2301190
On the Informational Asymmetry between Upper and Lower Bounds for Ultrametric Evolutionary Trees
This paper addresses the informational asymmetry for constructing an ultrametric evolutionary tree from upper and lower bounds on pairwise distances between n given species. We show that the tallest ultrametric tree exists and can be constructed in O(n2) time, while the existence of the shortest ultrametric tree depends on whether the lower bounds are ultrametric. The tallest tree construction algorithm gives a very simple solution to the construction of an ultrametric tree. We also provide an efficient O(n2)-time algorithm for checking the uniqueness of an ultrametric tree, and study a query problem for testing whether an ultrametric tree satisfies both upper and lower bounds.
10712046
Algorithms for identifying protein cross-links via tandem mass spectrometry
Cross-linking technology combined with tandem mass spectrometry (MS-MS) is a powerful method that provides a rapid solution to the discovery of protein-protein interactions and protein structures. We studied the problem of detecting cross-linked peptides and cross-linked amino acids from tandem mass spectral data. Our method consists of two steps: the first step finds two protein subsequences whose mass sum equals a given mass measured from the mass spectrometry; and the second step finds the best cross-linked amino acids in these two peptide sequences that are optimally correlated to a given tandem mass spectrum. We designed fast and space-efficient algorithms for these two steps, and implemented and tested them on experimental data of cross-linked Hemoglobin proteins.
2057857
Gene-finding via tandem mass spectrometry
We propose a new gene-finding methodology that combines high performance liquid chromatograph (HPLC)-tandem mass spectrometry experiments with a fast computer algorithm to locate coding regions and introns. Proteins are first extracted from cells and digested by enzymes, and then the resulting peptides are separated and analyzed by HPLC-tandem mass spectrometry. We designed an algorithm to find DNA coding sequences, corresponding to open reading frames (ORF), in the genome such that their translated amino acid sequences are optimally correlated with these tandem mass spectra. In this algorithm, we also allow one gap, corresponding to an intron, between two DNA coding sequences, such that their concatenation becomes one coding sequence. Finally, the algorithm assembles these candidate coding sequences and introns into gene structures. Our algorithm was implemented to predict genes on 4 contigs with a total of 123 kbps using two sets of simulated digestion- HPLC-tandem mass spectrometry data of 2523 Caenorhabditis elegans Chromosome IV proteins, digested by trypsin and Asp-N respectively. Among 15 annotated genes in the forward strand, all 98 exons are hit by the predicted no-gap coding sequences, and 60 out of 83 introns are correctly predicted. We also tested gene structure prediction in a contig containing 3 genes. Combining splicing site predictions with predicted coding sequences and introns, we found all 3 gene structures.
31567164
Prediction of protein function using protein-protein interaction data
Assigning functions to novel proteins is one of the most important problems in the post-genomic era. We develop a novel approach that applies the theory of Markov random fields to infer a protein's functions using protein-protein interaction data and the functional annotations of its interaction protein partners. For each function of interest and a protein, we predict the probability that the protein has that function using Bayesian approaches. Unlike in other available approaches for protein annotation where a protein has or does not have a function of interest, we give a probability for having the function. This probability indicates how confident we are about the prediction. We apply our method to predict cellular functions (43 categories including a category "others") for yeast proteins defined in the Yeast Proteome Database, using the protein-protein interaction data from the Munich Information Center for Protein Sequences. We show that our approach outperforms other available methods for function prediction based on protein interaction data.
8315237
Local Lazy Regression: Making Use of the Neighborhood to Improve QSAR Predictions
Traditional quantitative structure-activity relationship (QSAR) models aim to capture global structure-activity trends present in a data set. In many situations, there may be groups of molecules which exhibit a specific set of features which relate to their activity or inactivity. Such a group of features can be said to represent a local structure-activity relationship. Traditional QSAR models may not recognize such local relationships. In this work, we investigate the use of local lazy regression (LLR), which obtains a prediction for a query molecule using its local neighborhood, rather than considering the whole data set. This modeling approach is especially useful for very large data sets because no a priori model need be built. We applied the technique to three biological data sets. In the first case, the root-mean-square error (RMSE) for an external prediction set was 0.94 log units versus 0.92 log units for the global model. However, LLR was able to characterize a specific group of anomalous molecules with much better accuracy (0.64 log units versus 0.70 log units for the global model). For the second data set, the LLR technique resulted in a decrease in RMSE from 0.36 log units to 0.31 log units for the external prediction set. In the third case, we obtained an RMSE of 2.01 log units versus 2.16 log units for the global model. In all cases, LLR led to a few observations being poorly predicted compared to the global model. We present an analysis of why this was observed and possible improvements to the local regression approach.
