme is well suited for the emerging massive multiple-input multiple-output (MIMO) systems, as well as conventional cellular systems with a small number of base-station antennas. The transmitters employ precoding in time domain to enable the simultaneous transmissions of many users, which could be even more than the number of receive antennas at the base station. The system is modeled as a linear system of equations with block-sparse unknowns. We first adopt the block orthogonal matching pursuit (BOMP) algorithm to recover the transmitted signals. We then develop an improved algorithm, named interference cancellation BOMP (ICBOMP), which takes advantage of error correction and detection coding to perform perfect interference cancellation during each iteration of BOMP algorithm. Conditions for guaranteed data recovery are identified. The simulation results demonstrate that the proposed scheme can accommodate more simultaneous transmissions than conventional schemes in typical small-packet transmission scenarios.Comment: submitted to IEEE Transactions on Wireless Communication