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README.md

@@ -11,19 +11,30 @@ Load any ESM2 models into a FastEsm model to dramatically speed up training and
 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.
 
-# FastESM2-650
-
-## A faster half-precision version of ESM2-650 with FlashAttention2 and longer context
-To enhance the weights with longer context and better fp16 support, we trained ESM2-650 50000 additional steps with a traditional MLM objective (20% masking) in fp16 mixed precision on [OMGprot50](https://huggingface.co/datasets/tattabio/OMG_prot50) up to sequence length of **2048**.
-
 ## Use with 🤗 transformers
 
+### Supported models
+```python
+model_dict = {
+    # Synthyra/ESM2-8M
+    'ESM2-8M': 'facebook/esm2_t6_8M_UR50D',
+    # Synthyra/ESM2-35M
+    'ESM2-35M': 'facebook/esm2_t12_35M_UR50D',
+    # Synthyra/ESM2-150M
+    'ESM2-150M': 'facebook/esm2_t30_150M_UR50D',
+    # Synthyra/ESM2-650M
+    'ESM2-650M': 'facebook/esm2_t33_650M_UR50D',
+    # Synthyra/ESM2-3B
+    'ESM2-3B': 'facebook/esm2_t36_3B_UR50D',
+}
+```
+
 ### For working with embeddings
 ```python
 import torch
 from transformers import AutoModel, AutoTokenizer
 
-model_path = 'Synthyra/FastESM2_650'
+model_path = 'Synthyra/ESM2-8M'
 model = AutoModel.from_pretrained(model_path, torch_dtype=torch.float16, trust_remote_code=True).eval()
 tokenizer = model.tokenizer
 
@@ -59,52 +70,61 @@ with torch.no_grad():
 print(attentions[-1].shape) # (2, 20, 11, 11) 
 ```
 
+### Contact prediction
+Because we can output attentions using the naive attention implementation, the contact prediction is also supported
+```python
+with torch.no_grad():
+    contact_map = model.predict_contacts(**tokenized).squeeze().cpu().numpy() # (seq_len, seq_len)
+```
+![image/png](https://cdn-uploads.huggingface.co/production/uploads/62f2bd3bdb7cbd214b658c48/9707OSXZ3Wdgn0Ni-55T-.png)
 
 ## 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
-)
+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 it will take.
 
-_ = 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
+Example:
+```python
+embedding_dict = model.embed_dataset(
+    sequences=[
+        'MALWMRLLPLLALLALWGPDPAAA', ... # list of protein sequences
+    ],
+    batch_size=2, # adjust for your GPU memory
+    max_len=512, # adjust for your needs
+    full_embeddings=False, # if True, no pooling is performed
+    embed_dtype=torch.float32, # cast to what dtype you want
+    pooling_type=['mean', 'cls'], # more than one pooling type will be concatenated together
+    num_workers=0, # if you have many cpu cores, we find that num_workers = 4 is fast for large datasets
+    sql=False, # if True, embeddings will be stored in SQLite database
+    sql_db_path='embeddings.db',
+    save=True, # if True, embeddings will be saved as a .pth file
+    save_path='embeddings.pth',
 )
+# embedding_dict is a dictionary mapping sequences to their embeddings as tensors for .pth or numpy arrays for sql
 ```
 
-## Model probes
-We employ linear probing techniques on various PLMs and standard datasets, similar our previous [paper](https://www.biorxiv.org/content/10.1101/2024.07.30.605924v1), to assess the intrinsic correlation between pooled hidden states and valuable properties. FastESM performs very well.
-
-The plot below showcases performance normalized between the negative control (random vector embeddings) and the best performer. Classification task scores are averaged between MCC and F1 (or F1max for multilabel) and regression tasks are averaged between Spearman rho and R2.
-![image/png](https://cdn-uploads.huggingface.co/production/uploads/62f2bd3bdb7cbd214b658c48/d1Xi6k1Q4-9By_MtzTvdV.png)
-
-## Comparison of half precisions
-Presumabely because we trained in mixed-precision fp16, fp16 has closer outputs to the fp32 weights then bf16. Therefore, we recommend loading in fp16.
-
-When summing the MSE of 1000 sequences vs. the fp32 weights:
-
-Average MSE for FP16: 0.00000140
-
-Average MSE for BF16: 0.00004125
+```
+model.embed_dataset()
+Args:
+    sequences: List of protein sequences
+    batch_size: Batch size for processing
+    max_len: Maximum sequence length
+    full_embeddings: Whether to return full residue-wise (True) embeddings or pooled (False)
+    pooling_type: Type of pooling ('mean' or 'cls')
+    num_workers: Number of workers for data loading, 0 for the main process
+    sql: Whether to store embeddings in SQLite database - will be stored in float32
+    sql_db_path: Path to SQLite database
+    
+Returns:
+    Dictionary mapping sequences to embeddings, or None if sql=True
+
+Note:
+    - If sql=True, embeddings can only be stored in float32
+    - sql is ideal if you need to stream a very large dataset for training in real-time
+    - save=True is ideal if you can store the entire embedding dictionary in RAM
+    - sql will be used if it is True and save is True or False
+    - If your sql database or .pth file is already present, they will be scanned first for already embedded sequences
+    - Sequences will be truncated to max_len and sorted by length in descending order for faster processing
+```
 
-### Inference speed
-We look at various ESM models and their throughput on an H100. FastESM is over twice as fast as ESM2-650 with longer sequences. Requires PyTorch 2.5+ for the most savings, see [SDPA](https://pytorch.org/docs/stable/generated/torch.nn.functional.scaled_dot_product_attention.html).
-![image/png](https://cdn-uploads.huggingface.co/production/uploads/62f2bd3bdb7cbd214b658c48/PvaBGfuJXEW2v_WLkt63y.png)
 
 ### 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).
@@ -117,4 +137,4 @@ If you use any of this implementation or work please cite it (as well as the [ES
 	doi          = { 10.57967/hf/3729 },
 	publisher    = { Hugging Face }
 }
-```
+```