2822926
Sorting with Fixed-length Reversals
Abstract A popular puzzle TOP-SPIN consists of a permutation of 20 numbered disks on an oval track, with a turnstile capable of reversing a string of 4 consecutive disks. The goal is to sort the disks into identity permutation using reversals. We consider the more general case of sorting n element permutations with a turnstile of size k. The problem of computing the reversal distances is of considerable importance in reconstructing the evolutionary history of the genome. The minimum reversal sequence sorting the one genome to another corresponds to the most likely evolutionary path between them. We give a complete solution for all n and k, of the number of equivalence classes of n-permutations under k-reversal, for both permutations and circular permutations. We also prove the upper and lower bounds on the reversal distances between two permutations.
6997568
Gathering-Load-Balanced Tree Protocol for Wireless Sensor Networks
Wireless communications and digital electronics have enabled the development of low-power, low-cost, multifunctional sensors. The functionality of sensor network mainly is the measurement collection. The previous proposed protocols mainly focus on broadcasting tree structure, but it may not be efficient in data gathering. In this paper, we propose novel tree architecture that is a dynamic, adjustable, load-balanced tree in sensor networks to decrease the energy utilization and to prolong the lifetime of sensors. A load-balanced tree can share the forwarding loads between non-leaf nodes. Due to the limit of tree topology, we try to adjust forming a tree that has similar amount of children between non-leaf nodes. When the energy of non-leaf node is lower than a designated threshold, the tree structure can be readjusted to prolong the lifetime of tree. In simulation, we compare our protocol with different adjustment phases and an existed protocol. From the result, our protocol can have better performance than others
8131087
Multipath-Based Multicasting Strategies for Wormhole-Routed Star Graph Interconnection Networks
The star graph interconnection network has been recognized as an attractive alternative to the popular hypercube network. In this paper, we present a multipath-based multicast routing model for wormholerouted star graph networks, propose two efficient multipath routing schemes, and contrast the performance of the proposed schemes with the performance of the scheme presented in our previous work. Both of the two proposed schemes have been proven to be deadlock-free. The first scheme, simplemultipath routing, uses multiple independent paths for concurrent multicasting. The second scheme, two-phase multipath routing, includes two phases: source-to-relay and relay-to-destination. For each phase, multicasting is carried out using simple multipath routing. Experimental results show that, for short and medium messages with small message startup latencies, the proposed schemes reduce multicast latency more efficiently than other schemes.
44631758
Agent-based forwarding strategies for reducing location management cost in mobile networks
A major issue with location management in mobile wireless networks is the high cost associated with location updates and searches. A search occurs when a caller needs to connect to a mobile user whose location is unknown to the caller and the network must locate the callee. An update occurs when a mobile user moves into a new registration area and the network is informed of the location change. We propose and analyze a class of new agent-based forwarding strategies with the objective to reduce the location management cost in mobile wireless networks. We develop analytical Markov models to compare the performance of the proposed strategies with existing location management schemes to demonstrate their feasibility and also to reveal conditions under which the proposed schemes are superior to existing ones.
12141135
Construction of classification trees via the classification-hierarchy table
Abstract The classification-tree method developed by Grochtmann and coworkers is a black box testing technique to assist test engineers to construct test cases systematically from the functional specifications, via the construction of classification trees. This paper supplements their studies by proposing a methodology to construct classification trees systematically from given sets of classifications and their associated classes, via the notion of the classification-hierarchy table. The intuition of the classification-hierarchy table is to capture the hierarchical relationship for every pair of distinct classifications from which classification trees can be constructed.
7383373
Scale-Driven Iterative Optimization for Brain Extraction and Registration
We present a novel framework to automatically separate brain region from other non-brain regions in head images. The idea of the proposed method is to estimate larger scale patterns in an image and then correct the boundaries iteratively. The scale estimation is based on the recently proposed total variation (TV) regularized L^1 functional. An iterative optimization method is used to refine non-convex and acute angle boundaries. The final algorithm is able to extract large scale patterns with arbitrary shapes, which is particularly suitable for brain extraction. In order to reduce the computation overhead in 3D data, a multi-level technique is proposed to exponentially improve the speed of the brain extraction process. Based on accurate results of brain extraction, a non-rigid brain registration algorithm is proposed to improve accuracy and consistency of existing registration methods. Experimental results on real 3D brain MR images demonstrate that the proposed methods outperform existing solutions. In addition, results are provided to show that the proposed algorithm can also be used to segment large scale patterns in general images.