Software
Software.Software History
Show minor edits - Show changes to output
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[[#blosom]]
!!!!!Sampling Minimal Boolean Expressions (minDNF)
The minDNF method samples minimal boolean expressions in DNF.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/minDNF.tar.gz | minDNF code]]:
>><<
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[[#schism]]
!!!!!Interesting Subspace Mining (SCHISM)
SCHISM finds interesting subspace clusters.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/SCHISM.tar.gz | SCHISM code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2004-schism]
** bibtexsummary:[zakipapers.bib,2005-schism:ijbidm]
>><<
\\\
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!!!!!Graph Pattern Sampling (MUSK)
to:
!!!!!Graph Pattern Sampling (Output Space Sampling)
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** [[Path:/~zaki/software/MUSK.tar.gz | MUSK code (coming soon)]]: for maximal patterns
** [[Path:/~zaki/software/OSS.tar.gz | Graph Sampling code (coming soon)]]: for all, support-biased and discriminative patterns
** [[Path:/~zaki/software/OSS.tar.gz | Graph Sampling code (coming soon)]]: for all, support-biased and discriminative patterns
to:
** [[Path:/~zaki/software/OSS.tar.gz | Graph Sampling code]]: for all, support-biased and discriminative graph pattern sampling
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** [[http://cran.r-project.org/web/packages/arulesSequences/index.html | aRulesSequences (R)]]: R package that contains the cSPADE code (Courtesy: Christian Buchta and Michael Hahsler, Vienna University of Economics and Business Administration).
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** [[Path:/~zaki/software/cSPADE-win.tgz | cSpade (win) code]]: same as above, but for the Windows platform (Courtesy: Daniel Diaz, University of Paris 1 - Pantheon Sorbonne).
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** [[Path:/~zaki/software/TPOSE-win.tgz | Utilities (win) code]]: same as above, but for the Windows platform (Courtesy: Daniel Diaz, University of Paris 1 - Pantheon Sorbonne).
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** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, minimal CNF expressions and '''xug''' find minimal DNF expressions.
to:
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, and-clauses, CNF and DNF expressions, '''xng''' finds closed CNF expressions and '''xug''' find closed DNF expressions.
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!!Graph Mining
to:
!!Graph Mining & Indexing
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\\\
[#grail]]
!!!!!Scalable Graph Reachability Indexing (GRAIL)
GRAIL uses random multiple interval labelings, and a variety of optimizations to perform rapid reachability testing in very large graphs (with millions of nodes and edges).
>>frame<<
* '''Download'''
** [[http://code.google.com/p/grail/ | GRAIL code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2010-grail]
>><<
\\\
[#grail]]
!!!!!Scalable Graph Reachability Indexing (GRAIL)
GRAIL uses random multiple interval labelings, and a variety of optimizations to perform rapid reachability testing in very large graphs (with millions of nodes and edges).
>>frame<<
* '''Download'''
** [[http://code.google.com/p/grail/ | GRAIL code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2010-grail]
>><<
\\\
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** [[Path:/~zaki/software/vogue | VOGUE code]]
to:
** [[Path:/~zaki/software/VOGUE | VOGUE code]]
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** bibtexsummary:[zakipapers.bib,2009-vogue:tkdd]
to:
** bibtexsummary:[zakipapers.bib,2010-vogue:tkdd]
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[[#sequences]]
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[[#trees]]
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[[#graphs]]
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[[#clustering]]
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[[#bioseq]]
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[[#proteins]]
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[[#data]]
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[[#dataend]]
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(:htoc start=1 end=2 class=htoneline:)
----
\\
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(:htoc start=1 end=2 class=htoneline:)
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----
\\
!!Microarray Gene Expression Clustering
\\
to:
\\\
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!!!!! Triclusters and Biclusters (TriCluster and MicroCluster)
to:
!!!!!Microarray Gene Expression Clustering (TriCluster and MicroCluster)
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!!Hidden Markov Models (HMM)
\\
\\
to:
!! Biological Sequence Analysis
This section contains code for sequence modeling via Hidden Markov Models, code for structured motif extraction and search, and genome-scale disk-based suffix tree indexing.
This section contains code for sequence modeling via Hidden Markov Models, code for structured motif extraction and search, and genome-scale disk-based suffix tree indexing.
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!!!!!Variable Order HMM with Duration (VOGUE)
to:
!!!!!Hidden Markov Models: Variable Order HMM with Duration (VOGUE)
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----
!!!!!
to:
\\\
!!!!!Genome Scale Indexing: Disk-based Suffix Trees (Trellis and Trellis+)
!!!!!Genome Scale Indexing: Disk-based Suffix Trees (Trellis and Trellis+)
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----
!!!!!sMotif
to:
\\\
!!!!!Structured Sequence Motifs: Search and Extraction (sMotif and exMotif)
!!!!!Structured Sequence Motifs: Search and Extraction (sMotif and exMotif)
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!!!!!Protein Docking
to:
!!!!!Protein Docking and Partial Shape Matching (ContextShapes)
ContextShapes does rigid-body protein docking. It uses a novel contextshapes data structure to represent local surface regions/shapes on the protein. All critical points on both the receptor and ligand are represented via context shapes, and the best docking is found via pair-wise matching.
ContextShapes does rigid-body protein docking. It uses a novel contextshapes data structure to represent local surface regions/shapes on the protein. All critical points on both the receptor and ligand are represented via context shapes, and the best docking is found via pair-wise matching.
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>>cframe width=80pct<<
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>>important<<
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complex and informative patterns types such as: '''%red%Itemsets, Sequences, Trees and Graphs%%'''.
to:
complex and informative patterns types such as: '''Itemsets, Sequences, Trees and Graphs'''.
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>>frame<<
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>>cframe width=80pct<<
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>>frame width=60pct<<
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>>frame<<
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>>frame width=60pct<<
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>>frame<<
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(:toc-back:)
\\
\\
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\\
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(:toc-back:)
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(:toc-back:)
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(:toc-back:)
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(:toc-back:)
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!!!!!Origami
to:
!!!!!Representative Orthogonal Graph Mining (Origami)
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!!!!!Graph Pattern Sampling
to:
!!!!!Graph Pattern Sampling (MUSK)
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(:toc-back:)
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This section contains code for mining categorical subspace clusters, shape based clusters, for clustering based on a lower bound on similarity, and a new outlier-based approach for initial cluster seed selection.
\\
\\
to:
This section contains code for mining categorical subspace clusters, shape based clusters, for clustering
based on a lower bound on similarity, and a new outlier-based approach for initial cluster seed selection.
based on a lower bound on similarity, and a new outlier-based approach for initial cluster seed selection.
