0000000000000000000000000000000000000000 023857ab03ede018873c06d00c97b52bd374c253 Kevin Kaichuang Yang <kevyan@Kevins-MacBook-Pro.local> 1589816784 -0400	clone: from MSRNE-ML@vs-ssh.visualstudio.com:v3/MSRNE-ML/sequence_models/sequence_models
023857ab03ede018873c06d00c97b52bd374c253 9d29d7772666b064277c643221e35e8ca740352e Kevin Kaichuang Yang <kevyan@Kevins-MacBook-Pro.local> 1589913438 -0400	commit: Better version of causal convolution.
9d29d7772666b064277c643221e35e8ca740352e 81310b6f2eac8e2015e351b5fb22ea96e7848fed Kevin Kaichuang Yang <kevyan@Kevins-MacBook-Pro.local> 1589913491 -0400	commit (amend): Better version of causal convolution.
81310b6f2eac8e2015e351b5fb22ea96e7848fed 5c9e1c39cc574267fad07745f844ebe6a92e9a80 Kevin Kaichuang Yang <kevyan@Kevins-MacBook-Pro.local> 1589913616 -0400	commit: Add ByteNet block.
5c9e1c39cc574267fad07745f844ebe6a92e9a80 8c036014151af5c1dc1237400ffca62167ac40ee Kevin Kaichuang Yang <kevyan@Kevins-MacBook-Pro.local> 1589995667 -0400	commit: Implement ByteNet.
8c036014151af5c1dc1237400ffca62167ac40ee 605aef6041efdeea00c60025f2a4d459bd516aa0 Kevin Kaichuang Yang <kevyan@Kevins-MacBook-Pro.local> 1590000128 -0400	commit: Complete and test masked cross entropy.
605aef6041efdeea00c60025f2a4d459bd516aa0 eb17b257ee4fb5b125cf06b097bf677e03d2aba2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1590000162 -0400	commit (amend): Complete and test masked cross entropy.
eb17b257ee4fb5b125cf06b097bf677e03d2aba2 44ac67da867e8740365ad7f8caa1c3656d525ebc Kevin Kaichuang Yang <kevyan@microsoft.com> 1590169056 -0400	pull origin hugh: Merge made by the 'recursive' strategy.
44ac67da867e8740365ad7f8caa1c3656d525ebc ca1ce93a243352db947205fb0e583df089b06d7d Kevin Kaichuang Yang <kevyan@microsoft.com> 1590681071 -0400	commit: Add more ByteNet variants.
ca1ce93a243352db947205fb0e583df089b06d7d 69fa35e6be281d563fe0247afd84fea78860b5ab Kevin Kaichuang Yang <kevyan@microsoft.com> 1590783430 -0400	commit: First attempt at a conductor module for the HVAE. Some tests.
69fa35e6be281d563fe0247afd84fea78860b5ab eed6bbba6452c46f930a733f58441010c48e3055 Kevin Kaichuang Yang <kevyan@microsoft.com> 1590783475 -0400	commit: First attempt at a HVAE.
eed6bbba6452c46f930a733f58441010c48e3055 4791656b1f3320fe434d72d070882df4cf3df827 Kevin Kaichuang Yang <kevyan@microsoft.com> 1590783507 -0400	pull origin hugh: Merge made by the 'recursive' strategy.
4791656b1f3320fe434d72d070882df4cf3df827 11b33a4a3756ff2c757db083536431afc7a08877 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591128029 -0400	commit: Bug fixes. Move Conductor to vae.py.
11b33a4a3756ff2c757db083536431afc7a08877 b6524a38e876820f2220c8d084a83f887dd2e59a Kevin Kaichuang Yang <kevyan@microsoft.com> 1591128286 -0400	pull origin master: Fast-forward
b6524a38e876820f2220c8d084a83f887dd2e59a b6524a38e876820f2220c8d084a83f887dd2e59a Kevin Kaichuang Yang <kevyan@microsoft.com> 1591130303 -0400	checkout: moving from master to hugh
b6524a38e876820f2220c8d084a83f887dd2e59a 8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c Kevin Kaichuang Yang <kevyan@microsoft.com> 1591130412 -0400	commit (merge): Keep convolutional.py.
8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c b6524a38e876820f2220c8d084a83f887dd2e59a Kevin Kaichuang Yang <kevyan@microsoft.com> 1591130426 -0400	checkout: moving from hugh to master
b6524a38e876820f2220c8d084a83f887dd2e59a 8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c Kevin Kaichuang Yang <kevyan@microsoft.com> 1591130441 -0400	merge hugh: Fast-forward
8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c 8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c Kevin Kaichuang Yang <kevyan@microsoft.com> 1591130487 -0400	checkout: moving from master to cleanup
8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c 35e501dfefe6188bcbc2f1c69ff24c1a15527fe3 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591130663 -0400	commit: Rename dataloader file. Rename collate function for mlm.
35e501dfefe6188bcbc2f1c69ff24c1a15527fe3 40845133b3a4d05ee93699fae13dee5cbc0983fc Kevin Kaichuang Yang <kevyan@microsoft.com> 1591131045 -0400	commit: Clean up imports and style.
40845133b3a4d05ee93699fae13dee5cbc0983fc 299f9102f7663165fdb24b040ecbcf9732afec4b Kevin Kaichuang Yang <kevyan@microsoft.com> 1591132932 -0400	commit: Fix and briefly test the sortish sampler.
299f9102f7663165fdb24b040ecbcf9732afec4b 15656488c9820c64bc443ca623e674fc015d01d0 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591133904 -0400	commit: Fix and briefly test the batch sampler.
15656488c9820c64bc443ca623e674fc015d01d0 d54d8956d8882e98fca0017f65b23412b41b1efc Kevin Kaichuang Yang <kevyan@microsoft.com> 1591133960 -0400	commit (amend): Fix and briefly test the batch sampler.
d54d8956d8882e98fca0017f65b23412b41b1efc e002aa0608a9466b4b4f454fa2255b98d2cc36f7 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591133989 -0400	commit (amend): Fix and briefly test the batch sampler.
e002aa0608a9466b4b4f454fa2255b98d2cc36f7 299f9102f7663165fdb24b040ecbcf9732afec4b Kevin Kaichuang Yang <kevyan@microsoft.com> 1591134325 -0400	reset: moving to HEAD~1
299f9102f7663165fdb24b040ecbcf9732afec4b 35e501dfefe6188bcbc2f1c69ff24c1a15527fe3 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591134334 -0400	reset: moving to HEAD~2
35e501dfefe6188bcbc2f1c69ff24c1a15527fe3 11b33a4a3756ff2c757db083536431afc7a08877 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591134359 -0400	reset: moving to HEAD~3
11b33a4a3756ff2c757db083536431afc7a08877 11b33a4a3756ff2c757db083536431afc7a08877 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591134379 -0400	reset: moving to HEAD
11b33a4a3756ff2c757db083536431afc7a08877 64f73ae41684b1b6daa6b36627f205cd862a41e1 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591196420 -0400	commit: Test samplers.
64f73ae41684b1b6daa6b36627f205cd862a41e1 4e8fee3156fc1efdd764a6c604d201b6700677e8 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591196460 -0400	commit: Add docstrings from Hugh's branch.
