community-detection
Summary¶
This command will return a clutering results from the input kgtk file. The algorithms are provided by graph_tool (blockmodel, nested and mcmc)
Input File¶
The input file should be a KGTK Edge file with the following columns or their aliases:
node1: the subject column (source node)label: the predicate column (property name)node2: the object column (target node)
Processing an Input File that is Not a KGTK Edge File¶
If your input file doesn't have node1, label, or node2 columns (or their aliases) at all, then it is
not a valid KGTK Edge file. In this case, you also have to pass the following command line option:
--input-mode=NONE
The Output File¶
The output file is an edge file that contains the following columns:
node1: this column contains each nodelabel: this column contains only 'in'node2: this column contains the resulting clusternode2;prob: this column contains the probability/confidence of clustering
Usage¶
usage: kgtk community-detection [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
[--method METHOD]
[--old-id-column-name COLUMN_NAME]
[--new-id-column-name COLUMN_NAME]
[--overwrite-id [optional true|false]]
[--verify-id-unique [optional true|false]]
[--id-style {node1-label-node2,node1-label-num,node1-label-node2-num,node1-label-node2-id,empty,prefix###,wikidata,wikidata-with-claim-id}]
[--id-prefix PREFIX] [--initial-id INTEGER]
[--id-prefix-num-width INTEGER]
[--id-concat-num-width INTEGER]
[--value-hash-width VALUE_HASH_WIDTH]
[--claim-id-hash-width CLAIM_ID_HASH_WIDTH]
[--claim-id-column-name CLAIM_ID_COLUMN_NAME]
[--id-separator ID_SEPARATOR]
[-v [optional True|False]]
Creating community detection from graph-tool using KGTK file, available options are blockmodel, nested and mcmc
optional arguments:
-h, --help show this help message and exit
-i INPUT_FILE, --input-file INPUT_FILE
The KGTK input file. (May be omitted or '-' for
stdin.)
-o OUTPUT_FILE, --output-file OUTPUT_FILE
The KGTK output file. (May be omitted or '-' for
stdout.)
--method METHOD Specify the clustering method to use.
--old-id-column-name COLUMN_NAME
The name of the old ID column. (default=id).
--new-id-column-name COLUMN_NAME
The name of the new ID column. (default=id).
--overwrite-id [optional true|false]
When true, replace existing ID values. When false,
copy existing ID values. When --overwrite-id is
omitted, it defaults to False. When --overwrite-id is
supplied without an argument, it is True.
--verify-id-unique [optional true|false]
When true, verify ID uniqueness using an in-memory set
of IDs. When --verify-id-unique is omitted, it
defaults to False. When --verify-id-unique is supplied
without an argument, it is True.
--id-style {node1-label-node2,node1-label-num,node1-label-node2-num,node1-label-node2-id,empty,prefix###,wikidata,wikidata-with-claim-id}
The ID generation style. (default=prefix###).
--id-prefix PREFIX The prefix for a prefix### ID. (default=E).
--initial-id INTEGER The initial numeric value for a prefix### ID.
(default=1).
--id-prefix-num-width INTEGER
The width of the numeric value for a prefix### ID.
(default=1).
--id-concat-num-width INTEGER
The width of the numeric value for a concatenated ID.
(default=4).
--value-hash-width VALUE_HASH_WIDTH
How many characters should be used in a value hash?
(default=6)
--claim-id-hash-width CLAIM_ID_HASH_WIDTH
How many characters should be used to hash the claim
ID? 0 means do not hash the claim ID. (default=8)
--claim-id-column-name CLAIM_ID_COLUMN_NAME
The name of the claim_id column. (default=claim_id)
--id-separator ID_SEPARATOR
The separator user between ID subfields. (default=-)
-v [optional True|False], --verbose [optional True|False]
Print additional progress messages (default=False).
