OpenScientificCodeRegistry/Database
Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.
05.6k
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/jesusgf1/hippie_benchmarking_release",4 "url": "https://github.com/JesusGF1/hippie_benchmarking_release",5 "host": "github.com",6 "commit": "6165daca6da283e5309f1c7840cf39bcb919dcf5",7 "license": "BSD-3-Clause",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "64576398040288dd21c12fa5e5fcb927e263801b13e8f14fd371ade7431954f6",14 "language": "License",15 "lines": 28,16 "truncated": false,17 "block": 3,18 "row": 810919 },20 {21 "path": "README.md",22 "sha256": "1b008d1a833e68f957fe72f77661795c9b8a9b6f3830baa0b25a88eff25889d0",23 "language": "Text",24 "lines": 189,25 "truncated": false,26 "block": 4,27 "row": 268728 },29 {30 "path": "analysis/CVAE_only_experiment_G0_classification_accuracy.py",31 "sha256": "3c81da703416a24ff14444249e5035b063ced3ea9b86732b865bae62e547e798",32 "language": "Python",33 "lines": 198,34 "truncated": false,35 "block": 3,36 "row": 2471137 },38 {39 "path": "analysis/CVAE_only_experiment_G1_cross_modal_imputation.py",40 "sha256": "1642b9357513244ddfaa2cc954ba0564cc7efb3496e075e342d29abf3846400f",41 "language": "Python",42 "lines": 110,43 "truncated": false,44 "block": 3,45 "row": 2186346 },47 {48 "path": "analysis/CVAE_only_experiment_G2_counterfactual_swap.py",49 "sha256": "b428d0403b2f7c110480c93a17f30dd5682e14908325488104d76913d89063d5",50 "language": "Python",51 "lines": 252,52 "truncated": false,53 "block": 3,54 "row": 2520455 },56 {57 "path": "analysis/CVAE_only_experiment_G2_cross_species.py",58 "sha256": "2a545f178638c7b4a73e7018abf816fcc9859b82a54e46dd81e5df15bcfb4694",59 "language": "Python",60 "lines": 223,61 "truncated": false,62 "block": 3,63 "row": 2491864 },65 {66 "path": "analysis/CVAE_only_experiment_G3_latent_interpolation.py",67 "sha256": "1b6b38d699ba22afe3786dc49c81b33975ccde6db80fffb49bff83b2f7f869d0",68 "language": "Python",69 "lines": 152,70 "truncated": false,71 "block": 3,72 "row": 2314573 },74 {75 "path": "analysis/CVAE_only_experiment_build_datasets.py",76 "sha256": "6fc0a66303323cb8fd9f21e36885fdfc388f84f519bede54a32755553b32c2c3",77 "language": "Python",78 "lines": 105,79 "truncated": false,80 "block": 3,81 "row": 2279282 },83 {84 "path": "analysis/CVAE_only_experiment_latent_flow_crosstech.py",85 "sha256": "606c35ad8e3e5970322ceb49f91f3873bd67141c03f6543525935da50ab7a594",86 "language": "Python",87 "lines": 187,88 "truncated": false,89 "block": 3,90 "row": 2446791 },92 {93 "path": "analysis/CVAE_only_experiment_plot.py",94 "sha256": "12352145b7aeed48b4854e90151f0be490d6a2e43d174191b3e6234345f09579",95 "language": "Python",96 "lines": 490,97 "truncated": false,98 "block": 3,99 "row": 27144100 },101 {102 "path": "analysis/CVAE_only_experiment_train_hippie.py",103 "sha256": "e54e9721e95eb0c5514a0f86f8c45c8aa463abe68eb3bfc6e16690604fc08d06",104 "language": "Python",105 "lines": 258,106 "truncated": false,107 "block": 3,108 "row": 25557109 },110 {111 "path": "analysis/CVAE_only_experiment_train_hippie_wf3dacg.py",112 "sha256": "321f866345f2cbc12d83c63389ba53ca6072993ed3f93a14f7cd386d75b55676",113 "language": "Python",114 "lines": 215,115 "truncated": false,116 "block": 3,117 "row": 24769118 },119 {120 "path": "analysis/CVAE_only_experiment_utils.py",121 "sha256": "bd9ad2281352e34b799b43b1fe96195be4423cbc27e5e662e1c6caea0eae0778",122 "language": "Python",123 "lines": 381,124 "truncated": false,125 "block": 3,126 "row": 26132127 },128 {129 "path": "analysis/CVAE_only_latent_flow.py",130 "sha256": "6352739fbe76834c9f25bfdc906ab7d5f04b370e96e6108bbb60e16239934898",131 "language": "Python",132 "lines": 108,133 "truncated": false,134 "block": 3,135 "row": 22421136 },137 {138 "path": "analysis/figure_2_panel_a_pipeline.py",139 "sha256": "0c438523e880ae89f0810211fd1d0646282d6edfd7dacd6a6078b3d14ef3cb90",140 "language": "Python",141 "lines": 118,142 "truncated": false,143 "block": 3,144 "row": 21757145 },146 {147 "path": "analysis/figure_2_panel_b_hull_profile.py",148 "sha256": "dbba228f182eb79d19ba2a6add5183dc95af55bc10731d637387eb4d89a8d97a",149 "language": "Python",150 "lines": 177,151 "truncated": false,152 "block": 3,153 "row": 23794154 },155 {156 "path": "analysis/figure_2_panel_c_hausser_ablation.py",157 "sha256": "87b5b9089306d1bf9791aa09f0bfe57367d0f174fd9fc51556ea8d844b66b829",158 "language": "Python",159 "lines": 190,160 "truncated": false,161 "block": 3,162 "row": 24041163 },164 {165 "path": "analysis/figure_2_panel_d_hausser_hyperparam.py",166 "sha256": "20c0d789350a88e3544f9f27c8bd161399e1b86ce0b1acf2c469783de32b0cf8",167 "language": "Python",168 "lines": 226,169 "truncated": false,170 "block": 3,171 "row": 24646172 },173 {174 "path": "analysis/figure_2_supp_nemo.py",175 "sha256": "9adb5083374d38f3f3e2d91ea32b4f0945e62d06da944f2539c9181e66701cc4",176 "language": "Python",177 "lines": 243,178 "truncated": false,179 "block": 3,180 "row": 25195181 },182 {183 "path": "analysis/figure_2_supp_physmap.py",184 "sha256": "b1ae7b256be306a24098bf1280e99ec0c912f3b3e5f6cf5d1ae7a2a28a79d6cd",185 "language": "Python",186 "lines": 238,187 "truncated": false,188 "block": 3,189 "row": 25039190 },191 {192 "path": "analysis/figure_2_supp_pipelines.py",193 "sha256": "1dba629ffc2f10de9cc6832a5feae5f636caefeb31ffa032dd395bece4a69e4a",194 "language": "Python",195 "lines": 100,196 "truncated": false,197 "block": 3,198 "row": 21381199 },200 {201 "path": "analysis/figure_3_panel_ab_profile.py",202 "sha256": "b9e9bda2a8abded369c678529eced60cd279faa12cf9e51b9ed59759491a0b0f",203 "language": "Python",204 "lines": 239,205 "truncated": false,206 "block": 3,207 "row": 24563208 },209 {210 "path": "analysis/figure_3_panel_bimodal_benchmark.py",211 "sha256": "354cb3c9e659d2a490b50b0591c30d2d70db89f45d5b0b64c42a49789a746078",212 "language": "Python",213 "lines": 218,214 "truncated": false,215 "block": 3,216 "row": 24620217 },218 {219 "path": "analysis/figure_3_panel_c_l4l5.py",220 "sha256": "65473fc03f78005342dcd35f7476375d78d6d8988debc1824d2bd10941d27cd4",221 "language": "Python",222 "lines": 226,223 "truncated": false,224 "block": 3,225 "row": 24825226 },227 {228 "path": "analysis/figure_3_panel_confusion_matrices.py",229 "sha256": "a7ebf2ba4f7630852fe090b600a18c43000d9cf7aae44d7722ef4eeab482af55",230 "language": "Python",231 "lines": 150,232 "truncated": false,233 "block": 3,234 "row": 23199235 },236 {237 "path": "analysis/figure_3_supp_isiacg_benchmark.py",238 "sha256": "3db79d58803b4cc53185aa278dcd1c56c8c2271a551628a43b1425c7e5e4f388",239 "language": "Python",240 "lines": 201,241 "truncated": false,242 "block": 3,243 "row": 24117244 },245 {246 "path": "analysis/figure_3_supp_isiacg_profile.py",247 "sha256": "2a8a9a425c1cbbb6e5a03819b8c71abe71828e6fffa0343366475ccd7b5d766c",248 "language": "Python",249 "lines": 232,250 "truncated": false,251 "block": 3,252 "row": 24508253 },254 {255 "path": "analysis/figure_4_panel_profiles.py",256 "sha256": "de98264bd49f44816704584925e3cfbbe9cb4d0b124cd328cd6c0d09ad4cfd5f",257 "language": "Python",258 "lines": 268,259 "truncated": false,260 "block": 3,261 "row": 25219262 },263 {264 "path": "analysis/figure_4_supp_trimodal_benchmark.py",265 "sha256": "9f107e7ad08e7cac250f8947b96cf0e01ce7eda58a54654250df5bd7be89a0d6",266 "language": "Python",267 "lines": 288,268 "truncated": false,269 "block": 3,270 "row": 25225271 },272 {273 "path": "analysis/figure_4_trimodal_benchmark.py",274 "sha256": "b4bb7870b3ab10c76ced28ca70c816f769c0899cbadb13fefb9be41060f5c9fe",275 "language": "Python",276 "lines": 490,277 "truncated": false,278 "block": 3,279 "row": 26906280 },281 {282 "path": "analysis/figure_5_panel_a_method_bars.py",283 "sha256": "94b3952a4b8ab56cc23083383efb0d49607f5548e25c6d7a3b9d2069be7b2374",284 "language": "Python",285 "lines": 117,286 "truncated": false,287 "block": 3,288 "row": 22649289 },290 {291 "path": "analysis/figure_5_panel_c_confusion.py",292 "sha256": "9f804304ef6537461fe0fc9b03a3b96892b93bfeea3140928f348b20cc4c748f",293 "language": "Python",294 "lines": 119,295 "truncated": false,296 "block": 3,297 "row": 22181298 },299 {300 "path": "analysis/figure_5_panel_d_umap.py",301 "sha256": "9d8cc0cd3070b98bcff013516ccea8abf088fea08b2346d5c55fdaf6ac31d44d",302 "language": "Python",303 "lines": 182,304 "truncated": false,305 "block": 3,306 "row": 24103307 },308 {309 "path": "analysis/figure_5_supp_analysis.py",310 "sha256": "9ac590d86b39faeb65ff55192bdef2a61e5a97638c4a2e5647c8c5871b1a2a31",311 "language": "Python",312 "lines": 335,313 "truncated": false,314 "block": 3,315 "row": 26457316 },317 {318 "path": "analysis/figure_5_supp_nopretrain.py",319 "sha256": "9e42dd2bcb2f2ae6ee2fcedcbd059055561a4336b4df3c911e7712b0567a41f0",320 "language": "Python",321 "lines": 129,322 "truncated": false,323 "block": 3,324 "row": 23169325 },326 {327 "path": "analysis/figure_7_brain_region_benchmark.py",328 "sha256": "f40a47a510e28c471186afe2db654886f6c340c2bad4fb2a61c6705f873680e0",329 "language": "Python",330 "lines": 343,331 "truncated": false,332 "block": 3,333 "row": 26358334 },335 {336 "path": "analysis/figure_polarity_supplement.py",337 "sha256": "3a08f9f347502752f8bf54c62a8fc8e8755f35082e677031cb5ac6c1e84ccb29",338 "language": "Python",339 "lines": 454,340 "truncated": false,341 "block": 3,342 "row": 26738343 },344 {345 "path": "analysis/figure_supp_umap_clustering.py",346 "sha256": "8916c6bbcedde15a4737b432bd8cc6c58105dd51c6e499022b05affd2f1beb18",347 "language": "Python",348 "lines": 608,349 "truncated": false,350 "block": 3,351 "row": 27360352 },353 {354 "path": "analysis/make_source_data.py",355 "sha256": "1b23206fcf63c7dd10210a9561990d182968902aff9c01e0967fc3ca70bc1016",356 "language": "Python",357 "lines": 225,358 "truncated": false,359 "block": 3,360 "row": 25051361 },362 {363 "path": "comparison_methods/nemo/iclr/eval/c4_nested_cross_validation.py",364 "sha256": "65be35dfbe74a2788a9b85ce5ca34c0788daa87f2c9dbbf53f8ad9577122e0fc",365 "language": "Python",366 "lines": 136,367 "truncated": false,368 "block": 3,369 "row": 23160370 },371 {372 "path": "comparison_methods/nemo/iclr/eval/c4_supervise_evaluation.py",373 "sha256": "984b91bbf82ec0050fb19838ed4a2a64fdf044803d4c7a816f4c5d797d165170",374 "language": "Python",375 "lines": 34,376 "truncated": false,377 "block": 3,378 "row": 19197379 },380 {381 "path": "comparison_methods/nemo/iclr/eval/c4_vae_evaluation.py",382 "sha256": "26c7041be541fb774e221d6cac3cdf435a557681b4b9b6b7caa86cba2241bbc7",383 "language": "Python",384 "lines": 118,385 "truncated": false,386 "block": 3,387 "row": 21512388 },389 {390 "path": "comparison_methods/nemo/iclr/eval/ibl_label_ratio_MLP.py",391 "sha256": "d235aebe768de224e87e4210c98f2a9c68f15caccb31dbd1e69c8f15614363ed",392 "language": "Python",393 "lines": 426,394 "truncated": false,395 "block": 3,396 "row": 26416397 },398 {399 "path": "comparison_methods/nemo/iclr/eval/ibl_label_ratio_linear.py",400 "sha256": "1969ab5034ebcb699eaa6ca42bcf549bc9bfd58f3e4107dd6789bfffe2037a6f",401 "language": "Python",402 "lines": 163,403 "truncated": false,404 "block": 3,405 "row": 23139406 },407 {408 "path": "comparison_methods/nemo/iclr/eval/label_ratio_sweep_per_class.py",409 "sha256": "075e9e772fc3a9932a03d76514f1b12533c1d3addf1284aaf737c07a18c719f9",410 "language": "Python",411 "lines": 162,412 "truncated": false,413 "block": 3,414 "row": 23734415 },416 {417 "path": "comparison_methods/nemo/iclr/eval/nearest_neighbor_region_decoder.py",418 "sha256": "810ceebb3dc431c8ab465c1bd15bddd819f9b0a5c013a4319c6da23c28b025c1",419 "language": "Python",420 "lines": 516,421 "truncated": false,422 "block": 3,423 "row": 26836424 },425 {426 "path": "comparison_methods/nemo/iclr/predict_region.ipynb",427 "sha256": "c98c3fe10feb56f33272ec0649c555a5302292f567856a9eab68a4799a0b1510",428 "language": "Jupyter",429 "lines": 105,430 "truncated": false,431 "block": 3,432 "row": 7228433 },434 {435 "path": "comparison_methods/nemo/iclr/predict_region.py",436 "sha256": "c76d5822fdb8ea06be993067c30c9bc810ec85df0d0374144d182543e0a47a41",437 "language": "Python",438 "lines": 116,439 "truncated": false,440 "block": 3,441 "row": 21824442 },443 {444 "path": "comparison_methods/nemo/iclr/train/acg_VAE_training_seed_sweep.py",445 "sha256": "abd08576874cb953f8574a6aa91b74b2e0b02a7cbafdcc30bba267c8f7480e54",446 "language": "Python",447 "lines": 267,448 "truncated": false,449 "block": 3,450 "row": 24539451 },452 {453 "path": "comparison_methods/nemo/iclr/train/wvf_VAE_training_seed_sweep.py",454 "sha256": "1d101d63efce7fbbbfc643a3865ad24fe3fa6e4c48eeec1d6b627f38edad7cda",455 "language": "Python",456 "lines": 