4e8fee3156fc1efdd764a6c604d201b6700677e8 725edba1a6734460930c4a665c9eee9265a78de9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591196871 -0400	commit: Remove dataloader_vanilla.py
725edba1a6734460930c4a665c9eee9265a78de9 8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c Kevin Kaichuang Yang <kevyan@microsoft.com> 1591196882 -0400	checkout: moving from cleanup to master
8b0fd3bb121f2aa203837a1fa3b3dafd7cb9613c f0ef3ddda4305aa90b98ca88094f6e06d1af3dd1 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591196885 -0400	merge cleanup: Merge made by the 'recursive' strategy.
f0ef3ddda4305aa90b98ca88094f6e06d1af3dd1 f0ef3ddda4305aa90b98ca88094f6e06d1af3dd1 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591196899 -0400	checkout: moving from master to hvae
f0ef3ddda4305aa90b98ca88094f6e06d1af3dd1 196207b0d94ded14a951ee9d80a810c0336c6d8b Kevin Kaichuang Yang <kevyan@microsoft.com> 1591198419 -0400	commit: Move Conductor tests and fix Conductor padding/stride.
196207b0d94ded14a951ee9d80a810c0336c6d8b 3f66a2abbe7cb7e36726784b41e3483814ef5ad3 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591292290 -0400	commit: Fix some formatting.
3f66a2abbe7cb7e36726784b41e3483814ef5ad3 cc675ec9707ccb98d6f6a8f6b05c30cbfd278030 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591292301 -0400	commit: Allow recurrent decoders.
cc675ec9707ccb98d6f6a8f6b05c30cbfd278030 080f3f95113e8f3f9247694969233e23558c333b Kevin Kaichuang Yang <kevyan@microsoft.com> 1591292318 -0400	commit: Test causal convolutions.
080f3f95113e8f3f9247694969233e23558c333b 1cef7418d7538eda84f6f64bf94b40f9e61a9c23 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591292367 -0400	commit: Combine data utils into one module. Refactor collate_fns.
1cef7418d7538eda84f6f64bf94b40f9e61a9c23 f0ef3ddda4305aa90b98ca88094f6e06d1af3dd1 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591292377 -0400	checkout: moving from hvae to master
f0ef3ddda4305aa90b98ca88094f6e06d1af3dd1 1cef7418d7538eda84f6f64bf94b40f9e61a9c23 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591292380 -0400	merge hvae: Fast-forward
1cef7418d7538eda84f6f64bf94b40f9e61a9c23 1cef7418d7538eda84f6f64bf94b40f9e61a9c23 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591299804 -0400	checkout: moving from master to pretrain
1cef7418d7538eda84f6f64bf94b40f9e61a9c23 b775a0afbb5059e0b9b30838ac909d1168af2d98 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591735196 -0400	commit: Add a comment.
b775a0afbb5059e0b9b30838ac909d1168af2d98 f2c9053410221f895401005f624a1c89e1699ee6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591735217 -0400	commit: Add collaters for LM and MLM.
f2c9053410221f895401005f624a1c89e1699ee6 3fb986a343169b986bd7df4aeece297946cf95e9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591735427 -0400	commit: Clean up imports.
3fb986a343169b986bd7df4aeece297946cf95e9 ee5f5fa7071ff0340bd3e201fcc18448fb01c4ab Kevin Kaichuang Yang <kevyan@microsoft.com> 1591736079 -0400	commit: Fix if/elif bug.
ee5f5fa7071ff0340bd3e201fcc18448fb01c4ab 1cef7418d7538eda84f6f64bf94b40f9e61a9c23 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591972761 -0400	checkout: moving from pretrain to master
1cef7418d7538eda84f6f64bf94b40f9e61a9c23 c750f819cc17eef15916182086006bbb184168e7 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591972768 -0400	pull origin master: Fast-forward
c750f819cc17eef15916182086006bbb184168e7 c750f819cc17eef15916182086006bbb184168e7 Kevin Kaichuang Yang <kevyan@microsoft.com> 1591987662 -0400	checkout: moving from master to master
c750f819cc17eef15916182086006bbb184168e7 cd703e7ec4668708698552cca5ba8f100bd96aa6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1592320404 -0400	pull origin master: Fast-forward
cd703e7ec4668708698552cca5ba8f100bd96aa6 0bc984f291315cc40254c3e5d79a9eb383b00fb7 Kevin Kaichuang Yang <kevyan@microsoft.com> 1594057811 -0400	commit: Add ability to do flat sequence datasets.
0bc984f291315cc40254c3e5d79a9eb383b00fb7 a945ac267181ef1840902eee3aeaa15f7e40ee2b Kevin Kaichuang Yang <kevyan@microsoft.com> 1596210157 -0400	commit: Fix bug in SimpleCollater.
a945ac267181ef1840902eee3aeaa15f7e40ee2b f01c58f4d6955bbe03dc0a65b0acadbf33f1d3e5 Kevin Kaichuang Yang <kevyan@microsoft.com> 1596210178 -0400	commit: Add collating for reversed language models.
f01c58f4d6955bbe03dc0a65b0acadbf33f1d3e5 eada61b4ef972f3b573e82943023ae576b6f4864 Kevin Kaichuang Yang <kevyan@microsoft.com> 1596649859 -0400	commit: Add dropout.
eada61b4ef972f3b573e82943023ae576b6f4864 39fd421f28d3d1675caaba249ba5c5be08ac51de Kevin Kaichuang Yang <kevyan@microsoft.com> 1596649872 -0400	pull origin master: Merge made by the 'recursive' strategy.
39fd421f28d3d1675caaba249ba5c5be08ac51de 46c51c1f3dca425eeb67d9d63b46bee6b691e75b Kevin Kaichuang Yang <kevyan@microsoft.com> 1597263150 -0400	commit: Refactor collaters to remove redundancy.
46c51c1f3dca425eeb67d9d63b46bee6b691e75b 0db4fc48e4a4c28535966918659e42ce3050e2c9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1597267208 -0400	commit: Add collater for simple ancestor prediction.
0db4fc48e4a4c28535966918659e42ce3050e2c9 26ac22d64ae56ebbd7b10ae8cf7393ee8a768698 Kevin Kaichuang Yang <kevyan@microsoft.com> 1597776158 -0400	commit: Improvements to trRosetta, including fixing whitespace, refactoring the directories for model weights, and allowing encoder only.
26ac22d64ae56ebbd7b10ae8cf7393ee8a768698 76d73fcc0120f75be0f199474df12952afcd158e Kevin Kaichuang Yang <kevyan@microsoft.com> 1597776172 -0400	commit: Fix whitespace.
76d73fcc0120f75be0f199474df12952afcd158e d044779313f5e43b439e3787e56ac917371b345f Kevin Kaichuang Yang <kevyan@microsoft.com> 1597776253 -0400	commit: Refactor constructors some more to have sensible defaults.
d044779313f5e43b439e3787e56ac917371b345f 0508efac25d690b4a8acf09f395fe86f63c904ec Kevin Kaichuang Yang <kevyan@microsoft.com> 1597776289 -0400	commit: Don't calculate beta sheets.
0508efac25d690b4a8acf09f395fe86f63c904ec a8a78e796cf19f65aee02a1a74a4eb83ec2df187 Kevin Kaichuang Yang <kevyan@microsoft.com> 1597785040 -0400	commit: Make a function that reads fastas.
a8a78e796cf19f65aee02a1a74a4eb83ec2df187 16746f9497860369ffeeeb812397f693cb2ed309 Kevin Kaichuang Yang <kevyan@microsoft.com> 1597785076 -0400	commit: Make the processor directly callable.
16746f9497860369ffeeeb812397f693cb2ed309 30c31160dcad164ade4c6bba2f70fddb468e56cc Kevin Kaichuang Yang <kevyan@microsoft.com> 1597785112 -0400	commit: Put individual models in an nn.ModuleList for correct submodule and parameter behavior.
