Ming-Yang Kao

Abstract: Zero-day polymorphic worms pose a serious threat to the security of Internet infrastructures. Given their rapid propagation, it is crucial to detect them at edge networks and automatically generate signatures in the early stages of infection. Most existing approaches for automatic signature generation need host information and are thus not applicable for deployment on high-speed network links. In this paper, we propose Hamsa, a network-based automated signature generation system for polymorphic worms which is fast, noise-tolerant and attack-resilient. Essentially, we propose a realistic model to analyze the invariant content of polymorphic worms which allows us to make analytical attack-resilience guarantees for the signature generation algorithm. Evaluation based on a range of polymorphic worms and polymorphic engines demonstrates that Hamsa significantly outperforms Polygraph (J. Newsome et al., 2005) in terms of efficiency, accuracy, and attack resilience.

Abstract: Tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged molecules of prefix and suffix peptide subsequences and then measures mass/charge ratios of ...

Abstract: In this paper, we study the complexity of self-assembly under models that are natural generalizations of the tile self-assembly model. In particular, we extend Rothemund and Winfree's study of the tile complexity of tile self-assembly [Proceedings of the 32nd Annual ACM Symposium on Theory of Computing, Portland, OR, 2000, pp. 459--468]. They provided a lower bound of $\Omega(\frac{\log N}{\log\log N})$ on the tile complexity of assembling an $N\times N$ square for almost all N. Adleman et al. [Proceedings of the 33rd Annual ACM Symposium on Theory of Computing, Heraklion, Greece, 2001, pp. 740--748] gave a construction which achieves this bound. We consider whether the tile complexity for self-assembly can be reduced through several natural generalizations of the model. One of our results is a tile set of size $O(\sqrt{\log N})$ which assembles an $N\times N$ square in a model which allows flexible glue strength between nonequal glues. This result is matched for almost all N by a lower bound dictated by Kolmogorov complexity. For three other generalizations, we show that the $\Omega(\frac{\log N}{\log\log N})$ lower bound applies to $N\times N$ squares. At the same time, we demonstrate that there are some other shapes for which these generalizations allow reduced tile sets. Specifically, for thin rectangles with length N and width k, we provide a tighter lower bound of $\Omega(\frac{N^{1/k}}{k})$ for the standard model, yet we also give a construction which achieves $O(\frac{\log N}{\log\log N})$ complexity in a model in which the temperature of the tile system is adjusted during assembly. We also investigate the problem of verifying whether a given tile system uniquely assembles into a given shape; we show that this problem is NP-hard for three of the generalized models.

Abstract: Tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged molecules of prefix and suffix peptide subsequences and then measures mass/charge ratios of these ions. The de novo peptide sequencing problem is to reconstruct the peptide sequence from a given tandem mass spectral data of k ions. By implicitly transforming the spectral data into an NC-spectrum graph G (V, E) where /V/ = 2k + 2, we can solve this problem in O(/V//E/) time and O(/V/2) space using dynamic programming. For an ideal noise-free spectrum with only b- and y-ions, we improve the algorithm to O(/V/ + /E/) time and O(/V/) space. Our approach can be further used to discover a modified amino acid in O(/V//E/) time. The algorithms have been implemented and tested on experimental data.

Abstract: This dynamic reference work provides solutions to vital algorithmic problems for scholars, researchers, practitioners, teachers and students in fields such as computer science, mathematics, statistics, biology, economics, financial software, and medical informatics. This second edition is broadly expanded, building upon the success of its former edition with more than 450 new and updated entries. These entries are designed to ensure algorithms are presented from growing areas of research such as bioinformatics, combinatorial group testing, differential privacy, enumeration algorithms, game theory, massive data algorithms, modern learning theory, social networks, and VLSI CAD algorithms. Over 630 entries are organized alphabetically by problem, with subentries allowing for distinct solutions. Each entry includes a description of the basic algorithmic problem; the input and output specifications; key results; examples of applications; citations to key literature, open problems, experimental results, links to data sets and downloadable code. All entries are peer-reviewed, written by leading experts in the fieldand each entry contains links to a summary of the authors research work. This defining reference is available in both print and onlinea dynamic living work with hyperlinks to related entries, cross references citations, and a myriad other valuable URLs. New and Updated entries include: Algorithmic Aspects of Distributed Sensor Networks, Algorithms for Modern Computers Bioinformatics Certified Reconstruction and Mesh Generation Combinatorial Group Testing Compression of Text and Data Structures Computational Counting Computational Economics Computational Geometry Differential Privacy Enumeration Algorithms Exact Exponential Algorithms Game Theory Graph Drawing Group Testing Internet Algorithms Kernels and Compressions Massive Data Algorithms Mathematical Optimization Modern Learning Theory Social Networks Stable Marriage Problems, k-SAT Algorithms Sublinear Algorithms Tile Self-Assembly VLSI CAD Algorithms

Abstract: To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.

Abstract: A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.

Abstract: WITH the ever-widening scope of modern mathematical analysis and its many ramifications, it is quite impossible to include, in a single volume of reasonable size, an adequate and exhaustive discussion of the calculus in its more advanced stages. It therefore becomes necessary, in planning a thoroughly sound course in the subject, to consider several important aspects of the vast field confronting a modern writer. The limitation of space renders the selection of subject-matter fundamentally dependent upon the aim of the course, which may or may not be related to the content of specific examination syllabuses. Logical development, too, may lead to the inclusion of many topics which, at present, may only be of academic interest, while others, of greater practical value, may have to be omitted. The experience and training of the writer may also have, more or less, a bearing on both these considerations.Advanced CalculusBy Dr. C. A. Stewart. Pp. xviii + 523. (London: Methuen and Co., Ltd., 1940.) 25s.