Projects:NonParametricClustering - Revision history

Ygao at 01:00, 16 November 2013

2013-11-16T01:00:40Z

Ygao at 16:12, 12 January 2012

2012-01-12T16:12:20Z

Melonakos at 19:46, 11 May 2010

2010-05-11T19:46:22Z

Melonakos at 20:23, 27 August 2009

2009-08-27T20:23:13Z

Melonakos at 17:45, 25 August 2009

2009-08-25T17:45:27Z

Melonakos at 19:28, 11 July 2009

2009-07-11T19:28:47Z

Xavier: /* Results */

2008-12-09T23:39:40Z

Results

Xavier: /* Description */

2008-12-09T23:38:52Z

Description

Xavier: /* Results */

2008-12-09T22:54:17Z

Results

Xavier: /* Results */

2008-12-09T22:41:20Z

Results

@@ Line 1: / Line 1: @@
-  Back to [[Algorithm:BU|Boston University Algorithms]]
+  Back to [[Algorithm:Stony Brook|Stony Brook University Algorithms]]
 __NOTOC__
 = Non Parametric Clustering for Biomolecular Structural Analysis =

@@ Line 1: / Line 1: @@
-  Back to [[Algorithm:GATech|Georgia Tech Algorithms]]
+  Back to [[Algorithm:BU|Boston University Algorithms]]
 __NOTOC__
 = Non Parametric Clustering for Biomolecular Structural Analysis =

@@ Line 59: / Line 59: @@
 = Publications =
 ''In Print''
-* [http://www.na-mic.org/publications/pages/display?search=NonParametricClustering&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&searchbytag=checked&sponsors=checked| NA-MIC Publications Database]
+* [http://www.na-mic.org/publications/pages/display?search=NonParametricClustering&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&searchbytag=checked&sponsors=checked| NA-MIC Publications Database on Non Parametric Clustering for Biomolecular Structural Analysis]
 ''In press''
 * X. Le Faucheur, E. Hershkovits, R. Tannenbaum and A. Tannenbaum. Non-Parametric Clustering for studying RNA conformation. Publication in submission.

@@ Line 1: / Line 1: @@
-  Back to [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|NA-MIC Collaborations]], [[Algorithm:GATech|Georgia Tech Algorithms]]
+  Back to [[Algorithm:GATech|Georgia Tech Algorithms]]
 __NOTOC__
 = Non Parametric Clustering for Biomolecular Structural Analysis =

@@ Line 1: / Line 1: @@
-Back to [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|NA-MIC Collaborations]], [[Algorithm:GATech|Georgia Tech Algorithms]]
+ Back to [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|NA-MIC Collaborations]], [[Algorithm:GATech|Georgia Tech Algorithms]]
 __NOTOC__
 = Non Parametric Clustering for Biomolecular Structural Analysis =

