OpenScientificCodeRegistry/Database

1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/imperial-mind-lab/graphtrip",4 "url": "https://github.com/Imperial-MIND-lab/graphTRIP",5 "host": "github.com",6 "commit": "0e658ac9bf6038a8eed9cc952a02c1c7930f37b6",7 "license": "BSD-3-Clause",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "7c22fc499c3ee7a05bbc6fd4a383bb0907864d504356c85970b33dfae58582e9",14   "language": "License",15   "lines": 28,16   "truncated": false,17   "block": 20,18   "row": 881119  },20  {21   "path": "README.md",22   "sha256": "4b8869f8561fb5d22a711e489b690b0fbe98bbdc5112da1a81cb3bc50d00276a",23   "language": "Text",24   "lines": 179,25   "truncated": false,26   "block": 21,27   "row": 318028  },29  {30   "path": "datasets.py",31   "sha256": "c815e7c8a01e2f10c72a29862074cc4173f07d7f37b6b880dcdf283abed64859",32   "language": "Python",33   "lines": 696,34   "truncated": false,35   "block": 20,36   "row": 2205437  },38  {39   "path": "experiments/attention_weights.py",40   "sha256": "b630230ff4a0f39637196cbab18d98cbfaa1f97a83ecb649de218507a6da240c",41   "language": "Python",42   "lines": 524,43   "truncated": false,44   "block": 20,45   "row": 2177846  },47  {48   "path": "experiments/estimate_propensity.py",49   "sha256": "4a224c8c928bcf12c8e1f25105b36c14fa3908065f0c51bc89c837fcb1b3ec09",50   "language": "Python",51   "lines": 491,52   "truncated": false,53   "block": 20,54   "row": 2155655  },56  {57   "path": "experiments/grail.py",58   "sha256": "968e6352f5a05eba0ea10a07de00c002d525dbddbc7165592f09006e473803da",59   "language": "Python",60   "lines": 573,61   "truncated": false,62   "block": 20,63   "row": 2195564  },65  {66   "path": "experiments/grail_parallel.py",67   "sha256": "eb7db0a4d0d7efec411d3b5b7039719111c18ec15702ec9ce6f7061654e1c9e3",68   "language": "Python",69   "lines": 704,70   "truncated": false,71   "block": 21,72   "row": 5173  },74  {75   "path": "experiments/ingredients/__init__.py",76   "sha256": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",77   "language": "Python",78   "lines": 1,79   "truncated": false,80   "block": 1,81   "row": 495682  },83  {84   "path": "experiments/ingredients/data_ingredient.py",85   "sha256": "453f322d1b7e1bc6ddb2ddb81157ebe576bf80ceb58fd045d932b00c05fdce91",86   "language": "Python",87   "lines": 911,88   "truncated": false,89   "block": 21,90   "row": 21791  },92  {93   "path": "experiments/ingredients/mlp_ingredient.py",94   "sha256": "009afed89156c8b15d3b4b5894323bd69cca884e6fd1a5e68dd5baeb9b4aaa7f",95   "language": "Python",96   "lines": 439,97   "truncated": false,98   "block": 20,99   "row": 21223100  },101  {102   "path": "experiments/ingredients/vgae_ingredient.py",103   "sha256": "c8d64e53da5728e5bc5cae3a22513bd6387155e210521c77b417f76573fc887e",104   "language": "Python",105   "lines": 473,106   "truncated": false,107   "block": 20,108   "row": 21494109  },110  {111   "path": "experiments/pca_benchmark.py",112   "sha256": "0e701c3da96d9bd58111ff0041d79a499c517b331aff45ae5ebedf3492e145cc",113   "language": "Python",114   "lines": 276,115   "truncated": false,116   "block": 20,117   "row": 20409118  },119  {120   "path": "experiments/permutation_importance.py",121   "sha256": "ea3c6afbd530c76881ecb83f0a804407df6302cfbd2e8ee8422cbb4947d6a3f4",122   "language": "Python",123   "lines": 295,124   "truncated": false,125   "block": 20,126   "row": 20704127  },128  {129   "path": "experiments/regional_attributions.py",130   "sha256": "fd2a1998ad15b248641a61482432bc5fee7e57edb523058d09c8f3f898388f67",131   "language": "Python",132   "lines": 340,133   "truncated": false,134   "block": 20,135   "row": 21129136  },137  {138   "path": "experiments/retrain_mlp.py",139   "sha256": "ba1b4db40d2ba42bad1ca75a81bcc213631b8b2f7ca059319dbc0f4952646180",140   "language": "Python",141   "lines": 366,142   "truncated": false,143   "block": 20,144   "row": 21233145  },146  {147   "path": "experiments/run_experiment.py",148   "sha256": "a09ddba7cd639723a7423bc3c6b4eb252b5daeb8d4b5868a1fed9457c873a4e4",149   "language": "Python",150   "lines": 166,151   "truncated": false,152   "block": 20,153   "row": 19267154  },155  {156   "path": "experiments/test_and_finetune.py",157   "sha256": "41d059ff002a6a19cdc9b9dbec97a5995cfc79fbb7670f5b60715bfba43737f5",158   "language": "Python",159   "lines": 364,160   "truncated": false,161   "block": 20,162   "row": 21364163  },164  {165   "path": "experiments/test_biomarkers.py",166   "sha256": "8a7fc6cbc603c662db7cb5ea92974f346f967b1511a3482f833cb022f6c5a2de",167   "language": "Python",168   "lines": 326,169   "truncated": false,170   "block": 20,171   "row": 20778172  },173  {174   "path": "experiments/train_cfrnet.py",175   "sha256": "1167f5a27a30c1b7b9ed417e4309ea4093e72733b29cb7e72ef82feed8ab978c",176   "language": "Python",177   "lines": 645,178   "truncated": false,179   "block": 20,180   "row": 22049181  },182  {183   "path": "experiments/train_jointly.py",184   "sha256": "4759ee4f4e46f7f563d624d3fb3d08f5a1c43e3174646ea74ad2f4a2a3cb8c2d",185   "language": "Python",186   "lines": 279,187   "truncated": false,188   "block": 20,189   "row": 20628190  },191  {192   "path": "experiments/train_linreg_on_clinical.py",193   "sha256": "5c0044a894cabae529c5f8b67bc30c667bb353a2659324239402f8a061cfb43e",194   "language": "Python",195   "lines": 238,196   "truncated": false,197   "block": 20,198   "row": 19753199  },200  {201   "path": "experiments/train_linreg_on_z.py",202   "sha256": "739501fb5a4f7e2f6ec9b6761734e6489345603d034d3e306654a26169b1d445",203   "language": "Python",204   "lines": 277,205   "truncated": false,206   "block": 20,207   "row": 20340208  },209  {210   "path": "experiments/train_mlp.py",211   "sha256": "2e375e9d874db63998f67af1f92324338270e9f54a11f889c750797afd90eb37",212   "language": "Python",213   "lines": 243,214   "truncated": false,215   "block": 20,216   "row": 19920217  },218  {219   "path": "experiments/train_scate.py",220   "sha256": "20c70a1c038aff8524686f540993b25038bc812d707dc25e2be1615021b78acb",221   "language": "Python",222   "lines": 588,223   "truncated": false,224   "block": 20,225   "row": 21915226  },227  {228   "path": "experiments/train_tlearners.py",229   "sha256": "b330fb1f3313fcbfe737bae230e485eac20fcf002830d97c837b2dc2caff4893",230   "language": "Python",231   "lines": 774,232   "truncated": false,233   "block": 21,234   "row": 197235  },236  {237   "path": "experiments/train_vgae.py",238   "sha256": "20debed92750a8f8bc620caa753e73afad84bbff515696bbfe18c9b57e6a7aef",239   "language": "Python",240   "lines": 272,241   "truncated": false,242   "block": 20,243   "row": 20381244  },245  {246   "path": "experiments/transfer_and_finetune.py",247   "sha256": "adab1c6dce5ce0f3ff35c50e613fe31f7a1eab53e35d2766198683959327554d",248   "language": "Python",249   "lines": 723,250   "truncated": false,251   "block": 21,252   "row": 115253  },254  {255   "path": "experiments/transfer_vgae.py",256   "sha256": "a12b67a68150c468540f596251df1e8c8a91e4a6b996aa6ad9fad8fb9ab0e0fd",257   "language": "Python",258   "lines": 461,259   "truncated": false,260   "block": 20,261   "row": 21749262  },263  {264   "path": "experiments/tsne_benchmark.py",265   "sha256": "6b9971a6d5b65e7e13e727ccdc5857b067507eb966e3f4773fcce14fcfdaeded",266   "language": "Python",267   "lines": 420,268   "truncated": false,269   "block": 20,270   "row": 21212271  },272  {273   "path": "job_scripts/posthoc_analysis.sh",274   "sha256": "fb016add6c89e4cc9e0d8f4ec8d6121b1e2bfcded2aa777b685cd12bbcfc1bb7",275   "language": "Shell",276   "lines": 17,277   "truncated": false,278   "block": 21,279   "row": 2002280  },281  {282   "path": "job_scripts/preprocessing.sh",283   "sha256": "985b1128120ef918b44f1e9ba2bdb2f2634656dcf01d2bf1050fb81d986daa32",284   "language": "Shell",285   "lines": 22,286   "truncated": false,287   "block": 21,288   "row": 2005289  },290  {291   "path": "job_scripts/primary_jobs.sh",292   "sha256": "e83b17c089e49e81448262ac4e6815c96d7d908cd706b3a569c554f0a5dd1817",293   "language": "Shell",294   "lines": 60,295   "truncated": false,296   "block": 21,297   "row": 2417298  },299  {300   "path": "job_scripts/secondary_jobs.sh",301   "sha256": "85d4e4e1cfc4f6978017abe9f7ac58f4f250a6e6c07af2e557d340fa2b8db31b",302   "language": "Shell",303   "lines": 107,304   "truncated": false,305   "block": 21,306   "row": 2704307  },308  {309   "path": "job_scripts/short_secondary_jobs.sh",310   "sha256": "bdf7d2648fe337ea784bd5c60703a8b25fe80df773b44521f20f542f2960f7f0",311   "language": "Shell",312   "lines": 49,313   "truncated": false,314   "block": 21,315   "row": 2386316  },317  {318   "path": "models/__init__.py",319   "sha256": "badf60e355efe969ac4dc781908104ffad6f241da06fc1016a5afcb863099c80",320   "language": "Python",321   "lines": 31,322   "truncated": false,323   "block": 20,324   "row": 14810325  },326  {327   "path": "models/models.py",328   "sha256": "1e61204338835cc8f9cb5d1384b89d207b1e3f29969ab9ef6c5adbb8efd518d6",329   "language": "Python",330   "lines": 1826,331   "truncated": false,332   "block": 21,333   "row": 446334  },335  {336   "path": "models/utils.py",337   "sha256": "e39f58ca617be3852d0adb16c94407c07afe300a44b0d4193b65643472b53eb6",338   "language": "Python",339   "lines": 97,340   "truncated": false,341   "block": 20,342   "row": 16638343  },344  {345   "path": "notebooks/demo.ipynb",346   "sha256": "76d76f80e6116ca93ce4e0cbe08cd10cbbbf73beb0fc6d303d0ad5f1431599bb",347   "language": "Jupyter",348   "lines": 140,349   "truncated": false,350   "block": 