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SODA
1997
ACM
95views Algorithms» more  SODA 1997»
13 years 6 months ago
Randomly Sampling Molecules
We give a polynomial-time algorithm for the following problem: Given a degree sequence in which each degree is bounded from above by a constant, select, uniformly at random, an un...
Leslie Ann Goldberg, Mark Jerrum
JCC
2007
70views more  JCC 2007»
13 years 4 months ago
Self-organizing superimposition algorithm for conformational sampling
Abstract: A novel self-organizing algorithm for conformational sampling is introduced, in which precomputed conformations of rigid fragments are used as templates to enforce the de...
Fangqiang Zhu, Dimitris K. Agrafiotis
ICCS
2004
Springer
13 years 10 months ago
Improved Sampling for Biological Molecules Using Shadow Hybrid Monte Carlo
Shadow Hybrid Monte Carlo (SHMC) is a new method for sampling the phase space of large biological molecules. It improves sampling by allowing larger time steps and system sizes in ...
Scott S. Hampton, Jesús A. Izaguirre
KDD
2004
ACM
139views Data Mining» more  KDD 2004»
14 years 5 months ago
Learning a complex metabolomic dataset using random forests and support vector machines
Metabolomics is the omics science of biochemistry. The associated data include the quantitative measurements of all small molecule metabolites in a biological sample. These datase...
Young Truong, Xiaodong Lin, Chris Beecher
JCB
2007
94views more  JCB 2007»
13 years 4 months ago
A Quantile Method for Sizing Optical Maps
Optical mapping is an integrated system for the analysis of single DNA molecules. It constructs restriction maps (noted as “optical map”) from individual DNA molecules present...
Haifeng Li, Anton Valouev, David C. Schwartz, Mich...