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Releases: nlpie/biomedicus

Release 3.4.3

09 Oct 15:34
v3.4.3
573bc8a
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Removed built-in service discovery functionality.

Release 3.4.2

01 Apr 14:32
v3.4.2
025a309
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Support for deploying the e2e pipeline using the docker image.

Release 3.4.0

14 Feb 16:49
v3.4.0
3684d39
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Added the End-to-end REST pipeline service, described here: https://nlpie.github.io/biomedicus/docs/deploy-pipeline.html.

Release 3.3.0

31 Oct 20:29
v3.3.0
246ca05
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What's Changed

  • Updated concepts to UMLS 2023AA
  • Fixed an issue with overlapping annotations for the same concepts
  • Dependency Updates

Breaking Changes

  • Removed support for Python 3.8 from biomedicus (deprecated, numpy no longer receiving updates on 3.8)

Full Changelog: v3.2.1...v3.3.0

Release 3.2.1

19 Apr 19:18
v3.2.1
a8d8604
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What's Changed

  • Dependency Updates (Torch 2.0, rocksdb 8.0)
  • Supports Python 3.8-3.11 now
  • Switched to performing negation detection using only negex by default.
  • Updated to MTAP 1.2.1. This introduces some breaking changes, click on the link for more info.
  • Moved everything in biomedicus_client.pipeline to biomedicus_client package.
  • Renamed some built-in pipeline and deployment configuration files (-conf.yml to .yml)

Release Milestone: https://github.com/nlpie/biomedicus/milestone/15?closed=1
Full Changelog: v3.1.0...v3.2.1

3.1.0

16 Mar 20:04
v3.1.0
c206392
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What's Changed

  • Dependencies for release versions are now pinned for more stable releases.
  • Fix for a number of RTF reader formatting issues. (#140, #141)
  • Fixed an issue where the sentences processor would fail when CUDA is available (#142)
  • Fixed an issue where deepen was failing due to incorrect offset indices on dependencies (#138)

Full Changelog: v3.0.0...v3.1.0

3.0.0

16 Mar 18:13
v3.0.0
65921e2
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Initial public release.

3.0 Release Candidate 4

03 Oct 16:29
v3.0.0-rc.4
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Pre-release

What's Changed

Full Changelog: v3.0.0-rc.3...v3.0.0-rc.4

3.0 Release Candidate 3

19 Aug 16:11
v3.0.0-rc.3
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Pre-release

Various bug fixes (Mainly RTF). Made it easier to programmatically create pipelines and use custom input sources. Better logging messages around configuration.

Breaking change:
The biomedicus run command argument for the output directory has switched to an option -o. The correct syntax is now

biomedicus run /path_to/input_dir/ -o /path_to/output_dir/ 

This is because the option is only used in the case of a serializer (default: json) and if the serializer is set to none the option will not be used.

3.0 Beta #6

11 Aug 22:58
v3.0-beta.6
7038f1b
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3.0 Beta #6 Pre-release
Pre-release

This update contains the following enhancements for BioMedICUS

  • Better negation detection via an adapted implementation of parsing-sensitive DEEPEN algorithm.
  • Improvements to concept detection and vocabularies updated to UMLS 2020AA.
  • BioMedICUS 2.x simple rule-based regex patterns section header detection.
  • Fixed a bug which could potentially cause time-outs during deployment.