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Recent Releases of lobster

lobster - v0.0.15

What's Changed

  • badges by @ncfrey in https://github.com/prescient-design/lobster/pull/140
  • Peer patch (fold, sub loc, proteinnet, ssp) by @taylormjs in https://github.com/prescient-design/lobster/pull/139
  • hot fix badge by @ncfrey in https://github.com/prescient-design/lobster/pull/142
  • improve model load logging by @ncfrey in https://github.com/prescient-design/lobster/pull/143
  • onnx compile by @ncfrey in https://github.com/prescient-design/lobster/pull/144
  • add timestamps to cached UME checkpoints by @karinazad in https://github.com/prescient-design/lobster/pull/145
  • cpu attn mask by @ncfrey in https://github.com/prescient-design/lobster/pull/149

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.14...v0.0.15

- Python
Published by karinazad 9 months ago

lobster - v0.0.14

What's Changed

  • upgrade flash attention to 2.8.0 by @karinazad in https://github.com/prescient-design/lobster/pull/122
  • Post train eval by @taylormjs in https://github.com/prescient-design/lobster/pull/119
  • rl init by @ncfrey in https://github.com/prescient-design/lobster/pull/121
  • Add 'rank' stage to DyAb model by @tomyyyD in https://github.com/prescient-design/lobster/pull/124
  • Add weight decay to UME by @karinazad in https://github.com/prescient-design/lobster/pull/125
  • Perturbation callback by @karinazad in https://github.com/prescient-design/lobster/pull/126
  • remove with torch.inference_mode() from tokens to latents in FlexBert by @karinazad in https://github.com/prescient-design/lobster/pull/127
  • grpo updates by @ncfrey in https://github.com/prescient-design/lobster/pull/128
  • bump torch by @kleinhenz in https://github.com/prescient-design/lobster/pull/132
  • ckpt by @kleinhenz in https://github.com/prescient-design/lobster/pull/130
  • CONTRIBUTING.md by @karinazad in https://github.com/prescient-design/lobster/pull/133
  • Transform for nucleotides to AA and SMILES by @karinazad in https://github.com/prescient-design/lobster/pull/136
  • rope tests by @ncfrey in https://github.com/prescient-design/lobster/pull/134
  • deps by @kleinhenz in https://github.com/prescient-design/lobster/pull/135
  • dxt by @ncfrey in https://github.com/prescient-design/lobster/pull/129
  • Add DGEB evaluation integration for UME models by @ncfrey in https://github.com/prescient-design/lobster/pull/137

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.13...v0.0.14

- Python
Published by ncfrey 9 months ago

lobster - v0.0.13

What's Changed

  • lightweight server by @ncfrey in https://github.com/prescient-design/lobster/pull/96
  • DiscoCLIP loss by @karinazad in https://github.com/prescient-design/lobster/pull/98
  • Make umap optional by @karinazad in https://github.com/prescient-design/lobster/pull/100
  • citation by @ncfrey in https://github.com/prescient-design/lobster/pull/99
  • FIx Ume example notebook by @karinazad in https://github.com/prescient-design/lobster/pull/102
  • Remove structural tokens from Ume tokenizers by @karinazad in https://github.com/prescient-design/lobster/pull/101
  • Add translation and reverse-translation transforms (DNA -> protein, protein -> DNA) by @karinazad in https://github.com/prescient-design/lobster/pull/103
  • more fa tests by @ncfrey in https://github.com/prescient-design/lobster/pull/105
  • Small DyAb bugfixes by @tomyyyD in https://github.com/prescient-design/lobster/pull/107
  • Add Symile multi-modal contrastive loss to Ume by @karinazad in https://github.com/prescient-design/lobster/pull/109
  • comparing fa2 by @ncfrey in https://github.com/prescient-design/lobster/pull/112
  • Refactor UME losses by @karinazad in https://github.com/prescient-design/lobster/pull/111
  • Add 'from_pretrained' to Ume by @karinazad in https://github.com/prescient-design/lobster/pull/113
  • Save DyAb hyperparameters by @tomyyyD in https://github.com/prescient-design/lobster/pull/116
  • Add CLAUDE.md documentation and maintenance tools by @ncfrey in https://github.com/prescient-design/lobster/pull/114
  • Ume embedding normalization + small fixes by @karinazad in https://github.com/prescient-design/lobster/pull/115

New Contributors

  • @tomyyyD made their first contribution in https://github.com/prescient-design/lobster/pull/107

