Feature Extraction
Transformers
PyTorch
Safetensors
English
t5
text2text-generation
protein language model
computational-biology
high-performance-computing
machine-learning
language-modeling
deep-learning
proteins
chemistry
natural-language-processing
rostlab
virtual-human-chc
Instructions to use virtual-human-chc/prot_t5_xl_uniref50 with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use virtual-human-chc/prot_t5_xl_uniref50 with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("feature-extraction", model="virtual-human-chc/prot_t5_xl_uniref50")# Load model directly from transformers import AutoTokenizer, AutoModelForSeq2SeqLM tokenizer = AutoTokenizer.from_pretrained("virtual-human-chc/prot_t5_xl_uniref50") model = AutoModelForSeq2SeqLM.from_pretrained("virtual-human-chc/prot_t5_xl_uniref50", device_map="auto") - Notebooks
- Google Colab
- Kaggle
Update README.md
Browse files
README.md
CHANGED
|
@@ -72,16 +72,6 @@ ProtT5-XL-UniRef50 is part of the **ProtTrans** family of models developed by **
|
|
| 72 |
- Rare or undetermined amino acids `"U, Z, O, B"` are mapped to `"X"`.
|
| 73 |
- Tokenization: spaces are inserted between amino acids, and special tokens are added.
|
| 74 |
|
| 75 |
-
### Output
|
| 76 |
-
|
| 77 |
-
- **Description:** Each amino acid is represented by a 1024-dimensional vector.
|
| 78 |
-
- **Output format:** tensor
|
| 79 |
-
- **Shape:** `[n, max_seq_len, 1024]` with `max_seq_len` the longest sequences (max of `m`)
|
| 80 |
-
- **Data format:** *(float)*
|
| 81 |
-
- **Postprocessing:**
|
| 82 |
-
- Per-protein embeddings are obtained by averaging the residue embeddings across the sequence.
|
| 83 |
-
- Averaged embedding size: `[n, 1024]`
|
| 84 |
-
|
| 85 |
### Model
|
| 86 |
|
| 87 |
- **Modality:** Protein sequences
|
|
@@ -92,7 +82,16 @@ ProtT5-XL-UniRef50 is part of the **ProtTrans** family of models developed by **
|
|
| 92 |
- Embeddings capture biophysical and structural information such as secondary structure, localization, and membrane properties.
|
| 93 |
- **Training data:**
|
| 94 |
- Pretrained on **UniRef50**, a non-redundant dataset of ~45 million protein sequences.
|
| 95 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 96 |
|
| 97 |
## Installation
|
| 98 |
|
|
|
|
| 72 |
- Rare or undetermined amino acids `"U, Z, O, B"` are mapped to `"X"`.
|
| 73 |
- Tokenization: spaces are inserted between amino acids, and special tokens are added.
|
| 74 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 75 |
### Model
|
| 76 |
|
| 77 |
- **Modality:** Protein sequences
|
|
|
|
| 82 |
- Embeddings capture biophysical and structural information such as secondary structure, localization, and membrane properties.
|
| 83 |
- **Training data:**
|
| 84 |
- Pretrained on **UniRef50**, a non-redundant dataset of ~45 million protein sequences.
|
| 85 |
+
|
| 86 |
+
### Output
|
| 87 |
+
|
| 88 |
+
- **Description:** Each amino acid is represented by a 1024-dimensional vector.
|
| 89 |
+
- **Output format:** tensor
|
| 90 |
+
- **Shape:** `[n, max_seq_len, 1024]` with `max_seq_len` the longest sequences (max of `m`)
|
| 91 |
+
- **Data format:** *(float)*
|
| 92 |
+
- **Postprocessing:**
|
| 93 |
+
- Per-protein embeddings are obtained by averaging the residue embeddings across the sequence.
|
| 94 |
+
- Averaged embedding size: `[n, 1024]`
|
| 95 |
|
| 96 |
## Installation
|
| 97 |
|