Update README.md

README.md

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-# Model Card for Model ID
-
-<!-- Provide a quick summary of what the model is/does. -->
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-
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-## Model Details
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-### Model Description
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-<!-- Provide a longer summary of what this model is. -->
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-This is the model card of a 🤗 transformers model that has been pushed on the Hub. This model card has been automatically generated.
-
-- **Developed by:** [More Information Needed]
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-### Model Sources [optional]
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-## Uses
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-<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->
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-### Direct Use
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-<!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. -->
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-### Downstream Use [optional]
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-<!-- This section is for the model use when fine-tuned for a task, or when plugged into a larger ecosystem/app -->
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-### Out-of-Scope Use
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-## Bias, Risks, and Limitations
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-### Recommendations
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-<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
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-Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
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-## How to Get Started with the Model
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-Use the code below to get started with the model.
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-## Training Details
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-### Training Data
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-<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
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-### Training Procedure
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-#### Preprocessing [optional]
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-#### Training Hyperparameters
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-- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->
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-#### Speeds, Sizes, Times [optional]
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-<!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. -->
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-## Evaluation
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-<!-- This section describes the evaluation protocols and provides the results. -->
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-### Testing Data, Factors & Metrics
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-#### Testing Data
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-#### Factors
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-<!-- These are the things the evaluation is disaggregating by, e.g., subpopulations or domains. -->
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-#### Metrics
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-### Results
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-#### Summary
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-## Model Examination [optional]
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-<!-- Relevant interpretability work for the model goes here -->
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-## Environmental Impact
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-<!-- Total emissions (in grams of CO2eq) and additional considerations, such as electricity usage, go here. Edit the suggested text below accordingly -->
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-Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).
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-- **Hardware Type:** [More Information Needed]
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-## Technical Specifications [optional]
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-### Model Architecture and Objective
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-### Compute Infrastructure
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-#### Hardware
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-#### Software
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-## Citation [optional]
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-**BibTeX:**
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-**APA:**
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-## Glossary [optional]
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-<!-- If relevant, include terms and calculations in this section that can help readers understand the model or model card. -->
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-## More Information [optional]
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-## Model Card Authors [optional]
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-## Model Card Contact
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+# FastESM
+FastESM is a Huggingface compatible plug in version of ESM2 rewritten with a newer PyTorch attention implementation.
+
+Load any ESM2 models into a FastEsm model to dramatically speed up training and inference without **ANY** cost in performance.
+
+Outputting attention maps (or the contact prediction head) is not natively possible with SDPA. You can still pass ```output_attentions``` to have attention calculated manually and returned.
+Various other optimizations also make the base implementation slightly different than the one in transformers.
+
+## Use with 🤗 transformers
+
+### For working with embeddings
+```python
+import torch
+from transformers import AutoModel, AutoTokenizer
+
+model_path = 'Synthyra/ESM2-650M'
+model = AutoModel.from_pretrained(model_path, torch_dtype=torch.float16, trust_remote_code=True).eval()
+tokenizer = model.tokenizer
+
+sequences = ['MPRTEIN', 'MSEQWENCE']
+tokenized = tokenizer(sequences, padding=True, return_tensors='pt')
+with torch.no_grad():
+    embeddings = model(**tokenized).last_hidden_state
+
+print(embeddings.shape) # (2, 11, 1280)
+```
+
+### For working with sequence logits
+```python
+import torch
+from transformers import AutoModelForMaskedLM, AutoTokenizer
+
+model = AutoModelForMaskedLM.from_pretrained(model_path, torch_dtype=torch.float16, trust_remote_code=True).eval()
+with torch.no_grad():
+    logits = model(**tokenized).logits
+
+print(logits.shape) # (2, 11, 33)
+```
+
+### For working with attention maps
+```python
+import torch
+from transformers import AutoModel, AutoTokenizer
+
+model = AutoModel.from_pretrained(model_path, torch_dtype=torch.float16, trust_remote_code=True).eval()
+with torch.no_grad():
+    attentions = model(**tokenized, output_attentions).attentions # tuples of (batch_size, num_heads, seq_len, seq_len)
+
+print(attentions[-1].shape) # (2, 20, 11, 11) 
+```
+
+## Embed entire datasets with no new code
+To embed a list of protein sequences **fast**, just call embed_dataset. Sequences are sorted to reduce padding tokens, so the initial progress bar estimation is usually much longer than the actual time.
+```python
+embeddings = model.embed_dataset(
+    sequences=sequences, # list of protein strings
+    batch_size=16, # embedding batch size
+    max_len=2048, # truncate to max_len
+    full_embeddings=True, # return residue-wise embeddings
+    full_precision=False, # store as float32
+    pooling_type='mean', # use mean pooling if protein-wise embeddings
+    num_workers=0, # data loading num workers
+    sql=False, # return dictionary of sequences and embeddings
+)
+
+_ = model.embed_dataset(
+    sequences=sequences, # list of protein strings
+    batch_size=16, # embedding batch size
+    max_len=2048, # truncate to max_len
+    full_embeddings=True, # return residue-wise embeddings
+    full_precision=False, # store as float32
+    pooling_type='mean', # use mean pooling if protein-wise embeddings
+    num_workers=0, # data loading num workers
+    sql=True, # store sequences in local SQL database
+    sql_db_path='embeddings.db', # path to .db file of choice
+)
+```
+
+
+### Citation
+If you use any of this implementation or work please cite it (as well as the [ESM2](https://www.science.org/doi/10.1126/science.ade2574) paper).
+```
+@misc {FastESM2,
+	author       = { Hallee, L. and Bichara, D. and Gleghorn, J, P. },
+	title        = { FastESM2 },
+	year         = 2024,
+	url          = { https://huggingface.co/Synthyra/FastESM2_650 },
+	doi          = { 10.57967/hf/3729 },
+	publisher    = { Hugging Face }
+}
+```