Browsing by Author "Li, Huian"
Now showing 1 - 5 of 5
Results Per Page
Sort Options
Item Comparison of Multi-Sample Variant Calling Methods for Whole Genome Sequencing(Institute of Electrical and Electronics Engineers, 2014-10) Nho, Kwangsik; West, John D.; Li, Huian; Henschel, Robert; Bharthur, Apoorva; Tavares, Michel C.; Saykin, Andrew J.; Department of Medicine, IU School of MedicineRapid advancement of next-generation sequencing (NGS) technologies has facilitated the search for genetic susceptibility factors that influence disease risk in the field of human genetics. In particular whole genome sequencing (WGS) has been used to obtain the most comprehensive genetic variation of an individual and perform detailed evaluation of all genetic variation. To this end, sophisticated methods to accurately call high-quality variants and genotypes simultaneously on a cohort of individuals from raw sequence data are required. On chromosome 22 of 818 WGS data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), which is the largest WGS related to a single disease, we compared two multi-sample variant calling methods for the detection of single nucleotide variants (SNVs) and short insertions and deletions (indels) in WGS: (1) reduce the analysis-ready reads (BAM) file to a manageable size by keeping only essential information for variant calling ("REDUCE") and (2) call variants individually on each sample and then perform a joint genotyping analysis of the variant files produced for all samples in a cohort ("JOINT"). JOINT identified 515,210 SNVs and 60,042 indels, while REDUCE identified 358,303 SNVs and 52,855 indels. JOINT identified many more SNVs and indels compared to REDUCE. Both methods had concordance rate of 99.60% for SNVs and 99.06% for indels. For SNVs, evaluation with HumanOmni 2.5M genotyping arrays revealed a concordance rate of 99.68% for JOINT and 99.50% for REDUCE. REDUCE needed more computational time and memory compared to JOINT. Our findings indicate that the multi-sample variant calling method using the JOINT process is a promising strategy for the variant detection, which should facilitate our understanding of the underlying pathogenesis of human diseases.Item Enhancing and Implementing Fully Transparent Internet Voting(IEEE, 2015-08) Butterfield, Kevin; Li, Huian; Zou, Xukai; Li, Feng; Department of Computer & Information Science, School of ScienceVoting over the internet has been the focus of significant research with the potential to solve many problems. Current implementations typically suffer from a lack of transparency, where the connection between vote casting and result tallying is seen as a black box by voters. A new protocol was recently proposed that allows full transparency, never obfuscating any step of the process, and splits authority between mutually-constraining conflicting parties. Achieving such transparency brings with it challenging issues. In this paper we propose an efficient algorithm for generating unique, anonymous identifiers (voting locations) that is based on the Chinese Remainder Theorem, we extend the functionality of an election to allow for races with multiple winners, and we introduce a prototype of this voting system implemented as a multiplatform web application.Item Enhancing and Implementing Fully Transparent Internet Voting(Office of the Vice Chancellor for Research, 2015-04-17) Butterfield, Kevin; Li, Huian; Zou, Xukai; Li, FengVoting over the internet has been the focus of significant research with the potential to solve many problems. Current implementations typically suffer from a lack of transparency, where the connection between vote casting and result tallying is seen as a black box by voters. A new protocol was recently proposed that allows full transparency, never obfuscating any step of the process, and splits authority between mutually-constraining conflicting parties. Achieving such transparency brings with it challenging issues. In this paper we propose an efficient algorithm for generating unique, anonymous identifiers (voting locations) that is based on the Chinese Remainder Theorem, extend the functionality of an election to allow for races with multiple winners, and introduce a prototype of this voting system implemented as a multiplatform web application.Item The Internet Based Electronic Voting Enabling Open and Fair Election(Office of the Vice Chancellor for Research, 2014-04-11) Zou, Xukai; Li, Huian; Sui, Yan; Peng, Wei; Li, FengVoting is the pillar of modern democracies. However, examination of current voting systems (including E-voting techniques) shows a gap between casting secret ballots and tallying and verifying individual votes. This gap is caused by either disconnection between the vote-casting process and the vote-tallying process, or opaque transition (e.g. due to encryption) from vote- casting to vote-tallying and thus, damages voter assurance, i.e. failing to answer the question: “Will your vote count?” We proposed a groundbreaking E-voting protocol that fills this gap and provides a fully transparent election. In this new voting system, this transition is seamless, viewable, and verifiable. As a result, the above question can be answered assuredly: “Yes, my vote counts!” The new E-voting protocol is fundamentally different from all existing voting/E-voting protocols in terms of both concepts and the underlying mechanisms. It consists of three innovative Technical Designs: TD1: universal verifiable voting vector; TD2: forward and backward mutual lock voting; and TD3: in-process verification and enforcement. The new technique is the first fully transparent E-voting protocol which fills the aforementioned gap. The trust is split equally among all tallying authorities who are of conflict-of-interest and will technologically restrain from each other. As a result, the new technique enables open and fair elections, even for minor or weak political parties. It is able to mitigate errors and risk and detect fraud and attacks including collusion, with convincingly high probability 1 − 2−(m−log(m))n (n: #voters and m ≥ 2:#candidates). It removes many existing requirements such as trusted central tallying authorities, tailored hardware or software, and complex cryptographic primitives. In summary, the new e- voting technique delivers voter assurance and can transform the present voting booth based voting and election practice. Besides voting and elections, the new technique can also be adapted to other applications such as student class evaluation, rating and reputation systems.Item Transparent, Auditable, and Stepwise Verifiable Online E-Voting Enabling an Open and Fair Election(MDPI, 2017-08-17) Zou, Xukai; Li, Huian; Li, Feng; Peng, Wei; Sui, Yan; Computer and Information Science, School of ScienceMany e-voting techniques have been proposed but not widely used in reality. One of the problems associated with most existing e-voting techniques is the lack of transparency, leading to a failure to deliver voter assurance. In this work, we p verifiable, viewable, and mutual restraining e-voting protocol that exploits the existing multi-party political dynamics such as in the US. The new e-voting protocol consists of three original technical contributions—universal verifiable voting vector, forward and backward mutual lock voting, and in-process check and enforcement—that, along with a public real time bulletin board, resolves the apparent conflicts in voting such as anonymity vs. accountability and privacy vs. verifiability. Especially, the trust is split equally among tallying authorities who have conflicting interests and will technically restrain each other. The voting and tallying processes are transparent/viewable to anyone, which allow any voter to visually verify that his vote is indeed counted and also allow any third party to audit the tally, thus, enabling open and fair election. Depending on the voting environment, our interactive protocol is suitable for small groups where interaction is encouraged, while the non-interactive protocol allows large groups to vote without interaction.