Code

Zoo#4

Code

Open

yuanqing-wang wants to merge 103 commits intoyuanqing-wang:mainyuanqing-wang/malt:mainfrom choderalab:zoochoderalab/malt:zooCopy head branch name to clipboard

+1,121-1,245

Commits

Commits on Feb 5, 2022

• Adding pIC50 dataset.

  miretchin

  committed
  99f45f6

  Copy full SHA for 99f45f6

Commits on Feb 6, 2022

• Adding a sequential acquisition notebook and fixing a deprecation error.

  miretchin

  committed
  426c234

  Copy full SHA for 426c234

• Experimenting with Thompson Sampling.

  miretchin

  committed
  7c16580

  Copy full SHA for 7c16580

• Adding thompson sampling.

  miretchin

  committed
  3ad34c6

  Copy full SHA for 3ad34c6

Commits on Feb 7, 2022

• Adding random and thompson sampling.

  miretchin

  committed
  d36fb1d

  Copy full SHA for d36fb1d

• Verified random now works.

  miretchin

  committed
  58d1704

  Copy full SHA for 58d1704

• Added a random player without model.

  miretchin

  committed
  a0472c9

  Copy full SHA for a0472c9

• Added thompson sampling policy.

  miretchin

  committed
  90f4809

  Copy full SHA for 90f4809

Commits on Feb 11, 2022

• New data structure that has a more flexible �atch and �iew for use in multi-output training loops.

  miretchin

  committed
  42d20af

  Copy full SHA for 42d20af

Commits on Feb 15, 2022

• Adding a little interactive playground for understanding use-cases of our new Molecule data structure.

  miretchin

  committed
  d5a6472

  Copy full SHA for d5a6472

• Generalized the Point object into a Molecule object.

  miretchin

  committed
  5f10de1

  Copy full SHA for 5f10de1

Commits on Feb 16, 2022

• Generalizing the Molecule, adding slicing, enforcing values of same length.

  miretchin

  committed
  2026f21

  Copy full SHA for 2026f21

• Made Molecule base class less opinionated. Just accepts a dictionary and that's all.

  miretchin

  committed
  4b104d1

  Copy full SHA for 4b104d1

• Further generalize the Molecule base class.

  miretchin

  committed
  22de00a

  Copy full SHA for 22de00a

Commits on Feb 17, 2022

• Fixed batch to work with new Molecule class.

  miretchin

  committed
  8a116ab

  Copy full SHA for 8a116ab

• Removed the commented out __getitem__ that was old.

  miretchin

  committed
  85cb907

  Copy full SHA for 85cb907

• Generalized dataset to handle either a Molecule or AssayedMolecule (only difference is the batching function, which comes from malt.data.utils.

  miretchin

  committed
  a0076c7

  Copy full SHA for a0076c7

Commits on Feb 18, 2022

• Added tests that pass.

  miretchin

  committed
  1d9f867

  Copy full SHA for 1d9f867

Commits on Feb 19, 2022

• Creating a Gpytorch playground.

  miretchin

  committed
  27c6449

  Copy full SHA for 27c6449

• removed some data files, added a gpytorch playground.

  miretchin

  committed
  f178385

  Copy full SHA for f178385

Commits on Feb 20, 2022

• Created a minimal example from the GPyTorch website for exact GPs with feature extractors.

  miretchin

  committed
  0ec6651

  Copy full SHA for 0ec6651

• Got our DGL graph conv nets working with GPytorch for exact GPs!

  miretchin

  committed
  9b6935a

  Copy full SHA for 9b6935a

Commits on Feb 22, 2022

• Merge pull request #1 from choderalab/bayesopt

  Show description for 5685de7
  miretchin

  authored
  5685de7

  Copy full SHA for 5685de7

• Fixed datastructure and added some scripts for demonstrating pIC50 and data structures.

  miretchin

  committed
  d156ae2

  Copy full SHA for d156ae2

• Merge pull request #2 from choderalab/data

  Show description for c9cd248
  miretchin

  authored
  c9cd248

  Copy full SHA for c9cd248

• Delete lipophilicity_dglgraph.bin

  Show description for 54ce788
  miretchin

  authored
  54ce788

  Copy full SHA for 54ce788

• Added a better collate function.

  miretchin

  committed
  00f0fdd

  Copy full SHA for 00f0fdd

• Update trainer.py

  Show description for c9ede1d
  miretchin

  authored
  c9ede1d

  Copy full SHA for c9ede1d

• Merge pull request #3 from choderalab/data

  Show description for e0d6a9c
  miretchin

  authored
  e0d6a9c

  Copy full SHA for e0d6a9c

• Updating the exact GP notebook for GPyTorch.

  miretchin

  committed
  dbc0961

  Copy full SHA for dbc0961

Commits on Mar 26, 2022

• Fixed the tests!