Examples¶
Default model (blockmodel)¶
The following file will be used to illustrate some of the capabilities of kgtk reachable-nodes.
head examples/docs/community-detection-arnold.tsv
| node1 | label | node2 |
|---|---|---|
| 'Joseph P. Kennedy Jr.'@en | P3373 | 'Rosemary Kennedy'@en |
| 'Joseph P. Kennedy Jr.'@en | P3373 | 'Kathleen Cavendish, Marchioness of Hartington'@en |
| 'Joseph P. Kennedy Jr.'@en | P3373 | 'Jean Kennedy Smith'@en |
| 'Joseph P. Kennedy Jr.'@en | P3373 | 'Eunice Kennedy Shriver'@en |
| 'Joseph P. Kennedy Jr.'@en | P3373 | 'Patricia Kennedy Lawford'@en |
| 'Joseph P. Kennedy Jr.'@en | P3373 | 'John F. Kennedy'@en |
| 'Christopher G. Kennedy'@en | P22 | 'Robert F. Kennedy'@en |
| 'Christopher G. Kennedy'@en | P25 | 'Ethel Skakel Kennedy'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Robert F. Kennedy Jr.'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Joseph P. Kennedy II'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Michael LeMoyne Kennedy'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'David A. Kennedy'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Rory Kennedy'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Kathleen Kennedy Townsend'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Kerry Kennedy'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Courtney Kennedy Hill'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Douglas Harriman Kennedy'@en |
| 'Christopher G. Kennedy'@en | P3373 | 'Max Kennedy'@en |
| 'Courtney Kennedy Hill'@en | P22 | 'Robert F. Kennedy'@en |
| 'Courtney Kennedy Hill'@en | P25 | 'Ethel Skakel Kennedy'@en |
Find the communities using blockmodel.
kgtk community-detection -i examples/docs/community-detection-arnold.tsv --method blockmodel
| node1 | label | node2 |
|---|---|---|
| Christopher Lawford | in | cluster_6 |
| Peter Lawford | in | cluster_2 |
| Patricia Kennedy Lawford | in | cluster_7 |
| Jean Edith Olssen | in | cluster_13 |
| Victoria Lawford | in | cluster_2 |
| Sydney Lawford | in | cluster_2 |
| Robin Lawford | in | cluster_6 |
| Mary Rowan | in | cluster_6 |
| Deborah Gould | in | cluster_6 |
| Patricia Seaton | in | cluster_6 |
| David Christopher Lawford | in | cluster_13 |
| Savannah Rose Lawford | in | cluster_13 |
| Matthew Valentine Lawford | in | cluster_13 |
| Andrew Cuomo | in | cluster_31 |
| Kerry Kennedy | in | cluster_31 |
| Ted Kennedy | in | cluster_19 |
| John F. Kennedy | in | cluster_23 |
| Joseph P. Kennedy Sr. | in | cluster_24 |
| Rose Kennedy | in | cluster_24 |
| Joan Bennett Kennedy | in | cluster_20 |
| Victoria Reggie Kennedy | in | cluster_20 |
| Robert F. Kennedy | in | cluster_22 |
| Rosemary Kennedy | in | cluster_24 |
| Kathleen Cavendish, Marchioness of Hartington | in | cluster_24 |
| Jean Kennedy Smith | in | cluster_24 |
| Eunice Kennedy Shriver | in | cluster_23 |
| Joseph P. Kennedy Jr. | in | cluster_24 |
| Kara Kennedy | in | cluster_20 |
| Edward M. Kennedy Jr. | in | cluster_20 |
| Patrick J. Kennedy | in | cluster_20 |
| Robert F. Kennedy Jr. | in | cluster_31 |
| Ethel Skakel Kennedy | in | cluster_31 |
