Initial version

README.md

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+---
+pipeline_tag: sentence-similarity
+tags:
+- sentence-transformers
+- feature-extraction
+- sentence-similarity
+- transformers
+- embeddings
+- static-embeddings
+language: en
+license: apache-2.0
+---
+
+# PubMedBERT Embeddings 2M
+
+This is a distilled version of [PubMedBERT Embeddings](https://huggingface.co/NeuML/pubmedbert-base-embeddings) using the [Model2Vec](https://github.com/MinishLab/model2vec) library. It uses static embeddings, allowing text embeddings to be computed orders of magnitude faster on both GPU and CPU. It is designed for applications where computational resources are limited or where real-time performance is critical.
+
+## Usage (txtai)
+
+This model can be used to build embeddings databases with [txtai](https://github.com/neuml/txtai) for semantic search and/or as a knowledge source for retrieval augmented generation (RAG).
+
+```python
+import txtai
+
+# Create embeddings
+embeddings = txtai.Embeddings(
+  path="neuml/pubmedbert-base-embeddings-2M",
+  content=True,
+)
+embeddings.index(documents())
+
+# Run a query
+embeddings.search("query to run")
+```
+
+## Usage (Sentence-Transformers)
+
+Alternatively, the model can be loaded with [sentence-transformers](https://www.SBERT.net).
+
+```python
+from sentence_transformers import SentenceTransformer
+from sentence_transformers.models import StaticEmbedding
+
+# Initialize a StaticEmbedding module
+static = StaticEmbedding.from_model2vec("neuml/pubmedbert-base-embeddings-2M")
+model = SentenceTransformer(modules=[static])
+
+sentences = ["This is an example sentence", "Each sentence is converted"]
+embeddings = model.encode(sentences)
+print(embeddings)
+```
+
+## Usage (Model2Vec)
+
+The model can also be used directly with Model2Vec.
+
+```python
+from model2vec import StaticModel
+
+# Load a pretrained Model2Vec model
+model = StaticModel.from_pretrained("neuml/pubmedbert-base-embeddings-2M")
+
+# Compute text embeddings
+sentences = ["This is an example sentence", "Each sentence is converted"]
+embeddings = model.encode(sentences)
+print(embeddings)
+```
+
+## Evaluation Results
+
+The following compares performance of this model against the models previously compared with [PubMedBERT Embeddings](https://huggingface.co/NeuML/pubmedbert-base-embeddings#evaluation-results). The following datasets were used to evaluate model performance.
+
+- [PubMed QA](https://huggingface.co/datasets/pubmed_qa)
+  - Subset: pqa_labeled, Split: train, Pair: (question, long_answer)
+- [PubMed Subset](https://huggingface.co/datasets/awinml/pubmed_abstract_3_1k)
+  - Split: test, Pair: (title, text)
+  - _Note: The previously used [PubMed Subset](https://huggingface.co/datasets/zxvix/pubmed_subset_new) dataset is no longer available but a similar dataset is used here_
+- [PubMed Summary](https://huggingface.co/datasets/scientific_papers)
+  - Subset: pubmed, Split: validation, Pair: (article, abstract)
+
+The [Pearson correlation coefficient](https://en.wikipedia.org/wiki/Pearson_correlation_coefficient) is used as the evaluation metric.
+
+| Model                                                                              | PubMed QA | PubMed Subset | PubMed Summary | Average   |
+| ---------------------------------------------------------------------------------- | --------- | ------------- | -------------- | --------- |
+| [all-MiniLM-L6-v2](https://hf.co/sentence-transformers/all-MiniLM-L6-v2)           | 90.40     | 95.92         | 94.07          | 93.46     |
+| [bge-base-en-v1.5](https://hf.co/BAAI/bge-base-en-v1.5)                            | 91.02     | 95.82         | 94.49          | 93.78     |
+| [gte-base](https://hf.co/thenlper/gte-base)                                        | 92.97     | 96.90         | 96.24          | 95.37     |
+| [**pubmedbert-base-embeddings-2M**](https://hf.co/neuml/pubmedbert-base-embeddings-2M) | **88.62**     | **93.08**         | **93.24**          | **91.65**     |
+| [pubmedbert-base-embeddings-8M](https://hf.co/neuml/pubmedbert-base-embeddings-8M) | 90.05     | 94.29         | 94.15          | 92.83     |
+| [pubmedbert-base-embeddings](https://hf.co/neuml/pubmedbert-base-embeddings)       | 93.27     | 97.00         | 96.58          | 95.62     |
+| [S-PubMedBert-MS-MARCO](https://hf.co/pritamdeka/S-PubMedBert-MS-MARCO)            | 90.86     | 93.68         | 93.54          | 92.69     |
+
+As we can see, this model while not the top scoring model is certainly competitive.
+
+## Runtime performance
+
+As another test, let's see how long each model takes to index 120K article abstracts using the following code. All indexing is done with a RTX 3090 GPU. 
+
+```python
+from datasets import load_dataset
+from tqdm import tqdm
+from txtai import Embeddings
+
+ds = load_dataset("ccdv/pubmed-summarization", split="train")
+
+embeddings = Embeddings(path="path to model", content=True, backend="numpy")
+embeddings.index(tqdm(ds["abstract"]))
+```
+
+| Model                                                                              | Params (M) | Index time (s) |
+| ---------------------------------------------------------------------------------- | ---------- | -------------- |
+| [all-MiniLM-L6-v2](https://hf.co/sentence-transformers/all-MiniLM-L6-v2)           | 22         | 117            |
