---
tags:
- ColBERT
- PyLate
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:598752
- loss:KDLossWrapper
base_model: cambridgeltl/SapBERT-UMLS-2020AB-all-lang-from-XLMR
pipeline_tag: sentence-similarity
library_name: PyLate
---
# PyLate model based on cambridgeltl/SapBERT-UMLS-2020AB-all-lang-from-XLMR
This is a [PyLate](https://github.com/lightonai/pylate) model finetuned from [cambridgeltl/SapBERT-UMLS-2020AB-all-lang-from-XLMR](https://huggingface.co/cambridgeltl/SapBERT-UMLS-2020AB-all-lang-from-XLMR). It maps sentences & paragraphs to sequences of 128-dimensional dense vectors and can be used for semantic textual similarity using the MaxSim operator.
## Model Details
### Model Description
- **Model Type:** PyLate model
- **Base model:** [cambridgeltl/SapBERT-UMLS-2020AB-all-lang-from-XLMR](https://huggingface.co/cambridgeltl/SapBERT-UMLS-2020AB-all-lang-from-XLMR)
- **Document Length:** 96 tokens
- **Query Length:** 96 tokens
- **Output Dimensionality:** 128 tokens
- **Similarity Function:** MaxSim
### Model Sources
- **Documentation:** [PyLate Documentation](https://lightonai.github.io/pylate/)
- **Repository:** [PyLate on GitHub](https://github.com/lightonai/pylate)
- **Hugging Face:** [PyLate models on Hugging Face](https://huggingface.co/models?library=PyLate)
### Full Model Architecture
```
ColBERT(
(0): Transformer({'max_seq_length': 95, 'do_lower_case': False, 'architecture': 'PeftModelForFeatureExtraction'})
(1): Dense({'in_features': 768, 'out_features': 128, 'bias': False, 'activation_function': 'torch.nn.modules.linear.Identity', 'use_residual': False})
)
```
## Usage
First install the PyLate library:
```bash
pip install -U pylate
```
### Retrieval
Use this model with PyLate to index and retrieve documents. The index uses [FastPLAID](https://github.com/lightonai/fast-plaid) for efficient similarity search.
#### Indexing documents
Load the ColBERT model and initialize the PLAID index, then encode and index your documents:
```python
from pylate import indexes, models, retrieve
# Step 1: Load the ColBERT model
model = models.ColBERT(
model_name_or_path="pylate_model_id",
)
# Step 2: Initialize the PLAID index
index = indexes.PLAID(
index_folder="pylate-index",
index_name="index",
override=True, # This overwrites the existing index if any
)
# Step 3: Encode the documents
documents_ids = ["1", "2", "3"]
documents = ["document 1 text", "document 2 text", "document 3 text"]
documents_embeddings = model.encode(
documents,
batch_size=32,
is_query=False, # Ensure that it is set to False to indicate that these are documents, not queries
show_progress_bar=True,
)
# Step 4: Add document embeddings to the index by providing embeddings and corresponding ids
index.add_documents(
documents_ids=documents_ids,
documents_embeddings=documents_embeddings,
)
```
Note that you do not have to recreate the index and encode the documents every time. Once you have created an index and added the documents, you can re-use the index later by loading it:
```python
# To load an index, simply instantiate it with the correct folder/name and without overriding it
index = indexes.PLAID(
index_folder="pylate-index",
index_name="index",
)
```
#### Retrieving top-k documents for queries
Once the documents are indexed, you can retrieve the top-k most relevant documents for a given set of queries.
