Commits

Branch selector

 main

User selector

All users

Datepicker

All time

Commit History

Commits on Dec 18, 2025

• Handle API rate limit in evaluations (rate_limit_rpm)

  lunaticstarr

  committed
  fbf056f

  Copy full SHA for fbf056f

Commits on Dec 16, 2025

• Enable multiple try for empty predictions; update prompts for protein family/subtype.

  lunaticstarr

  committed
  b9ec58d

  Copy full SHA for b9ec58d

• Undo the cleaning of descriptor words - some of them are important in protein labels.

  lunaticstarr

  committed
  7422e32

  Copy full SHA for 7422e32

Commits on Dec 11, 2025

• handle complex in auto mode by searching all given databases

  lunaticstarr

  committed
  474cd4e

  Copy full SHA for 474cd4e

• remove modification/descriptor words from LLM synonyms for database search except for chemicals

  lunaticstarr

  committed
  b3626f8

  Copy full SHA for b3626f8

• update prompts for protein; improved prompts for auto type

  lunaticstarr

  committed
  26cf071

  Copy full SHA for 26cf071

Commits on Dec 7, 2025

• update prompts for complex

  lunaticstarr

  committed
  c99a807

  Copy full SHA for c99a807

Commits on Nov 30, 2025

• Remove tests/results from repo and ignore going forward

  lunaticstarr

  committed
  15190b1

  Copy full SHA for 15190b1

• Auto type detection (tested on chebi and uniprot); remove duplicated annotations from model_info; consider bqmodel qualifier

  lunaticstarr

  committed
  5a6a49e

  Copy full SHA for 5a6a49e

Commits on Oct 28, 2025

• split prompts for larger models into chunks

  lunaticstarr

  committed
  748ca5f

  Copy full SHA for 748ca5f

• streamline the prompts, e.g., remove empty display names and reactions IDs

  lunaticstarr

  committed
  17c0d26

  Copy full SHA for 17c0d26

Commits on Sep 17, 2025

• Merge pull request #4 from janisshin/feature/reaction-direct-LLM-anno

  Show description for c10e178
  lunaticstarr

  authored
  c10e178

  Copy full SHA for c10e178

Commits on Sep 8, 2025

• Merge branch 'main' of https://github.com/sys-bio/AAAIM

  janisshin

  committed
  ccf1752

  Copy full SHA for ccf1752

• Rename and edit reaction reference files

  janisshin

  committed
  5848be9

  Copy full SHA for 5848be9

• Clean up kegg rulebased and direct LLM methods and accessories

  janisshin

  committed
  eb4b347

  Copy full SHA for eb4b347

Commits on Sep 4, 2025

• chore: incorporate etity_type 'reaction' handling

  janisshin

  committed
  fc94a41

  Copy full SHA for fc94a41

• feat: LLM query for reactions--direct synonym comparison

  janisshin

  committed
  ccc28b4

  Copy full SHA for ccc28b4

• add orthology; streamline text cleaning

  janisshin

  committed
  e2a5b41

  Copy full SHA for e2a5b41

Commits on Sep 2, 2025

• Merge pull request #3 from janisshin/bugfix/improve-rxn-similarity-scoring

  Show description for 9cf3169
  lunaticstarr

  authored
  9cf3169

  Copy full SHA for 9cf3169

• add more data for KEGG RAG

  janisshin

  committed
  a1cec3e

  Copy full SHA for a1cec3e

Commits on Aug 31, 2025

• canceling of spectator species

  janisshin

  committed
  9b8ac75

  Copy full SHA for 9b8ac75

Commits on Aug 27, 2025

• Merge remote-tracking branch 'upstream/main'

  janisshin

  committed
  ebd9f00

  Copy full SHA for ebd9f00

• ground truth toy models

  janisshin

  committed
  8d4dc73

  Copy full SHA for 8d4dc73

• savepoint

  janisshin

  committed
  fad42a2

  Copy full SHA for fad42a2

• update: using ChEBI instead of KEGG

  janisshin

  committed
  92d22ce

  Copy full SHA for 92d22ce

• savepoint for KEGG compound flat downloads

  janisshin

  committed
  0bbf238

  Copy full SHA for 0bbf238

• class extension: ReactionRecommendation

  janisshin

  committed
  e5a91cd

  Copy full SHA for e5a91cd

• added more comments and reaction string to output

  janisshin

  committed
  a53b120

  Copy full SHA for a53b120

• removed redundancy

  janisshin

  committed
  7d6ce5f

  Copy full SHA for 7d6ce5f

• refactor KEGG recommendations to handle cofactors more effectively

  janisshin

  committed
  104bb96

  Copy full SHA for 104bb96

• added single arrow for consideration

  janisshin

  committed
  f3ca422

  Copy full SHA for f3ca422

Commits on Aug 26, 2025

• separate filter_kegg_reactions fn

  janisshin

  committed
  20f975f

  Copy full SHA for 20f975f

Commits on Aug 22, 2025

• fix bugs in protein annotation, add qualifier information for both workflow and evaluation functions

  lunaticstarr

  committed
  6594fed

  Copy full SHA for 6594fed

Commits on Aug 19, 2025

• update chebi2kegg map

  janisshin

  committed
  f96cbf8

  Copy full SHA for f96cbf8

Commits on Aug 13, 2025

• Merge branch 'main' of github.com:sys-bio/AAAIM

  lunaticstarr

  committed
  600e4c3

  Copy full SHA for 600e4c3

Pagination

Previous

Next