Public interface for doing affinity propagation clustering. More...

#include <APCluster.hh>

Inheritance diagram for protocols::cluster::APCluster:

Public Member Functions
	APCluster (core::Size total_pts, core::Size max_sims_per_pt=0)
	Create new clustering class for total_pts input data points. Optionally, set a limit on the number of similarities stored per point. More...

virtual	~APCluster ()

virtual void	set_sim (core::Size i, core::Size k, core::Real sim)
	How appropriate is k as an exemplar for i? More...

virtual bool	cluster (core::Size maxits, core::Size convits, core::Real lambda)
	Run the actual clustering algorithm. More...

virtual core::Size	num_pts () const

virtual core::Size	get_exemplar_for (core::Size i) const
	Return the index of the point that is the exemplar for point i. More...

virtual core::Size	get_num_exemplars () const
	The number of exemplars selected (number of clusters). Monotonically related to the self-preferences s(k,k). More...

virtual void	get_all_exemplars (utility::vector1< core::Size > &exemplars) const
	Return the indices of data points chosen as exemplars (cluster centers). More...

virtual void	get_cluster_for (core::Size k, utility::vector1< core::Size > &cluster) const
	Returns the indices of points with the specified exemplar k. Note that k is the index of an (input) data point that was chosen as an exemplar, not some "cluster index" between 1 and get_num_exemplars(). More...

virtual core::Real	get_net_sim () const
	The sum of similarities s(i,k) between every data point i and its exemplar k, plus the self preferences of the exemplars. The algorithm should minimize this value – if it dips and climbs again, increase lambda. More...

virtual bool	save_binary (std::string const &filename) const
	Saves the (sparse) similarity matrix and current cluster assignments (if any), but not the accumulated evidence from the last clustering [ r(i,k) and a(i,k) ]. File format is custom binary and is not portable (host endian-ness). More...

virtual bool	load_binary (std::string const &filename)
	Wipes all currently held data and reads in similarity values and cluster assignments. Afterwards, points may be re-clustered with different parameters if desired. File format is custom binary and is not portable (host endian-ness). More...

Protected Member Functions
virtual void	freeze ()

virtual void	reinitialize ()

virtual void	update_r_ik (core::Real lambda)

virtual void	update_a_ik (core::Real lambda)

virtual core::Size	assign_exemplars ()

virtual void	save_best_exemplars ()

virtual void	restore_best_exemplars ()

Private Attributes
utility::vector1< DataPoint >	pts_

core::Size	max_sims_per_pt_

bool	is_frozen_

Detailed Description

Public interface for doing affinity propagation clustering.

Based on Frey and Dueck, "Clustering by Passing Messages Between Data Points", Science 315 (2007). Useful for choosing a set of representative data points (exemplars) out of a large set (e.g. all decoys from a large Rosetta run) given a measure of similarity (e.g. RMSD, maxsub, GDT, ...).

As I understand it, this procedures tries to maximize the sum of similarities between each data point and its exemplar, while balancing that with total number of clusters. Reasonable measures of similarity would be negative RMSD, log-likelihoods, or squared distance (i.e. squared error), depending on what the points represent. Note there is no requirement for symmetry: s(i,j) need not equal s(j,i). The self-similarity s(k,k) ("preference") for each point controls the likelihood it will be selected as an exemplar, and thus indirectly controls the total number of clusters. There is no way to directly specify a specific number of clusters. The authors suggest that using the median of all other similarities will give a moderate number of clusters, and using the minimum of the other similaries will give a small number of clusters.

This implementation is designed for clustering very large numbers of data points with sparse similarity [ s(i,k) = -Inf for most i,k ]. Similarities for each input point are kept in a heap so that you can limit to only the L highest for each. (This scheme is quite likely to break symmetry, as some points will have more close neighbors than others.) Alternately, you may choose to do your own pre-filtering and only enter the G globally highest similarities between any points in the data set. Run time (per cycle) is linear in the number of similarities, or O(N^2) in the limit of a dense similarity matrix.

I follow the conventions of the original paper, where "i" is the index of some generic data point, and "k" is the index of a data point being considered as an exemplar (cluster center).

Definition at line 132 of file APCluster.hh.

Constructor & Destructor Documentation

protocols::cluster::APCluster::APCluster	(	core::Size	total_pts,
		core::Size	max_sims_per_pt = `0`
	)

Create new clustering class for total_pts input data points. Optionally, set a limit on the number of similarities stored per point.

Definition at line 60 of file APCluster.cc.

References max_sims_per_pt_, and pts_.

protocols::cluster::APCluster::~APCluster ( )

virtual

Definition at line 74 of file APCluster.cc.

Member Function Documentation

core::Size protocols::cluster::APCluster::assign_exemplars ( )

protectedvirtual

Definition at line 340 of file APCluster.cc.

References protocols::cluster::DataPoint::a_kk, protocols::cluster::DataPoint::candidates, protocols::cluster::DataPoint::curr_exemplar, protocols::cluster::DataPoint::i, protocols::cluster::Exemplar::k, core::chemical::element::N, pts_, protocols::cluster::DataPoint::r_kk, and protocols::cluster::Exemplar::s_ik.

Referenced by cluster().

bool protocols::cluster::APCluster::cluster	(	core::Size	maxits,
		core::Size	convits,
		core::Real	lambda
	)

virtual

Run the actual clustering algorithm.

Parameters

maxits	maximum number of iterations, period; 100 - 4000 reasonable.
convits	terminate after clusters don't change for this many iterations, 10 - 400 reasonable.
lambda	damping factor, 0.50 - 0.95 is a reasonable range

Returns: true if the clustering converges and false otherwise. Failure to converge is not necessarily a problem – you may be close to a good solution. Try increasing maxits and/or making lambda closer to 1 if you want convergence.

