Browsing by Author "Wu, Yi-Chung"

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A 135-mW Fully Integrated Data Processor for Next-Generation Sequencing
(2017-12-01)
Wu, Yi-Chung
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Chang, Chia-Hua
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Hung, Jui-Hung
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Yang, Chia-Hsiang
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分子醫學與生物工程研究所
Next-generation sequencing (NGS) enables high-throughput sequencing, in which short DNA fragments can be sequenced in a massively parallel fashion. However, the essential algorithm behind the succeeding NGS data analysis, DNA mapping, is still excessively time consuming. DNA mapping can be partitioned into two parts: suffix array (SA) sorting and backward searching. Dedicated hardware designs for the less-complex backward searching have been proposed, but feasible hardware for the most complicated part, SA sorting, has never been explored. Based on the memory-efficient sBWT algorithm, this work is the first integrated NGS data processor for the entire DNA mapping. The k-ordered Ferragina and Manzini index used in the sBWT algorithm is leveraged to improve storage capacity and reduce hardware complexity. The proposed NGS data processor realizes the sBWT algorithm through bucket sorting, suffix grouping, and suffix sorting circuits. Key design parameters are analyzed to achieve the optimal performance with respect to hardware cost and execution time. Fabricated in 40-nm CMOS, the NGS data processor dissipates 135 mW at 200 MHz from a 0.9-V supply. With 1-GB external memory, the chip can analyze human DNA within 10 min. This work achieves 43 065x and 8 971x [3208x and 402x] higher energy efficiency (throughput-to-area ratio) than the high-end CPU and GPU solutions, respectively.
A 135mW Fully Integrated Data Processor for Next-Generation Sequencing
(2017-01-01)
Wu, Yi-Chung
;
Hung, Jui-Hung
;
Yang, Chia-Hsiang
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交大名義發表
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National Chiao Tung University
A Bone-Guided Cochlear Implant CMOS Microsystem Preserving Acoustic Hearing
(2017-01-01)
Qian, Xin-Hong
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Wu, Yi-Chung
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Yang, Tzu-Yi
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Cheng, Cheng-Hsiang
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Chu, Hsing-Chien
In this paper, a bone-guided cochlear implant (BGCI) SOC microsystem is proposed and designed. The BGCI microsystem uses four or more electrodes placed on the bone surface of the cochlea and one on the round window to preserve partially the acoustic hearing. The external SOC of the BGCI processes the acoustic signals and generates stimulation patterns and command that are transmitted to the implanted chip through the 13.56MHz wireless power and bidirectional data telemetry. The implanted chip with 4-channel high-voltage-tolerant stimulator generates biphasic stimulation currents up to 800 mu A and sends back the power indication and electrode impedance error signals to the external SOC. Electrical tests on the fabricated BGCI has been performed. The in-vivo animal tests on guinea pigs has shown the evoked Wave III of EABR waveforms. The proposed BGCI can be applied to patients with high-frequency hearing loss, tinnitus, and dizziness.
Design and In Vivo Verification of a CMOS Bone-Guided Cochlear Implant Microsystem
(2019-11-01)
Qian, Xin-Hong
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Wu, Yi-Chung
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Yang, Tzu-Yi
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Cheng, Cheng-Hsiang
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Chu, Hsing-Chien
Objective: To develop and verify a CMOS bone-guided cochlear implant (BGCI) microsystem with electrodes placed on the bone surface of the cochlea and the outside of round window for treating high-frequency hearing loss. Methods: The BGCI microsystem consists of an external unit and an implanted unit. The external system-on-chip is designed to process acoustic signals through an acquisition circuit and an acoustic DSP processor to generate stimulation patterns and commands that are transmitted to the implanted unit through a 13.56 MHz wireless power and bidirectional data telemetry. In the wireless power telemetry, a voltage doubler/tripler (2X/3X) active rectifier is used to enhance the power conversion efficiency and generate 2 and 3 V output voltages. In the wireless data telemetry, phase-locked loop based binary phase-shift keying and load-shift keying modulators/demodulators are adopted for the downlink and uplink data through high-Q coils, respectively. The implanted chip with four-channel high-voltage-tolerant stimulator generates biphasic stimulation currents up to 800 mu A. Results: Electrical tests on the fabricated BGCI microsystem have been performed to verify the chip functions. The in vivo animal tests in guinea pigs have shown the evoked third wave of electrically evoked auditory brainstem response waveforms. It is verified that auditory nerves can be successfully stimulated and acoustic hearing can be partially preserved. Conclusion and Significance: Different from traditional cochlear implants, the proposed BGCI microsystem is less invasive, preserves partially acoustic hearing, and provides an effective alternative for treating high-frequency hearing loss.
Integration of Energy-Recycling Logic and Wireless Power Transfer for Ultra-Low-Power Implantables
(2017-01-01)
Lin, Hsin-Tzu
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Wu, Yi-Chung
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Hsieh, Ping-Hsuan
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Yang, Chia-Hsiang
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電子工程學系及電子研究所
This paper presents an integration of energy-recycling logic circuits with a wireless power transfer receiving module for ultra-low-power applications, such as transcutaneous biomedical implantables. In the prototype design, one inductive coil implanted inside the body receives wireless power and supplies the following electronics. While part of the loading is composed of conventional CMOS logics, the rest is implemented with energy-recycling logic circuits. Energy-recycling logic and the associated adiabatic operation achieve excellent energy efficiency by transferring and recycling energy between digital logic blocks along with the signal propagation. The required AC supplies further lead to a natural integration with wireless power transfer and therefore obviate the need for a rectifier that contributes to substantial power loss. As a proof of concept, a finite-impulse-response filter is designed in 90-nm CMOS process. Simulation results show a 59.3% power reduction as compared to static CMOS counterpart.
sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping
(2016-11-15)
Chang, Chia-Hua
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Chou, Min-Te
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Wu, Yi-Chung
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Hong, Ting-Wei
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Li, Yun-Lung
Motivation: The Full-text index in Minute space (FM-index) derived from the Burrows-Wheeler transform (BWT) is broadly used for fast string matching in large genomes or a huge set of sequencing reads. Several graphic processing unit (GPU) accelerated aligners based on the FM-index have been proposed recently; however, the construction of the index is still handled by central processing unit (CPU), only parallelized in data level (e.g. by performing block-wise suffix sorting in GPU), or not scalable for large genomes. Results: To fulfill the need for a more practical, hardware-parallelizable indexing and matching approach, we herein propose sBWT based on a BWT variant (i.e. Schindler transform) that can be built with highly simplified hardware-acceleration-friendly algorithms and still suffices accurate and fast string matching in repetitive references. In our tests, the implementation achieves significant speedups in indexing and searching compared with other BWT-based tools and can be applied to a variety of domains.