30c31160dcad164ade4c6bba2f70fddb468e56cc e18071a6b530dc23edd85b9e1dfdaa6161abf045 Kevin Kaichuang Yang <kevyan@microsoft.com> 1597785947 -0400	commit (merge): Merge docstrings and my changes.
e18071a6b530dc23edd85b9e1dfdaa6161abf045 01d719be28d51b04fa5f30c08a50ac8ec5896c44 Kevin Kaichuang Yang <kevyan@microsoft.com> 1598383078 -0400	commit: Add function to calculate weights based on similarity. Fix bugs and add functionality to parse_fasta.
01d719be28d51b04fa5f30c08a50ac8ec5896c44 453eae2d36e0f066b46aa0907588b04e5e05e84a Kevin Kaichuang Yang <kevyan@microsoft.com> 1598990023 -0400	commit: Add ffindex dataset.
453eae2d36e0f066b46aa0907588b04e5e05e84a 6598a7699df4aab2d280c8768c4805e2173df5c9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1598990060 -0400	commit: Don't move ensemple to GPU automatically.
6598a7699df4aab2d280c8768c4805e2173df5c9 87d32ae6b27bef02e22ab591ebb7abc8118dd9de Kevin Kaichuang Yang <kevyan@microsoft.com> 1598990120 -0400	commit: Clean up one-hot-embedding code and inverse.
87d32ae6b27bef02e22ab591ebb7abc8118dd9de d7e9f2a3a8dd2c06ae730da7eb1ac7885a261d69 Kevin Kaichuang Yang <kevyan@microsoft.com> 1599663526 -0400	commit: Improvements to dataloading for uniboost.
d7e9f2a3a8dd2c06ae730da7eb1ac7885a261d69 f3b7822a5ff48d20b377d39719bc962dad7dec3a Kevin Kaichuang Yang <kevyan@microsoft.com> 1600180813 -0400	commit: Strip characters that trrosetta doesn't recognize
f3b7822a5ff48d20b377d39719bc962dad7dec3a 8ccbb55c9d643483899d1590fb8bf89f293eb3bb Kevin Kaichuang Yang <kevyan@microsoft.com> 1600180845 -0400	commit: Put trrosetta weights in the pt data directory.
8ccbb55c9d643483899d1590fb8bf89f293eb3bb 6812c1f25f99a1daf5fd2b86763b3f1dbdde3a5b Kevin Kaichuang Yang <kevyan@microsoft.com> 1600368909 -0400	pull origin master: Fast-forward
6812c1f25f99a1daf5fd2b86763b3f1dbdde3a5b abadd2eb9ee4b7e6bd40df85654d531fc0b446c2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1600451990 -0400	commit: Remove mmseqs clustering code.
abadd2eb9ee4b7e6bd40df85654d531fc0b446c2 4fb73e6918a3b4b474922872cf302c6ee3c33e4c Kevin Kaichuang Yang <kevyan@microsoft.com> 1601313202 -0400	commit: Make a dataset for uniref/uniclust.
4fb73e6918a3b4b474922872cf302c6ee3c33e4c fa3a81684df4cc92591e8fc393424547441a4047 Kevin Kaichuang Yang <kevyan@microsoft.com> 1601313232 -0400	commit: Deal with empty sequences properly when masking.
fa3a81684df4cc92591e8fc393424547441a4047 1c0779ddfd1a1577b5561b2ced46dd21f04bf598 Kevin Kaichuang Yang <kevyan@microsoft.com> 1601313309 -0400	commit: Don't track scratch files.
1c0779ddfd1a1577b5561b2ced46dd21f04bf598 fc83c9d691e53e10e013b7a5a0274466bcc568f4 Kevin Kaichuang Yang <kevyan@microsoft.com> 1601313316 -0400	pull origin master: Merge made by the 'recursive' strategy.
fc83c9d691e53e10e013b7a5a0274466bcc568f4 3e4dee6f26d9e6ac9a2e0718a90d3ec386663ad7 Kevin Kaichuang Yang <kevyan@microsoft.com> 1601574860 -0400	commit: Initial loaders for structure.
3e4dee6f26d9e6ac9a2e0718a90d3ec386663ad7 31c50f07ecd797ff3c8735240a9b8ee88306dc0e Kevin Kaichuang Yang <kevyan@microsoft.com> 1601574873 -0400	commit: Small improvements to gnn.
31c50f07ecd797ff3c8735240a9b8ee88306dc0e 1f910fbf05f8b3516fb79d152a2ac6504ee237d5 Kevin Kaichuang Yang <kevyan@microsoft.com> 1601574895 -0400	commit: Add top-n accuracy.
1f910fbf05f8b3516fb79d152a2ac6504ee237d5 53cdfd8c20edc5942e53c4688177c97bee65f874 Kevin Kaichuang Yang <kevyan@microsoft.com> 1601659993 -0400	pull origin master: Fast-forward
53cdfd8c20edc5942e53c4688177c97bee65f874 a84e95080fe8e7a11d0ff5d6476145c65b6054ee Kevin Kaichuang Yang <kevyan@microsoft.com> 1601660890 -0400	commit: Store trrosetta bins in constants. Return syn_dist as an numpy array.
a84e95080fe8e7a11d0ff5d6476145c65b6054ee 060a5768f13b06f8a49b0ad371640f49fa09b97a Kevin Kaichuang Yang <kevyan@microsoft.com> 1601661066 -0400	commit: Fix missing assignment and spacing in argmax2value
060a5768f13b06f8a49b0ad371640f49fa09b97a b54c2a2693956fff5f8d493a6a17eb13c4fe5d9e Kevin Kaichuang Yang <kevyan@microsoft.com> 1601999924 -0400	pull origin master: Fast-forward
b54c2a2693956fff5f8d493a6a17eb13c4fe5d9e edf8226e73995594dfc8b8e3274296c281554661 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602027777 -0400	commit: Add option to extract structures from zip on the fly.
edf8226e73995594dfc8b8e3274296c281554661 9f07444db76466281ca83e8db75b514b1258c6a6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602027825 -0400	commit: Lots of small formatting and bug fixes.
9f07444db76466281ca83e8db75b514b1258c6a6 75f5d95e4301c92a1525ea96ac3228d3464b7d12 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602028253 -0400	commit (merge): Merge branch 'master' of vs-ssh.visualstudio.com:v3/MSRNE-ML/sequence_models/sequence_models
75f5d95e4301c92a1525ea96ac3228d3464b7d12 187713b308113183377a28d4c4125011e869096d Kevin Kaichuang Yang <kevyan@microsoft.com> 1602036963 -0400	commit: 2D ByteNet, 2D attention pooling, and a StructureConditioner for trRosetta outputs.
187713b308113183377a28d4c4125011e869096d 96a8cf47770ea849c295dda79b5d79b146ef0063 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602085106 -0400	commit: Rename the structure convnet.
96a8cf47770ea849c295dda79b5d79b146ef0063 627c40c58af6b4b9f91641354b4d3bf5b07f73bd Kevin Kaichuang Yang <kevyan@microsoft.com> 1602178806 -0400	commit: Use degrees, not radians.
627c40c58af6b4b9f91641354b4d3bf5b07f73bd 7f291c46d986aa142983dd18cdd823052dc74cc0 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602178870 -0400	commit: Refactor models.
7f291c46d986aa142983dd18cdd823052dc74cc0 0b2b896da3da295c9e308856c0250da236d31936 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602178975 -0400	commit: Remove old cnn structure encoder.