  miretchin

  committed
  f85b656

  Copy full SHA for f85b656

• Merge branch 'main' into gpytorch

  miretchin

  authored
  8f84ab7

  Copy full SHA for 8f84ab7

Commits on Mar 28, 2022

• Fixed the training loop to accommodate new inclusive API for GPyTorch and hardcoded model.

  miretchin

  committed
  8dfdade

  Copy full SHA for 8dfdade

Commits on Apr 10, 2022

• Added some scripts for comparing hardcoded vs. GPyTorch. Biggest takeaway -> the dimensionality of the target tensor matters a lot.

  miretchin

  committed
  6c16601

  Copy full SHA for 6c16601

Commits on May 8, 2022

• Created gpytorch tests! Fixed the training loop, player, regressor, and data APIs.

  miretchin

  committed
  9d57d7d

  Copy full SHA for 9d57d7d

• Added more working tests.

  miretchin

  committed
  d787948

  Copy full SHA for d787948

Commits on May 29, 2022

• Fixed a bunch of tests. Still a few that need to be fixed.

  miretchin

  committed
  afc7f14

  Copy full SHA for afc7f14

Commits on May 30, 2022

• Fixed ALL the tests! The only thing we need to investigate is the appending to Dataset(). It somehow sets a new class init signature and every time after that if you call Dataset(), it'll give you …

  Show description for 9000a67
  miretchin

  committed
  9000a67

  Copy full SHA for 9000a67

• Removed binary files.

  miretchin

  committed
  e05d6db

  Copy full SHA for e05d6db

Commits on May 31, 2022

• Make is so that you can define the exact GP models without providing data. Also, fixed the training loop and benchmarked using some new notebooks. Also added multi-objective stepping.

  miretchin

  committed
  1689891

  Copy full SHA for 1689891

Commits on Jun 13, 2022

• delete binary

  yuanqing-wang

  committed
  e7c8c30

  Copy full SHA for e7c8c30

• added doctests to molecule

  yuanqing-wang

  committed
  066eeb7

  Copy full SHA for 066eeb7

Commits on Jun 14, 2022

• dataset docstring

  yuanqing-wang

  committed
  7a56b45

  Copy full SHA for 7a56b45

• added doctests for dataset

  yuanqing-wang

  committed
  808b769

  Copy full SHA for 808b769

• delete scripts

  yuanqing-wang

  committed
  09dc51b

  Copy full SHA for 09dc51b

Commits on Jun 15, 2022

• core function

  yuanqing-wang

  committed
  14dbf8a

  Copy full SHA for 14dbf8a

• make y a special key

  yuanqing-wang

  committed
  99d705a

  Copy full SHA for 99d705a

• simplify dataset implementation

  yuanqing-wang

  committed
  9daa8b4

  Copy full SHA for 9daa8b4

• dataset tests passed

  yuanqing-wang

  committed
  9bd78cd

  Copy full SHA for 9bd78cd

• representation example

  yuanqing-wang

  committed
  b52d13c

  Copy full SHA for b52d13c

• get rid of hard-coded version if that's no longered needed

  yuanqing-wang

  committed
  fbfe32e

  Copy full SHA for fbfe32e

• deleted hard-code gpytorch

  yuanqing-wang

  committed
  b851f36

  Copy full SHA for b851f36

• keep data 1d for now

  yuanqing-wang

  committed
  ceb224b

  Copy full SHA for ceb224b

Commits on Jun 20, 2022

• get rid of the hand-coded one

  yuanqing-wang

  committed
  d038a81

  Copy full SHA for d038a81

• get rid of marginal likelihood

  yuanqing-wang

  committed
  7e2723e

  Copy full SHA for 7e2723e

• passed tests

  yuanqing-wang

  committed
  99f0674

  Copy full SHA for 99f0674

Commits on Jun 21, 2022

• rename CI

  yuanqing-wang

  committed
  e025ac5

  Copy full SHA for e025ac5

• expand dimensions in NN regression

  yuanqing-wang

  committed
  78f2084

  Copy full SHA for 78f2084

• training script

  yuanqing-wang

  committed
  3f561a3

  Copy full SHA for 3f561a3

Commits on Jun 22, 2022

• Merge pull request #5 from choderalab/refactor

  Show description for 1ba4725
  yuanqing-wang

  authored
  1ba4725

  Copy full SHA for 1ba4725

• Merge pull request #4 from choderalab/gpytorch

  Show description for 30e2e0e
  yuanqing-wang

  authored
  30e2e0e

  Copy full SHA for 30e2e0e

Commits on Oct 5, 2022

• supervised test

  yuanqing-wang

  committed
  1753cf6

  Copy full SHA for 1753cf6

• Removing reference to unexisting conda-installer in matrix.