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.12...v0.0.13

- Python
Published by karinazad 10 months ago

lobster - v0.0.12

What's Changed

  • Ume SMILES tokenizer fix by @karinazad in https://github.com/prescient-design/lobster/pull/66
  • Ume perplexity logging by @karinazad in https://github.com/prescient-design/lobster/pull/67
  • Update README.md by @ncfrey in https://github.com/prescient-design/lobster/pull/69
  • Ume fix perplexity device by @karinazad in https://github.com/prescient-design/lobster/pull/68
  • Add to Ume tokenizers by @karinazad in https://github.com/prescient-design/lobster/pull/71
  • RNS metric implementation by @karinazad in https://github.com/prescient-design/lobster/pull/73
  • Ume modality-specific embeddings by @karinazad in https://github.com/prescient-design/lobster/pull/72
  • add conversion transforms by @cgrambow in https://github.com/prescient-design/lobster/pull/74
  • Fix peer by @taylormjs in https://github.com/prescient-design/lobster/pull/70
  • add SMILES conversion transform and transform tests by @cgrambow in https://github.com/prescient-design/lobster/pull/75
  • Ume remove modality embeddings by @karinazad in https://github.com/prescient-design/lobster/pull/76
  • add maxinputlength option to conversion transforms by @cgrambow in https://github.com/prescient-design/lobster/pull/78
  • Initial InfoNCE contrastive experiments (with pos emb bugfix) by @sjmielke in https://github.com/prescient-design/lobster/pull/77
  • Ume weighted contrastive loss by @karinazad in https://github.com/prescient-design/lobster/pull/79
  • Update README.md by @ncfrey in https://github.com/prescient-design/lobster/pull/83
  • Ume weighted contrastive loss pt2 by @karinazad in https://github.com/prescient-design/lobster/pull/86
  • make flash-attn optional for Ume, enable CPU-only inference and testing by @ncfrey in https://github.com/prescient-design/lobster/pull/90
  • Ume remove paired tokenization by @karinazad in https://github.com/prescient-design/lobster/pull/92
  • Ume evaluation by @karinazad in https://github.com/prescient-design/lobster/pull/87
  • make flash attention optional by @kleinhenz in https://github.com/prescient-design/lobster/pull/95

New Contributors

  • @sjmielke made their first contribution in https://github.com/prescient-design/lobster/pull/77

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.11...v0.0.12

- Python
Published by kleinhenz 10 months ago

lobster - v0.0.11

What's Changed

  • Add AtomicaDataset by @karinazad in https://github.com/prescient-design/lobster/pull/63
  • Ume conversion/interaction tokenizer + fix SMILES and nucleotide tokenizers by @karinazad in https://github.com/prescient-design/lobster/pull/65

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.10...v0.0.11

- Python
Published by karinazad 12 months ago

lobster - v0.0.10

What's Changed

  • fix scheduler params by @karinazad in https://github.com/prescient-design/lobster/pull/64

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.9...v0.0.10

- Python
Published by karinazad 12 months ago

lobster - v0.0.9

What's Changed

  • unpin flash_attn by @karinazad in https://github.com/prescient-design/lobster/pull/62

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.8...v0.0.9

- Python
Published by karinazad 12 months ago

lobster - v0.0.8

What's Changed

  • update flash attention wheels by @karinazad in https://github.com/prescient-design/lobster/pull/61

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.7...v0.0.8

- Python
Published by karinazad 12 months ago

lobster - v0.0.7

What's Changed

  • Ume datamodule, iterable datasets, concat and multiplexed datasets, throughput+tokens per second callback by @karinazad in https://github.com/prescient-design/lobster/pull/39
  • transformer architecture analyzer by @karinazad in https://github.com/prescient-design/lobster/pull/40
  • fix HF datasets tests, add mocking by @karinazad in https://github.com/prescient-design/lobster/pull/42
  • configure lr scheduler by @ncfrey in https://github.com/prescient-design/lobster/pull/41
  • Structure tokens by @ncfrey in https://github.com/prescient-design/lobster/pull/43
  • LG hugging face dataset by @Sidney-Lisanza in https://github.com/prescient-design/lobster/pull/44
  • Add 3D Pinder to Ume datamodule by @karinazad in https://github.com/prescient-design/lobster/pull/45
  • Ume tokenizers and dataset sampling options by @karinazad in https://github.com/prescient-design/lobster/pull/46
  • PEER dataset(s) + callback by @taylormjs in https://github.com/prescient-design/lobster/pull/47
  • Ume model class and embeddings tutorial notebook by @karinazad in https://github.com/prescient-design/lobster/pull/48
  • Ume datamodule - allow downloads of HF datasets by @karinazad in https://github.com/prescient-design/lobster/pull/50
  • delete ckpt by @ncfrey in https://github.com/prescient-design/lobster/pull/51
  • extend smiles tokenizer by @cgrambow in https://github.com/prescient-design/lobster/pull/49
  • Ume model, per-modality loss, UmeTokenizerTransform by @karinazad in https://github.com/prescient-design/lobster/pull/52
  • Add OpenGenome2 by @taylormjs in https://github.com/prescient-design/lobster/pull/53
  • Add ZINC dataset, add limit to HF iterable datasets by @karinazad in https://github.com/prescient-design/lobster/pull/54
  • Ume datamodule - fix _get_dataset_sizes with limit by @karinazad in https://github.com/prescient-design/lobster/pull/56
  • Ume evaluation callbacks - switch to Ume tokenizers, expose evaluate by @karinazad in https://github.com/prescient-design/lobster/pull/57
  • slurm script time interval, Ume config, ModernBERT max length by @karinazad in https://github.com/prescient-design/lobster/pull/59
  • configs by @ncfrey in https://github.com/prescient-design/lobster/pull/55
  • Calm splits by @taylormjs in https://github.com/prescient-design/lobster/pull/58
  • dataloader checkpoint callback by @karinazad in https://github.com/prescient-design/lobster/pull/60

