---
tags:
- ColBERT
- PyLate
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:599884
- loss:KDLossWrapper
base_model: FremyCompany/BioLORD-2023
pipeline_tag: sentence-similarity
library_name: PyLate
---
# PyLate model based on FremyCompany/BioLORD-2023
This is a [PyLate](https://github.com/lightonai/pylate) model finetuned from [FremyCompany/BioLORD-2023](https://huggingface.co/FremyCompany/BioLORD-2023). 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:** [FremyCompany/BioLORD-2023](https://huggingface.co/FremyCompany/BioLORD-2023)
- **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: 599,884 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 |
donepezil (gh) 10 mg tablet, 60 | donepezil 10 mg oral tablet box of 60 | q2955867_0 | 43293533 | 715997 | donepezil 10 mg oral tablet box of 28 | donepezil 10 mg delayed release oral tablet box of 56 | donepezil 10 mg delayed release oral tablet box of 120 |
| 夓å¢ęæåé 2.0å
注å°å [ēęæę¬£] | ceftezole sodium 2000 mg injectable solution [yitixin] | q35876872_1 | 35871757 | 35872072 | ceftezole sodium 4000 mg injectable solution [yitixin] | ceftezole sodium 4000 mg injectable solution [yitixin] | ceftezole sodium 4000 mg injectable solution [yitixin] |
| acetaminophen 325mg, tramadol hcl 37.5mg | acetaminophen 325 mg / tramadol 37.5 mg oral tablet [tramacet] | q42386298_1 | 21111882 | 21131311 | azathioprine 50 mg oral tablet [azanin] | olanzapine 20 mg oral tablet [olanzapin 1a pharma] | levomenthol 6.5 mg/ml medicated liquid soap [pinimenthol] |
* Loss: thirawat_trainer.training.colbert.KDLossWrapper
### Evaluation Dataset
#### Unnamed Dataset
* Size: 2,287 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 |
|:--------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|
| type | string | string | string | int | int | string | string | string |
| details | clobazam 10mg/5ml oral suspension | clobazam 2 mg/ml oral suspension | q21276207_0 | 21025670 | 19050832 | clobazam 0.15 mg/ml oral suspension | clobazam 0.5 mg/ml oral suspension | clobazam 10 mg/ml oral solution |
| nappy rash soothing and healing (david hosking's) cream, 120 g | 120000 mg benzoin resin 0.01 mg/mg / camphor 0.01 mg/mg / lanolin 0.5 mg/mg / storax prepared 0.008 mg/mg / zinc oxide 0.15 mg/mg topical ointment [nappy rash soothing and healing] | q43329690_0 | 43281402 | 40161252 | 118 ml dibasic sodium phosphate heptahydrate 59.3 mg/ml / sodium phosphate, monobasic 161 mg/ml rectal solution [fleet ready-to-use] | 1 ml domperidone 10 mg/ml powder for oral suspension [nauzelin] | 70000 mg arnica extract 0.1 mg/mg topical ointment [arnikae] |
| 0.3 g clindamycin phosphate [kexinlin] | clindamycin 300 mg [kexinlin] | q36644900_0 | 35874078 | 19085270 | clindamycin 300 mg [zhuoli] | clindamycin 300 mg [clindamycin aristo] | clindamycin 300 mg [clindamycin billix] |
* Loss: thirawat_trainer.training.colbert.KDLossWrapper
### Training Hyperparameters
#### Non-Default Hyperparameters
- `eval_strategy`: epoch
- `per_device_train_batch_size`: 128
- `gradient_accumulation_steps`: 2
- `learning_rate`: 2e-05
- `warmup_ratio`: 0.1
- `bf16`: True
- `dataloader_num_workers`: 4
- `remove_unused_columns`: False
- `load_best_model_at_end`: True
#### All Hyperparameters