0b2b896da3da295c9e308856c0250da236d31936 0c0218d97f44ac3d192e68cf0da77aae52206953 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602178984 -0400	commit: Make code more readable.
0c0218d97f44ac3d192e68cf0da77aae52206953 bcff21578b652f9aa38253f798013b4c886862c7 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602179060 -0400	commit: Move structure bin to num conversion and add a collater for distances and angles.
bcff21578b652f9aa38253f798013b4c886862c7 85f53015d44c74e8f2b420db85c3557361d2cd7e Kevin Kaichuang Yang <kevyan@microsoft.com> 1602254533 -0400	commit: Add option to randomly subsample sequences over a certain length.
85f53015d44c74e8f2b420db85c3557361d2cd7e e4c724f0fe27264b42efb7729a9408d2e2b77c2b Kevin Kaichuang Yang <kevyan@microsoft.com> 1602254583 -0400	commit: Only mask structure tensor for size.
e4c724f0fe27264b42efb7729a9408d2e2b77c2b 6669c32f7ec2dce90bc686c9e1169a4826f67dc8 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602254600 -0400	commit: Fix masking bugs in attention layer.
6669c32f7ec2dce90bc686c9e1169a4826f67dc8 fde158d223a65679870caf94b2877652c48676e4 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602254608 -0400	pull origin master: Merge made by the 'recursive' strategy.
fde158d223a65679870caf94b2877652c48676e4 25fa06fed1529294dcb3c2d1e2b99546b7394739 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602522307 -0400	commit: Handle backwards structures.
25fa06fed1529294dcb3c2d1e2b99546b7394739 a6bb1399266c7fadca1d67cd5d4df5df9ddbb369 Kevin Kaichuang Yang <kevyan@microsoft.com> 1602522316 -0400	pull origin master: Merge made by the 'recursive' strategy.
a6bb1399266c7fadca1d67cd5d4df5df9ddbb369 da038d4af9aaf9d56d2f5fafd7d0d047443f446d Kevin Kaichuang Yang <kevyan@microsoft.com> 1603215856 -0400	commit: Remove pdb processing script.
da038d4af9aaf9d56d2f5fafd7d0d047443f446d 48113384f03d522cde58ec603e32c132a7e76ff0 Kevin Kaichuang Yang <kevyan@microsoft.com> 1603215890 -0400	commit: Add function to extract metrics from training script stdout.
48113384f03d522cde58ec603e32c132a7e76ff0 e3713458d52cef210049338782fee08673b0aeba Kevin Kaichuang Yang <kevyan@microsoft.com> 1603216017 -0400	commit: Remove support for zipped structures. Add support for pdb coordinates.
e3713458d52cef210049338782fee08673b0aeba d4f27d0802b7982b68a29e1b60a1d20229bdade3 Kevin Kaichuang Yang <kevyan@microsoft.com> 1603216259 -0400	commit: Fix length/offset issues when using gnn for next-token prediction.
d4f27d0802b7982b68a29e1b60a1d20229bdade3 1aae1284306426321db98d5a6abaf3afe2b9eeab Kevin Kaichuang Yang <kevyan@microsoft.com> 1603216274 -0400	commit: Shuffle better in SortishSampler.
1aae1284306426321db98d5a6abaf3afe2b9eeab f56e9ef730a0ff5e0940345125b64f3c3891048f Kevin Kaichuang Yang <kevyan@microsoft.com> 1603217596 -0400	commit: At most ell - 1 neighbors.
f56e9ef730a0ff5e0940345125b64f3c3891048f c06f8866d602c26ae8f9152d3233f2afe73cb4aa Kevin Kaichuang Yang <kevyan@microsoft.com> 1603217715 -0400	pull origin master: Merge made by the 'recursive' strategy.
c06f8866d602c26ae8f9152d3233f2afe73cb4aa 2abf52f40c8ce993ed045c339c7dacd84f95ddec Kevin Kaichuang Yang <kevyan@microsoft.com> 1603218940 -0400	commit: Split data.py into three modules.
2abf52f40c8ce993ed045c339c7dacd84f95ddec 2abf52f40c8ce993ed045c339c7dacd84f95ddec Kevin Kaichuang Yang <kevyan@microsoft.com> 1603482594 -0400	checkout: moving from master to h5py
2abf52f40c8ce993ed045c339c7dacd84f95ddec 8e64b61a77d516b5bcb7813a4521cd2acd4a6da6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1603482623 -0400	commit: Use consolidated h5pys instead of individual npzs to store structures.
8e64b61a77d516b5bcb7813a4521cd2acd4a6da6 2abf52f40c8ce993ed045c339c7dacd84f95ddec Kevin Kaichuang Yang <kevyan@microsoft.com> 1603482655 -0400	checkout: moving from h5py to master
2abf52f40c8ce993ed045c339c7dacd84f95ddec a696ef184a1e8258191d3a7b57a6d5193e18e946 Kevin Kaichuang Yang <kevyan@microsoft.com> 1603916470 -0400	pull origin master: Fast-forward
a696ef184a1e8258191d3a7b57a6d5193e18e946 8834233543b3e57ad5b89631edf09ca5b3b01dc6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1604422587 -0500	commit: Return y as a tensor.
8834233543b3e57ad5b89631edf09ca5b3b01dc6 a198f67680c3ae85ff9bb451ee201411547f87e5 Kevin Kaichuang Yang <kevyan@microsoft.com> 1604422596 -0500	commit: Fix 1D attention.
a198f67680c3ae85ff9bb451ee201411547f87e5 1d3e6f7d3f522e374cdac0d81288b865a65b51ed Kevin Kaichuang Yang <kevyan@microsoft.com> 1604422952 -0500	commit (merge): Merge branch 'master' of vs-ssh.visualstudio.com:v3/MSRNE-ML/sequence_models/sequence_models
1d3e6f7d3f522e374cdac0d81288b865a65b51ed 7569cf680c758052de4724c782f9ed4849a68d7a Kevin Kaichuang Yang <kevyan@microsoft.com> 1604431049 -0500	commit: Fix extra bits I didn't catch during merge.
7569cf680c758052de4724c782f9ed4849a68d7a d400684251e804574479c6430663d3eee0ff9813 Kevin Kaichuang Yang <kevyan@microsoft.com> 1604616649 -0500	commit: Fix shape for classification vs regression.
d400684251e804574479c6430663d3eee0ff9813 59f98b046f1c727411046f000f31cf1a9a933f96 Kevin Kaichuang Yang <kevyan@microsoft.com> 1604616687 -0500	commit: Remove unnecessary reshape.
59f98b046f1c727411046f000f31cf1a9a933f96 4210ef61661389aa066b9be98a258e89d0580065 Kevin Kaichuang Yang <kevyan@microsoft.com> 1604691895 -0500	pull origin master: Fast-forward
4210ef61661389aa066b9be98a258e89d0580065 d4396f04a084289f5514e8ecda362ada39537f1f Kevin Kaichuang Yang <kevyan@microsoft.com> 1604954244 -0500	commit: Machinery to predict TAPE contacts.
d4396f04a084289f5514e8ecda362ada39537f1f 5c6168200019c9993d5dad115d5ab7b6e4a9cdf7 Kevin Kaichuang Yang <kevyan@microsoft.com> 1604954543 -0500	commit (merge): Merge changes.
5c6168200019c9993d5dad115d5ab7b6e4a9cdf7 073286ff9bdf57a4f6f4e1f9335e2cc6824151d1 Kevin Kaichuang Yang <kevyan@microsoft.com> 1605556179 -0500	commit: Add cosine loss.
