{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":766093911,"defaultBranch":"master","name":"GenAIRR","ownerLogin":"MuteJester","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2024-03-02T10:19:46.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/56339082?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1725267045.0","currentOid":""},"activityList":{"items":[{"before":"44e915da49b8b504c7b85d787a7df4e5d45529d7","after":"143f583cc6a0c8533db4c822d08e2f57bc8dbd93","ref":"refs/heads/master","pushedAt":"2024-09-01T10:48:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Minor S5F Mutation Model Runtime Efficiency Improvements","shortMessageHtmlLink":"Minor S5F Mutation Model Runtime Efficiency Improvements"}},{"before":"0913f5af8f32594db5d300fea2994333f48beb97","after":"44e915da49b8b504c7b85d787a7df4e5d45529d7","ref":"refs/heads/master","pushedAt":"2024-08-29T09:17:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Updated RandomDataConfigGenerator.py to support the new trimming distribution structure","shortMessageHtmlLink":"Updated RandomDataConfigGenerator.py to support the new trimming dist…"}},{"before":"779f39d593b0c69e2a1f1db78848fcfadfb8141b","after":"0913f5af8f32594db5d300fea2994333f48beb97","ref":"refs/heads/master","pushedAt":"2024-08-29T08:58:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Updated RandomDataConfigGenerator.py to support the new trimming distribution structure","shortMessageHtmlLink":"Updated RandomDataConfigGenerator.py to support the new trimming dist…"}},{"before":"1c4ba6d524b7b573eb71f01b4dd4ee20cdc1bda6","after":"779f39d593b0c69e2a1f1db78848fcfadfb8141b","ref":"refs/heads/master","pushedAt":"2024-08-29T08:32:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"There was an issue in the ambiguity maps that were supposed to fix the ground truth list after the np trimmings, the map was built from a mix of states some expecting the trim length and some the end of the sequence, now everything is uniform and corrected, the maps expect the trim length when queried, tests were added to validate this correction method for both light and heavy BCR chains, dataconfigs are up to date with these changes after this update.\n\nAdditionally a class was implemented that takes a DataConfig object and automatically derives this maps : derive_similarity_maps.py","shortMessageHtmlLink":"There was an issue in the ambiguity maps that were supposed to fix th…"}},{"before":"084dc46f7345bb560a6290d460f2bedeff8bcf60","after":"1c4ba6d524b7b573eb71f01b4dd4ee20cdc1bda6","ref":"refs/heads/master","pushedAt":"2024-08-28T15:37:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Changed the Trimming Sampling Logic, Now There is a 4 Level Key System, first key is the trimming end i.e V_3,D_5 etc...\nSecond key is the family i.e IGHV10 ... and the third key is the family+the gene /asc i.e IGHV10-G3 the fourth level key is the trimming length which will give a likelihood value, the first 3 keys can be considered as a navigation to the trimming distribution of that position given the family and gene/asc","shortMessageHtmlLink":"Changed the Trimming Sampling Logic, Now There is a 4 Level Key Syste…"}},{"before":"fce1bd924f8d5d6fd98392e5eccc331f7bea2620","after":"084dc46f7345bb560a6290d460f2bedeff8bcf60","ref":"refs/heads/master","pushedAt":"2024-08-15T10:12:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Add support for a new mutation model that combines S5F with random substitutions","shortMessageHtmlLink":"Add support for a new mutation model that combines S5F with random su…"}},{"before":"44020406e5d634a14c903e6bc6f575f51edf6eeb","after":"fce1bd924f8d5d6fd98392e5eccc331f7bea2620","ref":"refs/heads/master","pushedAt":"2024-08-15T09:02:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Added TCR Simulation Example","shortMessageHtmlLink":"Added TCR Simulation Example"}},{"before":"44534542c53a7a7034c1c64378c65834712850e0","after":"44020406e5d634a14c903e6bc6f575f51edf6eeb","ref":"refs/heads/master","pushedAt":"2024-08-15T08:38:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Added Support to TCRB Simulation","shortMessageHtmlLink":"Added Support to TCRB Simulation"}},{"before":"cf8243aa4705ddcb4a56e4872210fbde0056fbf7","after":"44534542c53a7a7034c1c64378c65834712850e0","ref":"refs/heads/master","pushedAt":"2024-08-13T15:10:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Added Multiple Test for Core Simulation Functionality","shortMessageHtmlLink":"Added Multiple Test for Core Simulation Functionality"}},{"before":"c1098ce696dcc4b24ac62ce671646a1fd4fb014c","after":"cf8243aa4705ddcb4a56e4872210fbde0056fbf7","ref":"refs/heads/master","pushedAt":"2024-08-11T15:05:02.