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Commits on Dec 15, 2025

• fix: streamline gradient scaling and logging in training loop

  FridrichMethod

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Commits on Dec 10, 2025

• fix: treat UNK as free design

  tianyu-lu

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Commits on Dec 5, 2025

• Revise MotifBench benchmark note in README

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  tianyu-lu

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Commits on Nov 26, 2025

• Merge pull request #3 from ProteinDesignLab/akioshirali-colab

  tianyu-lu

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Commits on Nov 17, 2025

• Update README.md

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  akioshirali

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Commits on Nov 13, 2025

• allow paths in environment variables to be unspecified

  richardshuai

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Commits on Nov 5, 2025

• bugfix: missing sigma scaling in initial noise

  tianyu-lu

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Commits on Oct 31, 2025

• Add jaxtyping version 0.3.2 to uv.lock

  tianyu-lu

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Commits on Oct 13, 2025

• Update placeholder Foldseek path in README

  tianyu-lu

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Commits on Oct 6, 2025

• Update README.md

  richardshuai

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Commits on Oct 1, 2025

• fix: update checkpoint keys for model state dictionary consistency

  FridrichMethod

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Commits on Sep 25, 2025

• Merge commit '55c298a6164ee2aa5b332ee455ab5959c773327c'

  FridrichMethod

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• refactor: replace torch.from_numpy with torch.as_tensor for consistency in tensor creation

  FridrichMethod

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• refactor: remove unused bb_atoms parameter from load_feats_from_pdb function

  FridrichMethod

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• refactor: streamline noise level handling in loss weight calculation

  FridrichMethod

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• Merge commit '135a7cb1d3f4fcd9aa1ab8a8e3f2d3d1cd00cb90'

  FridrichMethod

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• refactor: ensure run_dir is not None when logging wandb run directory

  FridrichMethod

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• refactor: standardize s_max values to float format across configuration files

  FridrichMethod

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• refactor: remove subsample_eval_set from training configurations for consistency

  FridrichMethod

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• refactor: remove sc_num_seqs from training configurations for consistency

  FridrichMethod

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• refactor: remove n_eval_samples from training configurations for consistency

  FridrichMethod

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• refactor: remove eval_loss_t from training configurations for consistency

  FridrichMethod

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• refactor: remove length_ranges_per_chain from training configurations for consistency

  FridrichMethod

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• refactor: update n_examples_for_sigma_data to 512 for consistency across training configurations

  FridrichMethod

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• refactor: streamline backbone atom indexing by using predefined constants

  FridrichMethod

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• refactor: enhance PDB reading error handling and logging for multiple models

  FridrichMethod

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• Merge commit '4696c86a62b1c11bd62d79717d32b81922124192' into dev

  FridrichMethod

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• refactor: improve sampler logic and ensure proper handling of exhausted primary samples

  FridrichMethod

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• Merge commit 'd686633bd9739ebd6d2343e25aac93a9f09ba997'

  FridrichMethod

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• chore: update version to 1.3.2 in __init__.py

  FridrichMethod

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• refactor: change logger warning to debug for PDB example reloading

  FridrichMethod

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• refactor: streamline data processing in dataset and training modules

  FridrichMethod

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• refactor: update get_backbone_mask function to use type hints and improve documentation

  FridrichMethod

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Commits on Sep 24, 2025

• Merge commit 'b1e3ac5f97a65f0d9c71d8b0e6610d0e4c9dd045' into dev

  FridrichMethod

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• Compatible foldseek bin in Colab

  tianyu-lu

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