073286ff9bdf57a4f6f4e1f9335e2cc6824151d1 6bfa1c8414f174625dcf1065069b39814af83111 Kevin Kaichuang Yang <kevyan@microsoft.com> 1605556283 -0500	commit: Add ability to return pdb coordinates directly.
6bfa1c8414f174625dcf1065069b39814af83111 ac17474e11a3b2bcb10052ffe8e857358f88e057 Kevin Kaichuang Yang <kevyan@microsoft.com> 1605556296 -0500	commit: Attempt at a structure predictor.
ac17474e11a3b2bcb10052ffe8e857358f88e057 90cbda4de909a88adaa7b28d3a6ac1e896130017 Kevin Kaichuang Yang <kevyan@microsoft.com> 1605556314 -0500	commit: Add linear warmup.
90cbda4de909a88adaa7b28d3a6ac1e896130017 55805e6b5a2104b8c25fb1791aafe2a00f8268da Kevin Kaichuang Yang <kevyan@microsoft.com> 1605556325 -0500	commit: Use exponential decay and mask correctly.
55805e6b5a2104b8c25fb1791aafe2a00f8268da 9b545a48ec2d0248a5af86f9621feb0f1a6be5a0 Kevin Kaichuang Yang <kevyan@microsoft.com> 1605556340 -0500	pull origin master: Merge made by the 'recursive' strategy.
9b545a48ec2d0248a5af86f9621feb0f1a6be5a0 8aed8c54ca1d2acbe926685d0664003473c0abf6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1606158826 -0500	commit: Add transformer learning rate schedule.
8aed8c54ca1d2acbe926685d0664003473c0abf6 bd5f07710c7c3019e47194c7a99b26e47d044b5d Kevin Kaichuang Yang <kevyan@microsoft.com> 1606331399 -0500	commit: Return 0 and not nan when everything is masked.
bd5f07710c7c3019e47194c7a99b26e47d044b5d edbe9a2e4ad6370c725e0c35c15cb55822ce7fdb Kevin Kaichuang Yang <kevyan@microsoft.com> 1606331421 -0500	commit: Return 0 and not nan when everything is masked.
edbe9a2e4ad6370c725e0c35c15cb55822ce7fdb 1e625ddad72b102901361e8daabddccb8d2a96af Kevin Kaichuang Yang <kevyan@microsoft.com> 1606331463 -0500	commit: Move aaindex stuff out of utils to fix imports.
1e625ddad72b102901361e8daabddccb8d2a96af b6120edeb3fd774f5ed3cc0abf9d0d4366007251 Kevin Kaichuang Yang <kevyan@microsoft.com> 1606331493 -0500	commit: Fix bug in attention layers.
b6120edeb3fd774f5ed3cc0abf9d0d4366007251 1bfc50c731dd6b375b2f9eeb8aa8379b85b63102 Kevin Kaichuang Yang <kevyan@microsoft.com> 1606331526 -0500	commit: Add ability to combine linear and quadratic terms.
1bfc50c731dd6b375b2f9eeb8aa8379b85b63102 914a3ecd7067f297a6a652c0d9f04a57dd4910c0 Kevin Kaichuang Yang <kevyan@microsoft.com> 1606331761 -0500	commit (merge): Merge.
914a3ecd7067f297a6a652c0d9f04a57dd4910c0 cd222fb713453ab3f65959a0552930a28d85920c Kevin Kaichuang Yang <kevyan@microsoft.com> 1608009622 -0500	commit: Add ability to not embed at beginning of 1d Bytenet.
cd222fb713453ab3f65959a0552930a28d85920c 6d00a70a69987b9d1805316199e7529cedec03d2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1608009674 -0500	commit: Update logs parser.
6d00a70a69987b9d1805316199e7529cedec03d2 ca29266585409563e73d398795a2dab0536ed523 Kevin Kaichuang Yang <kevyan@microsoft.com> 1608009701 -0500	commit: Add ability to set max len in TAPE datasets.
ca29266585409563e73d398795a2dab0536ed523 2d175f2f0b474b9bf62839c1ea8fd9bf73c479ae Kevin Kaichuang Yang <kevyan@microsoft.com> 1610568854 -0500	commit: Specify devices properly.
2d175f2f0b474b9bf62839c1ea8fd9bf73c479ae bf20e94ad034c45069ad936a5daf4ba67f9cfe54 Kevin Kaichuang Yang <kevyan@microsoft.com> 1610568887 -0500	commit: Add masking and clean up skip connections.
bf20e94ad034c45069ad936a5daf4ba67f9cfe54 b693f62ace2e207605fdcb680779032729bcf23f Kevin Kaichuang Yang <kevyan@microsoft.com> 1610568924 -0500	commit: Fix alphabet conversion.
b693f62ace2e207605fdcb680779032729bcf23f 8e2f2c2922abe9b3f0d3ea7d14d59c845814b1b5 Kevin Kaichuang Yang <kevyan@microsoft.com> 1610568942 -0500	pull origin master: Merge made by the 'recursive' strategy.
8e2f2c2922abe9b3f0d3ea7d14d59c845814b1b5 94801e57444b741dd966818e48f9b1ab7608d9cf Kevin Kaichuang Yang <kevyan@microsoft.com> 1611954004 -0500	commit: Add option to not do softmax.
94801e57444b741dd966818e48f9b1ab7608d9cf 058d2a29abdfb59f214d5fe770d355fa7dd1902a Kevin Kaichuang Yang <kevyan@microsoft.com> 1612210409 -0500	commit: Add ability to use learned parameters in instance norms.
058d2a29abdfb59f214d5fe770d355fa7dd1902a 9fe80b297e143df07b4febbace9c2ec41f994912 Kevin Kaichuang Yang <kevyan@microsoft.com> 1612210445 -0500	commit: Fix how structures are masked.
9fe80b297e143df07b4febbace9c2ec41f994912 7cea6d496e1b7a13d598cba81e841dfb38145593 Kevin Kaichuang Yang <kevyan@microsoft.com> 1612210480 -0500	commit: Add option to output trrosetta bins for structures.
7cea6d496e1b7a13d598cba81e841dfb38145593 270fb0b0436249a4dc91aac618f7739119a8948b Kevin Kaichuang Yang <kevyan@microsoft.com> 1612210533 -0500	commit: Decide whether to unsqueeze the mask in a way that works with 2d inputs.
270fb0b0436249a4dc91aac618f7739119a8948b b6d1ff9da084edc6ee2892ebcf0f7c199092f598 Kevin Kaichuang Yang <kevyan@microsoft.com> 1612464518 -0500	commit: Propagate input_mask into the individual blocks.
b6d1ff9da084edc6ee2892ebcf0f7c199092f598 f119dd049cb6d597af861ea58764741e0d6438fc Kevin Kaichuang Yang <kevyan@microsoft.com> 1612464807 -0500	commit: Add dropout.
f119dd049cb6d597af861ea58764741e0d6438fc a4456397db216cab6de74dea72097aeac5663839 Kevin Kaichuang Yang <kevyan@microsoft.com> 1612921149 -0500	commit: Add a proper masked instance norm layer.
a4456397db216cab6de74dea72097aeac5663839 30e3968bc1435ad1a5c3ece8a247f339a4a962d2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1613071476 -0500	commit: Allow sequence clipping for secondary structure.
30e3968bc1435ad1a5c3ece8a247f339a4a962d2 811fdbf7a293bfceeeae761c94db75a5405677b2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1614120682 -0500	commit: Allow clipping to max length for remote homology.
811fdbf7a293bfceeeae761c94db75a5405677b2 7b920971d4bfc84e4d022d2a9bbe2147d79f0db6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1614120689 -0500	pull origin master: Merge made by the 'recursive' strategy.