+| BM25                                                                               | -          | 18             |
+| [bge-base-en-v1.5](https://hf.co/BAAI/bge-base-en-v1.5)                            | 109        | 518            |
+| [gte-base](https://hf.co/thenlper/gte-base)                                        | 109        | 523            | 
+| [**pubmedbert-base-embeddings-2M**](https://hf.co/neuml/pubmedbert-base-embeddings-2M) | **2**  | **17**         |
+| [pubmedbert-base-embeddings-8M](https://hf.co/neuml/pubmedbert-base-embeddings-8M) | 8  | 18         |
+| [pubmedbert-base-embeddings](https://hf.co/neuml/pubmedbert-base-embeddings)       | 109        | 462            |
+| [S-PubMedBert-MS-MARCO](https://hf.co/pritamdeka/S-PubMedBert-MS-MARCO)            | 109        | 465            |
+
+Clearly a static model's main upside is speed. It's important to note that if storage savings is the only concern, then take a look at [PubMedBERT Embeddings Matryoshka](https://huggingface.co/NeuML/pubmedbert-base-embeddings-matryoshka). The 256 dimension model scores higher than this model, so does the 64 dimension model. The tradeoff is that the runtime performance is still as slow as the base model.
+
+If runtime performance is the major concern, then a static model offers the best blend of accuracy and speed. Model2Vec models only need CPUs to run, no GPU required. Note how this model takes the same amount of time as building a BM25 index, which is normally an order of magnitude faster than vector models.
+
+## Training
+
+This model was trained using the [Tokenlearn](https://github.com/MinishLab/tokenlearn) library. First data was featurized with the following script.
+
+```bash
+python -m tokenlearn.featurize --model-name "neuml/pubmedbert-base-embeddings" --dataset-path "training-articles" --output-dir "features"
+```
+
+_Note that the same random sample of articles as [described here](https://medium.com/neuml/embeddings-for-medical-literature-74dae6abf5e0) are used for the dataset `training-articles`._
+
+From there, the following training script builds the model. The final model is weighted using [BM25](https://en.wikipedia.org/wiki/Okapi_BM25) instead of the default SIF weighting method. 
+
+```python
+from pathlib import Path
+
+import numpy as np
+
+from model2vec import StaticModel
+from more_itertools import batched
+from sklearn.decomposition import PCA
+from tokenlearn.train import collect_means_and_texts, train_model
+from tqdm import tqdm
+from txtai.scoring import ScoringFactory
+
+def tokenweights():
+  tokenizer = model.tokenizer
+
+  # Tokenize into dataset
+  dataset = []
+  for t in tqdm(batched(texts, 1024)):
+      encodings = tokenizer.encode_batch_fast(t, add_special_tokens=False)
+      for e in encodings:
+          dataset.append((None, e.ids, None))
+
+  # Build scoring index
+  scoring = ScoringFactory.create({"method": "bm25", "terms": True})
+  scoring.index(dataset)
+
+  # Calculate mean value of weights array per token
+  tokens = np.zeros(tokenizer.get_vocab_size())
+  for token in scoring.idf:
+    tokens[token] = np.mean(scoring.terms.weights(token)[1])
+
+  return tokens
+
+# Collect paths for training data
+paths = sorted(Path("features").glob("*.json"))
+texts, vectors = collect_means_and_texts(paths)
+
+# Train the model
+model = train_model("neuml/pubmedbert-base-embeddings", texts, vectors)
+
+# Weight the model
+weights = tokenweights()
+
+# Remove NaNs from embedding, if any
+embedding = np.nan_to_num(model.embedding)
+
+# Apply PCA
+embedding = PCA(n_components=embedding.shape[1]).fit_transform(embedding)
+
+# Apply weights
+embedding *= weights[:, None]
+
+# Update model embedding and normalize
+model.embedding, model.normalize = embedding, True
+
+# Save model
+model.save_pretrained("output path")
+```
+
+The following table compares the accuracy results for each of the methods
+
+| Model                                                | PubMed QA | PubMed Subset | PubMed Summary | Average   |
+| -----------------------------------------------------| --------- | ------------- | -------------- | --------- |
+| **pubmedbert-base-embeddings-8M-BM25**               | **90.05** | **94.29**     | **94.15**      | **92.83** |
+| pubmedbert-base-embeddings-8M-M2V (No training)      | 69.84     | 70.77         | 71.30          | 70.64     |
+| pubmedbert-base-embeddings-8M-SIF                    | 88.75     | 93.78         | 93.05          | 91.86     |
+
+As we can see, the BM25 weighted model has the best results for the evaluated datasets
+
+## Acknowledgement
+
+This model is built on the great work from the [Minish Lab](https://github.com/MinishLab) team consisting of [Stephan Tulkens](https://github.com/stephantul) and [Thomas van Dongen](https://github.com/Pringled).
+
+Read more at the following links.
+
+- [Model2Vec](https://github.com/MinishLab/model2vec)
+- [Tokenlearn](https://github.com/MinishLab/tokenlearn)
+- [Minish Lab Blog](https://minishlab.github.io/)

config.json

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+{"model_type": "model2vec", "architectures": ["StaticModel"], "tokenizer_name": "neuml/pubmedbert-base-embeddings", "apply_pca": 64, "apply_zipf": true, "hidden_dim": 64, "seq_length": 1000000, "normalize": true}

model.safetensors

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