Issues

• Release request: publish the merged nmslib dependency update (#559)

  allenai/scispacy#628 · Filter by author xrl opened on Sep 10, 2026

• fix: typo 'constuctor' → 'constructor' in CandidateGenerator error message

  allenai/scispacy#601 · Filter by author rtmalikian opened on Jun 19, 2026
  1

• fix: unclosed file handles in read_full_med_mentions() and read_ner_from_tsv()

  allenai/scispacy#599 · Filter by author rtmalikian opened on Jun 19, 2026
  1

• fix: unclosed file handle in evaluate_ner() when dumping metrics

  allenai/scispacy#597 · Filter by author rtmalikian opened on Jun 19, 2026
  2

• fix: which_look_like Hearst pattern uses hyponym twice instead of hypernym

  allenai/scispacy#595 · Filter by author rtmalikian opened on Jun 19, 2026
  1

• fix: misleading variable name in create_tfidf_ann_index — number_of_non_empty_tfidfs counts empty vectors

  allenai/scispacy#593 · Filter by author rtmalikian opened on Jun 19, 2026
  1

• fix: set-list zip produces incorrect span pairings in PerClassScorer (candidate_generation.py)

  allenai/scispacy#592 · Filter by author rtmalikian opened on Jun 19, 2026
  1

• fix: truncate cache filenames to avoid OSError on eCryptfs/encfs filesystems

  allenai/scispacy#590 · Filter by author rtmalikian opened on Jun 18, 2026
  1

• 📚 Daily Automated arXiv Updates for AI4Bio Papers

  allenai/scispacy#561 · Filter by author YuzeHao2023 opened on Jan 20, 2026

• What types of entities can each scispaCy model recognize?

  allenai/scispacy#550 · Filter by author rferrazd opened on Sep 10, 2025
  2

• Support for Python 3.13 and spaCy 3.8.7

  allenai/scispacy#545 · Filter by author source19069 opened on Aug 4, 2025
  3

• File name too long

  allenai/scispacy#539 · Filter by author youknow16 opened on May 28, 2025
  1

• Mismatch in Entity Annotation between SpaCy Models (en_ner_bionlp13cg_md and en_ner_jnlpba_md)

  allenai/scispacy#538 · Filter by author shshossain opened on Apr 13, 2025

• Incompatibility with numpy v2 - ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

  allenai/scispacy#536 · Filter by author widgetface opened on Feb 19, 2025
  2

• UMLS Entity Linker throws BadZipFile error

  allenai/scispacy#534 · Filter by author markediger-mdsol opened on Nov 22, 2024
  1

• Filtering CUI/TUI returned entities?

  allenai/scispacy#516 · Filter by author ddofer opened on Jun 20, 2024
  1

• Interactive demo is not working

  allenai/scispacy#515 · Filter by author xuanyshi opened on May 22, 2024
  2

• Configuration for model locations

  enhancement
  allenai/scispacy#469 · Filter by author buddha314 opened on Feb 28, 2023
  3

• Error running sample code: OSError: [Errno 36] File name too long

  bug
  allenai/scispacy#447 · Filter by author kryptec opened on Aug 17, 2022
  1

• Training scispacy pipelines require recreating the vocab file

  bug
  allenai/scispacy#440 · Filter by author Hammad-NobleAI opened on Jul 14, 2022
  9

• Entity linking future directions

  enhancement
  allenai/scispacy#429 · Filter by author eric-czech opened on Apr 14, 2022
  4

• any guidance on ontonotes prep?

  documentation
  allenai/scispacy#421 · Filter by author mprorock opened on Feb 24, 2022
  1

• Enhancement: Provide option to modify cache folder for entity linker knowledge base downloads

  enhancement
  allenai/scispacy#415 · Filter by author davidshumway opened on Jan 26, 2022
  2

• Slow loading of the pipe scispacy_linker

  enhancement
  allenai/scispacy#402 · Filter by author vlievin opened on Oct 25, 2021
  9

• Combining Entities Recognized by Different Models & by the AbbreviationDetector

  enhancementhelp wanted
  allenai/scispacy#388 · Filter by author Salamander230 opened on Aug 5, 2021
  3