| Joseph P. Kennedy II | in | cluster_31 |
| Michael LeMoyne Kennedy | in | cluster_31 |
| David A. Kennedy | in | cluster_31 |
| Rory Kennedy | in | cluster_31 |
| Kathleen Kennedy Townsend | in | cluster_31 |
| Christopher G. Kennedy | in | cluster_31 |
| Courtney Kennedy Hill | in | cluster_31 |
| Douglas Harriman Kennedy | in | cluster_31 |
| Max Kennedy | in | cluster_31 |
| Jacqueline Kennedy Onassis | in | cluster_42 |
| Caroline Kennedy | in | cluster_42 |
| John F. Kennedy Jr. | in | cluster_42 |
| Patrick Bouvier Kennedy | in | cluster_42 |
| Arabelle Kennedy | in | cluster_42 |
| Maria Shriver | in | cluster_57 |
| Sargent Shriver | in | cluster_52 |
| Arnold Schwarzenegger | in | cluster_63 |
| Bobby Shriver | in | cluster_52 |
| Timothy Shriver | in | cluster_48 |
| Anthony Shriver | in | cluster_52 |
| Mark Shriver | in | cluster_48 |
| Christina Schwarzenegger | in | cluster_58 |
| Christopher Schwarzenegger | in | cluster_58 |
| Katherine Schwarzenegger | in | cluster_58 |
| Patrick Schwarzenegger | in | cluster_63 |
| Joseph Baena | in | cluster_58 |
| Mildred Patricia Baena | in | cluster_57 |
| Aurelia Schwarzenegger | in | cluster_60 |
| Gustav Schwarzenegger | in | cluster_60 |
| Jadrny | in | cluster_60 |
| Meinhard Schwarzenegger | in | cluster_60 |
| Patrick M. Knapp Schwarzenegger | in | cluster_60 |
| Robert Sargent Shriver | in | cluster_48 |
| Hilda Shriver | in | cluster_48 |
| Malissa Feruzzi | in | cluster_48 |
| Jack Pratt | in | cluster_69 |
| Chris Pratt | in | cluster_69 |
| Anna Faris | in | cluster_69 |
| Alina Shriver | in | cluster_48 |
| Rogelio Baena | in | cluster_48 |
| Marilyn Monroe | in | cluster_42 |
nested model¶
kgtk community-detection -i examples/docs/community-detection-arnold.tsv --method nested
| node1 | label | node2 |
|---|---|---|
| Christopher Lawford | in | cluster_0_10_43 |
| Peter Lawford | in | cluster_0_2_43 |
| Patricia Kennedy Lawford | in | cluster_0_10_0 |
| Jean Edith Olssen | in | cluster_0_2_43 |
| Victoria Lawford | in | cluster_0_10_43 |
| Sydney Lawford | in | cluster_0_2_43 |
| Robin Lawford | in | cluster_0_2_43 |
| Mary Rowan | in | cluster_0_2_43 |
| Deborah Gould | in | cluster_0_10_43 |
| Patricia Seaton | in | cluster_0_7_43 |
| David Christopher Lawford | in | cluster_0_2_43 |
| Savannah Rose Lawford | in | cluster_0_10_43 |
| Matthew Valentine Lawford | in | cluster_0_2_43 |
| Andrew Cuomo | in | cluster_0_7_14 |
| Kerry Kennedy | in | cluster_0_7_14 |
| Ted Kennedy | in | cluster_0_10_34 |
| John F. Kennedy | in | cluster_0_2_38 |
| Joseph P. Kennedy Sr. | in | cluster_0_10_65 |
| Rose Kennedy | in | cluster_0_10_65 |
| Joan Bennett Kennedy | in | cluster_0_2_40 |
| Victoria Reggie Kennedy | in | cluster_0_7_40 |
| Robert F. Kennedy | in | cluster_0_10_35 |
| Rosemary Kennedy | in | cluster_0_10_65 |
| Kathleen Cavendish, Marchioness of Hartington | in | cluster_0_7_65 |
| Jean Kennedy Smith | in | cluster_0_7_65 |
| Eunice Kennedy Shriver | in | cluster_0_10_38 |
| Joseph P. Kennedy Jr. | in | cluster_0_2_65 |
| Kara Kennedy | in | cluster_0_2_40 |
