Channel estimation (CE) is one of the critical signal-processing tasks of the wireless physical layer (PHY). Recent deep learning (DL) based CE have outperformed statistical approaches such as least-square-based CE (LS) and linear minimum mean square error-based CE (LMMSE). However, existing CE approaches have not yet been realized on system-on-chip (SoC). The first contribution of this paper is to efficiently implement the existing state-of-the-art CE algorithms on Zynq SoC (ZSoC), comprising of ARM processor and field programmable gate array (FPGA), via hardware-software co-design and fixed point analysis. We validate the superiority of DL-based CE and LMMSE over LS for various signal-to-noise ratios (SNR) and wireless channels in terms of mean square error (MSE) and bit error rate (BER). We also highlight the high complexity, execution time, and power consumption of DL-based CE and LMMSE approaches. To address this, we propose a novel compute-efficient LS-augmented interpolated deep neural network (LSiDNN) based CE algorithm and realize it on ZSoC. The proposed LSiDNN offers 88-90% lower execution time and 38-85% lower resource utilization than state-of-the-art DL-based CE for identical MSE and BER. LSiDNN offers significantly lower MSE and BER than LMMSE, and the gain improves with increased mobility between transceivers. It offers 75% lower execution time and 90-94% lower resource utilization than LMMSE.

With the introduction of spectrum sharing and heterogeneous services in next-generation networks, the base stations need to sense the wideband spectrum and identify the spectrum resources to meet the quality-of-service, bandwidth, and latency constraints. Sub-Nyquist sampling (SNS) enables digitization for sparse wideband spectrum without needing Nyquist speed analog-to-digital converters (ADCs). However, SNS demands additional signal processing algorithms for spectrum reconstruction, such as the well-known orthogonal matching pursuit (OMP) algorithm. OMP is also widely used in other compressed sensing applications. The first contribution of this work is efficiently mapping the OMP algorithm on the Zynq system-on-chip (ZSoC) consisting of an ARM processor and field-programmable gate array (FPGA). Experimental analysis shows a significant degradation in OMP performance for sparse spectrum. Also, OMP needs prior knowledge of spectrum sparsity. We address these challenges via deep-learning (DL)-based architectures and efficiently map them on the ZSoC platform as a second contribution. Via hardware–software codesign (HSCD), different versions of the proposed architecture obtained by partitioning between software (SW) (ARM processor) and hardware (HW) (FPGA) are considered. The resource, power, and execution time comparisons for given memory constraints and a wide range of word lengths (WLs) are presented for these architectures.

Bioinformatics (2010) 26(18), i420–i425. The authors would like to apologize for an error in the calculation of the number of bases, number of flow values and average read length. Our reads turned out to be a lot shorter than previously reported. None of these errors has implications on the method or the results. The corrected table is shown below. Data basis for building the empirical distributions aAfter 454 quality-trimming. bWithout N's. cHomopolymer lengths 1–5, equals to number of homopolymer runs in BLAST results. The error also affects Figure 1b, where the left part of the plot is to be compared with the right set of curves. The corrected figure is shown below. (b) Absolute frequencies of flow values (E.coli). Left: original data, no quality-trimming; right: quality-trimmed. The trimming algorithm enhances the separation of the homopolymer length distributions and levels out discrepancies between the nucleotides such that the curves for the four nucleotides are nearly identical.

MOTIVATION: The commercial launch of 454 pyrosequencing in 2005 was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to approximately 500 base pairs and are thus approaching read lengths obtained from traditional Sanger sequencing. Study design of sequencing projects would benefit from being able to simulate experiments. RESULTS: We explore 454 raw data to investigate its characteristics and derive empirical distributions for the flow values generated by pyrosequencing. Based on our findings, we implement Flowsim, a simulator that generates realistic pyrosequencing data files of arbitrary size from a given set of input DNA sequences. We finally use our simulator to examine the impact of sequence lengths on the results of concrete whole-genome assemblies, and we suggest its use in planning of sequencing projects, benchmarking of assembly methods and other fields. AVAILABILITY: Flowsim is freely available under the General Public License from http://blog.malde.org/index.php/flowsim/.

BACKGROUND: The four heterogeneous childhood cancers, neuroblastoma, non-Hodgkin lymphoma, rhabdomyosarcoma, and Ewing sarcoma present a similar histology of small round blue cell tumor (SRBCT) and thus often leads to misdiagnosis. Identification of biomarkers for distinguishing these cancers is a well studied problem. Existing methods typically evaluate each gene separately and do not take into account the nonlinear interaction between genes and the tools that are used to design the diagnostic prediction system. Consequently, more genes are usually identified as necessary for prediction. We propose a general scheme for finding a small set of biomarkers to design a diagnostic system for accurate classification of the cancer subgroups. We use multilayer networks with online gene selection ability and relational fuzzy clustering to identify a small set of biomarkers for accurate classification of the training and blind test cases of a well studied data set. RESULTS: Our method discerned just seven biomarkers that precisely categorized the four subgroups of cancer both in training and blind samples. For the same problem, others suggested 19-94 genes. These seven biomarkers include three novel genes (NAB2, LSP1 and EHD1 - not identified by others) with distinct class-specific signatures and important role in cancer biology, including cellular proliferation, transendothelial migration and trafficking of MHC class antigens. Interestingly, NAB2 is downregulated in other tumors including Non-Hodgkin lymphoma and Neuroblastoma but we observed moderate to high upregulation in a few cases of Ewing sarcoma and Rabhdomyosarcoma, suggesting that NAB2 might be mutated in these tumors. These genes can discover the subgroups correctly with unsupervised learning, can differentiate non-SRBCT samples and they perform equally well with other machine learning tools including support vector machines. These biomarkers lead to four simple human interpretable rules for the diagnostic task. CONCLUSION: Although the proposed method is tested on a SRBCT data set, it is quite general and can be applied to other cancer data sets. Our scheme takes into account the interaction between genes as well as that between genes and the tool and thus is able find a very small set and can discover novel genes. Our findings suggest the possibility of developing specialized microarray chips or use of real-time qPCR assays or antibody based methods such as ELISA and western blot analysis for an easy and low cost diagnosis of the subgroups.

Many attempts have been made to analyze gene expression data. Typical goals of such analysis include discovery of subclasses, designing predictors/classifiers for diseases, identifying marker genes, and trying to get a deeper understanding of underlying biological process. Success of each of these tasks strongly depends on the features used to solve the problem. The high dimensional nature of expression profiles makes the task very difficult. Consequently, many researchers have used some feature selection criteria to reduce the dimensionality of the problem. These approaches are off-line in nature, as feature selection is done in a separate phase from the system design phase. These approaches ignore the fact that utility of features depends on both the problem that is solved and the tool that is used to solve the problem. We here propose to use a novel neural scheme that picks up the necessary features on-line when the system learns the classification task. Because it considers all the features at one go, it does not miss any subtle combination of these features. We demonstrate the effectiveness of our on-line feature selection (OFS) scheme to distinguish between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) cancer expression data set. Our scheme could identify only five genes that can produce results as good as or even better than what is reported in the literature on this data set. It identifies an important marker gene that alone has a very good discriminating power. This analysis method is quite general in nature and can be effectively used in other areas of bioinformatics. © 2006 Wiley Periodicals, Inc. Int J Int Syst 21: 453–467, 2006.