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Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most(More)
Modern global routers employ various routing methods to improve routing speed and quality. Maze routing is the most time-consuming process for existing global routing algorithms. This paper presents two bounded-length maze routing (BLMR) algorithms (optimal-BLMR and heuristic-BLMR) that perform much faster routing than traditional maze routing algorithms.(More)
Extracting sequence information from raw images of fluorescence is the foundation underlying several high-throughput sequencing platforms. Some of the main challenges associated with this technology include reducing the error rate, assigning accurate base-specific quality scores, and reducing the cost of sequencing by increasing the throughput per run. To(More)
Modern global routers use various routing methods to improve routing speed and the quality. Maze routing is the most time-consuming process for existing global routing algorithms. This paper presents two bounded-length maze routing (BLMR) algorithms (optimal-BLMR and heuristic-BLMR) to perform much faster routing than traditional maze routing algorithms.(More)
An important approach for efficient support vector machine (SVM) model selection is to use differentiable bounds of the leave-one-out (loo) error. Past efforts focused on finding tight bounds of loo (e.g., radius margin bounds, span bounds). However, their practical viability is still not very satisfactory. Duan, Keerthi, and Poo (2003) showed that radius(More)
Immense amounts of raw instrument data (i.e., images of fluorescence) are currently being generated using ultra high-throughput sequencing platforms. An important computational challenge associated with this rapid advancement is to develop efficient algorithms that can extract accurate sequence information from raw data. To address this challenge, we(More)
In this paper, we show that decomposition methods with alpha seed-ing are extremely useful for solving a sequence of linear SVMs with more data than attributes. This strategy is motivated from (Keerthi and Lin 2003) which proved that for an SVM with data not linearly separable, after C is large enough, the dual solutions are at the same face. We explain why(More)
An analog front end for diagnosing and monitoring the behavior of the heart is presented. This sensing front end has two low-power processing devices, including a 5(th)-order Butterworth operational transconductance-C (OTA-C) filter and an 8-bit successive approximation analog-to-digital converter (SAADC). The components fabricated in a 0.18-microm CMOS(More)
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