univi 0.3.4__py3-none-any.whl

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Files changed (40) hide show
  1. univi/__init__.py +120 -0
  2. univi/__main__.py +5 -0
  3. univi/cli.py +60 -0
  4. univi/config.py +340 -0
  5. univi/data.py +345 -0
  6. univi/diagnostics.py +130 -0
  7. univi/evaluation.py +632 -0
  8. univi/hyperparam_optimization/__init__.py +17 -0
  9. univi/hyperparam_optimization/common.py +339 -0
  10. univi/hyperparam_optimization/run_adt_hparam_search.py +109 -0
  11. univi/hyperparam_optimization/run_atac_hparam_search.py +109 -0
  12. univi/hyperparam_optimization/run_citeseq_hparam_search.py +137 -0
  13. univi/hyperparam_optimization/run_multiome_hparam_search.py +145 -0
  14. univi/hyperparam_optimization/run_rna_hparam_search.py +111 -0
  15. univi/hyperparam_optimization/run_teaseq_hparam_search.py +146 -0
  16. univi/interpretability.py +399 -0
  17. univi/matching.py +394 -0
  18. univi/models/__init__.py +8 -0
  19. univi/models/decoders.py +249 -0
  20. univi/models/encoders.py +848 -0
  21. univi/models/mlp.py +36 -0
  22. univi/models/tokenizers.py +376 -0
  23. univi/models/transformer.py +249 -0
  24. univi/models/univi.py +1284 -0
  25. univi/objectives.py +46 -0
  26. univi/pipeline.py +194 -0
  27. univi/plotting.py +126 -0
  28. univi/trainer.py +478 -0
  29. univi/utils/__init__.py +5 -0
  30. univi/utils/io.py +621 -0
  31. univi/utils/logging.py +16 -0
  32. univi/utils/seed.py +18 -0
  33. univi/utils/stats.py +23 -0
  34. univi/utils/torch_utils.py +23 -0
  35. univi-0.3.4.dist-info/METADATA +908 -0
  36. univi-0.3.4.dist-info/RECORD +40 -0
  37. univi-0.3.4.dist-info/WHEEL +5 -0
  38. univi-0.3.4.dist-info/entry_points.txt +2 -0
  39. univi-0.3.4.dist-info/licenses/LICENSE +21 -0
  40. univi-0.3.4.dist-info/top_level.txt +1 -0
univi-0.3.4.dist-info/RECORD ADDED
@@ -0,0 +1,40 @@
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+ univi/__init__.py,sha256=dCXDyZMzyubquI0xAg8qT4QMOP3hDLUH8U5eztFThtY,3507
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+ univi/__main__.py,sha256=Q1J7RaaiIfYd6osp2TOiBiS4B8xc8ZCMVwFAOjEii1U,99
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+ univi/cli.py,sha256=bw2P17oPn1ZOHs0t3MDyoUgtnmGw3LORxWREOQBkx-I,2154
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+ univi/config.py,sha256=2heJGyNWEo0kReRT-DpY_O345x3xRm-IYBWEABM8fk4,13437
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+ univi/data.py,sha256=a52AeGVT_cmItO-9An6KzS6-bKTmBncdkjIPdWnGgIo,11795
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+ univi/diagnostics.py,sha256=kNpb6-S-obVrpzOm3Hv1Nsvm7K8VtI386lbebbU-Geg,4257
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+ univi/evaluation.py,sha256=zrrTV0aiQq8Cmldk6bgvbiaEunQG3bL__741Ts8SZKI,21906
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+ univi/interpretability.py,sha256=yM3VM-vRSf6Un_qFckZ5SQxVlVDvtWOe8RPndmHetR0,13896
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+ univi/matching.py,sha256=oZ4BzzUSQfkGpqTEzjBDnWbq6VfjugTgaLX3yT33hvY,11549
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+ univi/objectives.py,sha256=kLdkrBXPbLd6pUd89d1eqi16KbC4_Oi8n-YP9Pg3Tx0,1220
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+ univi/pipeline.py,sha256=Ks5aiHHv1eKOttyr-bCHXkoxc6wn1fH_pv9NloI38Hc,7044
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+ univi/plotting.py,sha256=cM6SeZqSt0A51pLjouyuhyCpRcIRBeRcpFHUwD_l6qg,3653
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+ univi/trainer.py,sha256=nT2aWgP0Mg13wYvozbeiJACmPZ68rAY6tPSDyv4ZveY,17639
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+ univi/hyperparam_optimization/__init__.py,sha256=SDpb3SolbLzwvMzOH7f9WkZG9Q-iEjpnmPtlF31rUFk,615
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+ univi/hyperparam_optimization/common.py,sha256=a1eerXhdXQFb1AFg5623Jz8-3QxNzVsOj5G5pkbeUbQ,10593
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+ univi/hyperparam_optimization/run_adt_hparam_search.py,sha256=8jkDtRIxT2gh-edx1CXknb_kBQC7FvjBLml4IPubaFo,3170
