Code

Task denoising method dca#431

Code

Merged

scottgigante-immunai merged 189 commits intoopenproblems-bio:mainopenproblems-bio/openproblems:mainfrom wes-lewis:task-denoising-method-dcawes-lewis/SingleCellOpenProblems:task-denoising-method-dcaCopy head branch name to clipboardJul 13, 2022

+78-3

Commits

Commits on Mar 22, 2021

• Create alra.py

  Show description for dc0c756
  wes-lewis

  authored
  dc0c756

  Copy full SHA for dc0c756

• pre-commit

  github-actions[bot]

  committed
  6b19b08

  Copy full SHA for 6b19b08

Commits on Mar 16, 2022

• import alra

  scottgigante-immunai

  committed
  8d922dc

  Copy full SHA for 8d922dc

• pre-commit

  github-actions[bot]

  committed
  431110e

  Copy full SHA for 431110e

• set alra version

  scottgigante-immunai

  committed
  72b04e8

  Copy full SHA for 72b04e8

• Merge branch 'scottgigante/bugfix/alra_import' of github.com:scottgigante-immunai/openproblems into scottgigante/bugfix/alra_import

  scottgigante-immunai

  committed
  41246b7

  Copy full SHA for 41246b7

• Merge branch 'main' into scottgigante/bugfix/alra_import

  scottgigante-immunai

  committed
  9e88b0b

  Copy full SHA for 9e88b0b

Commits on Mar 17, 2022

• split up alra oneliner

  scottgigante-immunai

  committed
  718dd93

  Copy full SHA for 718dd93

• debug

  scottgigante-immunai

  committed
  09f2a4e

  Copy full SHA for 09f2a4e

• fix syntax error

  scottgigante-immunai

  committed
  9616ee7

  Copy full SHA for 9616ee7

• pre-commit

  github-actions[bot]

  committed
  21835a3

  Copy full SHA for 21835a3

• use dgCMatrix

  scottgigante-immunai

  committed
  3f8afb7

  Copy full SHA for 3f8afb7

• Merge branch 'scottgigante/bugfix/alra_import' of github.com:scottgigante-immunai/openproblems into scottgigante/bugfix/alra_import

  scottgigante-immunai

  committed
  01e904a

  Copy full SHA for 01e904a

• Merge branch 'main' into scottgigante/bugfix/alra_import

  scottgigante

  authored
  5936885

  Copy full SHA for 5936885

Commits on Mar 29, 2022

• output is stored in obsm

  scottgigante-immunai

  committed
  f776042

  Copy full SHA for f776042

• remove prints

  scottgigante-immunai

  committed
  a45ebb4

  Copy full SHA for a45ebb4

Commits on Apr 1, 2022

• Merge branch 'main' into scottgigante/bugfix/alra_import

  scottgigante-immunai

  committed
  29d1ebc

  Copy full SHA for 29d1ebc

Commits on Apr 7, 2022

• Merge branch 'main' into scottgigante/bugfix/alra_import

  scottgigante-immunai

  authored
  6cb82e5

  Copy full SHA for 6cb82e5

Commits on Apr 11, 2022

• Merge branch 'method-alra' into scottgigante/bugfix/alra_import

  wes-lewis

  authored
  47d4147

  Copy full SHA for 47d4147

• pre-commit

  github-actions[bot]

  committed
  13a7c0b

  Copy full SHA for 13a7c0b

• Merge pull request #1 from scottgigante-immunai/scottgigante/bugfix/alra_import