7b920971d4bfc84e4d022d2a9bbe2147d79f0db6 568198ba012e0ffa152b7d696b1b34d90838b0c6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1614801084 -0500	commit: Add a dataset for trrosetta.
568198ba012e0ffa152b7d696b1b34d90838b0c6 046b76903282322cca96154befa9fe469850f3a4 Kevin Kaichuang Yang <kevyan@microsoft.com> 1614802904 -0500	commit: Add collater for MSAs with structures.
046b76903282322cca96154befa9fe469850f3a4 21d3daa0d87ed1163943dfcb6239cc85ab3e048f Kevin Kaichuang Yang <kevyan@microsoft.com> 1614802936 -0500	commit: Add utils for working with pdb files.
21d3daa0d87ed1163943dfcb6239cc85ab3e048f dcaa0e1dede08013022e9551e98784155667c580 Kevin Kaichuang Yang <kevyan@microsoft.com> 1614802977 -0500	commit: Allow preprocessing to take in tensors.
dcaa0e1dede08013022e9551e98784155667c580 a514af7dd52dbe0476e75ebe19f96f0c161a713d Kevin Kaichuang Yang <kevyan@microsoft.com> 1614977376 -0500	commit: Don't use magic numbers for the number of node and edge features.
a514af7dd52dbe0476e75ebe19f96f0c161a713d 6f429996884d90c4d825bb8d67ac62244e715ac8 Kevin Kaichuang Yang <kevyan@microsoft.com> 1614977411 -0500	commit: Use sine and cosine for edge embeddings and allow precomputed sines and cosines.
6f429996884d90c4d825bb8d67ac62244e715ac8 aad80932fbdacdc2e71ef442588244eb0b52c545 Kevin Kaichuang Yang <kevyan@microsoft.com> 1615923125 -0400	commit: Be more strict about masking out nans.
aad80932fbdacdc2e71ef442588244eb0b52c545 c2d9131e2fde005594e3c29646babafafb161a69 Kevin Kaichuang Yang <kevyan@microsoft.com> 1615936123 -0400	commit: Add a regression version of trRosetta.
c2d9131e2fde005594e3c29646babafafb161a69 10e2a1f15e355e0a793268a22d654ead647d02aa Kevin Kaichuang Yang <kevyan@microsoft.com> 1616190571 -0400	commit: Add collater for seq->trr
10e2a1f15e355e0a793268a22d654ead647d02aa d9dc7007622ac0b0f1997d2e8b2392599d89de63 Kevin Kaichuang Yang <kevyan@microsoft.com> 1616190629 -0400	commit: Make last elu optional.
d9dc7007622ac0b0f1997d2e8b2392599d89de63 b000c32a25976d67fb0f54c0d2c7e3b38df37b3a Kevin Kaichuang Yang <kevyan@microsoft.com> 1616190641 -0400	commit: Use hardtanh instead of tanh.
b000c32a25976d67fb0f54c0d2c7e3b38df37b3a 043b5f2661ffc6e0c24a6cf17ccff9b7d169eb89 Kevin Kaichuang Yang <kevyan@microsoft.com> 1616190704 -0400	commit: Put de-binning function here.
043b5f2661ffc6e0c24a6cf17ccff9b7d169eb89 c0efbdb6a98ca1dbf3bb0b98d0177afad12bde9a Kevin Kaichuang Yang <kevyan@microsoft.com> 1616190722 -0400	commit: Use cholesky for matrix inverse.
c0efbdb6a98ca1dbf3bb0b98d0177afad12bde9a 4b363b90d0f1b34f6d32b45a867538363064fcde Kevin Kaichuang Yang <kevyan@microsoft.com> 1618275633 -0400	commit: Add gnn regressor.
4b363b90d0f1b34f6d32b45a867538363064fcde 87a3c225db6301fb40a700d3839b0ba959c7f76b Kevin Kaichuang Yang <kevyan@microsoft.com> 1618275652 -0400	commit: Utilities for interpretability project.
87a3c225db6301fb40a700d3839b0ba959c7f76b 72ae7a0e2970c5cd4c8425765a9ab8197d1db2d6 Kevin Kaichuang Yang <kevyan@microsoft.com> 1618275715 -0400	pull origin master: Merge made by the 'recursive' strategy.
72ae7a0e2970c5cd4c8425765a9ab8197d1db2d6 becef3fa747870cfb4f54c04b798f6a15655d907 Kevin Kaichuang Yang <kevyan@microsoft.com> 1619211609 -0400	commit: Add structure-only gnn.
becef3fa747870cfb4f54c04b798f6a15655d907 17d5715a995288aaef30cd6ea745b7b19080522a Kevin Kaichuang Yang <kevyan@microsoft.com> 1619211656 -0400	commit: Add conditioned ByteNetLM and streamline conditioned Bytenet.
17d5715a995288aaef30cd6ea745b7b19080522a f0ea0d3bd1a3c6cff7fd9ab00ee906d91c0bf8d2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1619806693 -0400	commit: Fix bug that was dropping the last batch.
f0ea0d3bd1a3c6cff7fd9ab00ee906d91c0bf8d2 ce81248a55c509b3fb94a556b18623eb3a73c5ca Kevin Kaichuang Yang <kevyan@microsoft.com> 1619806713 -0400	commit: Add positional embedding layer.
ce81248a55c509b3fb94a556b18623eb3a73c5ca 69cac83ac038a11c4727a9740056bec713b30e70 Kevin Kaichuang Yang <kevyan@microsoft.com> 1619806737 -0400	commit: Add option to use positional embedding.
69cac83ac038a11c4727a9740056bec713b30e70 cffd73801226bf5c620330dd904e432f3087872a Kevin Kaichuang Yang <kevyan@microsoft.com> 1619806744 -0400	pull origin master: Merge made by the 'recursive' strategy.
cffd73801226bf5c620330dd904e432f3087872a 4c543ed6911153512888c3d559c5b82180e1ec1c Kevin Kaichuang Yang <kevyan@microsoft.com> 1620071101 -0400	commit: Mask backwards correctly.
4c543ed6911153512888c3d559c5b82180e1ec1c 9ee0e16754add24b5b803d00d5952cac3f765aaa Kevin Kaichuang Yang <kevyan@microsoft.com> 1620848809 -0400	commit: Fix bug and allow passthrough src embedding.
9ee0e16754add24b5b803d00d5952cac3f765aaa ac3f3ca99c11010cabce6a9ab04fd1a3047a6ee2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1620849588 -0400	commit: Embed sequences properly.
ac3f3ca99c11010cabce6a9ab04fd1a3047a6ee2 8271d2096a8e02f4957fedc058f892d328435461 Kevin Kaichuang Yang <kevyan@microsoft.com> 1620858394 -0400	commit: Fix bidirectional.
8271d2096a8e02f4957fedc058f892d328435461 44fe860481100ce96ae6ce9f4429e620631272f2 Kevin Kaichuang Yang <kevyan@microsoft.com> 1620933138 -0400	commit: Break the bidirectional case into its own class.
44fe860481100ce96ae6ce9f4429e620631272f2 6bcbc659c6600c4e6e0486800060dae87ccd8c57 Kevin Kaichuang Yang <kevyan@microsoft.com> 1621027846 -0400	commit: Fix all GNNs.
6bcbc659c6600c4e6e0486800060dae87ccd8c57 1b1c9b6c9278598cb96a320a72659b03af92099c Kevin Kaichuang Yang <kevyan@microsoft.com> 1621027861 -0400	commit: Handle cases with no newline at eof correctly.