| Edward M. Kennedy Jr. | in | cluster_0_7_40 |
| Patrick J. Kennedy | in | cluster_0_7_40 |
| Robert F. Kennedy Jr. | in | cluster_0_10_14 |
| Ethel Skakel Kennedy | in | cluster_0_2_14 |
| Joseph P. Kennedy II | in | cluster_0_2_14 |
| Michael LeMoyne Kennedy | in | cluster_0_2_14 |
| David A. Kennedy | in | cluster_0_10_14 |
| Rory Kennedy | in | cluster_0_7_14 |
| Kathleen Kennedy Townsend | in | cluster_0_10_14 |
| Christopher G. Kennedy | in | cluster_0_2_14 |
| Courtney Kennedy Hill | in | cluster_0_4_14 |
| Douglas Harriman Kennedy | in | cluster_0_10_14 |
| Max Kennedy | in | cluster_0_10_14 |
| Jacqueline Kennedy Onassis | in | cluster_0_10_57 |
| Caroline Kennedy | in | cluster_0_2_57 |
| John F. Kennedy Jr. | in | cluster_0_10_57 |
| Patrick Bouvier Kennedy | in | cluster_0_2_57 |
| Arabelle Kennedy | in | cluster_0_7_57 |
| Maria Shriver | in | cluster_0_2_51 |
| Sargent Shriver | in | cluster_0_10_33 |
| Arnold Schwarzenegger | in | cluster_0_10_69 |
| Bobby Shriver | in | cluster_0_2_33 |
| Timothy Shriver | in | cluster_0_10_33 |
| Anthony Shriver | in | cluster_0_2_33 |
| Mark Shriver | in | cluster_0_10_33 |
| Christina Schwarzenegger | in | cluster_0_2_69 |
| Christopher Schwarzenegger | in | cluster_0_10_69 |
| Katherine Schwarzenegger | in | cluster_0_7_69 |
| Patrick Schwarzenegger | in | cluster_0_7_69 |
| Joseph Baena | in | cluster_0_2_69 |
| Mildred Patricia Baena | in | cluster_0_2_69 |
| Aurelia Schwarzenegger | in | cluster_0_4_69 |
| Gustav Schwarzenegger | in | cluster_0_10_69 |
| Jadrny | in | cluster_0_2_69 |
| Meinhard Schwarzenegger | in | cluster_0_10_69 |
| Patrick M. Knapp Schwarzenegger | in | cluster_0_2_69 |
| Robert Sargent Shriver | in | cluster_0_2_33 |
| Hilda Shriver | in | cluster_0_10_33 |
| Malissa Feruzzi | in | cluster_0_2_33 |
| Jack Pratt | in | cluster_0_7_69 |
| Chris Pratt | in | cluster_0_7_69 |
| Anna Faris | in | cluster_0_2_69 |
| Alina Shriver | in | cluster_0_2_33 |
| Rogelio Baena | in | cluster_0_2_69 |
| Marilyn Monroe | in | cluster_0_2_65 |
MCMC model¶
kgtk community-detection -i examples/docs/community-detection-arnold.tsv --method mcmc
| node1 | label | node2 | node2;prob |
|---|---|---|---|
| Christopher Lawford | in | cluster_0 | 1.0 |
| Peter Lawford | in | cluster_0 | 1.0 |
| Patricia Kennedy Lawford | in | cluster_1 | 0.806980698069807 |
| Jean Edith Olssen | in | cluster_0 | 1.0 |
| Victoria Lawford | in | cluster_0 | 1.0 |
| Sydney Lawford | in | cluster_0 | 1.0 |
| Robin Lawford | in | cluster_0 | 1.0 |
| Mary Rowan | in | cluster_0 | 0.9998999899989999 |
| Deborah Gould | in | cluster_0 | 0.9998999899989999 |
| Patricia Seaton | in | cluster_0 | 1.0 |
| David Christopher Lawford | in | cluster_0 | 0.9998999899989999 |
| Savannah Rose Lawford | in | cluster_0 | 0.9998999899989999 |
| Matthew Valentine Lawford | in | cluster_0 | 0.9997999799979999 |
| Andrew Cuomo | in | cluster_2 | 0.9457945794579458 |
| Kerry Kennedy | in | cluster_2 | 1.0 |
| Ted Kennedy | in | cluster_3 | 0.8140814081408141 |
| John F. Kennedy | in | cluster_3 | 0.9794979497949795 |