  ijpulidos

  committed
  cfad8a0

  Copy full SHA for cfad8a0

• Merge pull request #6 from choderalab/fix-ci

  Show description for 3237750
  yuanqing-wang

  authored
  3237750

  Copy full SHA for 3237750

• get rid of metrics

  yuanqing-wang

  committed
  00a16bb

  Copy full SHA for 00a16bb

• Merge branch 'main' of https://github.com/choderalab/malt

  yuanqing-wang

  committed
  c05ccfa

  Copy full SHA for c05ccfa

• get rid of rbf

  yuanqing-wang

  committed
  ceb368f

  Copy full SHA for ceb368f

Commits on Oct 7, 2022

• feed train_targets

  yuanqing-wang

  committed
  cefcc5a

  Copy full SHA for cefcc5a

Commits on Oct 12, 2022

• refactor to hide likelihood

  yuanqing-wang

  committed
  e4ba727

  Copy full SHA for e4ba727

• passing tests

  yuanqing-wang

  committed
  b9d4761

  Copy full SHA for b9d4761

• passing tests

  yuanqing-wang

  committed
  7c5ca65

  Copy full SHA for 7c5ca65

• clean up trainer

  yuanqing-wang

  committed
  2e2b9cc

  Copy full SHA for 2e2b9cc

• supervised training script

  yuanqing-wang

  committed
  35d8946

  Copy full SHA for 35d8946

• Merge pull request #7 from choderalab/gp_debug

  Show description for 9e24911
  yuanqing-wang

  authored
  9e24911

  Copy full SHA for 9e24911

Commits on Oct 13, 2022

• running scripts

  yuanqing-wang

  committed
  7054da4

  Copy full SHA for 7054da4

• scripts

  yuanqing-wang

  committed
  89ec4b8

  Copy full SHA for 89ec4b8

• lsf scripts

  yuanqing-wang

  committed
  8ddb4de

  Copy full SHA for 8ddb4de

• scripts

  yuanqing-wang

  committed
  3aa28d0

  Copy full SHA for 3aa28d0

• Merge pull request #8 from choderalab/gp_debug

  Show description for 4373468
  yuanqing-wang

  authored
  4373468

  Copy full SHA for 4373468

• scrtips

  yuanqing-wang

  committed
  88e204e

  Copy full SHA for 88e204e

Commits on Oct 16, 2022

• NN debug

  yuanqing-wang

  committed
  6dea83f

  Copy full SHA for 6dea83f

• use pip, not conda

  yuanqing-wang

  committed
  c5ddead

  Copy full SHA for c5ddead

• Merge pull request #9 from choderalab/gp_debug

  Show description for eb28c86
  yuanqing-wang

  authored
  eb28c86

  Copy full SHA for eb28c86

• dist

  yuanqing-wang

  committed
  f42fb78

  Copy full SHA for f42fb78

• old pep440

  yuanqing-wang

  committed
  c9cd045

  Copy full SHA for c9cd045

Commits on Oct 17, 2022

• unsqueeze

  yuanqing-wang

  committed
  a3fd514

  Copy full SHA for a3fd514

• no thompson sampling to pass tests

  yuanqing-wang

  committed
  d888ad5

  Copy full SHA for d888ad5

• require gpytorch

  yuanqing-wang

  committed
  e9e2cc5

  Copy full SHA for e9e2cc5

• pytest + github actions

  yuanqing-wang

  committed
  7b97243

  Copy full SHA for 7b97243

• fix docs

  yuanqing-wang

  committed
  5a656d1

  Copy full SHA for 5a656d1

• no need for a random player

  yuanqing-wang

  committed
  70b6b35

  Copy full SHA for 70b6b35

• passing tests

  yuanqing-wang

  committed
  658bd48

  Copy full SHA for 658bd48

• Update DOC.yml

  yuanqing-wang

  authored
  742ac29

  Copy full SHA for 742ac29

• Update setup.py

  yuanqing-wang

  authored
  70eb450

  Copy full SHA for 70eb450

• delete devtools

  yuanqing-wang

  committed
  e3e6f66

  Copy full SHA for e3e6f66

• Update index.rst

  yuanqing-wang

  authored
  678bdda

  Copy full SHA for 678bdda

• Update conf.py

  yuanqing-wang

  authored
  c967774

  Copy full SHA for c967774

• Update conf.py

  yuanqing-wang

  authored
  75b99b6

  Copy full SHA for 75b99b6

• documentation titles

  yuanqing-wang

  committed
  63ddfe8

  Copy full SHA for 63ddfe8

• model zoo

  yuanqing-wang

  committed
  1e843f3

  Copy full SHA for 1e843f3

• model zoo

  yuanqing-wang

  committed
  89f7b8d

  Copy full SHA for 89f7b8d

• fix imports

  yuanqing-wang

  committed
  5e6221a

  Copy full SHA for 5e6221a

Commits on Oct 18, 2022

• requirements

  yuanqing-wang

  committed
  59883bb

  Copy full SHA for 59883bb