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Ming-Yang Kao

Bio: Ming-Yang Kao is an academic researcher from Northwestern University. The author has contributed to research in topics: Time complexity & Planar graph. The author has an hindex of 37, co-authored 202 publications receiving 4438 citations. Previous affiliations of Ming-Yang Kao include Tufts University & Indiana University.


Papers
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Journal ArticleDOI
TL;DR: An efficient algorithm is developed that can discover a hidden motif from a set of sequences for any alphabet Σ with |Σ|≥ 2 and is applicable to DNA motif discovery.
Abstract: We study a natural probabilistic model for motif discovery. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet Σ. A motif Geg1g2… gm is a string of m characters. Each background sequence is implanted with a probabilistically generated approximate copy of G. For a probabilistically generated approximate copy b1b2… bm of G, every character is probabilistically generated such that the probability for bin gi is at most α. In this article, we develop an efficient algorithm that can discover a hidden motif from a set of sequences for any alphabet Σ with vΣvg 2 and is applicable to DNA motif discovery. We prove that for α c0, e, and Δ2 such that if there are at least c0 log n input sequences, then in O(n2/h(log n)O(1)) time this algorithm finds the motif with probability at least 3/4 for every Gi Σρ-Ψρ, h,e(Σ), where n the length of longest sequences, ρ is the length of the motif, h is a parameter with ρg 4hg Δ2log n, and Ψρ, h,e(Σ) is a small subset of at most 2−Θ(e2 h) fraction of the sequences in Σρ.

3 citations

Book ChapterDOI
16 Dec 1996
TL;DR: This paper considers the problem of adding the smallest number of edges to make a bipartite graph componentwise fully biconnected while preserving its bipartiteness and presents a linear-time algorithm for the problem.
Abstract: A graph is componentwise fully biconnected if every connected component either is an isolated vertex or is biconnected. We consider the problem of adding the smallest number of edges to make a bipartite graph componentwise fully biconnected while preserving its bipartiteness. This problem has important applications for protecting sensitive information in cross tabulated tables. This paper presents a linear-time algorithm for the problem.

3 citations

Posted Content
TL;DR: This paper develops three polynomial-time techniques for pricing European Asian options with provably small errors, where the stock prices follow binomial trees or trees of higher-degree.
Abstract: This paper develops three polynomial-time pricing techniques for European Asian options with provably small errors, where the stock prices follow binomial trees or trees of higher-degree. The first technique is the first known Monte Carlo algorithm with analytical error bounds suitable for pricing single-stock options with meaningful confidence and speed. The second technique is a general recursive bucketing-based scheme that can use the Aingworth-Motwani-Oldham aggregation algorithm, Monte-Carlo simulation and possibly others as the base-case subroutine. This scheme enables robust trade-offs between accuracy and time over subtrees of different sizes. For long-term options or high frequency price averaging, it can price single-stock options with smaller errors in less time than the base-case algorithms themselves. The third technique combines Fast Fourier Transform with bucketing-based schemes for pricing basket options. This technique takes polynomial time in the number of days and the number of stocks, and does not add any errors to those already incurred in the companion bucketing scheme. This technique assumes that the price of each underlying stock moves independently.

3 citations

Book ChapterDOI
Ming-Yang Kao1
24 Feb 1994
TL;DR: This paper gives an optimal linear-time algorithm for testing whether there exist nontrivial analytic invariants in terms of the suppressed cells in a given set of suppressed cells and presents NP-completeness results and an almost lineartime algorithm for the problem of suppressing the minimum number of cells in addition to the sensitive ones.
Abstract: To protect sensitive information in a cross tabulated table, it is a common practice to suppress some of the cells in the table. An analytic invariant is a power series in terms of the suppressed cells that has a unique feasible value and a convergence radius equal to +∞. Intuitively, the information contained in an invariant is not protected even though the values of the suppressed cells are not disclosed. This paper gives an optimal linear-time algorithm for testing whether there exist nontrivial analytic invariants in terms of the suppressed cells in a given set of suppressed cells. This paper also presents NP-completeness results and an almost lineartime algorithm for the problem of suppressing the minimum number of cells in addition to the sensitive ones so that the resulting table does not leak analytic invariant information about a given set of suppressed cells.

3 citations

Journal ArticleDOI
TL;DR: In this article, the authors presented a new approach called the enhanced double digest problem (EDD), which can be solved in linear time in certain theoretically interesting cases and is shown to be NP-hard.
Abstract: The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. Although this new problem is also NP-hard, it can be solved in linear time in certain theoretically interesting cases.

3 citations


Cited by
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Journal ArticleDOI

3,734 citations

Journal ArticleDOI
03 Jun 2011-Science
TL;DR: This work experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays.
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.

1,249 citations

Journal ArticleDOI
TL;DR: A new de novo sequencing software package, PEAKS, is described, to extract amino acid sequence information without the use of databases, using 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.
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.

1,239 citations

Journal ArticleDOI
21 Jul 2011-Nature
TL;DR: It is suggested that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment.
Abstract: The impressive capabilities of the mammalian brain—ranging from perception, pattern recognition and memory formation to decision making and motor activity control—have inspired their re-creation in a wide range of artificial intelligence systems for applications such as face recognition, anomaly detection, medical diagnosis and robotic vehicle control Yet before neuron-based brains evolved, complex biomolecular circuits provided individual cells with the ‘intelligent’ behaviour required for survival However, the study of how molecules can ‘think’ has not produced an equal variety of computational models and applications of artificial chemical systems Although biomolecular systems have been hypothesized to carry out neural-network-like computations in vivo and the synthesis of artificial chemical analogues has been proposed theoretically, experimental work has so far fallen short of fully implementing even a single neuron Here, building on the richness of DNA computing and strand displacement circuitry, we show how molecular systems can exhibit autonomous brain-like behaviours Using a simple DNA gate architecture that allows experimental scale-up of multilayer digital circuits, we systematically transform arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades that function as small neural networks Our approach even allows us to implement a Hopfield associative memory with four fully connected artificial neurons that, after training in silico, remembers four single-stranded DNA patterns and recalls the most similar one when presented with an incomplete pattern Our results suggest that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment

884 citations