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Added New Tutorials On Advanced Sequence Generation","shortMessageHtmlLink":"Added New Tutorials On Advanced Sequence Generation"}},{"before":"344dba8fb83001f6ae6a9e6cb15c38d31cb668f0","after":"c1098ce696dcc4b24ac62ce671646a1fd4fb014c","ref":"refs/heads/master","pushedAt":"2024-07-17T14:46:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Fixed Long Constant Alleles in DataConfigs","shortMessageHtmlLink":"Fixed Long Constant Alleles in DataConfigs"}},{"before":"4705274e0d366a5d26a96c0e89aa3c2f75c23a3d","after":"344dba8fb83001f6ae6a9e6cb15c38d31cb668f0","ref":"refs/heads/master","pushedAt":"2024-07-17T08:48:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Fixed Constant Allele DataConfig Bad Save, all constant alleles contained exactly the same DNA sequence for all chains, this issue is now fixed.\n\nAdd support for custom generation of sequence using argument that accept specific Allele objects use them instead of randomly sampling for each v,d and j allele.","shortMessageHtmlLink":"Fixed Constant Allele DataConfig Bad Save, all constant alleles conta…"}},{"before":"bd286680300c47d9c6b6892588f17d44b5809cda","after":"4705274e0d366a5d26a96c0e89aa3c2f75c23a3d","ref":"refs/heads/master","pushedAt":"2024-06-28T15:35:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Asc Table Fix","shortMessageHtmlLink":"Asc Table Fix"}},{"before":"65e5010bb129dd3c74237b9056b94e46b9b6e297","after":"bd286680300c47d9c6b6892588f17d44b5809cda","ref":"refs/heads/master","pushedAt":"2024-06-28T15:33:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Asc Table Fix","shortMessageHtmlLink":"Asc Table Fix"}},{"before":"3c8b2d429e90a51f5809b765cfe461b9ee6562eb","after":"65e5010bb129dd3c74237b9056b94e46b9b6e297","ref":"refs/heads/master","pushedAt":"2024-06-26T14:38:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Added Simulation Logic Of Light and Heavy Chain Sequences with Constant Region.","shortMessageHtmlLink":"Added Simulation Logic Of Light and Heavy Chain Sequences with Consta…"}},{"before":"523d2e553aacc8ec830bee665a715165f5a201a4","after":"3c8b2d429e90a51f5809b765cfe461b9ee6562eb","ref":"refs/heads/master","pushedAt":"2024-06-26T12:37:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Added Constant Region Data to Model Allele Structure + Added .c_alleles dictionary to each builtin dataconfig object (heavy and light chain).","shortMessageHtmlLink":"Added Constant Region Data to Model Allele Structure + Added .c_allel…"}},{"before":"7e237276dbf1ab366081aefcf3f5983aaa8501db","after":"523d2e553aacc8ec830bee665a715165f5a201a4","ref":"refs/heads/master","pushedAt":"2024-06-25T10:25:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Refactored Code Structure of Heavy and Light Chain Base Classes For Future Flexibility in Construction Step Addition (Like Constant Region)","shortMessageHtmlLink":"Refactored Code Structure of Heavy and Light Chain Base Classes For F…"}},{"before":"a641d4b76d4cbb72e74b718711fb7c2755e98667","after":"7e237276dbf1ab366081aefcf3f5983aaa8501db","ref":"refs/heads/master","pushedAt":"2024-06-25T08:30:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Fixed Missing Logic in fix position ambiguity after trimming is reconstructed ny NP regions, gemrline and sequence start and end were updated as need but the trim length was not updated, causing errors when addressing the D ambiguity map. Also added a few TODOs we should address","shortMessageHtmlLink":"Fixed Missing Logic in fix position ambiguity after trimming is recon…"}},{"before":"6f2e984125b8d137fcb46f3403605fdef8e25d25","after":"a641d4b76d4cbb72e74b718711fb7c2755e98667","ref":"refs/heads/master","pushedAt":"2024-06-23T07:31:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Adjusted the deletion function in the lightchain sequence object to remove max function, now it matches the heavy chain structure","shortMessageHtmlLink":"Adjusted the deletion function in the lightchain sequence object to