| cf1e13c | satoken | 10 May 2021, 13:26:23 UTC | Add files via upload | 10 May 2021, 13:26:23 UTC |
| f6af4c9 | Kengo SATO | 14 January 2020, 02:53:38 UTC | add the information of the web server | 14 January 2020, 02:53:38 UTC |
| 3e1239e | Kengo Sato | 28 March 2019, 05:01:39 UTC | bugfix, remove autoconf | 28 March 2019, 05:01:39 UTC |
| 7f8bfbf | Kengo SATO | 27 June 2018, 06:05:28 UTC | version up | 27 June 2018, 06:05:28 UTC |
| eab12ea | Kengo Sato | 30 May 2018, 08:30:05 UTC | fix deprecated | 30 May 2018, 08:30:05 UTC |
| 392eda9 | Kengo Sato | 30 May 2018, 06:07:12 UTC | small fix | 30 May 2018, 06:07:12 UTC |
| 556f75d | Kengo SATO | 30 May 2018, 05:23:29 UTC | minimum hairpin length for constraints | 30 May 2018, 05:23:29 UTC |
| 5328d35 | Kengo Sato | 29 May 2018, 03:28:59 UTC | new option | 29 May 2018, 03:28:59 UTC |
| 2b71baf | Kengo Sato | 29 May 2018, 02:25:33 UTC | add defines | 29 May 2018, 02:25:33 UTC |
| a618697 | Kengo SATO | 27 May 2018, 13:24:57 UTC | fix a critical bug | 27 May 2018, 13:24:57 UTC |
| da909d2 | Kengo Sato | 24 May 2018, 09:46:10 UTC | A small fix | 24 May 2018, 09:46:10 UTC |
| f117eb9 | Kengo Sato | 24 May 2018, 09:43:18 UTC | support cmake build | 24 May 2018, 09:44:53 UTC |
| 5b7bc54 | Kengo SATO | 24 October 2017, 06:25:29 UTC | line feeds | 24 October 2017, 06:25:29 UTC |
| acf6213 | Kengo SATO | 24 October 2017, 06:23:54 UTC | MIT license | 24 October 2017, 06:23:54 UTC |
| 3c07d0c | Kengo SATO | 24 October 2017, 05:58:43 UTC | add preprint URL | 24 October 2017, 05:58:43 UTC |
| 6df517f | Kengo Sato | 23 August 2017, 02:42:37 UTC | new default parameters | 23 August 2017, 02:42:37 UTC |
| 8a56c39 | Kengo Sato | 23 July 2017, 14:20:02 UTC | control the verbosity level | 23 July 2017, 14:20:02 UTC |
| 80296b8 | Kengo Sato | 18 July 2017, 01:31:52 UTC | display the loss for each epoch | 18 July 2017, 01:31:52 UTC |
| 5afd7f2 | Kengo SATO | 17 July 2017, 15:13:41 UTC | display the Viterbi score for the verbose output | 17 July 2017, 15:13:41 UTC |
| 5eb2dcc | Kengo Sato | 17 July 2017, 14:25:19 UTC | fix the CONTRAfold model | 17 July 2017, 14:25:19 UTC |
| 7ed9139 | Kengo Sato | 17 July 2017, 02:40:26 UTC | options for variable length of nucleotides features | 17 July 2017, 02:40:26 UTC |
| 074a8fe | Kengo Sato | 16 July 2017, 14:33:35 UTC | fix a bug | 16 July 2017, 14:33:35 UTC |
| 50039dd | Kengo Sato | 15 July 2017, 05:56:45 UTC | fix a bug | 15 July 2017, 05:56:45 UTC |
| 3ffb385 | Kengo Sato | 14 July 2017, 13:19:04 UTC | fix a bug around bp length | 14 July 2017, 13:19:04 UTC |
| 6eeb310 | Kengo Sato | 14 July 2017, 11:32:43 UTC | fix the output of parameters | 14 July 2017, 11:32:43 UTC |
| 3276a5b | Kengo Sato | 14 July 2017, 10:49:35 UTC | control verbosity for AdaGrad detail printing | 14 July 2017, 10:49:35 UTC |
| 410db4f | Kengo Sato | 14 July 2017, 02:26:46 UTC | ViennaRNA integration | 14 July 2017, 02:26:46 UTC |