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!!!!!CLICKS
to:
!!!!!Categorical Subspace Clustering (CLICKS)
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!!!!!Sparcl
to:
!!!!!Arbitrary Shape Clustering (Sparcl)
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!!!!!Robin
to:
!!!!!K-means Initialization (Robin)
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(:toc-back:)
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!!!!!TriCluster and MicroCluster
to:
!!!!! Triclusters and Biclusters (TriCluster and MicroCluster)
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(:toc-back:)
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(:toc-back:)
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!!!!!Trellis and Trellis+
to:
!!!!!Disk-based Suffix Trees (Trellis and Trellis+)
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(:toc-back:)
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(:toc-back:)
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(:toc-back:)
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** [[Path:/~zaki/software/IBM-datagen.tar.gz | IBM Datagen program]: contains the IBM synthetic dataset generator for itemset patterns
to:
** [[Path:/~zaki/software/IBM-datagen.tar.gz | IBM Datagen program]]: contains the IBM synthetic dataset generator for itemset patterns
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>><<
to:
>><<
(:toc-back:)
(:toc-back:)
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VOGUE is a variable order and gapped HMM with with duration. It uses sequence mining to extract frequent patterns in the data. It then uses these patterns to build a variable order HMM with explicit duration on the gap states, for sequence modeling and classification.
to:
VOGUE is a variable order and gapped HMM with with duration. It uses sequence mining to extract frequent patterns in the data. It then uses these patterns to build a variable order HMM with explicit duration on the gap states, for sequence modeling and classification. VOGUE was applied to model protein sequences, as well as a number of other sequence datasets including weblogs.
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----
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----
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!!Genome Scale Indexing
\\
\\
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----
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to:
----
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!!!!!Flexible and Non-sequential Protein Structure Alignment (SNAP/STSA and FlexSnap)
SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA {[zakipapers.bib,2008-snap]}. FlexSnap allows the ability to find both flexible and non-sequential allignments.
SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA {[zakipapers
to:
!!Structured Sequence Motifs: Search and Extraction
\\
!!!!!sMotif and exMotif
sMotif and exMotif are two complementary for searching and extracting/mining structured sequence motifs DNA sequences. A structured motif consists of simple motifs separated by different gap lengths. The simple motif may be a simple pattern or a position weighted matrix or profile. Given a template structured motif (pattern or profile), sMotif finds all matches in a given set of sequences. On the other hand, exMotif mines novel motifs matching some minimal conditions on the gaps and frequency.
\\
!!!!!sMotif and exMotif
sMotif and exMotif are two complementary for searching and extracting/mining structured sequence motifs DNA sequences. A structured motif consists of simple motifs separated by different gap lengths. The simple motif may be a simple pattern or a position weighted matrix or profile. Given a template structured motif (pattern or profile), sMotif finds all matches in a given set of sequences. On the other hand, exMotif mines novel motifs matching some minimal conditions on the gaps and frequency.
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** [[Path:/~zaki/software/SNAP/ | SNAP executables]]
** [[Path:/~zaki/software/FlexSNAP/ | FlexSNAP (coming soon)]]
to:
** [[Path:/~zaki/software/exMotif | exMotif code]]: for structured motif extraction
** [[Path:/~zaki/software/sMotif | sMotif code]]: for structured motif search
** [[Path:/~zaki/software/sMotif | sMotif code]]: for structured motif search
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** bibtexsummary:[zakipapers.bib,2009-snap:jbcb]
** bibtexsummary:[zakipapers.bib,2009-flexsnap]
** bibtexsummary:[zakipapers.bib,
to:
** bibtexsummary:[zakipapers.bib,2006-exmotif:amb]
** bibtexsummary:[zakipapers.bib,2006-smotif:amb]
** bibtexsummary:[zakipapers.bib,2006-smotif:amb]
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\\\
!!!Protein Docking (ContextShapes)
to:
\\
----
\\
!! Protein Structure
\\
!!!!!Flexible and Non-sequential Protein Structure Alignment (SNAP/STSA and FlexSnap)
SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA {[zakipapers.bib,2008-snap]}. FlexSnap allows the ability to find both flexible and non-sequential allignments.
----
\\
!! Protein Structure
\\
!!!!!Flexible and Non-sequential Protein Structure Alignment (SNAP/STSA and FlexSnap)
SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA {[zakipapers.bib,2008-snap]}. FlexSnap allows the ability to find both flexible and non-sequential allignments.
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** [[Path:/~zaki/software/ContextShapes | ContextShapes code]]
to:
** [[Path:/~zaki/software/SNAP/ | SNAP executables]]
** [[Path:/~zaki/software/FlexSNAP/ | FlexSNAP (coming soon)]]
** [[Path:/~zaki/software/FlexSNAP/ | FlexSNAP (coming soon)]]
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** bibtexsummary:[zakipapers.bib,2008-contextshapes:proteins]
to:
** bibtexsummary:[zakipapers.bib,2009-snap:jbcb]
** bibtexsummary:[zakipapers.bib,2009-flexsnap]
** bibtexsummary:[zakipapers.bib,2009-flexsnap]
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!!!!!Protein Indexing (PSIST)
PSIST uses suffix trees to index protein 3D structure. It first converts the 3D structure into a structure-feature sequence over a new structural alphabet, which is then used to index protein structures. The PSIST index makes it very fast to query for a matching structural fragment.
PSIST uses suffix trees to index protein 3D structure. It first converts the 3D structure into a structure-feature sequence over a new structural alphabet, which is then used to index protein structures. The PSIST index makes it very fast to query for a matching structural fragment.
to:
!!!!!Protein Docking (ContextShapes)
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** [[Path:/~zaki/software/PSIST.tar.gz | PSIST code]]
to:
** [[Path:/~zaki/software/ContextShapes | ContextShapes code]]
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** bibtexsummary:[zakipapers.bib,2008-psist:jpdc]
to:
** bibtexsummary:[zakipapers.bib,2008-contextshapes:proteins]
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\\
----
\
!!Real and Synthetic Datasets
The section contains various synthetic and real datasets used in some ofthe papers related to itemset, sequence, tree and XML mining.
----
The section contains various synthetic and real datasets used in some of
to:
\\\
!!!!!Protein Indexing (PSIST)
PSIST uses suffix trees to index protein 3D structure. It first converts the 3D structure into a structure-feature sequence over a new structural alphabet, which is then used to index protein structures. The PSIST index makes it very fast to query for a matching structural fragment.
!!!!!Protein Indexing (PSIST)
PSIST uses suffix trees to index protein 3D structure. It first converts the 3D structure into a structure-feature sequence over a new structural alphabet, which is then used to index protein structures. The PSIST index makes it very fast to query for a matching structural fragment.
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** [[Path:/~zaki/software/IBM-datagen.tgz | IBM Datagen program]: contains the IBM synthetic dataset generator for itemset patterns.
** [[Path/~zaki/software/TreeGen.tgz | Tree Generator]]: contains the synthetic tree generator described in {[zakipapers.bib,2005-treeminer:tkde]}.
** [[Path:/~zaki/software/DENSE_DB.tar.gz | Real Datasets]]: contains various real itemset datasets like '''chess''', '''connect''', '''mushroom''','''pumsb''' and so on, used in the papers on frequent, closed and maximal itemset mining.
** [[Path:/~zaki/software/CSLOGS.tar.gz | CSLOGS data ]]: The CSLOGS data was used for {[zakipapers.bib,2005-treeminer:tkde]}.
** [[Path:/~zaki/software/logml | Xrules Log Data ]]: The log data used for XML classification in {[zakipapers.bib,2006-xrules:mlj]}.
