Multimolecule

Commits
- 481675b: fix inplace modification error in rare cases (Zhiyuan Chen)
- 958eff6: deprecate NucleotidePrediction (Zhiyuan Chen)
- af10a64: update readme (Zhiyuan Chen)
- 5cf9601: improve dataset saving (Zhiyuan Chen)
- e30dc88: add RYOS dataset (Zhiyuan Chen)
- 04d092d: add EternaBench dataset (Zhiyuan Chen)
- 0b55920: update rnacentral variants name (Zhiyuan Chen)
- 1141aab: add RNAstarlign & ArchiveII datasets (Zhiyuan Chen)
- 35733a4: add Rivas dataset (Zhiyuan Chen)
- 9a365d0: fix pseudo-knots process in secondary structure (Zhiyuan Chen)
- 43e847e: minor fixes (Zhiyuan Chen)
- fa5adc3: ready for 0.0.6 (Zhiyuan Chen)

latest
Commits
- fa5adc3: ready for 0.0.6 (Zhiyuan Chen)

Commits
- c776a5d: add citation (Zhiyuan Chen)
- e02c90e: fix output type of rna ernie (Zhiyuan Chen)
- d7120dc: fix criterion when labels is NestedTensor (Zhiyuan Chen)
- 047faa8: Tokenizers won't add special token if passed None (Zhiyuan Chen)
- 6c15493: fix docs format (Zhiyuan Chen)
- bf820cd: update conversion_utils (Zhiyuan Chen)
- 10741ba: prediction heads accept NestedTensor as input_ids (Zhiyuan Chen)
- 0acee22: add DotBracketTokenizer (Zhiyuan Chen)
- 2150c76: add data (Zhiyuan Chen)
- 8d138a9: add datasets (Zhiyuan Chen)
- 2d070e0: add badges to readme (Zhiyuan Chen)

Commits
- b28bfe5: improve code quality (Zhiyuan Chen)
- 8ed0f1a: add modules.RotaryEmbedding (Zhiyuan Chen)
- bf1f65e: make RnaBert supports gradient checkpoint (Zhiyuan Chen)
- 561be58: make RnaMsm supports gradient checkpoint (Zhiyuan Chen)
- 1ded797: expose token_ids in PretrainedConfig (Zhiyuan Chen)
- a5031b4: rename Pretrain -> PreTrain for consistency (Zhiyuan Chen)
- 81c8936: fix type hints (Zhiyuan Chen)
- 25a443a: support count_parameters (Zhiyuan Chen)
- c632a77: add README (Zhiyuan Chen)
- 1c9514b: register models to AutoBackbone (Zhiyuan Chen)
- b48af26: fix <null> token is not recognised (Zhiyuan Chen)
- fef7fcb: add README of RNA-FM (Zhiyuan Chen)
- a483660: add README of RNABERT (Zhiyuan Chen)
- 881a7d0: add README of RNA-MSM (Zhiyuan Chen)
- 59ee118: add README of SpliceBERT (Zhiyuan Chen)
- 7554a94: add README of 3UTRBERT (Zhiyuan Chen)
- 5ee24bd: add README of UTR-LM (Zhiyuan Chen)
- 2bddca3: add document site (Zhiyuan Chen)
- 47b8a96: improve tokenizer design (Zhiyuan Chen)
- 0ace669: add mrna-fm (Zhiyuan Chen)
- 1dd1e65: fix lm_head weight (Zhiyuan Chen)
- 7ea36b9: improve docs (Zhiyuan Chen)
- cc288bd: add dna and protein tokenizer (Zhiyuan Chen)
- c9bc441: add sinusoidal position embedding (Zhiyuan Chen)
- 1b81880: add CaLm (Zhiyuan Chen)
- d85c4bb: add Inosine token in RNA vocab (Zhiyuan Chen)
- 303e8a3: add RiNALMo (Zhiyuan Chen)
- d19bd2a: add ERNIE-RNA (Zhiyuan Chen)
- f7d3ab5: remove downstream (Zhiyuan Chen)
- 4915e6f: rename Classification to Prediction (Zhiyuan Chen)
- fed720d: add corresponding AutoModelForPrediction (Zhiyuan Chen)
- 4b716ce: add modeling_output (Zhiyuan Chen)
- 52eed9f: improve doctest (Zhiyuan Chen)
- 2718a32: fix ContactPredictionHead (Zhiyuan Chen)
- ffa0213: rewrite RnaBertForPreTraining (Zhiyuan Chen)
- e18cf00: rewrite RnaFmForPretraining (Zhiyuan Chen)
- 9fedd52: rewrite RnaMsmForPretraining (Zhiyuan Chen)
- 8fb3ad4: rewrite UtrLmForPretraining (Zhiyuan Chen)
- 74f283a: improve SpliceBert & UtrBert for pretraining (Zhiyuan Chen)
- ac76344: add contact prediction models (Zhiyuan Chen)
- 369513c: add module docment (Zhiyuan Chen)
- 61c5687: improve head design (Zhiyuan Chen)
- 650edb8: update models doc (Zhiyuan Chen)
- e180f39: improve Tokenizer design (Zhiyuan Chen)
- 6fa7283: add RNAErnie (Zhiyuan Chen)
- 5a08afe: clean up docs and utils (Zhiyuan Chen)
- 0ef34df: add model widgets (Zhiyuan Chen)

