@@ -53,57 +53,33 @@ The algorithm is defined with the `operator` (`-op`) parameter. By default, it i
5353## Usage
5454You can call the functions directly with given args as
5555```
56- usage: kgtk graph-embeddings [-h] [-i INPUT_FILE_PATH ] [-o OUTPUT_FILE_PATH ]
57- [-l] [-T] [- ot] [-r True|False] [-d] [-s]
56+ usage: kgtk graph-embeddings [-h] [-i INPUT_FILE ] [-o OUTPUT_FILE] [-l] [-T ]
57+ [-ot] [-r True|False] [-d] [-s]
5858 [-c dot|cos|l2|squared_l2]
59- [-op linear|diagonal|complex_diagonal|translation ]
60- [-e] [- b True|False] [-w] [-bs]
59+ [-op RESCAL|DistMult|ComplEx|TransE] [-e ]
60+ [-b True|False] [-w] [-bs]
6161 [-lf ranking|logistic|softmax] [-lr] [-ef]
6262 [-dr True|False] [-ge True|False]
63+ [--no-output-header [True|False]]
6364 [-v [optional True|False]]
64- [--column-separator COLUMN_SEPARATOR]
65- [--input-format INPUT_FORMAT]
66- [--compression-type COMPRESSION_TYPE]
67- [--error-limit ERROR_LIMIT]
68- [--use-mgzip [optional True|False]]
69- [--mgzip-threads MGZIP_THREADS]
70- [--gzip-in-parallel [optional True|False]]
71- [--gzip-queue-size GZIP_QUEUE_SIZE]
72- [--mode {NONE,EDGE,NODE,AUTO}]
73- [--force-column-names FORCE_COLUMN_NAMES [FORCE_COLUMN_NAMES ...]]
74- [--header-error-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
75- [--skip-header-record [optional True|False]]
76- [--unsafe-column-name-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
77- [--initial-skip-count INITIAL_SKIP_COUNT]
78- [--every-nth-record EVERY_NTH_RECORD]
79- [--record-limit RECORD_LIMIT]
80- [--tail-count TAIL_COUNT]
81- [--repair-and-validate-lines [optional True|False]]
82- [--repair-and-validate-values [optional True|False]]
83- [--blank-required-field-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
84- [--comment-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
85- [--empty-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
86- [--fill-short-lines [optional True|False]]
87- [--invalid-value-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
88- [--long-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
89- [--prohibited-list-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
90- [--short-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
91- [--truncate-long-lines [TRUNCATE_LONG_LINES]]
92- [--whitespace-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}]
65+
66+ Generate graph embedding in kgtk tsv format, here we use PytorchBigGraph as low-level implementation
9367
9468optional arguments:
9569 -h, --help show this help message and exit
96- -i INPUT_FILE_PATH, --input-file INPUT_FILE_PATH
97- The KGTK input file. (default=-)
98- -o OUTPUT_FILE_PATH, --output-file OUTPUT_FILE_PATH
99- The KGTK output file. (default=-).
70+ -i INPUT_FILE, --input-file INPUT_FILE
71+ The KGTK input file. (May be omitted or '-' for
72+ stdin.)
73+ -o OUTPUT_FILE, --output-file OUTPUT_FILE
74+ The KGTK output file. (May be omitted or '-' for
75+ stdout.)
10076 -l , --log Setting the log path [Default: None]
10177 -T , --temporary_directory
10278 Sepecify the directory location to store temporary
10379 file
10480 -ot , --output_format
105- Outputformat for embeddings [Default: w2v] Choice: kgtk
106- | w2v | glove
81+ Outputformat for embeddings [Default: w2v] Choice:
82+ kgtk | w2v | glove
10783 -r True|False, --retain_temporary_data True|False
10884 When opearte graph, some tempory files will be
10985 generated, set True to retain these files
@@ -122,8 +98,9 @@ optional arguments:
12298 -op RESCAL|DistMult|ComplEx|TransE, --operator RESCAL|DistMult|ComplEx|TransE
12399 The transformation to apply to the embedding of one of
124100 the sides of the edge (typically the right-hand one)
125- before comparing it with the other one. It reflects
126- which model that embedding uses. [Default:ComplEx]
101+ before comparing it with the other one. It
102+ reflectswhich model that embedding uses.
103+ [Default:ComplEx]
127104 -e , --num_epochs The number of times the training loop iterates over
128105 all the edges.[Default:100]
129106 -b True|False, --bias True|False
@@ -145,111 +122,20 @@ optional arguments:
145122 The fraction of edges withheld from training and used
146123 to track evaluation metrics during training.
147124 [Defalut:0.0 training all edges ]
148- -dr True|False, --dynamic_relaitons True|False
125+ -dr True|False, --dynamic_relations True|False
149126 Whether use dynamic relations (when graphs with a
150127 large number of relations) [Default: True]
151128 -ge True|False, --global_emb True|False
152129 Whether use global embedding, if enabled, add to each
153130 embedding a vector that is common to all the entities
154131 of a certain type. This vector is learned during
155132 training.[Default: False]
133+ --no-output-header [True|False]
134+ When true, do not write a header to the output file
135+ (default=False).