** [[Path
** [[Path:/~zaki/software/DENSE_DB.tar.gz | Real Datasets]]: contains various real itemset datasets like '''chess''', '''connect''', '''mushroom''',
** [[Path
** [[Path:/~zaki/software/logml | Xrules Log Data ]]: The log data used for XML classification in {[zakipapers
to:
** [[Path:/~zaki/software/PSIST.tar.gz | PSIST code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2008-psist:jpdc]
>><<
\\\
!!!!!Protein Folding Pathways (UNFOLD)
UNFOLD uses a recursive min-cut on a weighted secondary structure element graph to predict the sequence of protein (un)folding events.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/UNFOLD.tar.gz | UNFOLD code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2004-pathways:bioinfo]
>><<
\\
----
\\
!!Real and Synthetic Datasets
The section contains various synthetic and real datasets used in some of the papers related to itemset, sequence, tree and XML mining.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/IBM-datagen.tar.gz | IBM Datagen program]: contains the IBM synthetic dataset generator for itemset patterns
** [[Path:/~zaki/software/TreeGen.tar.gz | Tree Generator]]: contains the synthetic tree generator described in {[zakipapers.bib,2005-treeminer:tkde]}
** [[Path:/~zaki/software/DENSE_DB.tar.gz | Real Datasets]]: contains various real itemset datasets like '''chess''', '''connect''', '''mushroom''', '''pumsb''' and so on, used in the papers on frequent, closed and maximal itemset mining
** [[Path:/~zaki/software/CSLOGS.tar.gz | CSLOGS data ]]: The CSLOGS data was used for {[zakipapers.bib,2005-treeminer:tkde]}
** [[Path:/~zaki/software/logml | Xrules Log Data ]]: The log data used for XML classification in {[zakipapers.bib,2006-xrules:mlj]}
** [[Path:/~zaki/software/Xrules-Synth-Data.tar.gz | Xrules synthetic datasets ]]: The synthetic classification data used for XML classification in {[zakipapers.bib,2006-xrules:mlj]}
** [[Path:/~zaki/software/plandata.gz | Plan dataset ]]: Planning dataset for sequence mining
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2008-psist:jpdc]
>><<
\\\
!!!!!Protein Folding Pathways (UNFOLD)
UNFOLD uses a recursive min-cut on a weighted secondary structure element graph to predict the sequence of protein (un)folding events.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/UNFOLD.tar.gz | UNFOLD code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2004-pathways:bioinfo]
>><<
\\
----
\\
!!Real and Synthetic Datasets
The section contains various synthetic and real datasets used in some of the papers related to itemset, sequence, tree and XML mining.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/IBM-datagen.tar.gz | IBM Datagen program]: contains the IBM synthetic dataset generator for itemset patterns
** [[Path:/~zaki/software/TreeGen.tar.gz | Tree Generator]]: contains the synthetic tree generator described in {[zakipapers.bib,2005-treeminer:tkde]}
** [[Path:/~zaki/software/DENSE_DB.tar.gz | Real Datasets]]: contains various real itemset datasets like '''chess''', '''connect''', '''mushroom''', '''pumsb''' and so on, used in the papers on frequent, closed and maximal itemset mining
** [[Path:/~zaki/software/CSLOGS.tar.gz | CSLOGS data ]]: The CSLOGS data was used for {[zakipapers.bib,2005-treeminer:tkde]}
** [[Path:/~zaki/software/logml | Xrules Log Data ]]: The log data used for XML classification in {[zakipapers.bib,2006-xrules:mlj]}
** [[Path:/~zaki/software/Xrules-Synth-Data.tar.gz | Xrules synthetic datasets ]]: The synthetic classification data used for XML classification in {[zakipapers.bib,2006-xrules:mlj]}
** [[Path:/~zaki/software/plandata.gz | Plan dataset ]]: Planning dataset for sequence mining
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[[#patutils]]
!!Itemset and Sequence Utilities
!!
to:
[[#blosom]]
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
Changed lines 124-128 from:
** [[Path:/~zaki/software/TPOSE.tar.gz | Utilities code]]: provides exttpose, getconf, and makebin
to:
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, '''xng''' finds minimal CNF expressions and '''xug''' find minimal DNF expressions.
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
Deleted lines 129-143:
[[#blosom]]
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, '''xng''' finds minimal CNF expressions and '''xug''' find minimal DNF expressions.
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
>><<
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!!Tree Mining
to:
[[#patutils]]
!!Itemset and Sequence Utilities
Provides the utilities needed for [[#eclat | Eclat]], [[#charm | Charm/Charm-L]], [[#genmax | GenMax]], [[#spade | Spade]] and [[#cspade | cSpade]].
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/TPOSE.tar.gz | Utilities code]]: provides exttpose, getconf, and makebin
>><<
!!Itemset and Sequence Utilities
Provides the utilities needed for [[#eclat | Eclat]], [[#charm | Charm/Charm-L]], [[#genmax | GenMax]], [[#spade | Spade]] and [[#cspade | cSpade]].
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/TPOSE.tar.gz | Utilities code]]: provides exttpose, getconf, and makebin
>><<
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----
\\
!!Tree Mining
\\
\\
!!Tree Mining
\\
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to:
\\
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----
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!!Datasets
to:
!!Real and Synthetic Datasets
The section contains various synthetic and real datasets used in some of the papers related to itemset, sequence, tree and XML mining.
The section contains various synthetic and real datasets used in some of the papers related to itemset, sequence, tree and XML mining.
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** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers
to:
** [[Path:/~zaki/software/IBM-datagen.tgz | IBM Datagen program]: contains the IBM synthetic dataset generator for itemset patterns.
** [[Path:/~zaki/software/TreeGen.tgz | Tree Generator]]: contains the synthetic tree generator described in {[zakipapers.bib,2005-treeminer:tkde]}.
** [[Path:/~zaki/software/DENSE_DB.tar.gz | Real Datasets]]: contains various real itemset datasets like '''chess''', '''connect''', '''mushroom''', '''pumsb''' and so on, used in the papers on frequent, closed and maximal itemset mining.
** [[Path:/~zaki/software/CSLOGS.tar.gz | CSLOGS data ]]: The CSLOGS data was used for {[zakipapers.bib,2005-treeminer:tkde]}.
** [[Path:/~zaki/software/logml | Xrules Log Data ]]: The log data used for XML classification in {[zakipapers.bib,2006-xrules:mlj]}.
** [[Path:/~zaki/software/TreeGen.tgz | Tree Generator]]: contains the synthetic tree generator described in {[zakipapers.bib,2005-treeminer:tkde]}.
** [[Path:/~zaki/software/DENSE_DB.tar.gz | Real Datasets]]: contains various real itemset datasets like '''chess''', '''connect''', '''mushroom''', '''pumsb''' and so on, used in the papers on frequent, closed and maximal itemset mining.
** [[Path:/~zaki/software/CSLOGS.tar.gz | CSLOGS data ]]: The CSLOGS data was used for {[zakipapers.bib,2005-treeminer:tkde]}.
** [[Path:/~zaki/software/logml | Xrules Log Data ]]: The log data used for XML classification in {[zakipapers.bib,2006-xrules:mlj]}.
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[[#blosom]]
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
!!
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
to:
[[#patutils]]
!!Itemset and Sequence Utilities
!!Itemset and Sequence Utilities
Changed lines 122-126 from:
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, '''xng''' finds minimal CNF expressions and '''xug''' find minimal DNF expressions.
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
to:
** [[Path:/~zaki/software/TPOSE.tar.gz | Utilities code]]: provides exttpose, getconf, and makebin
Added lines 124-138:
\\\
[[#blosom]]
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, '''xng''' finds minimal CNF expressions and '''xug''' find minimal DNF expressions.
