albert-base-v2

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esm2_t6_8M_UR50D

AI at Meta

ESM-2 is a state-of-the-art protein model trained on a masked language modelling objective. It is suitable for fine-tuning on a wide range of tasks that take protein sequences as input. For detailed information on the model architecture and training data, please refer to the accompanying paper. You may also be interested in some demo notebooks (PyTorch, TensorFlow) which demonstrate how to fine-tune ESM-2 models on your tasks of interest. Several ESM-2 checkpoints are available in the Hub with varying sizes. Larger sizes generally have somewhat better accuracy, but require much more memory and time to train

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caduceus-ps_seqlen-131k_d_model-256_n_layer-16

Kuleshov Group

To use the pre-trained model for masked language modeling, use the following snippet: Alternatively, you can instantiate a model from scratch to train on your own data as follows: This is the Caduceus-PS model with hidden dimension 256 and 16 MambaDNA layers. This model is reverse complement (RC) equivariant and thus no RC data augmentation is required when training this model, either during pre-training or for downstream fine-tuning. Note that the model hidden state will be twice that of a non-RC equivariant counterpart. For downstream task training and inference, and to ensure RC invariant outputs at downstream time, one can either run the downstream model on the hidden state and its RC…

Model · Fill mask

caduceus-ph_seqlen-131k_d_model-256_n_layer-16

Kuleshov Group

To use the pre-trained model for masked language modeling, use the following snippet: Alternatively, you can instantiate a model from scratch to train on your own data as follows: This is the Caduceus-Ph model with hidden dimension 256 and 16 MambaDNA layers. This model is not inherently reverse complement (RC) equivariant. Rather, it was pre-trained using RC data augmentation. Its intended usage is as follows: for downstream tasks, the model should be trained with RC data augmentation. At downstream task inference, the model should be run twice: once on a sequence and once on its RC. The output of these two applications should be combined (averaged) to form the downstream task prediction.…

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mdeberta-v3-base

Microsoft

DeBERTa improves the BERT and RoBERTa models using disentangled attention and enhanced mask decoder. With those two improvements, DeBERTa out perform RoBERTa on a majority of NLU tasks with 80GB training data. In DeBERTa V3, we further improved the efficiency of DeBERTa using ELECTRA-Style pre-training with Gradient Disentangled Embedding Sharing. Compared to DeBERTa, our V3 version significantly improves the model performance on downstream tasks. You can find more technique details about the new model from our paper. Please check the official repository for more implementation details and updates. mDeBERTa is multilingual version of DeBERTa which use the same structure as DeBERTa and was…

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deberta-v3-base

Microsoft

DeBERTa improves the BERT and RoBERTa models using disentangled attention and enhanced mask decoder. With those two improvements, DeBERTa out perform RoBERTa on a majority of NLU tasks with 80GB training data. In DeBERTa V3, we further improved the efficiency of DeBERTa using ELECTRA-Style pre-training with Gradient Disentangled Embedding Sharing. Compared to DeBERTa, our V3 version significantly improves the model performance on downstream tasks. You can find more technique details about the new model from our paper. Please check the official repository for more implementation details and updates. The DeBERTa V3 base model comes with 12 layers and a hidden size of 768. It has only 86M…

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Bio_ClinicalBERT

Emily Alsentzer

The Publicly Available Clinical BERT Embeddings paper contains four unique clinicalBERT models: initialized with BERT-Base (casedL-12H-768A-12) or BioBERT (BioBERT-Base v1.0 + PubMed 200K + PMC 270K) & trained on either all MIMIC notes or only discharge summaries. This model card describes the Bio+Clinical BERT model, which was initialized from BioBERT & trained on all MIMIC notes. The BioClinicalBERT model was trained on all notes from MIMIC III, a database containing electronic health records from ICU patients at the Beth Israel Hospital in Boston, MA. For more details on MIMIC, see here. All notes from the NOTEEVENTS table were included (~880M words). Each note in MIMIC was first split…