Kevin Kaichuang Yang
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af695772c4
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Increment version.
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2024-07-31 10:58:35 -04:00 |
Kevin Kaichuang Yang
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edaaa04182
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Merge pull request #22 from sarahalamdari/main
update alphabet
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2024-04-10 13:36:58 -07:00 |
sarahalamdari
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eb04f65295
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update alphabet
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2024-04-10 16:12:49 -04:00 |
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Kevin Kaichuang Yang
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354fde009b
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Specify pad token in LMCollater.
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2024-04-10 08:13:15 -04:00 |
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Kevin Kaichuang Yang
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b50869f6f0
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Set use_reentrant explicitly.
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2024-03-27 12:47:30 -04:00 |
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Kevin Kaichuang Yang
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c930f9fe08
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Newer versions of numpy don't allow jagged arrays.
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2024-03-25 17:24:40 -04:00 |
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Kevin Kaichuang Yang
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d5e664f526
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Clustered sampler.
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2024-03-25 17:07:34 -04:00 |
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Kevin Kaichuang Yang
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399be5e4ed
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Fix length bookkeeping.
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2024-03-14 10:00:56 -04:00 |
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Kevin Kaichuang Yang
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7cf76442b4
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Add collater for scl.
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2024-03-13 15:14:10 -04:00 |
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Kevin Kaichuang Yang
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13df666193
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Add enhancer alphabet.
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2024-03-13 15:14:00 -04:00 |
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Kevin Kaichuang Yang
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28ccf64690
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Add collater for scl.
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2024-03-13 15:13:39 -04:00 |
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Kevin Kaichuang Yang
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142b10a69b
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Add ability to sample batchsizes in multiples of x.
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2024-03-13 15:11:27 -04:00 |
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Kevin Kaichuang Yang
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6856e45dac
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Add ESM2 alphabet.
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2023-12-19 11:43:34 -05:00 |
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Kevin Kaichuang Yang
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c7fc0af894
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Add option to add start and stop tokens in seq-fitness collaters.
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2023-12-19 11:43:19 -05:00 |
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Kevin Kaichuang Yang
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6f77721d0a
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Add option not to tie weights in ESM models.
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2023-12-19 11:42:38 -05:00 |
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Kevin Kaichuang Yang
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0eecb6e22d
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Update the 2d cnn models.
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2023-01-18 14:45:14 -05:00 |
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Kevin Kaichuang Yang
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3d43b37221
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Redefine roberta head.
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2022-12-13 14:33:50 -05:00 |
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Kevin Kaichuang Yang
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eba33ea6e4
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Fix type error in MSA datasets.
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2022-12-13 14:32:29 -05:00 |
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Kevin Kaichuang Yang
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f39f194750
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Add GVP code.
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2022-12-13 14:31:37 -05:00 |
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Kevin Kaichuang Yang
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161825191a
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Update ARDM losses and collaters.
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2022-09-30 11:39:52 -04:00 |
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Kevin Kaichuang Yang
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e69e1e8aeb
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Change MSA constants to be easier for d3pm.
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2022-09-30 11:39:31 -04:00 |
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Kevin Kaichuang Yang
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885a24f980
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Actually fix constants.
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2022-08-29 11:37:57 -04:00 |
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Kevin Kaichuang Yang
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29226bfa75
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Increment version.
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2022-08-26 14:56:12 -04:00 |
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Kevin Kaichuang Yang
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6ce7214a2e
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Merge branch 'msadiff'
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2022-08-26 14:48:43 -04:00 |
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Kevin Kaichuang Yang
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7830d78b3f
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Merge branch 'main' of https://github.com/microsoft/protein-sequence-models
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2022-08-26 14:48:11 -04:00 |
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Kevin Kaichuang Yang
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9e09f90c24
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Fix constants.
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2022-08-26 14:47:36 -04:00 |
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Kevin Kaichuang Yang
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a706a6c076
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get rid of extra prints.
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2022-08-19 14:20:19 -04:00 |
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Kevin Kaichuang Yang
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cf87977035
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Increment version.
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2022-08-19 09:27:39 -04:00 |
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Kevin Kaichuang Yang
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b06bf7a4ce
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Add option to handle msa-transformer batching.
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2022-08-19 09:26:40 -04:00 |
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Kevin Kaichuang Yang
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4903ebac4c
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Only import wget if necessary
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2022-08-19 09:26:19 -04:00 |
Nitya Thakkar
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57072e49c3
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pulled new changes
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2022-08-17 11:51:13 -05:00 |
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Nitya Thakkar
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a62f886f4d
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added dataset class for zero shot
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2022-08-17 11:46:55 -05:00 |
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Nitya Thakkar
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ffe5355285
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A3M dataset for trrosetta test
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2022-08-15 16:51:28 -05:00 |
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Kevin Kaichuang Yang
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f913b2b266
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Merge pull request #11 from LouisRanjard/main
Update argument variable name.
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2022-08-11 23:14:14 -04:00 |
Louis
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9febf1a787
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Update argument variable name.
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2022-08-12 15:07:22 +12:00 |
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Kevin Kaichuang Yang
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1930966b18
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Merge branch 'main' of https://github.com/microsoft/protein-sequence-models
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2022-08-10 14:06:22 -04:00 |
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Kevin Kaichuang Yang
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7246166fc3
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Add new scripts and fix mif.
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2022-08-10 14:05:58 -04:00 |
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Kevin Kaichuang Yang
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457527eca7
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Update readme.
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2022-08-10 14:04:25 -04:00 |
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Nitya Thakkar
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51a6c5e54f
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dataset update
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2022-08-07 11:49:54 -05:00 |
Nitya Thakkar
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9e95b5d9ca
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updated loss function
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2022-07-29 13:16:15 -04:00 |
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Kevin Kaichuang Yang
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fd24ab85c5
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Merge pull request #10 from wukevin/patch-1
Test for reading gzip and non-gzipped pdb files
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2022-07-28 15:44:04 -04:00 |
Kevin Wu
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d418e77c27
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Test that reading a pdb file and its gzipped version produce same results
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2022-07-28 12:12:10 -07:00 |
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Kevin Kaichuang Yang
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4df218f2d3
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Merge pull request #9 from wukevin/patch-1
Support for parsing pdb.gz files
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2022-07-28 15:00:38 -04:00 |
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Kevin Wu
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6b2225d1ab
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Support for parsing pdb.gz files
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2022-07-28 11:52:43 -07:00 |
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Kevin Kaichuang Yang
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8df3de679d
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Document getting different representations from CARP.
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2022-07-27 15:54:41 -04:00 |
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Kevin Kaichuang Yang
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673459f22d
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Merge branch 'main' of https://github.com/microsoft/protein-sequence-models
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2022-07-27 15:49:18 -04:00 |
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Kevin Kaichuang Yang
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4c63f800e4
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Make it easy to extract layer-wise representations from CARP.
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2022-07-27 15:48:59 -04:00 |
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Nitya Thakkar
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a8005e2192
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updated openfold dataset alignment
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2022-07-26 14:51:31 -04:00 |
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Kevin Kaichuang Yang
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fda57669ab
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Add biorxiv link for BiGCARP.
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2022-07-25 11:37:01 -04:00 |
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Nitya Thakkar
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dd7a1edd76
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working dataset and sampler
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2022-07-19 15:21:41 -04:00 |