  Show description for 858065a
  wes-lewis

  authored
  858065a

  Copy full SHA for 858065a

Commits on Apr 12, 2022

• Merge branch 'main' into method-alra

  scottgigante-immunai

  authored
  7fe93fb

  Copy full SHA for 7fe93fb

Commits on Apr 19, 2022

• Update alra.py

  Show description for 655d1ec
  wes-lewis

  authored
  655d1ec

  Copy full SHA for 655d1ec

• fix csr casting

  wes-lewis

  authored
  c8a28af

  Copy full SHA for c8a28af

• Update alra.py

  Show description for abe564c
  wes-lewis

  authored
  abe564c

  Copy full SHA for abe564c

• pre-commit

  github-actions[bot]

  committed
  00e3b12

  Copy full SHA for 00e3b12

• add ValueError

  wes-lewis

  authored
  b31052c

  Copy full SHA for b31052c

• pre-commit

  github-actions[bot]

  committed
  c7665a2

  Copy full SHA for c7665a2

• simplify ValueError to avoid errors

  wes-lewis

  authored
  3104532

  Copy full SHA for 3104532

• pre-commit

  github-actions[bot]

  committed
  0a6bd4e

  Copy full SHA for 0a6bd4e

Commits on Apr 20, 2022

• cast to array for MSE

  Show description for 3143e25
  wes-lewis

  authored
  3143e25

  Copy full SHA for 3143e25

• pre-commit

  github-actions[bot]

  committed
  a18f887

  Copy full SHA for a18f887

Commits on Apr 25, 2022

• separate error line functions

  Show description for 8776950
  wes-lewis

  authored
  8776950

  Copy full SHA for 8776950

Commits on Apr 26, 2022

• Remove to_array()

  wes-lewis

  authored
  0070c9d

  Copy full SHA for 0070c9d

• pre-commit

  github-actions[bot]

  committed
  6b0386f

  Copy full SHA for 6b0386f

Commits on May 2, 2022

• Merge branch 'main' into method-alra

  scottgigante-immunai

  authored
  4e2e7c2

  Copy full SHA for 4e2e7c2

Commits on May 5, 2022

• Merge branch 'main' into method-alra

  scottgigante-immunai

  authored
  f18319c

  Copy full SHA for f18319c

Commits on May 9, 2022

• try casting to a matrix one more time

  wes-lewis

  authored
  8702150

  Copy full SHA for 8702150

• notate that wes' ALRA fork must be used instead

  wes-lewis

  authored
  38f6ee6

  Copy full SHA for 38f6ee6

• pre-commit

  github-actions[bot]

  committed
  87cf784

  Copy full SHA for 87cf784

• source from wes' code

  wes-lewis

  authored
  f978871

  Copy full SHA for f978871

• Merge branch 'main' into method-alra

  scottgigante-immunai

  authored
  36fb615

  Copy full SHA for 36fb615

• fix URL

  wes-lewis

  authored
  2bcfb8c

  Copy full SHA for 2bcfb8c

Commits on May 10, 2022

• shorten line lengths

  scottgigante-immunai

  authored
  3e54ab7

  Copy full SHA for 3e54ab7

• Check output is ndarray

  scottgigante-immunai

  authored
  62f8359

  Copy full SHA for 62f8359

Commits on May 13, 2022

• Merge branch 'main' into method-alra

  scottgigante-immunai

  authored
  06db9eb

  Copy full SHA for 06db9eb

Commits on May 14, 2022

• Fix typo

  scottgigante-immunai

  authored
  8c4f17c

  Copy full SHA for 8c4f17c

• Return dense data

  scottgigante-immunai

  authored
  0649df5

  Copy full SHA for 0649df5

• don't need tocsr now that the data is dense

  scottgigante-immunai

  authored
  e5d4228

  Copy full SHA for e5d4228

• Merge branch 'main' into method-alra

  scottgigante-immunai

  authored
  bc40e57

  Copy full SHA for bc40e57

• Return directly to denoised

  scottgigante-immunai

  authored
  2e774d1

  Copy full SHA for 2e774d1

• code cleanup

  scottgigante-immunai

  authored
  4bacd02

  Copy full SHA for 4bacd02

• Revert debugging

  scottgigante-immunai

  authored
  710d55f

  Copy full SHA for 710d55f

• Don't edit adata.obsm['train']

  scottgigante-immunai

  authored
  9c50ef0

  Copy full SHA for 9c50ef0

• access train_norm

  scottgigante-immunai

  authored
  14d3ca3

  Copy full SHA for 14d3ca3

• Add warning about editing adata.obsm['train']