286,457 "truncated": false,458 "block": 3,459 "row": 24925460 },461 {462 "path": "comparison_methods/nemo/replicate_c4_results.ipynb",463 "sha256": "c7aa52c2b534c290224d1b10e3d2d8c1e0ef35a303f0841c0ea28fde3e145da0",464 "language": "Jupyter",465 "lines": 215,466 "truncated": false,467 "block": 3,468 "row": 7571469 },470 {471 "path": "comparison_methods/nemo/scripts/allen_nwb_loader.py",472 "sha256": "4deb69ddad3cb222d8ac2263580c0a2795681a251cea2a15977a502f811cb6cd",473 "language": "Python",474 "lines": 497,475 "truncated": false,476 "block": 3,477 "row": 26541478 },479 {480 "path": "comparison_methods/nemo/scripts/compute_3dACG_IBL.py",481 "sha256": "06ac1c4aeeae64371168d52330393ccbd76031ab816380538115b6a969458b75",482 "language": "Python",483 "lines": 170,484 "truncated": false,485 "block": 3,486 "row": 23086487 },488 {489 "path": "comparison_methods/nemo/scripts/compute_3dacg_from_spikes.py",490 "sha256": "7137bfafe0919eb9a434c8266373a79753e963c8889e959a9cc9ec20a512fb8f",491 "language": "Python",492 "lines": 444,493 "truncated": false,494 "block": 3,495 "row": 26395496 },497 {498 "path": "comparison_methods/nemo/scripts/compute_NP_Ultra_dataset.py",499 "sha256": "1155a3725949396dc1b441c7acfa1e393b839e45364559889ba3eef2df6bf528",500 "language": "Python",501 "lines": 149,502 "truncated": false,503 "block": 3,504 "row": 22592505 },506 {507 "path": "comparison_methods/nemo/scripts/curate_and_process_ibl_dataset.py",508 "sha256": "86f9012b845dea6fbfff6f6ed37fdff06f224aa4006f6722c8f901517211bc20",509 "language": "Python",510 "lines": 260,511 "truncated": false,512 "block": 3,513 "row": 25307514 },515 {516 "path": "comparison_methods/nemo/scripts/gather_ibl_wvf_acg_pair.py",517 "sha256": "5ad5bb8e55f2762cd9986d167f880072dda8ebb5f45c282a8ed430f5369cb2f4",518 "language": "Python",519 "lines": 257,520 "truncated": false,521 "block": 3,522 "row": 24973523 },524 {525 "path": "comparison_methods/nemo/scripts/get_c4_wvf_acg3d_pairs.py",526 "sha256": "0fa8cb54e58beeeea4254bd21d4457d11557da590b4106a6fff85dfa71e82786",527 "language": "Python",528 "lines": 91,529 "truncated": false,530 "block": 3,531 "row": 20963532 },533 {534 "path": "comparison_methods/nemo/scripts/ibl_label_sweep.sh",535 "sha256": "4a74a398aa10279c0dd07e49f004270cb122de443f3217268ff00d6ec8d44268",536 "language": "Shell",537 "lines": 1,538 "truncated": false,539 "block": 4,540 "row": 1299541 },542 {543 "path": "comparison_methods/nemo/scripts/nemo_benchmark_evaluation.py",544 "sha256": "7fc08d392b886b81928d180a12faff62cdb51f737cf45955224b6b99c7f50b1e",545 "language": "Python",546 "lines": 1240,547 "truncated": false,548 "block": 3,549 "row": 27979550 },551 {552 "path": "comparison_methods/nemo/scripts/nemo_transductive_test.py",553 "sha256": "81aa3aa22d79847e981e3d6fd0e75a25c28399b55175927b340a63138f314ff0",554 "language": "Python",555 "lines": 540,556 "truncated": false,557 "block": 3,558 "row": 27265559 },560 {561 "path": "comparison_methods/nemo/scripts/run_c4_acg_vaes.sh",562 "sha256": "e7d3307f87ec132a1435f4e87764a074f96f1ca577a534821e77b1ec34b53010",563 "language": "Shell",564 "lines": 1,565 "truncated": false,566 "block": 4,567 "row": 1294568 },569 {570 "path": "comparison_methods/nemo/scripts/run_c4_wvf_vaes.sh",571 "sha256": "39b8df7031e650480178c8695cd59865e7023e72a281484d73ba4bb1ec4853bc",572 "language": "Shell",573 "lines": 13,574 "truncated": false,575 "block": 4,576 "row": 1402577 },578 {579 "path": "comparison_methods/nemo/scripts/run_mlp_probe_ultra.py",580 "sha256": "174403a6db90cc18a5a179e55fae1fa838549d5a2626cde71b038baed604c1d7",581 "language": "Python",582 "lines": 73,583 "truncated": false,584 "block": 3,585 "row": 20455586 },587 {588 "path": "comparison_methods/nemo/scripts/run_nemo_benchmark.sh",589 "sha256": "306134e830ce98186c870f1ae09e48931d09d3357246df26d8b0cdb21c8840c4",590 "language": "Shell",591 "lines": 186,592 "truncated": false,593 "block": 4,594 "row": 2199595 },596 {597 "path": "comparison_methods/nemo/scripts/run_transductive_nemo.sh",598 "sha256": "699f0fc671e8e692263130aaedf8243bc26c1cb8813c14f0e65e6b78dd66ddf7",599 "language": "Shell",600 "lines": 74,601 "truncated": false,602 "block": 4,603 "row": 1986604 },605 {606 "path": "comparison_methods/nemo/scripts/train_c4_nemo.sh",607 "sha256": "fd5bc04a546e7e44a0b16bc1da0a9856e6822ce20c6a1fd1256b16feb15d928d",608 "language": "Shell",609 "lines": 19,610 "truncated": false,611 "block": 4,612 "row": 1671613 },614 {615 "path": "comparison_methods/nemo/scripts/train_ibl_nemo.sh",616 "sha256": "a3f39aa894dca7e5c94d4fd57c2734f6483c822833851ca7f9e77a9c6f7c8f86",617 "language": "Shell",618 "lines": 6,619 "truncated": false,620 "block": 4,621 "row": 1320622 },623 {624 "path": "comparison_methods/nemo/scripts/train_ultra_nemo.sh",625 "sha256": "5004441f5fe6147343e52a61d9d1d0ee087c2e449ac18e5dbbc4566f5e60b737",626 "language": "Shell",627 "lines": 11,628 "truncated": false,629 "block": 4,630 "row": 1349631 },632 {633 "path": "comparison_methods/nemo/setup.py",634 "sha256": "512387ea8567af5919eaac660a59d5a2e8607eb5dd0c1feeefe4eb8067982f9c",635 "language": "Python",636 "lines": 6,637 "truncated": false,638 "block": 3,639 "row": 17593640 },641 {642 "path": "comparison_methods/nemo/src/celltype_ibl/models/ACG_augmentation_dataloader.py",643 "sha256": "8741aa7e6ab408218a7bf5629a38f5ac8de3f127b710569eb72b4917ebbb873c",644 "language": "Python",645 "lines": 144,646 "truncated": false,647 "block": 3,648 "row": 22789649 },650 {651 "path": "comparison_methods/nemo/src/celltype_ibl/models/AcgAug.py",652 "sha256": "96fac685e89203e9f6c058f12e2bba5dc9d78c6fffafe608a56185e44a32855a",653 "language": "Python",654 "lines": 173,655 "truncated": false,656 "block": 3,657 "row": 23184658 },659 {660 "path": "comparison_methods/nemo/src/celltype_ibl/models/BiModalEmbedding.py",661 "sha256": "473b8bca9b03405076b47040dc4e8a8da6b377e9cb42f0e02468ee2d755136a8",662 "language": "Python",663 "lines": 364,664 "truncated": false,665 "block": 3,666 "row": 25966667 },668 {669 "path": "comparison_methods/nemo/src/celltype_ibl/models/WvfAug.py",670 "sha256": "d412a77e6a6b4269170aaef39a5b3c7786348781d9eb07b558bd956a0f77b45c",671 "language": "Python",672 "lines": 88,673 "truncated": false,674 "block": 3,675 "row": 20856676 },677 {678 "path": "comparison_methods/nemo/src/celltype_ibl/models/bimodal_embedding_main_knn.py",679 "sha256": "f5db9eb8b3f5d1745a4c8045fe77a72402ea7b24ad46f86e16a323342c78e91f",680 "language": "Python",681 "lines": 1052,682 "truncated": false,683 "block": 3,684 "row": 27917685 },686 {687 "path": "comparison_methods/nemo/src/celltype_ibl/models/encoders.py",688 "sha256": "6c9c89794da2c7a98c0ecc5253202186bc39cd9d0b7df3fc74789c47eb99b091",689 "language": "Python",690 "lines": 255,691 "truncated": false,692 "block": 3,693 "row": 24301694 },695 {696 "path": "comparison_methods/nemo/src/celltype_ibl/models/linear_classifier.py",697 "sha256": "f5ccf6f54ea5f2b61482ecfb5df88bb0884d53b5e9b8e29ac21e0404d56f5d76",698 "language": "Python",699 "lines": 682,700 "truncated": false,701 "block": 3,702 "row": 27176703 },704 {705 "path": "comparison_methods/nemo/src/celltype_ibl/models/linear_classifier_multi_folds.py",706 "sha256": "99ffbd6d5ac568860a4a29fec317d40d79f9c09d9f5523454c5f13477a435bd9",707 "language": "Python",708 "lines": 681,709 "truncated": false,710 "block": 3,711 "row": 27184712 },713 {714 "path": "comparison_methods/nemo/src/celltype_ibl/models/linear_mlp_test.py",715 "sha256": "6dc6ca5caa8124b841f43c2e1b6ffd92f26b10d7eab0eb0bb13e957b15cf06d8",716 "language": "Python",717 "lines": 140,718 "truncated": false,719 "block": 3,720 "row": 23502721 },722 {723 "path": "comparison_methods/nemo/src/celltype_ibl/models/linear_probe.py",724 "sha256": "e91095c79213ec6e146c721e04805ce7dc6517513fb32f8182a2b8881b7d5f13",725 "language": "Python",726 "lines": 121,727 "truncated": false,728 "block": 3,729 "row": 21826730 },731 {732 "path": "comparison_methods/nemo/src/celltype_ibl/models/metrics.py",733 "sha256": "61c03c6b2abb1d996d1f50dee39d2cfe6debafc1656eccdbb3f532ea47eac4b3",734 "language": "Python",735 "lines": 40,736 "truncated": false,737 "block": 3,738 "row": 19266739 },740 {741 "path": "comparison_methods/nemo/src/celltype_ibl/models/mlp_classifier.py",742 "sha256": "d60eb7ec37d413d864b20f7f7abb0271eeaa20b66fa7068419a62321a33c301b",743 "language": "Python",744 "lines": 971,745 "truncated": false,746 "block": 3,747 "row": 