Definition at line 98 of file APCluster.cc.

References assign_exemplars(), freeze(), get_net_sim(), get_num_exemplars(), is_frozen_, reinitialize(), restore_best_exemplars(), save_best_exemplars(), protocols::TR(), update_a_ik(), and update_r_ik().

void protocols::cluster::APCluster::freeze ( )

protectedvirtual

Definition at line 194 of file APCluster.cc.

References protocols::cluster::DataPoint::candidate_for, protocols::cluster::DataPoint::candidates, is_frozen_, protocols::cluster::Exemplar::k, core::chemical::element::N, and pts_.

Referenced by cluster().

void protocols::cluster::APCluster::get_all_exemplars ( utility::vector1< core::Size > & exemplars ) const

virtual

Return the indices of data points chosen as exemplars (cluster centers).

Definition at line 153 of file APCluster.cc.

References protocols::cluster::DataPoint::curr_exemplar, protocols::cluster::DataPoint::i, core::chemical::element::N, and pts_.

void protocols::cluster::APCluster::get_cluster_for	(	core::Size	k,
		utility::vector1< core::Size > &	cluster
	)		const

virtual

Returns the indices of points with the specified exemplar k. Note that k is the index of an (input) data point that was chosen as an exemplar, not some "cluster index" between 1 and get_num_exemplars().

Definition at line 163 of file APCluster.cc.

References protocols::cluster::DataPoint::curr_exemplar, core::chemical::element::N, and pts_.

virtual core::Size protocols::cluster::APCluster::get_exemplar_for ( core::Size i ) const

inlinevirtual

Return the index of the point that is the exemplar for point i.

Definition at line 148 of file APCluster.hh.

References pts_.

core::Real protocols::cluster::APCluster::get_net_sim ( ) const

virtual

The sum of similarities s(i,k) between every data point i and its exemplar k, plus the self preferences of the exemplars. The algorithm should minimize this value – if it dips and climbs again, increase lambda.

Definition at line 173 of file APCluster.cc.

References protocols::cluster::DataPoint::candidates, protocols::cluster::DataPoint::curr_exemplar, protocols::cluster::Exemplar::k, core::chemical::element::N, pts_, protocols::cluster::Exemplar::s_ik, and protocols::cluster::DataPoint::s_kk.

Referenced by cluster().

core::Size protocols::cluster::APCluster::get_num_exemplars ( ) const

virtual

The number of exemplars selected (number of clusters). Monotonically related to the self-preferences s(k,k).

Definition at line 142 of file APCluster.cc.

References protocols::cluster::DataPoint::curr_exemplar, protocols::cluster::DataPoint::i, core::chemical::element::N, and pts_.

Referenced by cluster().

bool protocols::cluster::APCluster::load_binary ( std::string const & filename )

virtual

Wipes all currently held data and reads in similarity values and cluster assignments. Afterwards, points may be re-clustered with different parameters if desired. File format is custom binary and is not portable (host endian-ness).

Definition at line 465 of file APCluster.cc.

References protocols::cluster::DataPoint::candidates, protocols::cluster::DataPoint::curr_exemplar, protocols::cluster::DataPoint::i, is_frozen_, protocols::cluster::Exemplar::k, max_sims_per_pt_, core::chemical::element::N, pts_, protocols::cluster::read1(), protocols::cluster::Exemplar::s_ik, and protocols::cluster::DataPoint::s_kk.

virtual core::Size protocols::cluster::APCluster::num_pts ( ) const

inlinevirtual

Definition at line 146 of file APCluster.hh.

References pts_.

void protocols::cluster::APCluster::reinitialize ( )

protectedvirtual

Prepares the data points for another clustering run. Does not erase similarity data, etc.

Definition at line 217 of file APCluster.cc.

References protocols::cluster::Exemplar::a_ik, protocols::cluster::DataPoint::a_kk, protocols::cluster::DataPoint::best_exemplar, protocols::cluster::DataPoint::candidates, protocols::cluster::DataPoint::curr_exemplar, core::chemical::element::N, pts_, protocols::cluster::Exemplar::r_ik, and protocols::cluster::DataPoint::r_kk.

Referenced by cluster().

void protocols::cluster::APCluster::restore_best_exemplars ( )

protectedvirtual

Definition at line 424 of file APCluster.cc.

References protocols::cluster::DataPoint::best_exemplar, protocols::cluster::DataPoint::curr_exemplar, core::chemical::element::N, and pts_.

Referenced by cluster().

void protocols::cluster::APCluster::save_best_exemplars ( )

protectedvirtual

Definition at line 415 of file APCluster.cc.

References protocols::cluster::DataPoint::best_exemplar, protocols::cluster::DataPoint::curr_exemplar, core::chemical::element::N, and pts_.

Referenced by cluster().

bool protocols::cluster::APCluster::save_binary ( std::string const & filename ) const

virtual

Saves the (sparse) similarity matrix and current cluster assignments (if any), but not the accumulated evidence from the last clustering [ r(i,k) and a(i,k) ]. File format is custom binary and is not portable (host endian-ness).

Definition at line 441 of file APCluster.cc.

References protocols::cluster::DataPoint::candidates, protocols::cluster::DataPoint::curr_exemplar, protocols::cluster::DataPoint::i, protocols::cluster::Exemplar::k, max_sims_per_pt_, core::chemical::element::N, pts_, protocols::cluster::Exemplar::s_ik, protocols::cluster::DataPoint::s_kk, and protocols::cluster::write1().