| 25e4916 | Kengo Sato | 12 July 2017, 09:44:57 UTC | add an option for integrating the Turner parameters | 12 July 2017, 09:44:57 UTC |
| 14978fa | Kengo Sato | 12 July 2017, 08:02:54 UTC | link ViennaRNA package | 12 July 2017, 08:02:54 UTC |
| 73588e7 | Kengo Sato | 12 July 2017, 01:06:21 UTC | clean up | 12 July 2017, 01:06:21 UTC |
| a6e58a5 | Kengo Sato | 12 July 2017, 00:29:22 UTC | implementing vienna integration | 12 July 2017, 00:29:22 UTC |
| e34ee01 | Kengo SATO | 10 July 2017, 01:23:08 UTC | implement length features for vienna compatibility | 10 July 2017, 01:23:08 UTC |
| 94ee383 | Kengo Sato | 07 July 2017, 12:26:26 UTC | implementing vienna compatibility | 07 July 2017, 12:26:26 UTC |
| 38ed06e | Kengo SATO | 07 July 2017, 04:40:45 UTC | implementing import from vienna parameters | 07 July 2017, 04:40:45 UTC |
| 4d1881e | Kengo SATO | 06 July 2017, 14:56:16 UTC | change the order of base pairs | 06 July 2017, 14:56:16 UTC |
| 415565c | Kengo Sato | 06 July 2017, 10:51:13 UTC | use base complementarity for the parameter cache | 06 July 2017, 10:51:13 UTC |
| 7c7cc71 | Kengo Sato | 06 July 2017, 01:39:45 UTC | fix a critical bug | 06 July 2017, 01:39:45 UTC |
| 66e4d1d | Kengo SATO | 05 July 2017, 15:02:21 UTC | fix compilation errors | 05 July 2017, 15:02:21 UTC |
| 590418b | Kengo Sato | 03 July 2017, 13:06:20 UTC | implement new feature mapping | 03 July 2017, 13:06:20 UTC |
| 0db71ee | Kengo SATO | 03 July 2017, 01:11:14 UTC | implement new feature mapping | 03 July 2017, 01:11:14 UTC |
| 117fabe | Kengo SATO | 02 July 2017, 12:43:33 UTC | divide terminal mismatches for multi-loops and external loops | 02 July 2017, 12:43:33 UTC |
| 21618e4 | Kengo Sato | 30 June 2017, 11:44:31 UTC | separate terminal mismatches | 30 June 2017, 11:44:31 UTC |
| 4740fed | Kengo SATO | 25 June 2017, 14:12:22 UTC | refactoring | 25 June 2017, 14:12:22 UTC |
| 52c9627 | Kengo Sato | 24 June 2017, 08:53:01 UTC | refactoring | 24 June 2017, 08:53:01 UTC |
| 049c520 | Kengo Sato | 24 June 2017, 06:44:26 UTC | remove tries | 24 June 2017, 06:44:26 UTC |
| 1e88f7d | Kengo SATO | 24 June 2017, 03:05:47 UTC | refactoring | 24 June 2017, 03:05:47 UTC |
| 9ae3cee | Kengo Sato | 22 June 2017, 08:41:14 UTC | Merge branch 'feature_trie' | 22 June 2017, 08:41:14 UTC |
| a57a62f | Kengo SATO | 21 June 2017, 14:47:44 UTC | correct feature defines | 21 June 2017, 14:47:44 UTC |
| e025fdf | Kengo Sato | 21 June 2017, 13:23:30 UTC | longer nucleotides cache | 21 June 2017, 13:23:30 UTC |
| 7b8b73a | Kengo Sato | 19 June 2017, 05:14:16 UTC | do not use internal and hairpin cache | 19 June 2017, 05:14:16 UTC |
| ae45ee0 | Kengo SATO | 17 June 2017, 11:54:48 UTC | fix a bug around trie cache | 17 June 2017, 11:54:48 UTC |
| b22a107 | Kengo SATO | 16 June 2017, 15:05:58 UTC | bugfix around cache initialization | 16 June 2017, 15:05:58 UTC |
| cd2f4f7 | Kengo SATO | 16 June 2017, 14:48:42 UTC | fix boundary error in cache | 16 June 2017, 14:48:42 UTC |