  scottgigante-immunai

  authored
  856b45f

  Copy full SHA for 856b45f

• pre-commit

  github-actions[bot]

  committed
  438b208

  Copy full SHA for 438b208

• check train and test are not modified

  scottgigante-immunai

  authored
  4c8caaf

  Copy full SHA for 4c8caaf

• pre-commit

  github-actions[bot]

  committed
  4d14a4c

  Copy full SHA for 4d14a4c

• Retry ALRA on failure

  scottgigante-immunai

  authored
  4153803

  Copy full SHA for 4153803

• pre-commit

  github-actions[bot]

  committed
  26a3299

  Copy full SHA for 26a3299

• Switch t(as.matrix()) order

  scottgigante-immunai

  authored
  7e818f4

  Copy full SHA for 7e818f4

• Check dense data

  scottgigante-immunai

  authored
  3a59d98

  Copy full SHA for 3a59d98

• Return sparse data

  scottgigante-immunai

  authored
  11f7290

  Copy full SHA for 11f7290

• Check input data is sparse

  scottgigante-immunai

  authored
  ee148d1

  Copy full SHA for ee148d1

• Fix typo

  scottgigante-immunai

  authored
  1ff077e

  Copy full SHA for 1ff077e

• pre-commit

  github-actions[bot]

  committed
  b7fa68b

  Copy full SHA for b7fa68b

• Don't send the full AnnData to R

  scottgigante-immunai

  authored
  91503da

  Copy full SHA for 91503da

• Expect sparse input, dense array output

  scottgigante-immunai

  authored
  ff7a7a4

  Copy full SHA for ff7a7a4

• train and test must be floats

  scottgigante-immunai

  authored
  a97aa51

  Copy full SHA for a97aa51

• Convert back to float

  scottgigante-immunai

  authored
  73121bd

  Copy full SHA for 73121bd

• Fail on final attempt

  scottgigante-immunai

  authored
  a9754aa

  Copy full SHA for a9754aa

• put the retry inside python

  scottgigante-immunai

  authored
  6c5bd78

  Copy full SHA for 6c5bd78

• Remove the retry from R

  scottgigante-immunai

  authored
  7c52f57

  Copy full SHA for 7c52f57

• pre-commit

  github-actions[bot]

  committed
  ba7c4f5

  Copy full SHA for ba7c4f5

Commits on May 15, 2022

• layers['counts'] might not be sparse

  scottgigante-immunai

  authored
  5a7f1da

  Copy full SHA for 5a7f1da

• pre-commit

  github-actions[bot]

  committed
  71e1a98

  Copy full SHA for 71e1a98

• Log error each time

  scottgigante-immunai

  authored
  a9bffa4

  Copy full SHA for a9bffa4

• import logging

  scottgigante-immunai

  authored
  4344cc7

  Copy full SHA for 4344cc7

• pre-commit

  github-actions[bot]

  committed
  ba9e877

  Copy full SHA for ba9e877

• Better way to check matrices

  scottgigante-immunai

  authored
  d19a78b

  Copy full SHA for d19a78b

• pre-commit

  github-actions[bot]

  committed
  56fbf5a

  Copy full SHA for 56fbf5a

• fix array equal comparison

  scottgigante-immunai

  authored
  dfa2874

  Copy full SHA for dfa2874

• add explicit comment

  scottgigante-immunai

  authored
  1803505

  Copy full SHA for 1803505

• More explicit toarray

  scottgigante-immunai

  authored
  ab39e50

  Copy full SHA for ab39e50

• Can't check for untouched train/test

  scottgigante-immunai

  authored
  1abb2b8

  Copy full SHA for 1abb2b8

• Don't import scprep

  scottgigante-immunai

  authored
  2bb2414

  Copy full SHA for 2bb2414

• Merge branch 'main' into method-alra

  scottgigante-immunai

  authored
  6f21958

  Copy full SHA for 6f21958

• Just use a fixed target_sum

  scottgigante-immunai

  authored
  70837ee

  Copy full SHA for 70837ee

• Sample data should match API

  scottgigante-immunai

  authored
  b23945b

  Copy full SHA for b23945b

• pre-commit

  github-actions[bot]