New Contributors

  • @cgrambow made their first contribution in https://github.com/prescient-design/lobster/pull/49

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.6...v0.0.7

- Python
Published by karinazad 12 months ago

lobster - v0.0.6

What's Changed

  • Modern bert by @Sidney-Lisanza in https://github.com/prescient-design/lobster/pull/20
  • mgm script setup by @ncfrey in https://github.com/prescient-design/lobster/pull/21
  • add AminoAcidTokenizerFast by @kleinhenz in https://github.com/prescient-design/lobster/pull/16
  • adding predict_fab that formats pdb file with heavy and light chain by @fdreyer in https://github.com/prescient-design/lobster/pull/17
  • Add FlexBERT from ModernBERT by @edwag in https://github.com/prescient-design/lobster/pull/22
  • M320M dataset by @karinazad in https://github.com/prescient-design/lobster/pull/23
  • SMILES regex fast tokenizer by @karinazad in https://github.com/prescient-design/lobster/pull/24
  • Nucleotide tokenizer fast by @karinazad in https://github.com/prescient-design/lobster/pull/25
  • M320M and ChEMBL datamodules, tokenizer transform by @karinazad in https://github.com/prescient-design/lobster/pull/27
  • calm datamodule by @ncfrey in https://github.com/prescient-design/lobster/pull/28
  • FlexBERT tweaks by @edwag in https://github.com/prescient-design/lobster/pull/29
  • Allow input embeddings to be passed directly to FlexBERT by @edwag in https://github.com/prescient-design/lobster/pull/32
  • MoleculeACE linear probe evaluation callback by @karinazad in https://github.com/prescient-design/lobster/pull/31
  • deepspeed deps by @ncfrey in https://github.com/prescient-design/lobster/pull/33
  • Update push.yml by @ncfrey in https://github.com/prescient-design/lobster/pull/36
  • minimal esmc-small implementation by @fdreyer in https://github.com/prescient-design/lobster/pull/37
  • configs by @ncfrey in https://github.com/prescient-design/lobster/pull/38
  • Add CalmPropertyDataset & CalmLinearProbe Callbacks by @taylormjs in https://github.com/prescient-design/lobster/pull/34

New Contributors

  • @Sidney-Lisanza made their first contribution in https://github.com/prescient-design/lobster/pull/20
  • @fdreyer made their first contribution in https://github.com/prescient-design/lobster/pull/17
  • @edwag made their first contribution in https://github.com/prescient-design/lobster/pull/22
  • @karinazad made their first contribution in https://github.com/prescient-design/lobster/pull/23
  • @taylormjs made their first contribution in https://github.com/prescient-design/lobster/pull/34

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.5...v0.0.6

- Python
Published by kleinhenz about 1 year ago

lobster - v0.0.5

What's Changed

  • deps take 2 by @kleinhenz in https://github.com/prescient-design/lobster/pull/19

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.4...v0.0.5

- Python
Published by kleinhenz about 1 year ago

lobster - v0.0.4

What's Changed

  • don't publish every commit to main by @kleinhenz in https://github.com/prescient-design/lobster/pull/11
  • Fix typos by @chaitjo in https://github.com/prescient-design/lobster/pull/12
  • DyAb by @hofmannjl in https://github.com/prescient-design/lobster/pull/13
  • dependencies by @kleinhenz in https://github.com/prescient-design/lobster/pull/18

New Contributors

  • @chaitjo made their first contribution in https://github.com/prescient-design/lobster/pull/12
  • @hofmannjl made their first contribution in https://github.com/prescient-design/lobster/pull/13

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.3...v0.0.4

- Python
Published by kleinhenz about 1 year ago

lobster - v0.0.3

What's Changed

  • real pypi publish by @ncfrey in https://github.com/prescient-design/lobster/pull/10

Full Changelog: https://github.com/prescient-design/lobster/compare/v0.0.2...v0.0.3

- Python
Published by kleinhenz over 1 year ago

lobster - v0.0.2

test release 2 🦞 🦞

- Python
Published by kleinhenz over 1 year ago

lobster - v0.0.1

test release 🦞

- Python
Published by kleinhenz over 1 year ago