27650748 },749 {750 "path": "comparison_methods/nemo/src/celltype_ibl/models/mlp_classifier_multi_folds.py",751 "sha256": "781e97f2d5416dbefcc926a6425b8d3d995e56c51afef98a11e7500705d77b3d",752 "language": "Python",753 "lines": 1019,754 "truncated": false,755 "block": 3,756 "row": 27672757 },758 {759 "path": "comparison_methods/nemo/src/celltype_ibl/params/config.py",760 "sha256": "fc4ce7e088b0d261fea7d2b478cd181dac97b27b929226ec670b0e9ae58eebec",761 "language": "Python",762 "lines": 79,763 "truncated": false,764 "block": 3,765 "row": 20461766 },767 {768 "path": "comparison_methods/nemo/src/celltype_ibl/params/set_params.py",769 "sha256": "7518c05704f8a0e98a8073f7e30c1a26e648d739b0a34ad2f38588679b631cbd",770 "language": "Python",771 "lines": 161,772 "truncated": false,773 "block": 3,774 "row": 23830775 },776 {777 "path": "comparison_methods/nemo/src/celltype_ibl/utils/c4_data_utils.py",778 "sha256": "591b07968a288c65fb3ffd1219eeb35c7472ae246994e22c4f5c0f27695191b3",779 "language": "Python",780 "lines": 1381,781 "truncated": false,782 "block": 3,783 "row": 28021784 },785 {786 "path": "comparison_methods/nemo/src/celltype_ibl/utils/c4_vae_util.py",787 "sha256": "5b5a94e749ebca9b1d4e09a527a292b86a088e233f796cf1c82cdc3908d39958",788 "language": "Python",789 "lines": 259,790 "truncated": false,791 "block": 3,792 "row": 24634793 },794 {795 "path": "comparison_methods/nemo/src/celltype_ibl/utils/cell_explorer_data_util.py",796 "sha256": "93123fd26ce6501b18e33e566857a5490d7a7960a4e653997bdffbff2ed95014",797 "language": "Python",798 "lines": 92,799 "truncated": false,800 "block": 3,801 "row": 21432802 },803 {804 "path": "comparison_methods/nemo/src/celltype_ibl/utils/cross_session_validation.py",805 "sha256": "5f7244d77ef3fee41dd8078507ed87f3317ea9109a937674fc8dd26cf466540d",806 "language": "Python",807 "lines": 20,808 "truncated": false,809 "block": 3,810 "row": 18568811 },812 {813 "path": "comparison_methods/nemo/src/celltype_ibl/utils/ibl_data_util.py",814 "sha256": "f3214ad483667e5647ea903d371be054cbb2b873ab8f36fb509cd2cc2c503a3d",815 "language": "Python",816 "lines": 274,817 "truncated": false,818 "block": 3,819 "row": 25124820 },821 {822 "path": "comparison_methods/nemo/src/celltype_ibl/utils/ibl_data_visualization.py",823 "sha256": "03a23122f76ee3af891289f6bd5c92196c9d2dc1ebf8168eed0437ef173d5ade",824 "language": "Python",825 "lines": 319,826 "truncated": false,827 "block": 3,828 "row": 24989829 },830 {831 "path": "comparison_methods/nemo/src/celltype_ibl/utils/ibl_eval_utils.py",832 "sha256": "40e3365075f334ffad92da97636f20ac85f48ab916327a5c4d31a257dc1d4a8e",833 "language": "Python",834 "lines": 93,835 "truncated": false,836 "block": 3,837 "row": 21516838 },839 {840 "path": "comparison_methods/nemo/src/celltype_ibl/utils/kenji_allen_data_utils.py",841 "sha256": "7e022780d7abd6a68b5f26342302b1f9e1e8efbc1c64a0f6cc942150c3d6821f",842 "language": "Python",843 "lines": 73,844 "truncated": false,845 "block": 3,846 "row": 20405847 },848 {849 "path": "comparison_methods/nemo/src/celltype_ibl/utils/nested_cv_util.py",850 "sha256": "bd575061bf78ad24de8aaa51cf5d95ee9fb5f843500a9ba63e79a906cec43f03",851 "language": "Python",852 "lines": 58,853 "truncated": false,854 "block": 3,855 "row": 20427856 },857 {858 "path": "comparison_methods/nemo/src/celltype_ibl/utils/preprocess.py",859 "sha256": "bdfcc35a092ad601e5b12f029e3104857860b27dad2ef54b955741a1aa256c10",860 "language": "Python",861 "lines": 102,862 "truncated": false,863 "block": 3,864 "row": 21225865 },866 {867 "path": "comparison_methods/nemo/src/celltype_ibl/utils/ultra_data_util.py",868 "sha256": "090c8a148437b765f446df7971c5dba42fa20a2396f00df156b2fb8c56ea0be4",869 "language": "Python",870 "lines": 139,871 "truncated": false,872 "block": 3,873 "row": 22494874 },875 {876 "path": "comparison_methods/nemo/src/celltype_ibl/utils/visualize_util.py",877 "sha256": "92f2886c7ab4892dcb6a3a86acd26007cbea626cf8a24613532e53d1556dcd5b",878 "language": "Python",879 "lines": 522,880 "truncated": false,881 "block": 3,882 "row": 26764883 },884 {885 "path": "comparison_methods/physmap/physmap_knn_crossdataset.r",886 "sha256": "f786ec73439aefb3af5c113a1c4a5f7cab7ca85d37bc462d9cbdaf73d9f314dc",887 "language": "R",888 "lines": 460,889 "truncated": false,890 "block": 4,891 "row": 1068892 },893 {894 "path": "comparison_methods/physmap/physmap_script.r",895 "sha256": "66f7f011873913913f560df709e22611416ee36efae0e86eb110cb97fb4eb146",896 "language": "R",897 "lines": 785,898 "truncated": false,899 "block": 4,900 "row": 1147901 },902 {903 "path": "comparison_methods/physmap/physmap_script_cross_dataset.r",904 "sha256": "02d065f30c1dbfaba7b385f9b8e1e9c407e0b81c31faa114b2fe44d2efd948b1",905 "language": "R",906 "lines": 585,907 "truncated": false,908 "block": 4,909 "row": 1110910 },911 {912 "path": "comparison_methods/physmap/physmap_script_holdout.r",913 "sha256": "5cc25bed86d2c6d290195876526d36db6aa5a51922b0a21e29b20e70d7d083fd",914 "language": "R",915 "lines": 657,916 "truncated": false,917 "block": 4,918 "row": 1131919 },920 {921 "path": "comparison_methods/physmap/physmap_script_pca.r",922 "sha256": "c7a5799d45284a5008ad712cd603023b9d8cac5449798bfd247bbe13a7d5c8bb",923 "language": "R",924 "lines": 586,925 "truncated": false,926 "block": 4,927 "row": 1119928 },929 {930 "path": "comparison_methods/physmap/run_physmap.sh",931 "sha256": "9e0e7ed26241ccb2312eaf3e24762cdb005014175fda0777b88800993d0e451a",932 "language": "Shell",933 "lines": 79,934 "truncated": false,935 "block": 4,936 "row": 2006937 },938 {939 "path": "comparison_methods/physmap/run_physmap_crossdataset.sh",940 "sha256": "eea6dcb19a9ff9e10c837bf4b43fc59f1235bc46052bc1042fe953c08f475546",941 "language": "Shell",942 "lines": 86,943 "truncated": false,944 "block": 4,945 "row": 2068946 },947 {948 "path": "comparison_methods/physmap/run_physmap_holdout.sh",949 "sha256": "26dc2b8f824f5245fa7c26948a8120b06a5499b9e196fb4f53f4935998753c53",950 "language": "Shell",951 "lines": 142,952 "truncated": false,953 "block": 4,954 "row": 2126955 },956 {957 "path": "comparison_methods/physmap/setup_script.R",958 "sha256": "e4367e5634c53fb8f9e1f7d8f003967c39fa19faafa1199427b9763dc3e646a5",959 "language": "R",960 "lines": 51,961 "truncated": false,962 "block": 4,963 "row": 308964 },965 {966 "path": "comparison_methods/wf-rf/wf_rf_benchmark_evaluation.py",967 "sha256": "e7ed3b0ce78975860b73a4b1ebb11b4f04ce350e61618dd828af021500a5f757",968 "language": "Python",969 "lines": 638,970 "truncated": false,971 "block": 3,972 "row": 27485973 },974 {975 "path": "examples/smoke_test_hf_checkpoint.py",976 "sha256": "386847c1b94defee1113b925de12f8193712f3fb6de62ea360ab8d408f7be661",977 "language": "Python",978 "lines": 160,979 "truncated": false,980 "block": 3,981 "row": 23077982 },983 {984 "path": "hippie/augmentations.py",985 "sha256": "8e868260693717a9c728fe94660c9509d8dbadbc27864bab6198c39ea247966f",986 "language": "Python",987 "lines": 214,988 "truncated": false,989 "block": 3,990 "row": 24503991 },992 {993 "path": "hippie/backbones.py",994 "sha256": "50f6febb2db918bb0279b34ac009571e41026bcb101c826182582f562e56032a",995 "language": "Python",996 "lines": 183,997 "truncated": false,998 "block": 3,999 "row": 239781000 },1001 {1002 "path": "hippie/cli.py",1003 "sha256": "a85d9b836e84b829602770245350fc8c2f370917f4e4c42867e557407d573e13",1004 "language": "Python",1005 "lines": 161,1006 "truncated": false,1007 "block": 3,1008 "row": 229011009 },1010 {1011 "path": "hippie/compute_parity.py",1012 "sha256": "091d341e84bf26065f9ee792989e488f86cc0b910c9c801e4396483361bfbd55",1013 "language": "Python",1014 "lines": 297,1015 "truncated": false,1016 "block": 3,1017 "row": 252441018 },1019 {1020 "path": "hippie/dataloading.py",1021 "sha256": "ffe88c399ffc27fc10f864fd266fbe77bd630c03488948ed703845aeda85147c",1022 "language": "Python",1023 "lines": 162,1024 "truncated": false,1025 "block": 3,1026 "row": 237221027 },1028 {1029 "path": "hippie/multimodal_model.py",1030 "sha256": "8df12b96afb116f4ac39ef8d15b43ff97326f99965c7c4334a779d84950d3266",1031 "language": "Python",1032 "lines": 866,1033 "truncated": false,1034 "block": 3,1035 "row": 278131036 },1037 {1038 "path": "hippie/optimizers.py",1039 "sha256": "449578a135f667066b5d8f883aac43bcf9dc32f4a1bbd8e9a6b64c3b6414bf14",1040 "language": "Python",1041 "lines": 209,1042 "truncated": false,1043 "block": 3,1044 "row": 243791045 },1046 {1047 "path": "hippie/utils.py",1048 "sha256": "3dbb50664f58b3186c4b50556ea81b9c4b1934f1bbab1e09b67d2f94b26c18ac",1049 "language": "Python",1050 "lines": 191,1051 "truncated": false,1052 "block": 3,1053 "row": 240541054 },1055 {1056 "path": "hippie_wf3dacg/__init__.py",1057 "sha256": "e0e68bc874c3575c1b095ae36294b08f0ea0d0e05af0ed3d1348c404ddf2734c",1058 "language": "Python",1059 "lines": 56,1060 "truncated": false,1061 "block": 3,1062 "row": 197201063 },1064 {1065 "path": "hippie_wf3dacg/acg.py",1066 "sha256": "5d61494e9cc6d6383aeb6b65a06c5f697c947aa814a3fb69b653a52e9adaed4a",1067 "language": "Python",1068 "lines": 186,1069 "truncated": false,1070 "block": 3,1071 "row": 242561072 },1073 {1074 "path": "hippie_wf3dacg/dataloading.py",1075 "sha256": "b59159d4ad15b59b4065033aa02a922b22fc6272f71f0708716e1369643e51e7",1076 "language": "Python",1077 "lines": 297,1078 "truncated": false,1079 "block": 3,1080 "row": 256101081 },1082 {1083 "path": "hippie_wf3dacg/load_c4.py",1084 "sha256": "26ab0409df7419f888a87f1917a2f5aeb9a17bfdea9cbf85e0405608e30019a3",1085 "language": "Python",1086 "lines": 239,1087 "truncated": false,1088 "block": 3,1089 "row": 249851090 },1091 {1092 "path": "hippie_wf3dacg/model.py",1093 "sha256": "1fb0b148ec6bf8d3da70cca937be3dffd53d6d2a1e08faf25b03a23e793b131f",1094 "language": "Python",1095 "lines": 695,1096 "truncated": false,1097 "block": 3,1098 "row": 276261099 },1100 {1101 "path": "scripts/check_dataset_cache_consistency.py",1102 "sha256": "4f3905a7b7abf0ccae64cc54abe05eaa4a86e60158aae0acf0bf084e4808aab4",1103 "language": "Python",1104 "lines": 140,1105 "truncated": false,1106 "block": 3,1107 "row": 232871108 },1109 {1110 "path": "scripts/cross_dataset_script.py",1111 "sha256": "d2261c648c1268defb62b6325d7f6014c768926782b70d7acd851732f201c25a",1112 "language": "Python",1113 "lines": 1785,1114 "truncated": false,1115 "block": 4,1116 "row": 671117 },1118 {1119 "path": "scripts/download_c4_h5.py",1120 "sha256": "bbd3779e6e0a1616a1122e40caed00259643b9d29d8b49e59812fae5ce0a4fe7",1121 "language": "Python",1122 "lines": 94,1123 "truncated": false,1124 "block": 3,1125 "row": 217541126 },1127 {1128 "path": "scripts/pick_locked_configs.py",1129 "sha256": "dfd2bb48e1d9d179db6aee6f0862b02c2b5b23d42bac5048a353bf8e63b11432",1130 "language": "Python",1131 "lines": 262,1132 "truncated": false,1133 "block": 3,1134 "row": 253471135 },1136 {1137 "path": "scripts/run_all_figures.sh",1138 "sha256": "0ae38ef61c378a342a035fca177d076f49a0dd7f650183827b8e4f6e69737ae3",1139 "language": "Shell",1140 "lines": 99,1141 "truncated": false,1142 "block": 4,1143 "row": 21271144 },1145 {1146 "path": "scripts/train_hippie_wf3dacg.py",1147 "sha256": "2714f27b467fbc376beefcd76a00821ee366a329a271fe705e8c8bddba936e08",1148 "language": "Python",1149 "lines": 487,1150 "truncated": false,1151 "block": 3,1152 "row": 271381153 },1154 {1155 "path": "scripts/train_hippie_wf3dacg_cross_dataset.py",1156 "sha256": "b4861470a225d47d31cab3c6c9e79a02bc677a1f8ca6a52814c6bda3df6a654f",1157 "language": "Python",1158 "lines": 560,1159 "truncated": false,1160 "block": 3,1161 "row": 274081162 },1163 {1164 "path": "scripts/train_multimodal_holdout.py",1165 "sha256": "91391492ae861f686961f838d0c62e9d80de16671ae0233b6dd8186652b35c94",1166 "language": "Python",1167 "lines": 1314,1168 "truncated": false,1169 "block": 3,1170 "row": 280241171 },1172 {1173 "path": "scripts/train_multimodal_holdout_waveisi.py",1174 "sha256": "23e32127f217e07e6d93d132677c1a3b84f0c285247f3f049f30da582f983ab8",1175 "language": "Python",1176 "lines": 1113,1177 "truncated": false,1178 "block": 3,1179 "row": 279521180 },1181 {1182 "path": "scripts/train_multimodal_transductive.py",1183 "sha256": "18280604207a0e0fb6009c7506163aa5487cfcbb7dab7a6f40e2ccf14cf37877",1184 "language": "Python",1185 "lines": 2182,1186 "truncated": false,1187 "block": 4,1188 "row": 901189 },1190 {1191 "path": "scripts/train_multimodal_transductive_isiacg.py",1192 "sha256": "cd06ece1e1bc21ad0aa78a3e30be3f0ed6eb676e42f074a5cdc5869c21486818",1193 "language": "Python",1194 "lines": 1471,1195 "truncated": false,1196 "block": 3,1197 "row": 280451198 },1199 {1200 "path": "scripts/train_multimodal_transductive_waveisi.py",