Commits
- d99eeb5: run tests before publishing (Zhiyuan Chen)
- 89d52ae: fix rotary embedding in UtrLm and RnaFm (Zhiyuan Chen)
- 461ba05: fix attention mask of RnaMsm (Zhiyuan Chen)
- 3fcb921: fix head for utrlm and utrbert (Zhiyuan Chen)
- 2968292: unify classification head (Zhiyuan Chen)
- 9f8b2a7: rename Outputs of RnaMsm (Zhiyuan Chen)
- bde2098: add support of CrisprOffTarget tasks (Zhiyuan Chen)
- 83572c7: set default value of head in code (Zhiyuan Chen)
- 3747c05: improve token initialisation (Zhiyuan Chen)
- 9a41985: support delete_existing in convert_checkpoint (Zhiyuan Chen)
- 8011687: ensure pooler consistency (Zhiyuan Chen)
- 57039f7: rename tokenizers -> tokenisers to avoid conflicts (Zhiyuan Chen)
- e06fb22: relax the input_ids in ContactPredictionHead (Zhiyuan Chen)
- e2702d3: use strameline vocab by default if nmers > 1 (Zhiyuan Chen)
- 4b1cd97: add KMerTokenHead (Zhiyuan Chen)
- 3f9ec11: add head for nucleotide-level tasks (Zhiyuan Chen)
- 91b0201: add support of Nucleotide level tasks (Zhiyuan Chen)
- 449b56e: pytest now fails under 50 (Zhiyuan Chen)
- cb98098: set default transform_act to gelu (Zhiyuan Chen)
- 8e31573: fix type hints (Zhiyuan Chen)
- f74b91f: inspect if input_ids is NestedTensor (Zhiyuan Chen)
- 4ff51f9: ignore convert_checkpoint.py in testing (Zhiyuan Chen)
- c7cebc7: unify typehints (Zhiyuan Chen)
- 6c53582: unify criterion & build criterion into head (Zhiyuan Chen)
- f8c825b: make multimolecule.module for shared modulet diff develop (Zhiyuan Chen)
- 5dfc33c: fix token & nucleodite head (Zhiyuan Chen)
- b0c2b63: use mcrmse for multi regression tasks (Zhiyuan Chen)
- ce325f0: allow additional kwargs in Nucleotide-level tasks (Zhiyuan Chen)
- b61796b: add AutoModelForNucleotideClassification & AutoModelForCrisprOffTarget (Zhiyuan Chen)
- b981919: set model_max_length in covert_checkpoint (Zhiyuan Chen)
- 0c850cb: fix rnamsm output (Zhiyuan Chen)
- c229a7d: add copyright header (Zhiyuan Chen)
- c47578c: fix head config (Zhiyuan Chen)
- 6856ad8: fix model_max_length of RnaFm Tokenizer (Zhiyuan Chen)

Commits
- 0f62c93: fix imports (Zhiyuan Chen)
- 573deee: update gitignore (Zhiyuan Chen)
- cd27502: improve RnaTokenizer (Zhiyuan Chen)
- 2bea376: rewrite heads (Zhiyuan Chen)
- 5fd3353: support kmer in tokenizer (Zhiyuan Chen)
- 9c96615: reorganise rnabert (Zhiyuan Chen)
- 061a554: add support of RnaMsm (Zhiyuan Chen)
- 0273c7b: add support of SpliceBert (Zhiyuan Chen)
- d831fbd: add support of RnaFm (Zhiyuan Chen)
- 5b22b8e: add support of UtrLm (Zhiyuan Chen)
- 3ff3d2f: add support of 3UTR-BERT (Zhiyuan Chen)
- ce31a79: add strameline vocab to avoid excessive mem in kmer (Zhiyuan Chen)

Commits
- 3188088: Unify RNA Tokenizer (Zhiyuan Chen)