| a11de46 | Kengo Sato | 13 May 2017, 02:36:08 UTC | add a "soft constraints" option for prediction mode | 16 June 2017, 14:36:08 UTC |
| eac82ee | Kengo Sato | 11 May 2017, 08:42:12 UTC | bug fix around the weight of weak labeled data | 16 June 2017, 14:36:08 UTC |
| a82a3f0 | Kengo Sato | 16 June 2017, 14:35:24 UTC | fix iterator for parameters | 16 June 2017, 14:35:24 UTC |
| 35ac93b | Kengo Sato | 16 June 2017, 04:49:46 UTC | fix regex error | 16 June 2017, 04:49:46 UTC |
| 59e6420 | Kengo SATO | 11 June 2017, 14:03:56 UTC | enable the feature trie for inside, outside, etc. | 11 June 2017, 14:03:56 UTC |
| 62940e9 | Kengo SATO | 09 June 2017, 15:12:25 UTC | finish implementing cache mechanism | 09 June 2017, 15:12:25 UTC |
| 292a132 | Kengo Sato | 09 June 2017, 12:30:13 UTC | implementing cache mechanism | 09 June 2017, 12:30:13 UTC |
| dd0f9d9 | Kengo Sato | 09 June 2017, 11:09:06 UTC | symmetric features | 09 June 2017, 11:09:06 UTC |
| a95dd8d | Kengo SATO | 08 June 2017, 14:33:07 UTC | implement the cache system with feature trie | 08 June 2017, 14:33:07 UTC |
| 55930a7 | Kengo Sato | 06 June 2017, 10:12:12 UTC | add a special case | 06 June 2017, 10:12:12 UTC |
| 76535a3 | Kengo Sato | 06 June 2017, 09:32:02 UTC | cache mechanism for internal loops | 06 June 2017, 09:32:02 UTC |
| 03be0c6 | Kengo SATO | 01 June 2017, 14:23:50 UTC | modify for write parameters keeping uniqueness | 01 June 2017, 14:23:50 UTC |
| 8823e80 | Kengo Sato | 01 June 2017, 12:51:46 UTC | modify for internal loops | 01 June 2017, 12:51:46 UTC |
| d6782b2 | Kengo SATO | 30 May 2017, 14:01:51 UTC | cache indices for hairpin nucleotides | 30 May 2017, 14:01:51 UTC |
| f1e5096 | Kengo Sato | 30 May 2017, 09:57:09 UTC | new access function for hairpin loops | 30 May 2017, 09:57:09 UTC |
| e87d564 | Kengo Sato | 30 May 2017, 08:09:08 UTC | fix an error | 30 May 2017, 08:09:08 UTC |
| 172ecf9 | Kengo Sato | 30 May 2017, 07:54:00 UTC | indirect reference to parameter values | 30 May 2017, 07:54:00 UTC |
| 14ab98a | Kengo SATO | 26 May 2017, 14:59:28 UTC | work with trie | 26 May 2017, 14:59:28 UTC |
| 2415dec | Kengo SATO | 26 May 2017, 14:18:25 UTC | fix | 26 May 2017, 14:18:25 UTC |
| 34e126e | Kengo SATO | 26 May 2017, 13:50:34 UTC | fix for trie | 26 May 2017, 13:50:34 UTC |
| 6e8b7fc | Kengo Sato | 26 May 2017, 10:08:00 UTC | fix for trie | 26 May 2017, 10:08:00 UTC |
| 21d72cf | Kengo SATO | 26 May 2017, 07:13:27 UTC | modify some files to use trie | 26 May 2017, 07:13:27 UTC |
| c8702ba | Kengo Sato | 13 May 2017, 02:36:08 UTC | add a "soft constraints" option for prediction mode | 13 May 2017, 02:36:08 UTC |
| d0e5a6b | Kengo Sato | 11 May 2017, 08:42:12 UTC | bug fix around the weight of weak labeled data | 11 May 2017, 08:42:12 UTC |
| 0a6ee21 | Kengo Sato | 18 April 2017, 07:41:46 UTC | swap unpaired and paired in InferenceEngine::UseLossReactivity() | 18 April 2017, 07:41:46 UTC |
| bebe5ce | Kengo Sato | 18 April 2017, 05:12:40 UTC | swap unpaired and paired in InferenceEngine::UseSoftConstraint() | 18 April 2017, 05:12:40 UTC |