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
>><<
[[#blosom]]
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, '''xng''' finds minimal CNF expressions and '''xug''' find minimal DNF expressions.
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
>><<
Deleted lines 226-229:
----
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to:
----
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!!Graph Mining
\\
\\
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!!!Origami
to:
!!!!!Origami
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!!!Graph Pattern Sampling
to:
!!!!!Graph Pattern Sampling
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to:
\\
[[#clicks]]
[[#clicks]]
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[[#sparcl]]
Added line 301:
[[#robin]]
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to:
\\
[[#tricluster]]
!!!!!TriCluster and MicroCluster
Tricluster is the first tri-clustering algorithm for microarray expression clustering. It builds upon the new microCluster bi-clustering approach. Tricluster first mines all the bi-clusters across the gene-sample slices, and then it extends these into tri-clusters across time or space (depending on the third dimension). It can find both scaling and shifting patterns.
[[#tricluster]]
!!!!!TriCluster and MicroCluster
Tricluster is the first tri-clustering algorithm for microarray expression clustering. It builds upon the new microCluster bi-clustering approach. Tricluster first mines all the bi-clusters across the gene-sample slices, and then it extends these into tri-clusters across time or space (depending on the third dimension). It can find both scaling and shifting patterns.
Changed lines 327-328 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/TriCluster.tar.gz | Tricluster code]]
** [[Path:/~zaki/software/microCluster.tar.gz | microCluster code]]
** [[Path:/~zaki/software/microCluster.tar.gz | microCluster code]]
Changed lines 331-332 from:
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2005-tricluster]
** bibtexsummary:[zakipapers.bib,2005-microcluster:is]
** bibtexsummary:[zakipapers.bib,2005-microcluster:is]
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\\\
!!!!!MicroCluster
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
!!!!!MicroCluster
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
to:
\\
Deleted lines 336-348:
!!Hidden Markov Models
!!!!!VOGUE
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
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!!Genome Scale Indexing
!!!!!Trellis
to:
!!Hidden Markov Models (HMM)
\\
[[#vogue]]
!!!!!Variable Order HMM with Duration (VOGUE)
VOGUE is a variable order and gapped HMM with with duration. It uses sequence mining to extract frequent patterns in the data. It then uses these patterns to build a variable order HMM with explicit duration on the gap states, for sequence modeling and classification.
\\
[[#vogue]]
!!!!!Variable Order HMM with Duration (VOGUE)
VOGUE is a variable order and gapped HMM with with duration. It uses sequence mining to extract frequent patterns in the data. It then uses these patterns to build a variable order HMM with explicit duration on the gap states, for sequence modeling and classification.
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** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/vogue | VOGUE code]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2009-vogue:tkdd]
Changed lines 358-360 from:
!!Protein Structure Alignment
!!!!!Snap
to:
!!Genome Scale Indexing
\\
!!!!!Trellis and Trellis+
Trellis is a disk-based suffix tree indexing methods (with suffix links) that is capable of indexing the entire human genome on a commodity PC with limited memory. Trellis+ extends Trellis by further removing some memory limitations by using a novel guide suffix tree in memory.
\\
!!!!!Trellis and Trellis+
Trellis is a disk-based suffix tree indexing methods (with suffix links) that is capable of indexing the entire human genome on a commodity PC with limited memory. Trellis+ extends Trellis by further removing some memory limitations by using a novel guide suffix tree in memory.
Changed lines 367-368 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/trellis/TRELLIS_DIST.tar.gz | Trellis code]]: input sequence must be in memory
** [[Path:/~zaki/software/trellis/TRELLIS_BUFFER_DIST.tar.gz | Trellis+ code]]: removes all memory limitations
** [[Path:/~zaki/software/trellis/TRELLIS_BUFFER_DIST.tar.gz | Trellis+ code]]: removes all memory limitations
Changed lines 372-373 from:
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2007-trellis]
** bibtexsummary:[zakipapers.bib,2008-trellis+]
** bibtexsummary:[zakipapers.bib,2008-trellis+]
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!!!!!FlexSnap
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
to:
Changed lines 379-381 from:
!!Protein Docking
!!!!!ContextShapes
to:
!! Protein Structure
!!!!!Flexible and Non-sequential Protein Structure Alignment (SNAP/STSA and FlexSnap)
SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA {[zakipapers.bib,2008-snap]}. FlexSnap allows the ability to find both flexible and non-sequential allignments.
!!!!!Flexible and Non-sequential Protein Structure Alignment (SNAP/STSA and FlexSnap)
SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA {[zakipapers.bib,2008-snap]}. FlexSnap allows the ability to find both flexible and non-sequential allignments.
Changed lines 387-388 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/SNAP/ | SNAP executables]]
** [[Path:/~zaki/software/FlexSNAP/ | FlexSNAP (coming soon)]]
** [[Path:/~zaki/software/FlexSNAP/ | FlexSNAP (coming soon)]]
Changed lines 391-392 from:
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2009-snap:jbcb]
** bibtexsummary:[zakipapers.bib,2009-flexsnap]
** bibtexsummary:[zakipapers.bib,2009-flexsnap]
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!!!!!PSIST
to:
\\\
!!!!!Protein Docking (ContextShapes)
!!!!!Protein Docking (ContextShapes)
Changed lines 399-400 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/ContextShapes | ContextShapes code]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2008-contextshapes:proteins]
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to:
\\\
!!!!!Protein Indexing (PSIST)
PSIST uses suffix trees to index protein 3D structure. It first converts the 3D structure into a structure-feature sequence over a new structural alphabet, which is then used to index protein structures. The PSIST index makes it very fast to query for a matching structural fragment.
!!!!!Protein Indexing (PSIST)
PSIST uses suffix trees to index protein 3D structure. It first converts the 3D structure into a structure-feature sequence over a new structural alphabet, which is then used to index protein structures. The PSIST index makes it very fast to query for a matching structural fragment.
Changed lines 412-413 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/PSIST.tar.gz | PSIST code]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2008-psist:jpdc]
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----
\\
\\
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!!!!!Eclat
to:
!!!!!Frequent Itemsets (Eclat)
Changed lines 82-83 from:
!!!!!Charm, Charm-L and Non-redundant Rule Generation
to:
!!!!!Closed Itemsets (Charm, Charm-L) and Non-redundant Rule Generation
Changed lines 103-104 from:
!!!!!GenMax
to:
!!!!! Maximal Itemsets (GenMax)
Added lines 115-129:
\\\
[[#blosom]]
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, '''xng''' finds minimal CNF expressions and '''xug''' find minimal DNF expressions.
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
>><<
[[#blosom]]
!!!!!Frequent Boolean Expressions (BLOSOM)
The BLOSOM framework allows one to mine arbitrary frequent boolean expressions include AND clauses (itemsets), OR clauses, and CNF/DNF expressions. It focuses on mining the minimal boolean expressions.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/BLOSOM.tar.gz | BLOSOM code]]: '''mug''' find minimal or-clauses, '''xng''' finds minimal CNF expressions and '''xug''' find minimal DNF expressions.