r…"}},{"before":"33225cf75be7a8a924928643e0f688ac0e786687","after":"6f2e984125b8d137fcb46f3403605fdef8e25d25","ref":"refs/heads/master","pushedAt":"2024-06-11T15:54:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Updated Asc Tables in DataConfig Files","shortMessageHtmlLink":"Updated Asc Tables in DataConfig Files"}},{"before":"a9ca777c735a8167c1ab8de6a68bd9462abfdf73","after":"33225cf75be7a8a924928643e0f688ac0e786687","ref":"refs/heads/master","pushedAt":"2024-05-27T10:38:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ayeletperes","name":"Ayelet Peres","path":"/ayeletperes","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/26592225?s=80&v=4"},"commit":{"message":"bug in light chain productive call","shortMessageHtmlLink":"bug in light chain productive call"}},{"before":"afb235c3922be4f6a869a15212307206f554e709","after":"a9ca777c735a8167c1ab8de6a68bd9462abfdf73","ref":"refs/heads/master","pushedAt":"2024-05-26T12:00:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Minor Light Chain Fix","shortMessageHtmlLink":"Minor Light Chain Fix"}},{"before":"8ffeedecdf156012d1d68319b19ab2bb09f7e38f","after":"afb235c3922be4f6a869a15212307206f554e709","ref":"refs/heads/master","pushedAt":"2024-05-26T11:42:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ayeletperes","name":"Ayelet Peres","path":"/ayeletperes","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/26592225?s=80&v=4"},"commit":{"message":"fixed light chain functionality","shortMessageHtmlLink":"fixed light chain functionality"}},{"before":"97c18b462d6272dbc94a4ab097e67803bd58e071","after":"8ffeedecdf156012d1d68319b19ab2bb09f7e38f","ref":"refs/heads/master","pushedAt":"2024-05-25T10:10:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Dist Updated","shortMessageHtmlLink":"Dist Updated"}},{"before":"6b225bf9eeea1ef15656c7de0c47a37d45240caa","after":"97c18b462d6272dbc94a4ab097e67803bd58e071","ref":"refs/heads/master","pushedAt":"2024-05-25T09:59:53.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/master'","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/master'"}},{"before":"d88f3ec7b1d5b02d4304ca795db9349f875ef608","after":"6b225bf9eeea1ef15656c7de0c47a37d45240caa","ref":"refs/heads/master","pushedAt":"2024-05-25T09:59:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"Create python-publish.yml","shortMessageHtmlLink":"Create python-publish.yml"}},{"before":"a58a3c18fee65a757331eb50523a77c55d98ed9b","after":"d88f3ec7b1d5b02d4304ca795db9349f875ef608","ref":"refs/heads/master","pushedAt":"2024-05-22T15:27:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"MuteJester","name":"Thomas Konstantinovsky","path":"/MuteJester","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56339082?s=80&v=4"},"commit":{"message":"builtin dataconfig loading function after the \"frame\" was added to the allele class","shortMessageHtmlLink":"builtin dataconfig loading function after the \"frame\" was added to th…"}},{"before":"a09f96d39ae1a5388f0b3bde3df6a0769ca862df","after":"a58a3c18fee65a757331eb50523a77c55d98ed9b","ref":"refs/heads/master","pushedAt":"2024-05-21T02:56:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ayeletperes","name":"Ayelet Peres","path":"/ayeletperes","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/26592225?s=80&v=4"},"commit":{"message":"fixed bug in fix_productive_call_after_corruption_indel","shortMessageHtmlLink":"fixed bug in fix_productive_call_after_corruption_indel"}},{"before":"e8cc85a2f49548ec9008959c0fe3255d7eb2e9bf","after":"a09f96d39ae1a5388f0b3bde3df6a0769ca862df","ref":"refs/heads/master","pushedAt":"2024-04-24T13:42:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ayeletperes","name":"Ayelet Peres","path":"/ayeletperes","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/26592225?s=80&v=4"},"commit":{"message":"minor fix to final productivity check","shortMessageHtmlLink":"minor fix to final productivity check"}},{"before":"1a00a618c5cf43914ca7685cc3dfe48efe9adb93","after":"e8cc85a2f49548ec9008959c0fe3255d7eb2e9bf","ref":"refs/heads/master","pushedAt":"2024-04-18T15:00:58.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ayeletperes","name":"Ayelet Peres","path":"/ayeletperes","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/26592225?s=80&v=4"},"commit":{"message":"added corrupt_events_proba","shortMessageHtmlLink":"added corrupt_events_proba"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEqclkBwA","startCursor":null,"endCursor":null}},"title":"Activity · MuteJester/GenAIRR"}