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+ univi/hyperparam_optimization/run_atac_hparam_search.py,sha256=jUjGb2XYyNmd0y-RZccImcigcPawjsSXR0NsiW9GTkA,3208
18
+ univi/hyperparam_optimization/run_citeseq_hparam_search.py,sha256=rg9c88nexNbHqScWuzQNGqBFxFr8zAitJ9w1SS6nafc,4204
19
+ univi/hyperparam_optimization/run_multiome_hparam_search.py,sha256=_xj-PASym2f4XM64EUyySt9TgBLpDU1fMkHzO3n-0uY,4550
20
+ univi/hyperparam_optimization/run_rna_hparam_search.py,sha256=Pk7s-CpOznutmGG35X_WkgHq2ycaQrtSpipmGjVKRCQ,3263
21
+ univi/hyperparam_optimization/run_teaseq_hparam_search.py,sha256=TzVAKrSeeFMMlmEKacR7w1ndvTsQQF5IrrIOb2pwkW4,4565
22
+ univi/models/__init__.py,sha256=xjf0-DwUbWNc7_eMvvWPt1RlCOKvLVlsb-sO89JE1Zc,260
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+ univi/models/decoders.py,sha256=PVNuRJcJaYQnVsZtT_2ZFgTjzps1ITJOsDQwlO0NKrU,7524
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+ univi/models/encoders.py,sha256=LYXYsmg_k9vWkqbm9f8QRsCqCQEG7wTpd9yQ8dcKxcA,33706
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+ univi/models/mlp.py,sha256=JCGh7RVUY02iyRUfUdmmJi8IJAKW3ui9N9UZbPSzsG8,1020
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+ univi/models/tokenizers.py,sha256=1hqIFtYn7b3ZiKYk8RD-dlZJQT2ps--4pC0oVis59I4,13219
27
+ univi/models/transformer.py,sha256=d9nwAynG8iktvsefJGQ1A9cJA-Spi_o4dSFwXRHNTVA,8678
28
+ univi/models/univi.py,sha256=k7GU1MlczwDufQK3TGl8bMq4iOKxXnP6nr3ngZWayBE,52980
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+ univi/utils/__init__.py,sha256=RR6XNh67LUrMxUPKehlMEPqClunltIDIFtpAfsMf04o,75
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+ univi/utils/io.py,sha256=n6DBt_gIKgKoGJ2CxcS7RESoRMpMm3EBC4sevzflJcA,23065
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+ univi/utils/logging.py,sha256=33cXm2X0qFbF8LoJOwAceo2kMvAgZOR_diyXAscskxg,497
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+ univi/utils/seed.py,sha256=7RLyNL2OP2nzOkfOo_xPh8ZOy5-Q9Sw_CtfQLyu9gGc,434
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+ univi/utils/stats.py,sha256=aU98m7Wi0uZgNhWMJJF7OZil0OIMhafuIgbBg3r_Px8,550
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+ univi/utils/torch_utils.py,sha256=EC7IES7kXmH9i1OoQ5IGHkHe8dd27j__xjmefXBe9QM,623
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+ univi-0.3.4.dist-info/licenses/LICENSE,sha256=8g2N0f8fv0iMFidEpfEYYkG7HCe4JvheBiZcWBEg5rQ,1082
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+ univi-0.3.4.dist-info/METADATA,sha256=tmpNUBV2ZgjOy8LzzZ3t-QInOeD00I_HJL7FXlHnQ1U,32530
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+ univi-0.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ univi-0.3.4.dist-info/entry_points.txt,sha256=hNsZh4I1722iYY9XugiAw6nL75pw9oTSdmb8Ak6XaM4,41
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+ univi-0.3.4.dist-info/top_level.txt,sha256=sVrcedBMzHmzCRqqF_L6SQCTeQ5W3QBP2rN1z9_dfGc,6
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+ univi-0.3.4.dist-info/RECORD,,
univi-0.3.4.dist-info/WHEEL ADDED
@@ -0,0 +1,5 @@
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+ Wheel-Version: 1.0
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+ Generator: setuptools (80.9.0)
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+ Root-Is-Purelib: true
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+ Tag: py3-none-any
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+
univi-0.3.4.dist-info/entry_points.txt ADDED
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+ [console_scripts]
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+ univi = univi.cli:main
univi-0.3.4.dist-info/licenses/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2025 Andrew J. Ashford
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the “Software”), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
univi-0.3.4.dist-info/top_level.txt ADDED
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+ univi