To do so, initialize the ColBERT retriever with the index you want to search in, encode the queries and then retrieve the top-k documents to get the top matches ids and relevance scores:
```python
# Step 1: Initialize the ColBERT retriever
retriever = retrieve.ColBERT(index=index)
# Step 2: Encode the queries
queries_embeddings = model.encode(
["query for document 3", "query for document 1"],
batch_size=32,
is_query=True, # # Ensure that it is set to False to indicate that these are queries
show_progress_bar=True,
)
# Step 3: Retrieve top-k documents
scores = retriever.retrieve(
queries_embeddings=queries_embeddings,
k=10, # Retrieve the top 10 matches for each query
)
```
### Reranking
If you only want to use the ColBERT model to perform reranking on top of your first-stage retrieval pipeline without building an index, you can simply use rank function and pass the queries and documents to rerank:
```python
from pylate import rank, models
queries = [
"query A",
"query B",
]
documents = [
["document A", "document B"],
["document 1", "document C", "document B"],
]
documents_ids = [
[1, 2],
[1, 3, 2],
]
model = models.ColBERT(
model_name_or_path="pylate_model_id",
)
queries_embeddings = model.encode(
queries,
is_query=True,
)
documents_embeddings = model.encode(
documents,
is_query=False,
)
reranked_documents = rank.rerank(
documents_ids=documents_ids,
queries_embeddings=queries_embeddings,
documents_embeddings=documents_embeddings,
)
```
## Training Details
### Training Dataset
#### Unnamed Dataset
* Size: 598,752 training samples
* Columns: query, positive, query_id, target_id, group_id, negative_0, negative_1, and negative_2
* Approximate statistics based on the first 1000 samples:
| | query | positive | query_id | target_id | group_id | negative_0 | negative_1 | negative_2 |
|:--------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:---------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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| type | string | string | string | int | int | string | string | string |
| details |
åøę“č¬ ēå [åÆę®č¬] | ibuprofen oral tablet [kepufen] | q36653233_0 | 35870422 | 1177480 | ibuprofen topical ointment [vesicum] | ibuprofen extended release oral tablet [ibu 1a pharma] | ibuprofen oral tablet [jamp-ibuprofen] |
| avapro hct 300/12.5 tablet, 30 | hydrochlorothiazide 12.5 mg / irbesartan 300 mg oral tablet [avapro hct] box of 30 | q43362350_0 | 2936189 | 19081559 | hydrochlorothiazide 25 mg / irbesartan 300 mg delayed release oral tablet [irbesartan hydrochlorothiazide teva] box of 28 | hydrochlorothiazide 25 mg / irbesartan 300 mg oral tablet [irbesartan bz] box of 98 | hydrochlorothiazide 25 mg / irbesartan 300 mg delayed release oral tablet [karvezide] box of 280 |
| povidone-iodine (pfizer (perth)) 10% application, 500 ml, bottle | 500 ml povidone-iodine 100 mg/ml transdermal system by pfizer | q43321701_0 | 2907294 | 19083433 | 30 ml povidone-iodine 100 mg/ml topical solution by pfizer | 125 ml povidone-iodine 100 mg/ml topical solution [povidone iodee mylan] box of 1 by mylan | 100 ml povidone-iodine 100 mg/ml topical solution by bittermedizin |
* Loss: thirawat_trainer.training.colbert.KDLossWrapper
### Evaluation Dataset
#### Unnamed Dataset
* Size: 2,270 evaluation samples
* Columns: query, positive, query_id, target_id, group_id, negative_0, negative_1, and negative_2
* Approximate statistics based on the first 1000 samples:
| | query | positive | query_id | target_id | group_id | negative_0 | negative_1 | negative_2 |
|:--------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:---------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|
| type | string | string | string | int | int | string | string | string |
| details | fentanyl 100 microgram/hour patch, 5 | fentanyl 0.1 mg/hr transdermal system | q43342123_0 | 42902560 | 1154029 | fentanyl 0.158 mg/actuat nasal spray | fentanyl 0.05 mg/ml nasal spray | fentanyl 1.89 mg unknown combination pack medical aids |
| sodium benzoate 1.83g/5ml oral solution | benzoate 366 mg/ml oral solution | q21235913_0 | 21119205 | 21119204 | sodium chloride 23.2 mg/ml oral solution | fluticasone 0.125 mg/actuat inhalation powder | chlorhexidine 0.00001 mg/ml oral solution |
| meloxicam - meloxicam tablet | meloxicam 15 mg oral tablet | q45623828_0 | 1150347 | 1150347 | econazole 0.0314 mg/mg topical cream | nabumetone 400 mg oral tablet | domestic cow skin extract 50 mg/ml injectable solution |
* Loss: thirawat_trainer.training.colbert.KDLossWrapper
### Training Hyperparameters
#### Non-Default Hyperparameters
- `eval_strategy`: epoch
- `per_device_train_batch_size`: 64
- `gradient_accumulation_steps`: 2
- `learning_rate`: 2e-05
- `num_train_epochs`: 2
- `warmup_ratio`: 0.1
- `bf16`: True
- `dataloader_num_workers`: 4
- `remove_unused_columns`: False
#### All Hyperparameters