Results 1 - 10 of 1,597

MAFFT version 5: improvement in accuracy of multiple sequence alignment

by Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, Takashi Miyata - NUCLEIC ACIDS RES , 2005
"... The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed high ..."
Abstract - Cited by 801 (5 self) - Add to MetaCart
The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed

Cluster Ensembles - A Knowledge Reuse Framework for Combining Multiple Partitions

by Alexander Strehl, Joydeep Ghosh, Claire Cardie - Journal of Machine Learning Research , 2002
"... This paper introduces the problem of combining multiple partitionings of a set of objects into a single consolidated clustering without accessing the features or algorithms that determined these partitionings. We first identify several application scenarios for the resultant 'knowledge reuse&ap ..."
Abstract - Cited by 603 (20 self) - Add to MetaCart
' framework that we call cluster ensembles. The cluster ensemble problem is then formalized as a combinatorial optimization problem in terms of shared mutual information. In addition to a direct maximization approach, we propose three effective and efficient techniques for obtaining high-quality combiners

E.: Automatic clustering of orthologs and inparalogs from pairwise species comparisons.

by Maido Remm , Christian E V Storm , Erik L L Sonnhammer - Journal of Molecular Biology , 2001
"... Orthologs are genes in different species that originate from a single gene in the last common ancestor of these species. Such genes have often retained identical biological roles in the present-day organisms. It is hence important to identify orthologs for transferring functional information betwee ..."
Abstract - Cited by 311 (9 self) - Add to MetaCart
species. Ortholog clusters are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex

Multi-way distributional clustering via pairwise interactions

by Ron Bekkerman, Andrew Mccallum - In ICML , 2005
"... We present a novel unsupervised learning scheme that simultaneously clusters variables of several types (e.g., documents, words and authors) based on pairwise interactions between the types, as observed in co-occurrence data. In this scheme, multiple clustering systems are generated aiming at maximi ..."
Abstract - Cited by 60 (10 self) - Add to MetaCart
at maximizing an objective function that measures multiple pairwise mutual information between cluster variables. To implement this idea, we propose an algorithm that interleaves top-down clustering of some variables and bottom-up clustering of the other variables, with a local optimization correction routine

Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements

by Atul J. Butte, Isaac S. Kohane, I. S. Kohane - Pacific Symposium on Biocomputing , 2000
"... Increasing numbers of methodologies are available to find functional genomic clusters in RNA expression data. We describe a technique that computes comprehensive pair-wise mutual information for all genes in such a data set. An association with a high mutual information means that one gene is non-ra ..."
Abstract - Cited by 192 (1 self) - Add to MetaCart
Increasing numbers of methodologies are available to find functional genomic clusters in RNA expression data. We describe a technique that computes comprehensive pair-wise mutual information for all genes in such a data set. An association with a high mutual information means that one gene is non

Robust Data Clustering

by Ana L. N. Fred, Anil K. Jain , 2003
"... We address the problem of robust clustering by combining data partitions (forming a clustering ensemble) produced by multiple clusterings. We formulate robust clustering under an information-theoretical framework; mutual information is the underlying concept used in the definition of quantitative me ..."
Abstract - Cited by 273 (8 self) - Add to MetaCart
We address the problem of robust clustering by combining data partitions (forming a clustering ensemble) produced by multiple clusterings. We formulate robust clustering under an information-theoretical framework; mutual information is the underlying concept used in the definition of quantitative

The effect upon channel capacity in wireless communications of perfect and imperfect knowledge of the channel

by Muriel Médard - IEEE Trans. Inf. Theory , 2000
"... Abstract—We present a model for time-varying communication single-access and multiple-access channels without feedback. We consider the difference between mutual information when the receiver knows the channel perfectly and mutual information when the receiver only has an estimate of the channel. We ..."
Abstract - Cited by 271 (7 self) - Add to MetaCart
Abstract—We present a model for time-varying communication single-access and multiple-access channels without feedback. We consider the difference between mutual information when the receiver knows the channel perfectly and mutual information when the receiver only has an estimate of the channel

Sum Capacity of a Gaussian Vector Broadcast Channel

by Wei Yu, John M. Cioffi - IEEE Trans. Inform. Theory , 2002
"... This paper characterizes the sum capacity of a class of non-degraded Gaussian vectB broadcast channels where a singletransmitter with multiple transmit terminals sends independent information to multiple receivers. Coordinat+[ is allowed among the transmit teminals, but not among the different recei ..."
Abstract - Cited by 279 (21 self) - Add to MetaCart
This paper characterizes the sum capacity of a class of non-degraded Gaussian vectB broadcast channels where a singletransmitter with multiple transmit terminals sends independent information to multiple receivers. Coordinat+[ is allowed among the transmit teminals, but not among the different

Efficient Use of Side Information in MultipleAntenna Data Transmission over Fading Channels

by Aradhana Narula, Michael J. Lopez, Mitchell D. Trott, Gregory W. Wornell , 1998
"... We derive performance limits for two closely related communication scenarios involving a wireless system with multiple-element transmitter antenna arrays: a point-to-point system with partial side information at the transmitter, and a broadcast system with multiple receivers. In both cases, ideal be ..."
Abstract - Cited by 211 (4 self) - Add to MetaCart
We derive performance limits for two closely related communication scenarios involving a wireless system with multiple-element transmitter antenna arrays: a point-to-point system with partial side information at the transmitter, and a broadcast system with multiple receivers. In both cases, ideal

Closing the gap in the capacity of wireless networks via percolation theory

by Massimo Franceschetti, Olivier Dousse, David N. C. Tse, Patrick Thiran - IEEE TRANS. INFORMATION THEORY , 2007
"... An achievable bit rate per source–destination pair in a wireless network of � randomly located nodes is determined adopting the scaling limit approach of statistical physics. It is shown that randomly scattered nodes can achieve, with high probability, the same Ia � � transmission rate of arbitrari ..."
Abstract - Cited by 238 (8 self) - Add to MetaCart
is then obtained by performing pairwise coding and decoding at each hop along the paths, and using a time division multiple access scheme.
Results 1 - 10 of 1,597