BlueBrain/Search

Issues

• Run Text Mining on literature sample

  #627 opened 2 years ago by FrancescoCasalegno
  1

• Create Elasticsearch database with literature sample

  #621 opened 2 years ago by FrancescoCasalegno
  1

• Create JSONL configuration file for topic filtering

  #640 opened 2 years ago by FrancescoCasalegno
  0

• Unify abstract and section paragraphs

  #637 opened 2 years ago by jankrepl
  1

• Deploy embedding model on Kubernetes using Seldom

  #623 opened 2 years ago by FrancescoCasalegno
  3

• Implement `bbs_database upload-elasticsearch`

  #620 opened 2 years ago by FrancescoCasalegno
  0

• Remove Python 3.7 from the CI

  #636 opened 2 years ago by jankrepl
  1

• Unit test setup in the CI is extremely slow

  #635 opened 2 years ago by jankrepl
  1

• Add `to-month` argument to `download` entrypoint

  #588 opened 2 years ago by FrancescoCasalegno
  0

• Add Elasticsearch `articles` table

  #618 opened 2 years ago by FrancescoCasalegno
  4

• Add Question-Answer samples to our dataset using data from KG

  #616 opened 2 years ago by FrancescoCasalegno
  1

• Collect annotations for RE model

  #606 opened 3 years ago by FrancescoCasalegno
  5

• Add more than one acceptable answer in our Question-Answering dataset

  #617 opened 2 years ago by FrancescoCasalegno
  1

• Train and evaluate first RE models for `(GENE, is-in, BRAIN_REGION)`

  #613 opened 2 years ago by FrancescoCasalegno
  2

• Explore Re-Ranking models to improve results of Semantic Search

  #625 opened 2 years ago by FrancescoCasalegno
  0

• Reformulate Questions to clarify the required value to be extracted

  #624 opened 2 years ago by FrancescoCasalegno
  0

• Fine-tune Question-Answering model on our own data

  #622 opened 2 years ago by FrancescoCasalegno
  0

• Semantic search + Exact matches in ElasticSearch

  #610 opened 2 years ago by FrancescoCasalegno
  7

• Include topic info in JSON output parse of `bbs_database parse`

  #619 opened 2 years ago by FrancescoCasalegno
  0

• Question-Answering: collect example questions + run first analysis with pre-trained QA models

  #612 opened 2 years ago by FrancescoCasalegno
  4

• Evaluate Abstractive Question-Answering models

  #615 opened 2 years ago by FrancescoCasalegno
  0

• Investigate Question-Answering models working on tables

  #614 opened 2 years ago by FrancescoCasalegno
  0

• Collect batch n. 3 of NER annotations

  #611 opened 2 years ago by FrancescoCasalegno
  1

• Complete training set for NER by collecting more samples

  #604 opened 2 years ago by FrancescoCasalegno
  2

• Try improving NER model performance by using publicly available NER datasets

  #608 opened 2 years ago by FrancescoCasalegno
  9

• Perform Error Analysis of NER model predictions

  #607 opened 2 years ago by FrancescoCasalegno
  8

• Attempt removing Early Stopping

  #603 opened 2 years ago by FrancescoCasalegno
  4

• Investigate options for storing literature documents

  #609 opened 2 years ago by FrancescoCasalegno
  2

• Compare Huggingface vs. SpaCy performance on NER

  #602 opened 2 years ago by FrancescoCasalegno
  4

• Try improving NER model performance by leveraging ontotology-generated text

  #605 opened 2 years ago by FrancescoCasalegno
  4

• Compute learning curves for NER models

  #601 opened 2 years ago by FrancescoCasalegno
  2

• Download more `PMC` files: `oa_other` and `historical_ocr`

  #584 opened 3 years ago by FrancescoCasalegno
  1

• `bluesearch.utils.find_files` can be slow when doing regex

  #587 opened 3 years ago by jankrepl
  1

• Dynamically providing parameters containing "." does not work

  #594 opened 3 years ago by jankrepl
  0

• First sketch of the overall pipeline (+ research relevant tools/approaches)

  #562 opened 3 years ago by jankrepl
  2

• Run ETL pipeline and collect stats on downloads

  #572 opened 3 years ago by FrancescoCasalegno
  1

• Handle external signals to `topic-extract` gracefully

  #575 opened 3 years ago by jankrepl
  1

• `bbs_database download arxiv` fails with `invalid literal for int()`

  #585 opened 3 years ago by FrancescoCasalegno
  2

• `bbs_database command -vv` activates debug messages of 3rd party packages

  #565 opened 3 years ago by jankrepl
  0

• Use zipped files for `Pubmed` articles in `bbs_database parse` entrypoint

  #583 opened 3 years ago by EmilieDel
  0

• Potential bug in topic-extract

  #578 opened 3 years ago by jankrepl
  1

• Ignore `pytest.PytestUnraisableExceptionWarning` globally

  #580 opened 3 years ago by jankrepl
  0

• `bbs_database add` does not put the abstract in the sentences table

  #579 opened 3 years ago by jankrepl
  0

• Topic extraction takes all the files in the directory

  #577 opened 3 years ago by jankrepl
  0

• Make `add` handle duplicate articles

  #576 opened 3 years ago by jankrepl
  0

• Create NER model for `BRAIN_REGION`

  #573 opened 3 years ago by FrancescoCasalegno
  0

• Design an intermediary step between `bbs_database topic-filter` and `bbs_database parse`

  #559 opened 3 years ago by jankrepl
  1

• Evaluate using `Jina` for Blue Brain Search

  #567 opened 3 years ago by FrancescoCasalegno
  0

• Reuse extracted topic information

  #566 opened 3 years ago by jankrepl
  0

• Tox: move mypy to a separate env

  #560 opened 3 years ago by Stannislav
  0