| Joseph P. Kennedy Sr. | in | cluster_4 | 0.9993999399939995 |
| Rose Kennedy | in | cluster_4 | 0.9992999299929993 |
| Joan Bennett Kennedy | in | cluster_5 | 0.7872787278727873 |
| Victoria Reggie Kennedy | in | cluster_5 | 0.48514851485148514 |
| Robert F. Kennedy | in | cluster_6 | 1.0 |
| Rosemary Kennedy | in | cluster_4 | 0.9994999499949995 |
| Kathleen Cavendish, Marchioness of Hartington | in | cluster_4 | 0.9991999199919992 |
| Jean Kennedy Smith | in | cluster_4 | 0.9995999599959996 |
| Eunice Kennedy Shriver | in | cluster_1 | 0.866986698669867 |
| Joseph P. Kennedy Jr. | in | cluster_4 | 0.9990999099909991 |
| Kara Kennedy | in | cluster_5 | 0.7872787278727873 |
| Edward M. Kennedy Jr. | in | cluster_5 | 0.7872787278727873 |
| Patrick J. Kennedy | in | cluster_5 | 0.787078707870787 |
| Robert F. Kennedy Jr. | in | cluster_2 | 1.0 |
| Ethel Skakel Kennedy | in | cluster_2 | 1.0 |
| Joseph P. Kennedy II | in | cluster_2 | 1.0 |
| Michael LeMoyne Kennedy | in | cluster_2 | 1.0 |
| David A. Kennedy | in | cluster_2 | 1.0 |
| Rory Kennedy | in | cluster_2 | 1.0 |
| Kathleen Kennedy Townsend | in | cluster_2 | 1.0 |
| Christopher G. Kennedy | in | cluster_2 | 1.0 |
| Courtney Kennedy Hill | in | cluster_2 | 1.0 |
| Douglas Harriman Kennedy | in | cluster_2 | 1.0 |
| Max Kennedy | in | cluster_2 | 1.0 |
| Jacqueline Kennedy Onassis | in | cluster_5 | 1.0 |
| Caroline Kennedy | in | cluster_5 | 1.0 |
| John F. Kennedy Jr. | in | cluster_5 | 1.0 |
| Patrick Bouvier Kennedy | in | cluster_5 | 0.9998999899989999 |
| Arabelle Kennedy | in | cluster_5 | 1.0 |
| Maria Shriver | in | cluster_7 | 0.9790979097909791 |
| Sargent Shriver | in | cluster_7 | 0.9998999899989999 |
| Arnold Schwarzenegger | in | cluster_8 | 1.0 |
| Bobby Shriver | in | cluster_7 | 0.9998999899989999 |
| Timothy Shriver | in | cluster_7 | 0.9998999899989999 |
| Anthony Shriver | in | cluster_7 | 1.0 |
| Mark Shriver | in | cluster_7 | 0.9998999899989999 |
| Christina Schwarzenegger | in | cluster_8 | 0.9998999899989999 |
| Christopher Schwarzenegger | in | cluster_8 | 1.0 |
| Katherine Schwarzenegger | in | cluster_8 | 1.0 |
| Patrick Schwarzenegger | in | cluster_8 | 1.0 |
| Joseph Baena | in | cluster_8 | 1.0 |
| Mildred Patricia Baena | in | cluster_8 | 0.9997999799979999 |
| Aurelia Schwarzenegger | in | cluster_8 | 0.9998999899989999 |
| Gustav Schwarzenegger | in | cluster_8 | 0.9997999799979999 |
| Jadrny | in | cluster_8 | 0.987998799879988 |
| Meinhard Schwarzenegger | in | cluster_8 | 1.0 |
| Patrick M. Knapp Schwarzenegger | in | cluster_8 | 0.98999899989999 |
| Robert Sargent Shriver | in | cluster_7 | 0.9921992199219922 |
| Hilda Shriver | in | cluster_7 | 0.9938993899389938 |
| Malissa Feruzzi | in | cluster_7 | 0.9416941694169417 |
| Jack Pratt | in | cluster_8 | 0.9837983798379838 |
| Chris Pratt | in | cluster_8 | 0.9858985898589859 |
| Anna Faris | in | cluster_8 | 0.9840984098409841 |
| Alina Shriver | in | cluster_7 | 0.9413941394139413 |
| Rogelio Baena | in | cluster_8 | 0.9873987398739874 |
| Marilyn Monroe | in | cluster_5 | 0.49194919491949196 |