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L]]: this code can mine all minimal and closed and-clauses, i.e., all minimal and closed frequent itemsets.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-blosom]
>><<
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!!!!!Spade
to:
!!!!!Frequent Sequences (Spade)
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!!!!!cSpade
to:
!!!!!Sequence Constraints (cSpade)
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!!!!!SLEUTH
to:
!!!!! SLEUTH
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\\\
!!!!!XML Classification (XRules)
XRules uses [[#treeminer | frequent tree mining]] to mine discriminative patterns from tree-structured XML documents.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/XRULES.tar.gz | XRULES code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-xrules:mlj]
>><<
----
!!!!!XML Classification (XRules)
XRules uses [[#treeminer | frequent tree mining]] to mine discriminative patterns from tree-structured XML documents.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/XRULES.tar.gz | XRULES code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2006-xrules:mlj]
>><<
----
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to:
!!Graph Mining
Deleted lines 226-227:
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** [[Path:/~zaki/software/MUSK.tar.gz | MUSK code]]: for maximal patterns
** [[Path:/~zaki/software/MUSK.tar.gz | Graph Sampling code]]: for all, support-biased and discriminative patterns
** [[Path:/~zaki/software/
to:
** [[Path:/~zaki/software/MUSK.tar.gz | MUSK code (coming soon)]]: for maximal patterns
** [[Path:/~zaki/software/OSS.tar.gz | Graph Sampling code (coming soon)]]: for all, support-biased and discriminative patterns
** [[Path:/~zaki/software/OSS.tar.gz | Graph Sampling code (coming soon)]]: for all, support-biased and discriminative patterns
Changed lines 260-262 from:
!!Boolean Expression Mining
!!!!!BLOSOM
to:
!! Clustering
This section contains code for mining categorical subspace clusters, shape based clusters, for clustering based on a lower bound on similarity, and a new outlier-based approach for initial cluster seed selection.
!!!!!CLICKS
CLICKS finds subspace clusters in categorical data using a k-partite clique mining approach.
This section contains code for mining categorical subspace clusters, shape based clusters, for clustering based on a lower bound on similarity, and a new outlier-based approach for initial cluster seed selection.
!!!!!CLICKS
CLICKS finds subspace clusters in categorical data using a k-partite clique mining approach.
Changed lines 270-271 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/CLICKS.tar.gz | CLICKS code]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2007-clicks:dke]
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to:
\\\
!!!!!Sparcl
Sparcl finds shape-based clusters. It uses a two step approach: in the first step we select a relatively large number of candidate centroids (via [[#robin | ROBIN]]) to find seed clusters via the K-means algorithm and in the second step we use a novel similarity kernel to merge the initial seed clusters to yield the final arbitrary shaped clusters.
!!!!!Sparcl
Sparcl finds shape-based clusters. It uses a two step approach: in the first step we select a relatively large number of candidate centroids (via [[#robin | ROBIN]]) to find seed clusters via the K-means algorithm and in the second step we use a novel similarity kernel to merge the initial seed clusters to yield the final arbitrary shaped clusters.
Changed lines 283-284 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/SPARCL.tar.gz | SPARCL code (coming soon)]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2009-sparcl:kais]
Changed lines 290-292 from:
!!!!!Sparcl
to:
!!!!!Robin
ROBIN uses a new local outllier factor based initial seed selection to improve k-means style clustering.
ROBIN uses a new local outllier factor based initial seed selection to improve k-means style clustering.
Changed lines 295-296 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/ROBIN.tar.gz | ROBIN code (coming soon)]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2009-robin:prl]
Deleted lines 299-310:
!!!!!Robin
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
Deleted lines 300-310:
!!XML Classification
!!!!!Xrules
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
Changed lines 181-182 from:
SLEUTH extends the TreeMiner methodology to mine all frequent embedded or induced as well as ordered or unordered tree patterns.
to:
SLEUTH extends the [[#treeminer | TreeMiner]] methodology to mine all frequent embedded or induced as well as ordered or unordered tree patterns.
Deleted lines 189-190:
---
Added lines 192-194:
---
\\
\\
Added line 197:
[[#origami]]
Added lines 200-201:
Origami uses random walks over the graph partial order to mine a representative sample of the maximal frequent subgraph patterns. It next selects only the orthogonal representative patterns via a local clique-finding method.
Changed lines 204-205 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/ORIGAMI.tar.gz | Origami code (coming soon)]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2008-origami:sadm]
Changed lines 211-215 from:
!!!Musk
to:
[[#graphsamplng]]
!!!Graph Pattern Sampling
Whereas [[#origami | Origami]] can mine a sample of maximal graph patterns it does not provide any uniformity guarantee. MUSK {[zakipapers.bib,2009-musk]} proposes a Markov Chain Monte Carlo based approach to guarantee a uniform sample of all maximal patterns. The MCMC approach was further extended in {[zakipapers.bib,2009-graphsampling]} to mine a sample of all frequent patterns, to mine support-biased patterns and also to mine a sample of discriminative patterns.
!!!Graph Pattern Sampling
Whereas [[#origami | Origami]] can mine a sample of maximal graph patterns it does not provide any uniformity guarantee. MUSK {[zakipapers.bib,2009-musk]} proposes a Markov Chain Monte Carlo based approach to guarantee a uniform sample of all maximal patterns. The MCMC approach was further extended in {[zakipapers.bib,2009-graphsampling]} to mine a sample of all frequent patterns, to mine support-biased patterns and also to mine a sample of discriminative patterns.
Changed lines 218-219 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/MUSK.tar.gz | MUSK code]]: for maximal patterns
** [[Path:/~zaki/software/MUSK.tar.gz | Graph Sampling code]]: for all, support-biased and discriminative patterns
** [[Path:/~zaki/software/MUSK.tar.gz | Graph Sampling code]]: for all, support-biased and discriminative patterns
Changed lines 222-223 from:
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2009-musk]
** bibtexsummary:[zakipapers.bib,2009-graphsampling]
** bibtexsummary:[zakipapers.bib,2009-graphsampling]
Changed lines 225-234 from:
\\\
!!!OSS
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
!!!OSS
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
to:
\\
Changed lines 166-167 from:
Treeminer uses the vertical scope-list representation to mine frequent sequences {[2005-treeminer:tkde]}. Treeminer counts all embeddings, whereas Treeminer-D counts only distinct occurrences, which can be more appropriate for some datasets.
to:
Treeminer uses the vertical scope-list representation to mine frequent sequences {[zakipapers.bib,2005-treeminer:tkde]}. Treeminer counts all embeddings, whereas Treeminer-D counts only distinct occurrences, which can be more appropriate for some datasets.
Changed line 170 from:
** [[Path:/~zaki/software/TreeMiner.tar.gz | TreeMiner code]]
to:
** [[Path:/~zaki/software/TreeMiner.tar.gz | TreeMiner code]]: vtreeminer is the TreeMiner code, whereas htreeminer is the PatternMatcher code as mentioned in the paper below.
Added lines 181-182:
SLEUTH extends the TreeMiner methodology to mine all frequent embedded or induced as well as ordered or unordered tree patterns.
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** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/SLEUTH.tar.gz | SLEUTH code]]
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** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2005-sleuth:fi]
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to:
\\
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to:
** You also need to download utilities like getconf, exttpose from [[#patutils | Utilities]] section.
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----
Added lines 157-159:
----
\\
\\
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to:
\\
[[#treeminer]]
!!!!!TreeMiner and TreeMiner-D
Treeminer uses the vertical scope-list representation to mine frequent sequences {[2005-treeminer:tkde]}. Treeminer counts all embeddings, whereas Treeminer-D counts only distinct occurrences, which can be more appropriate for some datasets.