| 23ff5bd | Kengo Sato | 01 March 2017, 01:06:59 UTC | change the reactivity scores | 01 March 2017, 01:06:59 UTC |
| 83610d9 | Kengo Sato | 27 January 2017, 14:18:48 UTC | work around for unpaired reactivity data | 27 January 2017, 14:18:48 UTC |
| 96e52d6 | Kengo Sato | 23 January 2017, 07:12:46 UTC | modify the training algorithm for weak label data Do not update parameters related to base pairs using weak label data that contain no base pairs. | 23 January 2017, 07:12:46 UTC |
| b8019c8 | Kengo Sato | 23 January 2017, 03:48:05 UTC | remove some Japanese comments | 23 January 2017, 03:48:05 UTC |
| 4a14c23 | Kengo Sato | 23 January 2017, 00:32:50 UTC | modify loss function and soft constraints for weak-labeled data | 23 January 2017, 00:32:50 UTC |
| 8117005 | Kengo Sato | 21 January 2017, 07:38:07 UTC | fix a bug about regularization | 21 January 2017, 07:38:07 UTC |
| 072ed82 | Kengo Sato | 18 January 2017, 05:33:39 UTC | implement restarting where training stopped | 18 January 2017, 05:33:39 UTC |
| a8c0d33 | Kengo SATO | 16 January 2017, 08:08:49 UTC | support pseudouridine and maximum span of BP | 16 January 2017, 08:08:49 UTC |
| 2793107 | Kengo SATO | 15 January 2017, 14:46:52 UTC | fix a performance problem about C_SINGLE_MAX_LENGTH | 15 January 2017, 14:46:52 UTC |
| 8ee76c5 | Kengo Sato | 15 January 2017, 09:07:41 UTC | support data with both reactivities | 15 January 2017, 09:07:41 UTC |
| 024b8a4 | Kengo Sato | 15 January 2017, 02:29:47 UTC | fix a bug around loss function | 15 January 2017, 02:29:47 UTC |
| 7e8e33d | Kengo Sato | 14 January 2017, 07:46:48 UTC | run gengetopt | 14 January 2017, 07:46:48 UTC |
| 1f29e56 | Kengo Sato | 14 January 2017, 07:31:13 UTC | Adjust the weight for loss according to num of bp | 14 January 2017, 07:31:13 UTC |
| c13b7bb | Kengo SATO | 14 January 2017, 07:05:39 UTC | change some default options | 14 January 2017, 07:05:39 UTC |
| c13c1a3 | Kengo SATO | 12 January 2017, 14:54:54 UTC | implement training with the restart output the status of AdaGrad/RDA, and read it when restart. | 12 January 2017, 14:54:54 UTC |
| 1e3c2da | Kengo Sato | 12 January 2017, 05:40:16 UTC | fix a bug around complementarity check | 12 January 2017, 05:40:16 UTC |
| 47b288d | Kengo Sato | 12 January 2017, 04:38:34 UTC | Merge branch 'master' of ssh://gitbucket.dna.bio.keio.ac.jp:29418/satoken/ngsfold | 12 January 2017, 04:38:34 UTC |
| e1957b5 | Kengo Sato | 12 January 2017, 04:38:19 UTC | implement AdaGrad/FOBOS | 12 January 2017, 04:38:19 UTC |
| 2b27682 | Kengo SATO | 12 January 2017, 04:37:17 UTC | Merge branch 'master' of ssh://gitbucket.dna.bio.keio.ac.jp:29418/satoken/ngsfold | 12 January 2017, 04:37:17 UTC |
| 8e7b159 | Kengo SATO | 12 January 2017, 04:37:12 UTC | check complementarity at ParameterHash | 12 January 2017, 04:37:12 UTC |
| a8f37d2 | Kengo Sato | 12 January 2017, 02:46:30 UTC | implement counting features for debug | 12 January 2017, 02:46:30 UTC |