  committed
  b984c90

  Copy full SHA for b984c90

Commits on May 16, 2022

• flake8

  scottgigante-immunai

  authored
  caded4a

  Copy full SHA for caded4a

• no_denoising still needs to densify

  scottgigante-immunai

  authored
  7b8660b

  Copy full SHA for 7b8660b

• convert to csc

  scottgigante-immunai

  authored
  0987352

  Copy full SHA for 0987352

• pre-commit

  github-actions[bot]

  committed
  55921bd

  Copy full SHA for 55921bd

• Convert to csr

  scottgigante-immunai

  authored
  208a0d3

  Copy full SHA for 208a0d3

• conversion of sparse doesn't work, try anndata

  scottgigante-immunai

  authored
  2acd17d

  Copy full SHA for 2acd17d

• accept sce

  scottgigante-immunai

  authored
  8dfd0c8

  Copy full SHA for 8dfd0c8

• pre-commit

  github-actions[bot]

  committed
  cad5391

  Copy full SHA for cad5391

• Convert to dense

  scottgigante-immunai

  authored
  bff9fa4

  Copy full SHA for bff9fa4

• pre-commit

  github-actions[bot]

  committed
  1fdaf16

  Copy full SHA for 1fdaf16

• Convert to dense

  scottgigante-immunai

  authored
  b63619a

  Copy full SHA for b63619a

• pre-commit

  github-actions[bot]

  committed
  b71d239

  Copy full SHA for b71d239

• Try .tocsr()

  scottgigante-immunai

  authored
  35ab901

  Copy full SHA for 35ab901

Commits on May 17, 2022

• Create dca.py

  wes-lewis

  authored
  7dba013

  Copy full SHA for 7dba013

• pre-commit

  github-actions[bot]

  committed
  ff029ab

  Copy full SHA for ff029ab

• Create dca.py

  wes-lewis

  authored
  bbaf46a

  Copy full SHA for bbaf46a

• pre-commit

  github-actions[bot]

  committed
  221f417

  Copy full SHA for 221f417

• add dca

  wes-lewis

  authored
  cf95450

  Copy full SHA for cf95450

• add dca

  wes-lewis

  authored
  2b71c93

  Copy full SHA for 2b71c93

• Update dca.py

  wes-lewis

  authored
  ff44c8f

  Copy full SHA for ff44c8f

• Update dca.py

  Show description for 97f47ad
  wes-lewis

  authored
  97f47ad

  Copy full SHA for 97f47ad

• pre-commit

  github-actions[bot]

  committed
  82b28d3

  Copy full SHA for 82b28d3

• Update dca.py

  wes-lewis

  authored
  584ea3f

  Copy full SHA for 584ea3f

• Update dca.py

  wes-lewis

  authored
  e214e98

  Copy full SHA for e214e98

• Delete dca.py

  wes-lewis

  authored
  87e3c09

  Copy full SHA for 87e3c09

• Update requirements.txt

  wes-lewis

  authored
  6c80a67

  Copy full SHA for 6c80a67

• Update __init__.py

  wes-lewis

  authored
  72209dd

  Copy full SHA for 72209dd

• pre-commit

  github-actions[bot]

  committed
  6c5d803

  Copy full SHA for 6c5d803

• Update dca.py

  Show description for 84a9ae7
  wes-lewis

  authored
  84a9ae7

  Copy full SHA for 84a9ae7

• pre-commit

  github-actions[bot]

  committed
  551201d

  Copy full SHA for 551201d

• Update dca.py

  wes-lewis

  authored
  81cd986

  Copy full SHA for 81cd986

• pre-commit

  github-actions[bot]

  committed
  61064f4

  Copy full SHA for 61064f4

Commits on May 19, 2022

• put dca import inside method

  wes-lewis

  authored
  6e9e03e

  Copy full SHA for 6e9e03e

• pre-commit

  github-actions[bot]