[[#treeminer]]
!!!!!TreeMiner and TreeMiner-D
Treeminer uses the vertical scope-list representation to mine frequent sequences {[2005-treeminer:tkde]}. Treeminer counts all embeddings, whereas Treeminer-D counts only distinct occurrences, which can be more appropriate for some datasets.
Changed lines 170-171 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/TreeMiner.tar.gz | TreeMiner code]]
** [[Path:/~zaki/software/TreeMinerD.tar.gz | TreeMiner-D code]]
** [[Path:/~zaki/software/TreeMinerD.tar.gz | TreeMiner-D code]]
Changed lines 174-184 from:
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!TreeMiner-D
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!TreeMiner-D
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd
to:
** bibtexsummary:[zakipapers.bib,2005-treeminer:tkde]
Changed lines 92-93 from:
** [[Path:/~zaki/software/CHARM.tar.gz | Charm Code]]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L and Non-redundant Rules]]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L and Non-redundant Rules]]
to:
** [[Path:/~zaki/software/CHARM.tar.gz | Charm code]]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L and Non-redundant Rules code]]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L and Non-redundant Rules code]]
Changed line 109 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax code]]
Deleted lines 114-115:
----
Added lines 117-119:
----
\\
\\
Added lines 125-126:
Spade uses the vertical format for mining the set of all frequent sequences from a dataset of many sequences. It also mines the frequent sequences of itemsets.
Changed lines 129-130 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/SPADE.tar.gz | Spade code]]
** You also need to download utilities like getconf, exttpose from [[#patutils | Utilities]] section.
** You also need to download utilities like getconf, exttpose from [[#patutils | Utilities]] section.
Changed line 133 from:
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2001-spade:mlj]]
Added lines 139-145:
cSpade mines constrained frequent sequences. The constraints can take the form of length or width limitations on the
sequences, minimum or maximum gap constraints on consecutive
sequence elements, applying a time window on allowable
sequences, incorporating item constraints, and finding
sequences predictive of one or more classes. The class specific sequences can be used for sequence classification as
described in {[2000-featuremine:is]}.
sequences, minimum or maximum gap constraints on consecutive
sequence elements, applying a time window on allowable
sequences, incorporating item constraints, and finding
sequences predictive of one or more classes. The class specific sequences can be used for sequence classification as
described in {[2000-featuremine:is]}.
Changed lines 148-149 from:
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
to:
** [[Path:/~zaki/software/cSPADE.tar.gz | cSpade code]]
Changed line 151 from:
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2000-cspade]
Changed line 70 from:
>>frame<<
to:
>>frame width=60pct<<
Changed lines 73-74 from:
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
to:
** You also need to download utilities like getconf, exttpose from [[#patutils | Utilities]] section.
Changed lines 94-95 from:
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
to:
** You also need to download utilities like getconf, exttpose from [[#patutils | Utilities]] section.
Changed line 110 from:
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
to:
** You also need to download utilities like getconf, exttpose from [[#patutils | Utilities]] section.
Changed lines 72-73 from:
** [[Path:/~zaki/software/ECLAT.tar.gz]]
to:
** [[Path:/~zaki/software/ECLAT.tar.gz | Eclat code]]
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
Changed lines 79-81 from:
to:
\\\
[[#charm]]
[[#charm]]
Changed lines 85-86 from:
Charm-L adds the ability to construct the entire frequent concept lattice, that is, it adds the links
to:
Charm-L adds the ability to construct the entire frequent concept lattice (also called as the '''iceberg lattice'''), that is,
it adds the links
it adds the links
Changed lines 94-95 from:
to:
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
Changed lines 100-101 from:
to:
\\\
[[#genmax]]
[[#genmax]]
Added lines 105-118:
Genmax mines all maximal frequent itemsets via a backtracking approach with progressive focusing.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
** You also need to download utilities like getconf, exttpose from [[#patutiles | Utilities]] section.
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
Changed lines 124-132 from:
to:
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
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>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
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to:
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
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to:
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
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>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
---
\\
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
---
\\
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Added lines 185-194:
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
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>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
Changed lines 206-216 from:
to:
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
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!!!BLOSOM
to:
!!!!!BLOSOM
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
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!!!CLICKS
!!Sparcl
!!!Robin
to:
!!!!!CLICKS
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!Sparcl
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!Robin
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!Sparcl
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!Robin
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
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!!!Xrules
to:
!!!!!Xrules
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
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!!!TriCluster
!!
to:
!!!!!TriCluster
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!MicroCluster
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!MicroCluster
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
Changed lines 303-304 from:
!!!VOGUE
to:
!!!!!VOGUE
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
Changed lines 317-318 from:
!!!Trellis
to:
!!!!!Trellis
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
Changed lines 331-333 from:
!!!Snap
!!
to:
!!!!!Snap
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!FlexSnap
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
\\\
!!!!!FlexSnap
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
Changed lines 355-356 from:
!!!ContextShapes
to:
!!!!!ContextShapes
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
Changed lines 369-370 from:
!!!PSIST
to:
!!!!!PSIST
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
[[#patutils]]
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
[[#patutils]]
Changed lines 384-403 from:
!!Datasets
to:
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
!!Datasets
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
----
\\
!!Datasets
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/GENMAX.tar.gz | GenMax Code]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-genmax:dmkd]
>><<
Changed line 21 from:
>>sidenote width=270px<<
to:
>>sidenote width=35pct<<
Added lines 24-26:
[[#dmtl]]
Changed lines 40-41 from:
DMTL implements all algorithms following the vertical data mining approach. For itemsets, the implementation follows the [[#eclat | Eclat]] approach (without diffsets). For sequences it follows the [[#spade | Spade]] approach. For trees it implements the [[#sleuth | SLEUTH]] framework, which allows one to mine embedded/induced and ordered/unordered trees. Finally, the graph mining framework uses a novel vertical approach.
to:
DMTL implements all algorithms following the vertical data mining approach. For itemsets, the implementation
follows the [[#eclat | Eclat]] approach (without diffsets). For sequences it follows the [[#spade | Spade]] approach.
For trees it implements the [[#sleuth | SLEUTH]] framework, which allows one to mine embedded/induced and
ordered/unordered trees. Finally, the graph mining framework uses a novel vertical approach.
>>frame width=60pct<<
follows the [[#eclat | Eclat]] approach (without diffsets). For sequences it follows the [[#spade | Spade]] approach.
For trees it implements the [[#sleuth | SLEUTH]] framework, which allows one to mine embedded/induced and
ordered/unordered trees. Finally, the graph mining framework uses a novel vertical approach.
>>frame width=60pct<<
Changed lines 52-53 from:
to:
>><<
Changed lines 56-58 from:
!! Itemset Mining
The section contains the code for mining all frequent itemsets,closed itemsets, and all maximal frequent itemsets.
The section contains the code for mining all frequent itemsets,
to:
[[#itemsets]]
!! Itemset Mining and Association Rules
The section contains the code for mining all frequent itemsets, all closed itemsets, and all maximal frequent itemsets.
It also includes the code for constructing the concept lattice (or iceberg lattice) and generating nonredundant association rules.
!! Itemset Mining and Association Rules
The section contains the code for mining all frequent itemsets, all closed itemsets, and all maximal frequent itemsets.
It also includes the code for constructing the concept lattice (or iceberg lattice) and generating nonredundant association rules.
