Browsing by Subject "Error correction"

Now showing 1 - 7 of 7

Open Access
Assessment and correction of errors in DNA sequencing technologies
(2017-12) Fırtına, Can
Next Generation Sequencing technologies differ by several parameters where the choice to use whether short or long read sequencing platforms often leads to trade-offs between accuracy and read length. In this thesis, I first demonstrate the problems in reproducibility in analyses using short reads. Our comprehensive analysis on the reproducibility of computational characterization of genomic variants using high throughput sequencing data shows that repeats might be prone to ambiguous mapping. Short reads are more vulnerable to repeats and, thus, may cause reproducibility problems. Next, I introduce a novel algorithm Hercules, the first machine learning-based long read error correction algorithm. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection. In such cases researchers often combine both technologies and the more erroneous long reads are corrected using the short reads. Current approaches rely on various graph based alignment techniques and do not take the error profile of the underlying technology into account. Memory- and time- efficient machine learning algorithms that address these shortcomings have the potential to achieve better and more accurate integration of these two technologies. Our algorithm models every long read as a profile Hidden Markov Model with respect to the underlying platform's error profile. The algorithm learns a posterior transition/ emission probability distribution for each long read and uses this to correct errors in these reads. Using datasets from two DNA-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-corrected reads have the highest mapping rate among all competing algorithms and highest accuracy when most of the basepairs of a long read are covered with short reads.
Open Access
A bound on the zero-error list coding capacity
(IEEE, 1993) Arıkan, Erdal
We present a new bound on the zero-error list coding capacity, and using which, show that the list-of-3 capacity of the 4/3 channel is at most 6/19 bits, improving the best previously known bound of 3/8. The relation of the bound to the graph-entropy bound of Koerner and Marton is also discussed.
Open Access
An information-theoretic analysis of Grover's algorithm
(IEEE, 2003-06-07) Arıkan, Erdal
Grover discovered a quantum algorithm for identifying a target element in an unstructured search universe of N items in approximately 1r/4VN queries to a quantum oracle. For classical search using a classical oracle, the search complexity is of order N /2 queries since on average half of the items must be searched. In work preceding Grover's, Bennett et al. had shown that no quantum algorithm can solve the search problem in fewer than D(VN) queries. Thus, Grover's algorithm has optimal order of complexity. Here, we present an informationtheoretic analysis of Grover's algorithm and show that the square-root speed-up by Grover's algorithm is the best possible by any algorithm using the same quantum oracle.
Open Access
NS-SRAM: neighborhood solidarity SRAM for reliability enhancement of SRAM memories
(IEEE, 2016-08-09) Alouani, I.; Ahangari, Hamzeh; Öztürk, Özcan; Niar, S.
Technology shift and voltage scaling increased the susceptibility of Static Random Access Memories (SRAMs) to errors dramatically. In this paper, we present NS-SRAM, for Neighborhood Solidarity SRAM, a new technique to enhance error resilience of SRAMs by exploiting the adjacent memory bit data. Bit cells of a memory line are paired together in circuit level to mutually increase the static noise margin and critical charge of a cell. Unlike existing techniques, NS-SRAM aims to enhance both Bit Error Rate (BER) and Soft Error rate (SER) at the same time. Due to auto-adaptive joiners, each of the adjacent cells' nodes is connected to its counterpart in the neighbor bit. NS-SRAM enhances read-stability by increasing critical Read Static Noise Margin (RSNM), thereby decreasing faults when circuit operates under voltage scaling. It also increases hold-stability and critical charge to mitigate soft-errors. By the proposed technique, reliability of SRAM based structures such as cache memories and register files can drastically be improved with comparable area overhead to existing hardening techniques. Moreover it does not require any extra-memory, does not impact the memory effective size, and has no negative impact on performance. © 2016 IEEE.
Open Access
Reduction of effects of inactive array elements in phase aberration correction
(IEEE, 1993) Karaman, Mustafa; Köymen, Hayrettin; Atalar, Abdullah; O'Donnell, M.
Phase aberration correction based on time delay estimation via minimization of sum of absolute difference (SAD) between radio frequency (RF) signals of neighboring elements is studied in the presence of missing elements. To examine the influence of inactive elements, phase estimation error is measured for various combinations of different number of missing elements, aberration level, and SNR. The measurements are performed on an experimental RF data set. Aberration delays of missing elements are interpolated using the phase estimate between the nearest active elements. The B-scan images are reconstructed for qualitative examination.
Open Access
A simulation study of forward error correction for lost packet recovery in B-ISDN/ATM
(IEEE, 1993-05) Oğuz, Nihat Cem; Ayanoğlu, E.
We present the results of a simulation study for a virtual circuit connection over an ATM network where forward error correction is performed at both the ATM cell level and the packet data unit (PDU) level. A main conclusion of this study is that at low loads ATM cells from the same source dominate in the switch buffers, while at high loads there is a mixing of ATM cells from different sources. For the latter case. ATM cell level coding performs better, while for the former, PDU level coding performs better. The combination of the two techniques has the best overall performance.
Open Access
A simulation study of two-level forward error correction for lost packet recovery in B-ISDN/ATM
(IEEE, 1993) Oğuz, Nihat Cem; Ayanoğlu, E.
The major source of errors in B-ISDN/ATM systems is expected to be buffer overflow during congested conditions, resulting in lost packets. A single lost or errored ATM cell will cause retransmission of the entire packet data unit (PDU) that it belongs to. The performance of the end-to-end system can be made much less sensitive to cell loss by means of forward error correction. In this paper, we present the results of a simulation study for an ATM network where forward error correction is performed at both the cell level and the PDU level. The results indicate that (i) cell losses are highly correlated in time, and analytical models ignoring this fact will not yield accurate results, (ii) the correlation of cell losses is similar to burst errors in digital communication, and similar code interleaving techniques should be used, (iii) coding cells and PDUs separately provides this interleaving effect, and this joint code outperforms coding only at the cell level or only at the PDU level in almost all cases simulated.