Issues

• GPU out of memory

  wontfix
  deepmodeling/Uni-Mol#375 · Filter by author BernalFA opened on Aug 28, 2026

• [BUG] _Two differences between Unimol2 source code and unimol_tools package resulting in different embedding generating

  bug
  deepmodeling/Uni-Mol#371 · Filter by author Du-JP opened on Mar 31, 2026

• Preprocessing of raw .pdb protein files for Uni-Mol pocket encoder

  documentation
  deepmodeling/Uni-Mol#370 · Filter by author alexander-telepov opened on Feb 16, 2026

• I wanna know about the training time of Uni-Mol on the 3D structures of organic molecules

  deepmodeling/Uni-Mol#369 · Filter by author LiYong4128 opened on Feb 1, 2026

• [BUG] Wrong calculation on feat["pair_type"] in Uni-Mol2

  bug
  deepmodeling/Uni-Mol#368 · Filter by author xuanliugit opened on Jan 20, 2026

• 📚 Daily Automated arXiv Updates for AI4Chem Papers

  deepmodeling/Uni-Mol#367 · Filter by author YuzeHao2023 opened on Jan 18, 2026

• How to choose the model size we want and run the local model path?

  wontfix
  deepmodeling/Uni-Mol#366 · Filter by author Zhouzz22 opened on Jan 12, 2026
  1

• [Question] Clarification on units for QM9 property prediction benchmarks in Uni-Mol2

  documentation
  deepmodeling/Uni-Mol#365 · Filter by author YuX-Ren opened on Jan 4, 2026

• [BUG] Inconsistent representations between batch and single inference in Uni-Mol2 (Suspected Self-Attention Mask Issue)

  bug
  deepmodeling/Uni-Mol#364 · Filter by author thelittlewen opened on Jan 2, 2026
  2

• Even with only the random seed being different, the prediction results vary greatly.

  deepmodeling/Uni-Mol#362 · Filter by author jia-huang opened on Nov 12, 2025
  1

• How to run Uni-Dock v2 with docker?

  wontfix
  deepmodeling/Uni-Mol#360 · Filter by author jeremycheminf opened on Sep 8, 2025
  2

• test AUC

  deepmodeling/Uni-Mol#359 · Filter by author mxqmxqmxq opened on Sep 3, 2025
  2

• [BUG] wrong pose in unimol docking v2

  bug
  deepmodeling/Uni-Mol#358 · Filter by author yangjinhao1234 opened on Aug 21, 2025

• [BUG] total_train_steps was not calculated or passed in correctly

  bug
  deepmodeling/Uni-Mol#357 · Filter by author jia-huang opened on Aug 14, 2025
  2

• [BUG] _RuntimeError: p.is_cuda() INTERNAL ASSERT FAILED at "/home/runner/work/Uni-Core/Uni-Core/csrc/adam/interface.cpp":10, please report a bug to PyTorch. p must be a CUDA tensor

  bug
  deepmodeling/Uni-Mol#356 · Filter by author jia-huang opened on Aug 11, 2025
  1

• [Feature Request] _Replace with Title_Toxcast multi-label task property prediction

  enhancement
  deepmodeling/Uni-Mol#355 · Filter by author 3505675604 opened on Jul 23, 2025

• [BUG] the saved model only have parameters of classification head

  bug
  deepmodeling/Uni-Mol#354 · Filter by author kevin-wen1 opened on Jul 14, 2025
  2

• UniMol_Docking_v2: input_protein column should not be in input CSV when using batch_one2many

  documentation
  deepmodeling/Uni-Mol#353 · Filter by author tompan-123 opened on Jul 11, 2025

• Question about pre-trained ligand embeddings by Unimol tools

  wontfix
  deepmodeling/Uni-Mol#351 · Filter by author srdjan125 opened on Jul 9, 2025
  6

• [BUG] unimol2 LMDBDataset传的tmp_data_dir参数temp找不到

  bug
  deepmodeling/Uni-Mol#350 · Filter by author ZZZPeiei opened on Jul 9, 2025

• [BUG] unimol+: RuntimeError: Expected all tensors to be on the same device, but found at least two devices, cuda:{0,1,2,3} and cpu!

  bug
  deepmodeling/Uni-Mol#348 · Filter by author Linus-XZX opened on Jun 17, 2025

• [Feature Request] _Replace with Title_

  enhancement
  deepmodeling/Uni-Mol#346 · Filter by author ZZZPeiei opened on May 22, 2025

• [BUG] AttributeError: 'Trainer' object has no attribute 'scaler'

  bug
  deepmodeling/Uni-Mol#343 · Filter by author PatWalters opened on May 11, 2025
  3

• unimol_docking_v2 output .lmdb .pkl

  wontfix
  deepmodeling/Uni-Mol#342 · Filter by author JiangLab2020 opened on May 8, 2025
  1

• How to train unimol2 from scratch? Is there any tutorial?

  documentation
  deepmodeling/Uni-Mol#338 · Filter by author kingwzun opened on Apr 15, 2025
  2