Code

Literature evaluation updates#127

Code

Open

bsantan wants to merge 20 commits intomainUCDenver-ccp/Cartoomics:mainfrom literature_evaluation_updatesUCDenver-ccp/Cartoomics:literature_evaluation_updatesCopy head branch name to clipboard

+101,412-115

Commits

Commits on May 29, 2024

• evaluate abstracts and full text

  bsantan

  committed
  11e7a5d

  Copy full SHA for 11e7a5d

• concept_idf_annotated file

  bsantan

  committed
  3cab92d

  Copy full SHA for 3cab92d

• literature comparison changes for abstract and full text

  bsantan

  committed
  6e03755

  Copy full SHA for 6e03755

Commits on Aug 19, 2024

• adding nourah's script for RoBERTa's embeddings

  lagillenwater

  committed
  c41423e

  Copy full SHA for c41423e

Commits on Aug 28, 2024

• testing bioBERT for gene similarity

  lagillenwater

  committed
  473a807

  Copy full SHA for 473a807

• testing RoBERT for gene similarity

  lagillenwater

  committed
  75df746

  Copy full SHA for 75df746

Commits on Sep 3, 2024

• added tests for other genes

  lagillenwater

  committed
  96240e4

  Copy full SHA for 96240e4

• added tests for other genes

  lagillenwater

  committed
  c7f177f

  Copy full SHA for c7f177f

• created test using a biomedically trained RoBERTa model

  lagillenwater

  committed
  f005f31

  Copy full SHA for f005f31

Commits on Sep 5, 2024

• created script for performing text embedding evaluations

  lagillenwater

  committed
  b3a3f70

  Copy full SHA for b3a3f70

• updated test script to test text embedding evaluation

  lagillenwater

  committed
  d88f28c

  Copy full SHA for d88f28c

Commits on Sep 10, 2024

• adding packages to be installed to envrionment

  lagillenwater

  committed
  2b26570

  Copy full SHA for 2b26570

• updated test script to include heatmap creation

  lagillenwater

  committed
  8a0990a

  Copy full SHA for 8a0990a

• updated literature comparison to use text based output

  lagillenwater

  committed
  3bdc6bf

  Copy full SHA for 3bdc6bf

• testing

  lagillenwater

  committed
  3e548b9

  Copy full SHA for 3e548b9

• fixed bug for full text

  lagillenwater

  committed
  f91961d

  Copy full SHA for f91961d

• added functions

  lagillenwater

  committed
  b32c962

  Copy full SHA for b32c962

Commits on Sep 27, 2024

• updating test script to test nlp embedding based evaluation

  lagillenwater

  committed
  f06b24b

  Copy full SHA for f06b24b

• evaluation of Cartoomics pathways based on literature embedings

  lagillenwater

  committed
  7686504

  Copy full SHA for 7686504

• modified file for text input

  lagillenwater

  committed
  434fd9c

  Copy full SHA for 434fd9c