1b1c9b6c9278598cb96a320a72659b03af92099c 4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1621624903 -0400	commit: Add option for final layer norm.
4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 9677a22835077729aba9115307bff3ab66a6d730 Kevin Kaichuang Yang <kevyan@microsoft.com> 1621624909 -0400	checkout: moving from master to public_dev
9677a22835077729aba9115307bff3ab66a6d730 1548c3a70318cba8baa33c8f58310d6be89cdc10 Kevin Kaichuang Yang <kevyan@microsoft.com> 1623429365 -0400	commit: Add options to make ByteNets bigger and use different activations.
1548c3a70318cba8baa33c8f58310d6be89cdc10 4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1623429369 -0400	checkout: moving from public_dev to master
4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1623722229 -0400	checkout: moving from master to linear
4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1623722737 -0400	reset: moving to HEAD
4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1623722745 -0400	checkout: moving from linear to master
4081fa446b6cdc9df3ab7f42ee75cbeeb9bfd9d9 2c6ba9ee938f8c542e0932a50e9632517056c531 Kevin Kaichuang Yang <kevyan@microsoft.com> 1623722777 -0400	commit: Add options for gelu and not halving dimension within blocks.
2c6ba9ee938f8c542e0932a50e9632517056c531 616dcbe5b3c7c792371fc9d23b6ba4ba8df09942 Kevin Kaichuang Yang <kevyan@microsoft.com> 1623939697 -0400	pull origin master: Merge made by the 'recursive' strategy.
616dcbe5b3c7c792371fc9d23b6ba4ba8df09942 d0a6d3cc37919c5fd024d912a2b459c5414a7eec Kevin Kaichuang Yang <kevyan@microsoft.com> 1624073325 -0400	commit: Simplified implementation of esm-1b.
d0a6d3cc37919c5fd024d912a2b459c5414a7eec 7e328d1b0b1aa8d610b6b9bfebdc082fe3a53b17 Kevin Kaichuang Yang <kevyan@microsoft.com> 1624981754 -0400	commit: Fix indexing.
7e328d1b0b1aa8d610b6b9bfebdc082fe3a53b17 68cb58f2eb9bbdf6b3edb2f08bed5f66ad466b9f Kevin Kaichuang Yang <kevyan@microsoft.com> 1624981783 -0400	commit: Make the training log parser do tokens too.
68cb58f2eb9bbdf6b3edb2f08bed5f66ad466b9f 124ace6baca038fd4ce7c5a5e29323806c84d542 Kevin Kaichuang Yang <kevyan@microsoft.com> 1624982026 -0400	commit: Better descriptions.
124ace6baca038fd4ce7c5a5e29323806c84d542 1548c3a70318cba8baa33c8f58310d6be89cdc10 Kevin Kaichuang Yang <kevyan@microsoft.com> 1624982089 -0400	checkout: moving from master to public_dev
1548c3a70318cba8baa33c8f58310d6be89cdc10 1548c3a70318cba8baa33c8f58310d6be89cdc10 Kevin Kaichuang Yang <kevyan@microsoft.com> 1624982336 -0400	reset: moving to HEAD
1548c3a70318cba8baa33c8f58310d6be89cdc10 64ccb91a2bacfc6c4fd2050d3ed36b86bcaf63cb Kevin Kaichuang Yang <kevyan@microsoft.com> 1624989515 -0400	commit (merge): Merge from master.
64ccb91a2bacfc6c4fd2050d3ed36b86bcaf63cb 124ace6baca038fd4ce7c5a5e29323806c84d542 Kevin Kaichuang Yang <kevyan@microsoft.com> 1624989539 -0400	checkout: moving from public_dev to master
124ace6baca038fd4ce7c5a5e29323806c84d542 ac8a0abbb00c85a2b3f3e8a2350dc3e43d137baa Kevin Kaichuang Yang <kevyan@microsoft.com> 1627931909 -0400	commit: Add options for factorized linear layers and partially frozen embeddings.
ac8a0abbb00c85a2b3f3e8a2350dc3e43d137baa 8f7a67ae184e61daa30a9c6c8be9dbb59047e596 Kevin Kaichuang Yang <kevyan@microsoft.com> 1627931947 -0400	commit: Don't do last elu if not using prediction heads.
8f7a67ae184e61daa30a9c6c8be9dbb59047e596 acfca296cced523ea38c6b1b4957c58c6b6fa249 Kevin Kaichuang Yang <kevyan@microsoft.com> 1628190216 -0400	commit: More efficient reconstruction of weights.
acfca296cced523ea38c6b1b4957c58c6b6fa249 6862b7fa325397de1455c0598a71898bf1262ffc Kevin Kaichuang Yang <kevyan@microsoft.com> 1628191081 -0400	commit: Allow batching in DoubleEmbedding.
6862b7fa325397de1455c0598a71898bf1262ffc 4bf13881c800cf46d7caedaf02adeaff20d32504 Kevin Kaichuang Yang <kevyan@microsoft.com> 1628191189 -0400	commit (merge): Merge changes.
4bf13881c800cf46d7caedaf02adeaff20d32504 3f49723a3ea6327dd35eab5d9d1b3f645db9c346 Kevin Kaichuang Yang <kevyan@microsoft.com> 1628197727 -0400	commit: Force types to match.
3f49723a3ea6327dd35eab5d9d1b3f645db9c346 e87e483552b2d7284b5d1c687dff6459b454adec Kevin Kaichuang Yang <kevyan@microsoft.com> 1631995966 -0400	commit: Add option to tie embeddings.
e87e483552b2d7284b5d1c687dff6459b454adec e87e483552b2d7284b5d1c687dff6459b454adec Kevin Kaichuang Yang <kevyan@microsoft.com> 1631997812 -0400	checkout: moving from master to master
e87e483552b2d7284b5d1c687dff6459b454adec 64ccb91a2bacfc6c4fd2050d3ed36b86bcaf63cb Kevin Kaichuang Yang <kevyan@microsoft.com> 1631997881 -0400	checkout: moving from master to public_dev
64ccb91a2bacfc6c4fd2050d3ed36b86bcaf63cb cacc678fc5730aeaaa9c3e3ee9367db0bd8e743e Kevin Kaichuang Yang <kevyan@microsoft.com> 1631998271 -0400	commit: Add low rank pwff and double embedding.
cacc678fc5730aeaaa9c3e3ee9367db0bd8e743e 076dfb452dbc6b0d0702f815f5c8241d5a63d8ff Kevin Kaichuang Yang <kevyan@microsoft.com> 1631998339 -0400	commit: Add new options from master.
076dfb452dbc6b0d0702f815f5c8241d5a63d8ff 15c808a3d0cfdeeb8bfc3b648740a602562670ca Kevin Kaichuang Yang <kevyan@microsoft.com> 1632006415 -0400	commit: Add conditioned decoder.
15c808a3d0cfdeeb8bfc3b648740a602562670ca 15c808a3d0cfdeeb8bfc3b648740a602562670ca Kevin Kaichuang Yang <kevyan@microsoft.com> 1632153098 -0400	checkout: moving from public_dev to main
15c808a3d0cfdeeb8bfc3b648740a602562670ca e87e483552b2d7284b5d1c687dff6459b454adec Kevin Kaichuang Yang <kevyan@microsoft.com> 1632153107 -0400	checkout: moving from main to master
e87e483552b2d7284b5d1c687dff6459b454adec bd422d3f7e5f45591f021c987be0e25073142e07 Kevin Kaichuang Yang <kevyan@microsoft.com> 1635880747 -0400	commit: Fix down-embedding bug.
bd422d3f7e5f45591f021c987be0e25073142e07 6fa4f24d779e0ded3bbc912aeb5455942c01e10a Kevin Kaichuang Yang <kevyan@microsoft.com> 1635881755 -0400	commit: Remove hierarchical Bytenet and update Bytenet documentation.