  committed
  25d0869

  Copy full SHA for 25d0869

• Update dca.py

  wes-lewis

  authored
  b0c7c00

  Copy full SHA for b0c7c00

Commits on Jun 7, 2022

• Merge branch 'method-alra' of https://github.com/wes-lewis/SingleCellOpenProblems oof q

  wes-lewis

  committed
  6917611

  Copy full SHA for 6917611

• Merge branch 'master' into task-denoising-method-dca

  wes-lewis

  committed
  d5513fb

  Copy full SHA for d5513fb

• Merge pull request #7 from openproblems-bio/main

  Show description for 9d36c83
  wes-lewis

  authored
  9d36c83

  Copy full SHA for 9d36c83

Commits on Jun 13, 2022

• Update requirements.txt

  wes-lewis

  authored
  51af989

  Copy full SHA for 51af989

• pre-commit

  github-actions[bot]

  committed
  792ae3c

  Copy full SHA for 792ae3c

• Merge branch 'main' into task-denoising-method-dca

  scottgigante-immunai

  authored
  181fb62

  Copy full SHA for 181fb62

• Create README.md

  wes-lewis

  authored
  18eb84c

  Copy full SHA for 18eb84c

• Update README.md

  wes-lewis

  authored
  a2604e3

  Copy full SHA for a2604e3

• Create Dockerfile

  wes-lewis

  authored
  72ef3dd

  Copy full SHA for 72ef3dd

• Create requirements.txt

  wes-lewis

  authored
  4c815ed

  Copy full SHA for 4c815ed

• pre-commit

  github-actions[bot]

  committed
  ba764e2

  Copy full SHA for ba764e2

• Create requirements.txt

  wes-lewis

  authored
  3d5d5f5

  Copy full SHA for 3d5d5f5

• pre-commit

  github-actions[bot]

  committed
  02a103f

  Copy full SHA for 02a103f

Commits on Jun 14, 2022

• remove dca from python-extras readme

  wes-lewis

  authored
  70c9c08

  Copy full SHA for 70c9c08

• fix image specification

  wes-lewis

  authored
  f101cd6

  Copy full SHA for f101cd6

• remove dca from here

  wes-lewis

  authored
  f2b94b9

  Copy full SHA for f2b94b9

• Update Dockerfile

  wes-lewis

  authored
  ea5765d

  Copy full SHA for ea5765d

• pin dca 0.3*

  Show description for 5c82a75
  wes-lewis

  authored
  5c82a75

  Copy full SHA for 5c82a75

• Update dca.py

  wes-lewis

  authored
  eb7c857

  Copy full SHA for eb7c857

• Update __init__.py

  wes-lewis

  authored
  6410a87

  Copy full SHA for 6410a87

• Update requirements.txt

  wes-lewis

  authored
  3f90c05

  Copy full SHA for 3f90c05

• Update README.md

  wes-lewis

  authored
  cb21310

  Copy full SHA for cb21310

• Update README.md

  wes-lewis

  authored
  e15b50b

  Copy full SHA for e15b50b

• Update README.md

  wes-lewis

  authored
  45c68b9

  Copy full SHA for 45c68b9

• Update requirements.txt

  wes-lewis

  authored
  c1c22cf

  Copy full SHA for c1c22cf

• Update check_version api

  scottgigante-immunai

  authored
  1aa43c8

  Copy full SHA for 1aa43c8

• Merge branch 'main' into task-denoising-method-dca

  scottgigante-immunai

  authored
  6d3840d

  Copy full SHA for 6d3840d

• Require pyyaml==5.4.1 to prevent kopt error

  Show description for e1cc3a3
  scottgigante-immunai

  authored
  e1cc3a3

  Copy full SHA for e1cc3a3

• pre-commit

  github-actions[bot]

  committed
  7c84ae5

  Copy full SHA for 7c84ae5

• Fix keras version

  scottgigante-immunai

  authored
  3dbc058

  Copy full SHA for 3dbc058

Commits on Jun 15, 2022

• Update dca.py

  Show description for 193d724
  wes-lewis

  authored
  193d724

  Copy full SHA for 193d724

• pre-commit

  github-actions[bot]