Changed lines 66-67 from:
{[zakipapers.bib,1997-eclat]}, combined with the diffsets improvement {[zakipapers.bib,2003-diffsets]}. The code also contains the maxeclat, clique, and maxclique approaches mentioned in
to:
{[zakipapers.bib,1997-eclat]}, combined with the diffsets improvement {[zakipapers.bib,2003-diffsets]}.
The code also contains the maxeclat, clique, and maxclique approaches mentioned in
The code also contains the maxeclat, clique, and maxclique approaches mentioned in
Added line 70:
>>frame<<
Changed lines 72-73 from:
** [[Path:/~zaki/software/ECLAT.tar.gz | Download Page]]
to:
** [[Path:/~zaki/software/ECLAT.tar.gz]]
Changed lines 77-78 from:
to:
>><<
Changed lines 81-82 from:
Charm mines all the frequent closed itemsets as described in {[]}.
to:
Charm mines all the frequent closed itemsets as described in {[zakipapers.bib,2002-charm]}.
Charm-L adds the ability to construct the entire frequent concept lattice, that is, it adds the links
between all sub/super-concepts (or closed itemsets) {[zakipapers.bib,2005-charm:tkde]}.
This ability is used to mine the non-redundant association rules {[zakipapers.bib,2004-nonredundant:dmkd]}.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/CHARM.tar.gz | Charm Code]]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L and Non-redundant Rules]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-charm:tkde]
** bibtexsummary:[zakipapers.bib,2004-nonredundant:dmkd]
>><<
Charm-L adds the ability to construct the entire frequent concept lattice, that is, it adds the links
between all sub/super-concepts (or closed itemsets) {[zakipapers.bib,2005-charm:tkde]}.
This ability is used to mine the non-redundant association rules {[zakipapers.bib,2004-nonredundant:dmkd]}.
>>frame<<
* '''Download'''
** [[Path:/~zaki/software/CHARM.tar.gz | Charm Code]]
** [[Path:/~zaki/software/RULES.tar.gz | Charm-L and Non-redundant Rules]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2005-charm:tkde]
** bibtexsummary:[zakipapers.bib,2004-nonredundant:dmkd]
>><<
Added line 63:
** bibtexsummary:[zakipapers.bib,2003-diffsets]
Changed lines 65-69 from:
!!!!!
to:
!!!!!Charm, Charm-L and Non-redundant Rule Generation
Charm mines all the frequent closed itemsets as described in {[]}.
!!!!!
Charm mines all the frequent closed itemsets as described in {[]}.
!!!!!
Changed line 63 from:
** bibtexsummary:[zakipapers.bib,2009-eclat:tkde]
to:
** bibtexsummary:[zakipapers.bib,2000-eclat:tkde]
Changed lines 63-65 from:
** bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
to:
** bibtexsummary:[zakipapers.bib,2009-eclat:tkde]
** bibtexsummary:[zakipapers.bib,2003-diffsets]
** bibtexsummary:[zakipapers.bib,2003-diffsets]
Added line 52:
[[#eclat]]
Changed lines 55-56 from:
Eclat uses the original vertical tidset approach for mining all frequent itemsets {[zakipapes.bib,1997-eclat]}, combined with the diffsets improvement {[zakipapes.bib,2003-diffsets]}. The code also contains the maxeclat, clique, and maxclique approaches mentioned in {[zakipapes.bib,2000-eclat:tkde]}.
to:
Eclat uses the original vertical tidset approach for mining all frequent itemsets
{[zakipapers.bib,1997-eclat]}, combined with the diffsets improvement {[zakipapers.bib,2003-diffsets]}. The code also contains the maxeclat, clique, and maxclique approaches mentioned in
{[zakipapers.bib,2000-eclat:tkde]}.
{[zakipapers.bib,1997-eclat]}, combined with the diffsets improvement {[zakipapers.bib,2003-diffsets]}. The code also contains the maxeclat, clique, and maxclique approaches mentioned in
{[zakipapers.bib,2000-eclat:tkde]}.
Changed lines 70-72 from:
!!!Spade
!!!cSpade
!!!cSpade
to:
[[#spade]]
!!!!!Spade
!!!!!cSpade
!!!!!Spade
!!!!!cSpade
Changed lines 78-80 from:
!!!TreeMiner
!!!TreeMiner-D
!!!SLEUTH
to:
!!!!!TreeMiner
!!!!!TreeMiner-D
[[#sleuth]]
!!!!!SLEUTH
!!!!!TreeMiner-D
[[#sleuth]]
!!!!!SLEUTH
Added lines 37-38:
DMTL implements all algorithms following the vertical data mining approach. For itemsets, the implementation follows the [[#eclat | Eclat]] approach (without diffsets). For sequences it follows the [[#spade | Spade]] approach. For trees it implements the [[#sleuth | SLEUTH]] framework, which allows one to mine embedded/induced and ordered/unordered trees. Finally, the graph mining framework uses a novel vertical approach.
Changed lines 48-52 from:
!! Itemset Mining
Eclat
!!!Charm
!!!Charm-L
!!!GenMax
!!!Charm
to:
!! Itemset Mining
The section contains the code for mining all frequent itemsets, all closed itemsets, and all maximal frequent itemsets.
!!!!!Eclat
Eclat uses the original vertical tidset approach for mining all frequent itemsets {[zakipapes.bib,1997-eclat]}, combined with the diffsets improvement {[zakipapes.bib,2003-diffsets]}. The code also contains the maxeclat, clique, and maxclique approaches mentioned in {[zakipapes.bib,2000-eclat:tkde]}.
* '''Download'''
** [[Path:/~zaki/software/ECLAT.tar.gz | Download Page]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
!!!!!Charm
!!!!!Charm-L
!!!!!GenMax
The section contains the code for mining all frequent itemsets, all closed itemsets, and all maximal frequent itemsets.
!!!!!Eclat
Eclat uses the original vertical tidset approach for mining all frequent itemsets {[zakipapes.bib,1997-eclat]}, combined with the diffsets improvement {[zakipapes.bib,2003-diffsets]}. The code also contains the maxeclat, clique, and maxclique approaches mentioned in {[zakipapes.bib,2000-eclat:tkde]}.
* '''Download'''
** [[Path:/~zaki/software/ECLAT.tar.gz | Download Page]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
!!!!!Charm
!!!!!Charm-L
!!!!!GenMax
Changed lines 5-7 from:
>>important<<
'''Acknowledgments''': We gratefully acknowledge the funding from the following agencies/programs that made the research possible:
to:
>>frame<<
!!!!Acknowledgments
We gratefully acknowledge the funding from the following agencies/programs that made the research possible:
!!!!Acknowledgments
We gratefully acknowledge the funding from the following agencies/programs that made the research possible:
Deleted line 15:
Added lines 18-20:
----
\\
\\
Changed line 22 from:
(:toc-page Software/Software self=1:)
to:
(:*toc:)
Deleted line 23:
Changed lines 25-26 from:
to:
\\
Changed lines 29-30 from:
complex and informative patterns types such as: '''Itemsets, Sequences, Trees and Graphs'''.
to:
complex and informative patterns types such as: '''%red%Itemsets, Sequences, Trees and Graphs%%'''.
