Detecting Superbubbles in Assembly Graphs

We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap graph constructed from reads. From these graphs, many assembly algorithms first detect simple local graph structures (motifs), such as tips and bubbles, mainly to find sequencing errors. These motifs are easy to detect, but they are sometimes too simple to deal with more complex errors. The superbubble is an extension of the bubble, which is also important for analyzing assembly graphs. Though superbubbles are much more complex than ordinary bubbles, we show that they can be efficiently enumerated. We propose an average-case linear time algorithm (i.e., O(n+m) for a graph with n vertices and m edges) for graphs with a reasonable model, though the worst-case time complexity of our algorithm is quadratic (i.e., O(n(n+m))). Moreover, the algorithm is practically very fast: Our experiments show that our algorithm runs in reasonable time with a single CPU core even against a very large graph of a whole human genome.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Succinct Oblivious RAM

As online storage services become increasingly common, it is important that users\u27 private information is protected from database access pattern analyses. Oblivious RAM (ORAM) is a cryptographic primitive that enables users to perform arbitrary database accesses without revealing any information about the access pattern to the server. Previous ORAM studies focused mostly on reducing the access overhead. Consequently, the access overhead of the state-of-the-art ORAM constructions are almost at practical levels in certain application scenarios such as secure processors. However, we assume that the server space usage could become a new important issue in the coming big-data era. To enable large-scale computation in security-aware settings, it is necessary to rethink the ORAM server space cost using big-data standards. In this paper, we introduce "succinctness" as a theoretically tractable and practically relevant criterion of the ORAM server space efficiency in the big-data era. We, then, propose two succinct ORAM constructions that also exhibit state-of-the-art performance in terms of the bandwidth blowup and the user space. We also give non-asymptotic analyses and simulation results which indicate that the proposed ORAM constructions are practically effective

Wear Leveling Revisited

Wear leveling - a technology designed to balance the write counts among memory cells regardless of the requested accesses - is vital in prolonging the lifetime of certain computer memory devices, especially the type of next-generation non-volatile memory, known as phase change memory (PCM). Although researchers have been working extensively on wear leveling, almost all existing studies mainly focus on the practical aspects and lack rigorous mathematical analyses. The lack of theory is particularly problematic for security-critical applications. We address this issue by revisiting wear leveling from a theoretical perspective. First, we completely determine the problem parameter regime for which Security Refresh - one of the most well-known existing wear leveling schemes for PCM - works effectively by providing a positive result and a matching negative result. In particular, Security Refresh is not competitive for the practically relevant regime of large-scale memory. Then, we propose a novel scheme that achieves better lifetime, time/space overhead, and wear-free space for the relevant regime not covered by Security Refresh. Unlike existing studies, we give rigorous theoretical lifetime analyses, which is necessary to assess and control the security risk.Peer reviewe

多様なポストゲノムデータのためのアラインメントフリーなアルゴリズムの構造

学位の種別: 課程博士審査委員会委員 : （主査）東京大学教授 今井 浩, 東京大学教授 小林 直樹, 東京大学教授 五十嵐 健夫, 東京大学教授 杉山 将, 東京大学講師 笠原 雅弘University of Tokyo(東京大学

Detecting Superbubbles in Assembly Graphs

We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap graph constructed from reads. From these graphs, many assembly algorithms first detect simple local graph structures (motifs), such as tips and bubbles, mainly to find sequencing errors. These motifs are easy to detect, but they are sometimes too simple to deal with more complex errors. The superbubble is an extension of the bubble, which is also important for analyzing assembly graphs. Though superbubbles are much more complex than ordinary bubbles, we show that they can be efficiently enumerated. We propose an average-case linear time algorithm (i.e., O(n+m) for a graph with n vertices and m edges) for graphs with a reasonable model, though the worst-case time complexity of our algorithm is quadratic (i.e., O(n(n+m))). Moreover, the algorithm is practically very fast: Our experiments show that our algorithm runs in reasonable time with a single CPU core even against a very large graph of a whole human genome

Cold polypectomy in patients on antithrombotic medication

Background: The cold polypectomy (CP) technique has been increasingly used in recent years. However, there have been few studies about post-polypectomy bleeding (PPB) in patients who underwent CP and who were on antithrombotic drugs. The objective of this study was to determine the safety of CP in patients on antithrombotic medication. Methods: The subjects were patients who underwent CP in our hospital between April 2014 and March 2016. PPB rates were examined in relation to the use of antithrombotic medication. Results: CP was performed to remove 2,466 polyps in 1,003 patients. There were 549 polyps (22.3%) in186 patients in the antithrombotic group and 1,917 polyps (77.7%) in 817 patients in the non-antithrombotic group. PPB occurred in 0.55% (3/549) of patients in the antithrombotic group and in 0.10% (2/1,917) of patients in the non-antithrombotic group, showing no significant difference (p = 0.07). Patients in the antithrombotic group in whom PPB occurred included 1 aspirin user with 1 polyp and 1 aspirin plus clopidogrel user with 2 polyps. No PPB occurred in patients on other antithrombotic agents or receiving heparin bridging. There was no significant difference between PPB rates in patients with small polyps (6-9 mm) in the antithrombotic and non-antithrombotic groups, but there was a significant difference between PPB rates in the 2 groups for patients with diminutive group (1-5 mm). Conclusion: CP is a safe procedure even in patients on antithrombotic medication