6fa4f24d779e0ded3bbc912aeb5455942c01e10a 15c808a3d0cfdeeb8bfc3b648740a602562670ca Kevin Kaichuang Yang <kevyan@microsoft.com> 1635881758 -0400	checkout: moving from master to public_dev
15c808a3d0cfdeeb8bfc3b648740a602562670ca 15c808a3d0cfdeeb8bfc3b648740a602562670ca Kevin Kaichuang Yang <kevyan@microsoft.com> 1635881825 -0400	checkout: moving from public_dev to main
15c808a3d0cfdeeb8bfc3b648740a602562670ca 6fa4f24d779e0ded3bbc912aeb5455942c01e10a Kevin Kaichuang Yang <kevyan@microsoft.com> 1635881834 -0400	checkout: moving from main to master
6fa4f24d779e0ded3bbc912aeb5455942c01e10a 15c808a3d0cfdeeb8bfc3b648740a602562670ca Kevin Kaichuang Yang <kevyan@microsoft.com> 1635881846 -0400	checkout: moving from master to public_dev
15c808a3d0cfdeeb8bfc3b648740a602562670ca 00e0c33ae4bed83af6508efe875a511fbd82acb4 Kevin Kaichuang Yang <kevyan@microsoft.com> 1635882251 -0400	commit (merge): Merge changes from master.
00e0c33ae4bed83af6508efe875a511fbd82acb4 6fa4f24d779e0ded3bbc912aeb5455942c01e10a Kevin Kaichuang Yang <kevyan@microsoft.com> 1635882340 -0400	checkout: moving from public_dev to master
6fa4f24d779e0ded3bbc912aeb5455942c01e10a 2d6ff82345a1736a150973bf6d83e64bc01b2f08 Kevin Kaichuang Yang <kevyan@microsoft.com> 1639499603 -0500	commit: Fix backwards flag placement.
2d6ff82345a1736a150973bf6d83e64bc01b2f08 bec34bb749a3fd207429407cf27b8c9f2c20205c Kevin Kaichuang Yang <kevyan@microsoft.com> 1639780055 -0500	commit: Add docstrings and fix bugs.
bec34bb749a3fd207429407cf27b8c9f2c20205c 746df7d3b49c905632fd34bdadae70944e36dcca Kevin Kaichuang Yang <kevyan@microsoft.com> 1641384724 -0500	commit: Add task option again for MSAGapCollater.
746df7d3b49c905632fd34bdadae70944e36dcca 6458a6f617ebe6111724d8bec035c51723b8d58e Kevin Kaichuang Yang <kevyan@microsoft.com> 1641385588 -0500	commit: Document where starts and padding go.
6458a6f617ebe6111724d8bec035c51723b8d58e 6458a6f617ebe6111724d8bec035c51723b8d58e Kevin Kaichuang Yang <kevyan@microsoft.com> 1641386050 -0500	reset: moving to HEAD
6458a6f617ebe6111724d8bec035c51723b8d58e ee4d183e3111cd8069e50facb29bde5fd6af0ae9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1642212906 -0500	commit: Write mixup module.
ee4d183e3111cd8069e50facb29bde5fd6af0ae9 73cbe97fc24234d6b7e92f6b198f74b0e1e1ed09 Kevin Kaichuang Yang <kevyan@microsoft.com> 1645040902 -0500	commit: set padding and mask ids manually.
73cbe97fc24234d6b7e92f6b198f74b0e1e1ed09 f29b24d5b2890135f34255cc0a1d8ad4e7238300 Kevin Kaichuang Yang <kevyan@microsoft.com> 1645040918 -0500	commit: Add more RNA options.
f29b24d5b2890135f34255cc0a1d8ad4e7238300 e03e0c9bad155224bc3c6847c81ec3a5a226151a Kevin Kaichuang Yang <kevyan@microsoft.com> 1645040945 -0500	commit: Collaters for shortening.
e03e0c9bad155224bc3c6847c81ec3a5a226151a 837d9a167374d3fb64951ad2ed8d597439bf560e Kevin Kaichuang Yang <kevyan@microsoft.com> 1647627007 -0400	commit: Add ability to only return distances from structure.
837d9a167374d3fb64951ad2ed8d597439bf560e 1db113bf3d1f1f314bd96690467a358945b1e12e Kevin Kaichuang Yang <kevyan@microsoft.com> 1647627054 -0400	commit: Change formatting for trr datasets.
1db113bf3d1f1f314bd96690467a358945b1e12e 37a22d8e6b3c7e32f8e8bad827b53e20e4fb6bdd Kevin Kaichuang Yang <kevyan@microsoft.com> 1647627097 -0400	commit: Add option for initial number of features.
37a22d8e6b3c7e32f8e8bad827b53e20e4fb6bdd e8b5b4dbf7b209944982e8ab978abd982d5b00a9 Kevin Kaichuang Yang <kevyan@microsoft.com> 1647627155 -0400	commit: Simple functions for loading pretrained CNNs.
e8b5b4dbf7b209944982e8ab978abd982d5b00a9 2778c54336cc834de344e992e35876bbb4f9583b Kevin Kaichuang Yang <kevyan@microsoft.com> 1647628048 -0400	commit: add license.
2778c54336cc834de344e992e35876bbb4f9583b 86b230ae68bf812f3ec2d94ec4637377e289fa25 Kevin Kaichuang Yang <kevyan@microsoft.com> 1647628082 -0400	commit: Update version.
86b230ae68bf812f3ec2d94ec4637377e289fa25 3344dcd3155096649a4127ab00db26a90e118d74 Kevin Kaichuang Yang <kevyan@microsoft.com> 1647629350 -0400	commit: New install instructions and pretrained models.
3344dcd3155096649a4127ab00db26a90e118d74 74b7af194d25188ec94e250e7cb446774762d2e1 Kevin Kaichuang Yang <kevyan@microsoft.com> 1647629401 -0400	commit: Fix typo.
74b7af194d25188ec94e250e7cb446774762d2e1 a17466b0dc344a1ea8fdbebf22945a32c2eb6fe3 Kevin Kaichuang Yang <kevyan@microsoft.com> 1647630231 -0400	commit: Some notes on installation.
a17466b0dc344a1ea8fdbebf22945a32c2eb6fe3 e978aacb9d0b0da420c832a015b26ba55611c7ee Kevin Kaichuang Yang <kevyan@microsoft.com> 1652883417 -0400	commit: Add encoder-only option.
e978aacb9d0b0da420c832a015b26ba55611c7ee 383f070d7a9baa0fb994fe4b7b4ea82d179f5459 Kevin Kaichuang Yang <kevyan@microsoft.com> 1652883440 -0400	commit: Add utilities for fine-tuning and structure.
383f070d7a9baa0fb994fe4b7b4ea82d179f5459 1846408ca072545fa5abd2b188829fb904d9c782 Kevin Kaichuang Yang <kevyan@microsoft.com> 1652883469 -0400	commit: Add option for maxlen in CSVDataset.
1846408ca072545fa5abd2b188829fb904d9c782 f2be26244d81999b43ad5f5bb81165ee94034e49 Kevin Kaichuang Yang <kevyan@microsoft.com> 1653328272 -0400	pull github main: Merge made by the 'recursive' strategy.