156136
157137 -v [optional True|False], --verbose [optional True|False]
158138 Print additional progress messages (default=False).
159-
160- File options:
161- Options affecting processing.
162-
163- --column-separator COLUMN_SEPARATOR
164- Column separator (default=<TAB>).
165- --input-format INPUT_FORMAT
166- Specify the input format (default=None).
167- --compression-type COMPRESSION_TYPE
168- Specify the compression type (default=None).
169- --error-limit ERROR_LIMIT
170- The maximum number of errors to report before failing
171- (default=1000)
172- --use-mgzip [optional True|False]
173- Execute multithreaded gzip. (default=False).
174- --mgzip-threads MGZIP_THREADS
175- Multithreaded gzip thread count. (default=3).
176- --gzip-in-parallel [optional True|False]
177- Execute gzip in parallel. (default=False).
178- --gzip-queue-size GZIP_QUEUE_SIZE
179- Queue size for parallel gzip. (default=1000).
180- --mode {NONE,EDGE,NODE,AUTO}
181- Determine the KGTK file mode
182- (default=KgtkReaderMode.AUTO).
183-
184- Header parsing:
185- Options affecting header parsing.
186-
187- --force-column-names FORCE_COLUMN_NAMES [FORCE_COLUMN_NAMES ...]
188- Force the column names (default=None).
189- --header-error-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
190- The action to take when a header error is detected.
191- Only ERROR or EXIT are supported
192- (default=ValidationAction.EXIT).
193- --skip-header-record [optional True|False]
194- Skip the first record when forcing column names
195- (default=False).
196- --unsafe-column-name-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
197- The action to take when a column name is unsafe
198- (default=ValidationAction.REPORT).
199-
200- Pre-validation sampling:
201- Options affecting pre-validation data line sampling.
202-
203- --initial-skip-count INITIAL_SKIP_COUNT
204- The number of data records to skip initially
205- (default=do not skip).
206- --every-nth-record EVERY_NTH_RECORD
207- Pass every nth record (default=pass all records).
208- --record-limit RECORD_LIMIT
209- Limit the number of records read (default=no limit).
210- --tail-count TAIL_COUNT
211- Pass this number of records (default=no tail
212- processing).
213-
214- Line parsing:
215- Options affecting data line parsing.
216-
217- --repair-and-validate-lines [optional True|False]
218- Repair and validate lines (default=False).
219- --repair-and-validate-values [optional True|False]
220- Repair and validate values (default=False).
221- --blank-required-field-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
222- The action to take when a line with a blank node1,
223- node2, or id field (per mode) is detected
224- (default=ValidationAction.EXCLUDE).
225- --comment-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
226- The action to take when a comment line is detected
227- (default=ValidationAction.EXCLUDE).
228- --empty-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
229- The action to take when an empty line is detected
230- (default=ValidationAction.EXCLUDE).
231- --fill-short-lines [optional True|False]
232- Fill missing trailing columns in short lines with
233- empty values (default=False).
234- --invalid-value-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
235- The action to take when a data cell value is invalid
236- (default=ValidationAction.COMPLAIN).
237- --long-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
238- The action to take when a long line is detected
239- (default=ValidationAction.COMPLAIN).
240- --prohibited-list-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
241- The action to take when a data cell contains a
242- prohibited list (default=ValidationAction.COMPLAIN).
243- --short-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
244- The action to take when a short line is detected
245- (default=ValidationAction.COMPLAIN).
246- --truncate-long-lines [TRUNCATE_LONG_LINES]
247- Remove excess trailing columns in long lines
248- (default=False).
249- --whitespace-line-action {PASS,REPORT,EXCLUDE,COMPLAIN,ERROR,EXIT}
250- The action to take when a whitespace line is detected
251- (default=ValidationAction.EXCLUDE).
252-
253139```
254140## Examples
255141
@@ -274,7 +160,7 @@ The output_file.tsv may look like:
274160### Example 2
275161Running with more specific parameters (TransE algorithm and 200-dimensional vectors):
276162```
277- kgtk graph-embeddings
163+ kgtk graph-embeddings \
278164 --input-file input_file.tsv \
279165 --output-file output_file.tsv \
280166 --dimension 200 \
@@ -296,7 +182,7 @@ The `output_file.tsv` may look like:
296182### Example 3
297183Using glove format to generate graph embeddings
298184```
299- kgtk graph-embeddings
185+ kgtk graph-embeddings \
300186 --input-file input_file.tsv \
301187 --output-file output_file.tsv \
302188 --output_format glove
@@ -313,7 +199,7 @@ The `output_file.tsv` may look like:
313199### Example 4
314200Using kgtk format to generate graph embeddings
315201```
316- kgtk graph-embeddings
202+ kgtk graph-embeddings \
317203 --input-file input_file.tsv \
318204 --output-file output_file.tsv \
319205 --output_format kgtk --no-output-headers
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