  committed
  4838543

  Copy full SHA for 4838543

• Update dca.py

  wes-lewis

  authored
  40a6f5d

  Copy full SHA for 40a6f5d

• pre-commit

  github-actions[bot]

  committed
  81a66c4

  Copy full SHA for 81a66c4

Commits on Jun 20, 2022

• Merge pull request #9 from openproblems-bio/main

  Show description for fa8de52
  wes-lewis

  authored
  fa8de52

  Copy full SHA for fa8de52

Commits on Jun 21, 2022

• Update dca.py

  wes-lewis

  authored
  dd57e02

  Copy full SHA for dd57e02

• pre-commit

  github-actions[bot]

  committed
  d67622b

  Copy full SHA for d67622b

• Update dca.py

  wes-lewis

  authored
  7e4e68f

  Copy full SHA for 7e4e68f

• pre-commit

  github-actions[bot]

  committed
  019220f

  Copy full SHA for 019220f

• Add test args

  wes-lewis

  authored
  bd497c9

  Copy full SHA for bd497c9

• Merge branch 'main' into task-denoising-method-dca

  scottgigante-immunai

  authored
  e20b6c7

  Copy full SHA for e20b6c7

Commits on Jun 27, 2022

• fix thread count and pass epochs to dca

  wes-lewis

  authored
  fd45114

  Copy full SHA for fd45114

• pre-commit

  github-actions[bot]

  committed
  5811dbb

  Copy full SHA for 5811dbb

• add in masking

  wes-lewis

  authored
  4ceed52

  Copy full SHA for 4ceed52

• pre-commit

  github-actions[bot]

  committed
  8df6f8a

  Copy full SHA for 8df6f8a

• Merge branch 'main' into task-denoising-method-dca

  scottgigante-immunai

  authored
  d5b946b

  Copy full SHA for d5b946b

Commits on Jun 28, 2022

• Update README.md

  wes-lewis

  authored
  6c63c97

  Copy full SHA for 6c63c97

• Update README.md

  wes-lewis

  authored
  cd81217

  Copy full SHA for cd81217

• add removezeros and insert_at functions

  wes-lewis

  authored
  cac88e7

  Copy full SHA for cac88e7

• pre-commit

  github-actions[bot]

  committed
  ab1fcfb

  Copy full SHA for ab1fcfb

• Update dca.py

  wes-lewis

  authored
  ca0e758

  Copy full SHA for ca0e758

• pre-commit

  github-actions[bot]

  committed
  73e4355

  Copy full SHA for 73e4355

Commits on Jul 5, 2022

• Remove zero counts from train data

  scottgigante-immunai

  authored
  a3d423d

  Copy full SHA for a3d423d

• Remove filtering from DCA

  scottgigante-immunai

  authored
  ecfbc67

  Copy full SHA for ecfbc67

• Remove unused code

  scottgigante-immunai

  authored
  852a5dd

  Copy full SHA for 852a5dd

• pre-commit

  github-actions[bot]

  committed
  77f4de9

  Copy full SHA for 77f4de9

• Don't need a line break

  scottgigante-immunai

  authored
  234090b

  Copy full SHA for 234090b

• Update utils.py

  scottgigante-immunai

  authored
  7667668

  Copy full SHA for 7667668

• pre-commit

  github-actions[bot]

  committed
  d07e2a1

  Copy full SHA for d07e2a1

Commits on Jul 12, 2022

• Use epochs if passed

  scottgigante-immunai

  authored
  1da6d7c

  Copy full SHA for 1da6d7c

• Fix metric descriptions

  scottgigante-immunai

  authored
  4475d55

  Copy full SHA for 4475d55

• Merge branch 'main' into task-denoising-method-dca

  scottgigante-immunai

  authored
  001bbf8

  Copy full SHA for 001bbf8

• don't compute coverage on non-test args

  scottgigante-immunai

  authored
  2749be8

  Copy full SHA for 2749be8