File size: 4,215 Bytes
3a65b5b 0412bc6 45207dc 3a65b5b 0412bc6 cd46fff 0412bc6 cd46fff 0412bc6 cd46fff 0412bc6 cd46fff 0412bc6 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 |
---
pipeline_tag: sentence-similarity
tags:
- sentence-transformers
- feature-extraction
- sentence-similarity
- transformers
widget:
- source_sentence: "The up-regulation of miR-146a was also detected in cervical cancer tissues."
sentences: ["The expression of miR-146a has been found to be up-regulated in cervical cancer.", "Only concomitant ablation of ERK1 and ERK2 impairs tumor growth."]
example_title: "BioNLP Example"
---
# kamalkraj/BioSimCSE-BioLinkBERT-BASE
This is a [sentence-transformers](https://www.SBERT.net) model: It maps sentences & paragraphs to a 768 dimensional dense vector space and can be used for tasks like clustering or semantic search.
<!--- Describe your model here -->
## Usage (Sentence-Transformers)
Using this model becomes easy when you have [sentence-transformers](https://www.SBERT.net) installed:
```
pip install -U sentence-transformers
```
Then you can use the model like this:
```python
from sentence_transformers import SentenceTransformer
sentences = ["This is an example sentence", "Each sentence is converted"]
model = SentenceTransformer('kamalkraj/BioSimCSE-BioLinkBERT-BASE')
embeddings = model.encode(sentences)
print(embeddings)
```
## Usage (HuggingFace Transformers)
Without [sentence-transformers](https://www.SBERT.net), you can use the model like this: First, you pass your input through the transformer model, then you have to apply the right pooling-operation on-top of the contextualized word embeddings.
```python
from transformers import AutoTokenizer, AutoModel
import torch
#Mean Pooling - Take attention mask into account for correct averaging
def mean_pooling(model_output, attention_mask):
token_embeddings = model_output[0] #First element of model_output contains all token embeddings
input_mask_expanded = attention_mask.unsqueeze(-1).expand(token_embeddings.size()).float()
return torch.sum(token_embeddings * input_mask_expanded, 1) / torch.clamp(input_mask_expanded.sum(1), min=1e-9)
# Sentences we want sentence embeddings for
sentences = ['This is an example sentence', 'Each sentence is converted']
# Load model from HuggingFace Hub
tokenizer = AutoTokenizer.from_pretrained('kamalkraj/BioSimCSE-BioLinkBERT-BASE')
model = AutoModel.from_pretrained('kamalkraj/BioSimCSE-BioLinkBERT-BASE')
# Tokenize sentences
encoded_input = tokenizer(sentences, padding=True, truncation=True, return_tensors='pt')
# Compute token embeddings
with torch.no_grad():
model_output = model(**encoded_input)
# Perform pooling. In this case, mean pooling.
sentence_embeddings = mean_pooling(model_output, encoded_input['attention_mask'])
print("Sentence embeddings:")
print(sentence_embeddings)
```
## Evaluation Results
<!--- Describe how your model was evaluated -->
For an automated evaluation of this model, see the *Sentence Embeddings Benchmark*: [https://seb.sbert.net](https://seb.sbert.net?model_name=kamalkraj/BioSimCSE-BioLinkBERT-BASE)
## Training
The model was trained with the parameters:
**DataLoader**:
`torch.utils.data.dataloader.DataLoader` of length 7708 with parameters:
```
{'batch_size': 128, 'sampler': 'torch.utils.data.sampler.RandomSampler', 'batch_sampler': 'torch.utils.data.sampler.BatchSampler'}
```
**Loss**:
`sentence_transformers.losses.MultipleNegativesRankingLoss.MultipleNegativesRankingLoss` with parameters:
```
{'scale': 20.0, 'similarity_fct': 'cos_sim'}
```
Parameters of the fit()-Method:
```
{
"epochs": 1,
"evaluation_steps": 0,
"evaluator": "NoneType",
"max_grad_norm": 1,
"optimizer_class": "<class 'torch.optim.adamw.AdamW'>",
"optimizer_params": {
"lr": 5e-05
},
"scheduler": "WarmupLinear",
"steps_per_epoch": null,
"warmup_steps": 771,
"weight_decay": 0.01
}
```
## Full Model Architecture
```
SentenceTransformer(
(0): Transformer({'max_seq_length': 128, 'do_lower_case': False}) with Transformer model: BertModel
(1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False})
)
```
## Citing & Authors
<!--- Describe where people can find more information --> |