@@ Line 1: / Line 1: @@
 Back to [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|NA-MIC Collaborations]], [[Algorithm:GATech|Georgia Tech Algorithms]]
 __NOTOC__
 = Non Parametric Clustering for Biomolecular Structural Analysis =
@@ Line 16: / Line 15: @@
 |}
-== Clustering method ==
+''Clustering method''
 Our method of choice for the clustering of the data space is based on a physical Potts model. The N points of our dataset are referred as magnetic sites. Each site is assigned a Potts spin. Spin values are taken from a set of q distinct integers. An interaction term that is proportional to the distance between nearest neighbor’s data points is added to the model. The spin configuration of our model is dependent on a parameter T that physically corresponds to a temperature. Such Potts systems are known to form a phase with islands of similar Potts state (similar magnetic state). Revealing the clusters in the data space is converted into Monte Carlo search for the magnetic islands in the equivalent physical model. While this method is slow comparing to other non parametric hierarchical methods, it is by far superior in robustness and its classification is more coherent due to its physical interpretation. We compare our results to linkage-based clustering methods, which are popular non-parametric clustering methods.
-== Results ==
+''Results''
-=== Single Nucleotide ===
+''Single Nucleotide''
 The single nucleotide conformation is the basic structural unit of the RNA shape. The flexibility of a residue stems from the modes of motion of its backbone, which are restricted to 6 rotations. The backbone conformation distribution is strongly non-homogeneous and we then operate clustering in this 6-dimensional torsional space.
@@ Line 37: / Line 36: @@
 Also, we have compare our method to linkage-based clustering methods. These hierarchical methods necessitate more prior knowledge in order to select an optimal clustering configuration within the iterative data decomposition into clusters. Final clustering seems to be much easier to obtain and interpret with the Potts proposed model.
-=== Base Pair ===
+''Base Pair''
 Interactions within the RNA strand can bring residues that are initially far apart in the sequence into close proximity. Studying interacting base pair geometries can shed light on the folding process and the functionality of an RNA molecule. The Potts based clustering give the results presented in (Fig 3). Our analysis shows that we have been able to reconstruct with high fidelity -and somehow complete- the base pair classification one can find in data banks.
@@ Line 47: / Line 45: @@
 |}
-== Project status ==
+''Project status''
 Thus far we have applied the method to classify single nucleotide and base pair conformations. At the current stage we are developing classification nomenclature for base stacking, an interaction that have not been given an adequate physical model nor been classified.
-= Project aim =
+''Project aim''
 A variant of the Potts model classification can be used to find clustering in network of interactions between molecules. We plan to use the Potts model with results from projects of polymers adsorption that we are currently working on to develop model for docking interactions between polymers and between polymers and metal surfaces.
@@ Line 61: / Line 59: @@
 = Publications =
 ''In Print''
+* [http://www.na-mic.org/publications/pages/display?search=NonParametricClustering&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&searchbytag=checked&sponsors=checked| NA-MIC Publications Database]
 ''In press''
 * X. Le Faucheur, E. Hershkovits, R. Tannenbaum and A. Tannenbaum. Non-Parametric Clustering for studying RNA conformation. Publication in submission.

@@ Line 32: / Line 32: @@
 |+ '''Fig 2. Single Nucleotide Clustering'''
 |valign="top"|[[Image:SingleNucleotideBins.JPG|thumb|400px|3D projection of the clustering for the qualitattive observations.]]
-|valign="top"|[[Image:SingleNucleotidePotts.JPG|thumb|400px|3D projection of the clustering for the classification with the new clustering method.]]
+|valign="top"|[[Image:SingleNucleotidePotts.JPG|thumb|400px|3D projection of the clustering for the classification with the proposed clustering method.]]
 |}
@@ Line 46: / Line 46: @@
 |valign="top"|[[Image:BasePairClustersPotts.JPG|thumb|400px|Proposed clustering: the first 8 clusters correspond to the classification in the literature (Data Banks).]]
 |}
 == Project status ==

@@ Line 27: / Line 27: @@
 The single nucleotide conformation is the basic structural unit of the RNA shape. The flexibility of a residue stems from the modes of motion of its backbone, which are restricted to 6 rotations. The backbone conformation distribution is strongly non-homogeneous and we then operate clustering in this 6-dimensional torsional space.
-Comparison of the resulting clustering with previous prior knowledge reveals an excellent match (Fig 2).
+Comparison of the resulting clustering (3D projection) with previous prior knowledge reveals an excellent match (Fig 2).
 {|
@@ Line 34: / Line 34: @@
 |valign="top"|[[Image:SingleNucleotidePotts.JPG|thumb|400px|3D projection of the clustering for the classification with the new clustering method.]]
 |}
 {|
@@ Line 39: / Line 44: @@
 |valign="top"|[[Image:BasePairConformation.JPG|thumb|250px|2D projection of the clustering for the base pair geometry case. The coordinates of the projection are theta and omega. (a) All the data points before clustering. (b) After clustering with the algorithm the first seven clusters that correspond to the classification in the literature.]]
 |}
 ''Project status''

@@ Line 31: / Line 31: @@
 {|
 |+ '''Fig 2. Single Nucleotide Representations'''
-|valign="top"|[[Image:ASCIIBins.JPG|thumb|400px|3D projection of the clustering for the qualitattive observations.]]
+|valign="top"|[[Image:SingleNucleotideBins.JPG|thumb|400px|3D projection of the clustering for the qualitattive observations.]]
-|valign="top"|[[Image:ClusterBins.JPG|thumb|400px|3D projection of the clustering for the classification with the new clustering method.]]
+|valign="top"|[[Image:SingleNucleotidePotts.JPG|thumb|400px|3D projection of the clustering for the classification with the new clustering method.]]
 |}