Changed lines 37-43 from:
* [[http://sourceforge.net/projects/dmtl/ | Sourceforge Download Page]]
* bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
to:
* '''Download'''
** [[http://dmtl.sourceforge.net/ | Sourceforge Project Page]]
** [[http://sourceforge.net/projects/dmtl/ | Sourceforge Download Page]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
** [[http://dmtl.sourceforge.net/ | Sourceforge Project Page]]
** [[http://sourceforge.net/projects/dmtl/ | Sourceforge Download Page]]
*'''Relevant Publications'''
** bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
Changed line 1 from:
>>warning<<
to:
>>warning text-align=justify<<
Changed lines 5-12 from:
----
!!Acknowledgments
We
-
to:
>>important<<
'''Acknowledgments''': We gratefully acknowledge the funding from the following agencies/programs that made the research possible:
* NSF Information and Data Management program (Grant: IIS-0092978)
* NSF Next Generation Software program (Grant: EIA-0103708)
* DOE Office of Science (Grant: DE-FG02-02ER25538)
* CIA/NSA/DNI/IARPA Knowledge Discovery and Dissemination Program (Grants: EIA-0225715, ACI-0342411, CNS-0332960, CNS-0422637, CNS-0540232, IIS-0830218)
* NSF Emerging Models and Technologies for Computation program (Grant: EMT-0829835)
* NIH Biomedical Imaging and Bioengineering Institute (Grant: 1R01EB0080161-02)
>><<
>>sidenote width=270px<<
(:toc-page Software/Software self=1:)
>><<
'''Acknowledgments''': We gratefully acknowledge the funding from the following agencies/programs that made the research possible:
* NSF Information and Data Management program (Grant: IIS-0092978)
* NSF Next Generation Software program (Grant: EIA-0103708)
* DOE Office of Science (Grant: DE-FG02-02ER25538)
* CIA/NSA/DNI/IARPA Knowledge Discovery and Dissemination Program (Grants: EIA-0225715, ACI-0342411, CNS-0332960, CNS-0422637, CNS-0540232, IIS-0830218)
* NSF Emerging Models and Technologies for Computation program (Grant: EMT-0829835)
* NIH Biomedical Imaging and Bioengineering Institute (Grant: 1R01EB0080161-02)
>><<
>>sidenote width=270px<<
(:toc-page Software/Software self=1:)
>><<
Changed lines 1-3 from:
'''Disclaimer''': The software
to:
>>warning<<
'''Disclaimer''': The software on this page is provided on an '''as is''' basis for research purposes. There is no additional support offered, nor are the author(s) or their institutions liable under any circumstances.
>><<
(:*toc:)
'''Disclaimer''': The software on this page is provided on an '''as is''' basis for research purposes. There is no additional support offered, nor are the author(s) or their institutions liable under any circumstances.
>><<
(:*toc:)
Changed lines 8-12 from:
!!!Data Mining Template Library
!! ItemsetMining
to:
!!Acknowledgments
We gratefully acknowledge the funding from the following agencies that made the research possible:
National Science Foundation -- Information and Data Management program (IIS-0092978), and Next Generation Software program (EIA-0103708); and Department of Energy, Office of Science (DE-FG02-02ER25538)
----
!!Data Mining Template Library (DMTL)
DMTL is an open-source, high-performance, generic data mining toolkit, written in C++.
It provides a collection of generic algorithms and data structures for mining increasingly
complex and informative patterns types such as: '''Itemsets, Sequences, Trees and Graphs'''.
DMTL
utilizes a generic data mining approach, where all aspects of mining are controlled via a set
of properties. The kind of pattern to be mined, the kind of mining approach to use, and the
kind of data types and formats to mine over are all specified as a list of properties. This
provides tremendous flexibility to customize the toolkit for various applications.
!!!!!!Download:
* [[http://dmtl.sourceforge.net/ | Sourceforge Project Page]]
* [[http://sourceforge.net/projects/dmtl/ | Sourceforge Download Page]]
!!!!!!Relevant Publications
* bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
----
!! Itemset Mining
We gratefully acknowledge the funding from the following agencies that made the research possible:
National Science Foundation -- Information and Data Management program (IIS-0092978), and Next Generation Software program (EIA-0103708); and Department of Energy, Office of Science (DE-FG02-02ER25538)
----
!!Data Mining Template Library (DMTL)
DMTL is an open-source, high-performance, generic data mining toolkit, written in C++.
It provides a collection of generic algorithms and data structures for mining increasingly
complex and informative patterns types such as: '''Itemsets, Sequences, Trees and Graphs'''.
DMTL
utilizes a generic data mining approach, where all aspects of mining are controlled via a set
of properties. The kind of pattern to be mined, the kind of mining approach to use, and the
kind of data types and formats to mine over are all specified as a list of properties. This
provides tremendous flexibility to customize the toolkit for various applications.
!!!!!!Download:
* [[http://dmtl.sourceforge.net/ | Sourceforge Project Page]]
* [[http://sourceforge.net/projects/dmtl/ | Sourceforge Download Page]]
!!!!!!Relevant Publications
* bibtexsummary:[zakipapers.bib,2008-dmtl:dmkd]
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!! Itemset Mining
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(:*toc-float:)
to:
(:*toc-float Table of Contents:)
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!!!Charm-L
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!!!TreeMiner-D
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!!Clusering
to:
!!Boolean Expression Mining
!!!BLOSOM
!!Clustering
!!!CLICKS
!!!BLOSOM
!!Clustering
!!!CLICKS
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!!XML Classification
!!!Xrules
!!Microarray Gene Expression Clustering
!!!TriCluster
!!!MicroCluster
!!!Xrules
!!Microarray Gene Expression Clustering
!!!TriCluster
!!!MicroCluster
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!!!PSIST
to:
!!!PSIST
!!Utilities
!!Datasets
!!Utilities
!!Datasets
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(:*toc-float:)
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!!List of Software
(:*toc:)
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'''Disclaimer''': The software is provided on an '''as is''' basis for research purposes. There is no additional support offered, nor are the author(s) or their institutions liable under any circumstances.
----
!!List of Software
(:*toc:)
----
!! Generic Pattern Mining
!!!Data Mining Template Library
!! ItemsetMining
!!!Eclat
!!!Charm
!!!GenMax
!!Sequence Mining
!!!Spade
!!!cSpade
!!Tree Mining
!!!TreeMiner
!!!SLEUTH
!!Graph Mining
!!!Origami
!!!Musk
!!!OSS
!!Clusering
!!!Sparcl
!!!Robin
!!Hidden Markov Models
!!!VOGUE
!!Genome Scale Indexing
!!!Trellis
!!Protein Structure Alignment
!!!Snap
!!!FlexSnap
!!Protein Docking
!!!ContextShapes
!!Protein Indexing
!!!PSIST
----
!!List of Software
(:*toc:)
----
!! Generic Pattern Mining
!!!Data Mining Template Library
!! ItemsetMining
!!!Eclat
!!!Charm
!!!GenMax
!!Sequence Mining
!!!Spade
!!!cSpade
!!Tree Mining
!!!TreeMiner
!!!SLEUTH
!!Graph Mining
!!!Origami
!!!Musk
!!!OSS
!!Clusering
!!!Sparcl
!!!Robin
!!Hidden Markov Models
!!!VOGUE
!!Genome Scale Indexing
!!!Trellis
!!Protein Structure Alignment
!!!Snap
!!!FlexSnap
!!Protein Docking
!!!ContextShapes
!!Protein Indexing
!!!PSIST