20,351   "row": 8016352  },353  {354   "path": "notebooks/figures.ipynb",355   "sha256": "9bcdf8b7f2073ddccb16155f5cab99e20157e2c686fdeda81d042da3d4eecfc5",356   "language": "Jupyter",357   "lines": 1936,358   "truncated": false,359   "block": 20,360   "row": 8590361  },362  {363   "path": "notebooks/load_models_data.py",364   "sha256": "9c7a8ec4db3a0b3fc46fb09625faec8fd642b3f92b8e535c1cc9db57d9448b5e",365   "language": "Python",366   "lines": 109,367   "truncated": false,368   "block": 20,369   "row": 17467370  },371  {372   "path": "preprocessing/__init__.py",373   "sha256": "264e0e0c5bdb782812f5e7260f595fb5f6913682fbdaae0493c56f5abe4dc3a9",374   "language": "Python",375   "lines": 1,376   "truncated": false,377   "block": 20,378   "row": 12210379  },380  {381   "path": "preprocessing/metrics.py",382   "sha256": "7905719a4ddbd31a1f0ac4650be8690720aafc621bb7dd34ed3e3c160d0cdd66",383   "language": "Python",384   "lines": 847,385   "truncated": false,386   "block": 21,387   "row": 35388  },389  {390   "path": "preprocessing/preprocess.py",391   "sha256": "524abfcd63114ff914775d528a78ef21d49f9b6d0c2e709cc9feb8014f19c438",392   "language": "Python",393   "lines": 134,394   "truncated": false,395   "block": 20,396   "row": 18661397  },398  {399   "path": "preprocessing/react/concat_5HT_atlases.py",400   "sha256": "2ff4202653e36cba7f25f74bb70dc5edc937306e747549abc80986a7e55c4707",401   "language": "Python",402   "lines": 87,403   "truncated": false,404   "block": 20,405   "row": 17158406  },407  {408   "path": "preprocessing/react/create_subject_list.sh",409   "sha256": "ba4237ef966b427e3be3023c4488179796c9c428e823606cdafdc25fa15eab75",410   "language": "Shell",411   "lines": 9,412   "truncated": false,413   "block": 21,414   "row": 1899415  },416  {417   "path": "preprocessing/react/normalise_5HT_atlas.py",418   "sha256": "a911c2ddde12a1af854410696cfa28c24e92b3541a03039f0dcd60f25c0ed232",419   "language": "Python",420   "lines": 135,421   "truncated": false,422   "block": 20,423   "row": 17826424  },425  {426   "path": "preprocessing/react/react.sh",427   "sha256": "aafbaae5b59e91fd3ed028c2507ccf17f50c8be8340325c0ab251605585a105f",428   "language": "Shell",429   "lines": 39,430   "truncated": false,431   "block": 21,432   "row": 2313433  },434  {435   "path": "preprocessing/react/react_masks.sh",436   "sha256": "8fe4ef92128e62f0f8de70f9b2fcc1c9cfe3145a90f3e139c785db1d14610e8e",437   "language": "Shell",438   "lines": 32,439   "truncated": false,440   "block": 21,441   "row": 2211442  },443  {444   "path": "preprocessing/react/resample_and_mask_5HT_atlas.sh",445   "sha256": "44a1c167f373227b69f6687b1c4e59bfa6a62f0c7eebb39ed0c62ee6515d3130",446   "language": "Shell",447   "lines": 84,448   "truncated": false,449   "block": 21,450   "row": 2600451  },452  {453   "path": "scripts/ablation.py",454   "sha256": "7c1c8e6397cc73d1c2065b83d95b141b52f7c1664526d812a49c27c4cd65d9b7",455   "language": "Python",456   "lines": 236,457   "truncated": false,458   "block": 20,459   "row": 20262460  },461  {462   "path": "scripts/graphtrip.py",463   "sha256": "3a22df064607ca2c38424b8ae5f323029b79cab7cb4b4c097e5753f8270db3a3",464   "language": "Python",465   "lines": 165,466   "truncated": false,467   "block": 20,468   "row": 18887469  },470  {471   "path": "scripts/graphtrip_bdi.py",472   "sha256": "4cb390196196ee930387dd7b7a71600eece62b2f33fe938b66fca84cac5b6b57",473   "language": "Python",474   "lines": 110,475   "truncated": false,476   "block": 20,477   "row": 17694478  },479  {480   "path": "scripts/medusa.py",481   "sha256": "dff7622e077e15b2b27b4c4ef1577d8812a75879f8e94e25e2f1612cb145ca41",482   "language": "Python",483   "lines": 164,484   "truncated": false,485   "block": 20,486   "row": 19035487  },488  {489   "path": "scripts/posthoc.py",490   "sha256": "f05acaf9e6b49da6f3e206b9a630e6ef7955ebfe2e4fdc01e96b630c90676397",491   "language": "Python",492   "lines": 611,493   "truncated": false,494   "block": 21,495   "row": 5496  },497  {498   "path": "scripts/validation.py",499   "sha256": "59058e007099da432bfedd9e6d77074ff0aa780873678371a2548f1e6c3ea9f1",500   "language": "Python",501   "lines": 299,502   "truncated": false,503   "block": 20,504   "row": 21033505  },506  {507   "path": "scripts/xai_biomarkers.py",508   "sha256": "51b704a6ea9173287bbb6af45b0e282839759599579e1eb11570208d9b9cb1a9",509   "language": "Python",510   "lines": 129,511   "truncated": false,512   "block": 20,513   "row": 18429514  },515  {516   "path": "scripts/xai_regions.py",517   "sha256": "bd8e96421c8982acf18fb7a4bd9a76d150865931a701fc922e8b9b06afaeee9b",518   "language": "Python",519   "lines": 88,520   "truncated": false,521   "block": 20,522   "row": 17100523  },524  {525   "path": "utils/__init__.py",526   "sha256": "1f76dbb1a6596a6d38b96606984067da0607d408dd43899259b47a9365204152",527   "language": "Python",528   "lines": 4,529   "truncated": false,530   "block": 20,531   "row": 12327532  },533  {534   "path": "utils/annotations.py",535   "sha256": "3684aab436bb63cc9c8dbe31c623104c37dc7e3a9f9a94cea7c0d404efea1e41",536   "language": "Python",537   "lines": 249,538   "truncated": false,539   "block": 20,540   "row": 20096541  },542  {543   "path": "utils/configs.py",544   "sha256": "16992a2de0dac10914663804c5cebf50ac7a8b2d7dfe042b1c9868ebda09b036",545   "language": "Python",546   "lines": 362,547   "truncated": false,548   "block": 20,549   "row": 20874550  },551  {552   "path": "utils/files.py",553   "sha256": "faaa0a5a1fa3a4027b8753ca1b0df409df9e4fa8a50c3d7c413cdba5132cd0b2",554   "language": "Python",555   "lines": 110,556   "truncated": false,557   "block": 20,558   "row": 17208559  },560  {561   "path": "utils/helpers.py",562   "sha256": "1ae9ababf4945a84a012ae56dbd1b413aeacb102a6ca6875377801ddc2dd3418",563   "language": "Python",564   "lines": 566,565   "truncated": false,566   "block": 20,567   "row": 21695568  },569  {570   "path": "utils/plotting.py",571   "sha256": "c56c70d69eeaee8cb62121f20f0fcbed1be61159bf1c0b41ba6a52698f9fe10b",572   "language": "Python",573   "lines": 3400,574   "truncated": false,575   "block": 21,576   "row": 524577  },578  {579   "path": "utils/statsalg.py",580   "sha256": "b95c3714b65d2bb88b8b62f03a9afbbbd61643d08151cf887b459f659d173bf4",581   "language": "Python",582   "lines": 1710,583   "truncated": false,584   "block": 21,585   "row": 431586  }587 ]588}