fastembed-bio 0.1.0__py3-none-any.whl

fastembed_bio-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: fastembed-bio
+Version: 0.1.0
+Summary: Fast, light, accurate library for biological sequence embeddings (proteins, DNA, RNA)
+License: Apache License
+License-File: LICENSE
+License-File: NOTICE
+Keywords: vector,embedding,protein,esm2,bioinformatics,onnx,biological-sequences
+Author: Nathan LeRoy
+Author-email: nathanjleroy@gmail.com
+Requires-Python: >=3.10.0
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: huggingface-hub (>=0.20,<2.0)
+Requires-Dist: loguru (>=0.7.2,<0.8.0)
+Requires-Dist: mmh3 (>=4.1.0,<6.0.0)
+Requires-Dist: numpy (>=1.21) ; python_version == "3.11"
+Requires-Dist: numpy (>=1.21,<2.3.0) ; python_version == "3.10"
+Requires-Dist: numpy (>=1.26) ; python_version == "3.12"
+Requires-Dist: numpy (>=2.1.0) ; python_version == "3.13"
+Requires-Dist: numpy (>=2.3.0) ; python_version >= "3.14"
+Requires-Dist: onnxruntime (>1.20.0) ; python_version >= "3.13"
+Requires-Dist: onnxruntime (>=1.17.0,!=1.20.0) ; python_version >= "3.10" and python_version < "3.13"
+Requires-Dist: pillow (>=10.3.0,<11.0) ; python_version < "3.10"
+Requires-Dist: pillow (>=10.3.0,<12.0) ; python_version >= "3.10" and python_version < "3.13"
+Requires-Dist: pillow (>=11.0.0,<12.0) ; python_version >= "3.13"
+Requires-Dist: py-rust-stemmers (>=0.1.0,<0.2.0)
+Requires-Dist: requests (>=2.31,<3.0)
+Requires-Dist: tokenizers (>=0.15,<1.0)
+Requires-Dist: tqdm (>=4.66,<5.0)
+Project-URL: Homepage, https://github.com/nleroy917/fastembed-bio
+Project-URL: Repository, https://github.com/nleroy917/fastembed-bio
+Description-Content-Type: text/markdown
+
+# ⚡️ What is FastEmbed?
+
+FastEmbed is a lightweight, fast, Python library built for embedding generation. We [support popular text models](https://qdrant.github.io/fastembed/examples/Supported_Models/). Please [open a GitHub issue](https://github.com/qdrant/fastembed/issues/new) if you want us to add a new model.
+
+The default text embedding (`TextEmbedding`) model is Flag Embedding, presented in the [MTEB](https://huggingface.co/spaces/mteb/leaderboard) leaderboard. It supports "query" and "passage" prefixes for the input text. Here is an example for [Retrieval Embedding Generation](https://qdrant.github.io/fastembed/qdrant/Retrieval_with_FastEmbed/) and how to use [FastEmbed with Qdrant](https://qdrant.github.io/fastembed/qdrant/Usage_With_Qdrant/).
+
+## 📈 Why FastEmbed?
+
+1. Light: FastEmbed is a lightweight library with few external dependencies. We don't require a GPU and don't download GBs of PyTorch dependencies, and instead use the ONNX Runtime. This makes it a great candidate for serverless runtimes like AWS Lambda. 
+
+2. Fast: FastEmbed is designed for speed. We use the ONNX Runtime, which is faster than PyTorch. We also use data parallelism for encoding large datasets.
+
+3. Accurate: FastEmbed is better than OpenAI Ada-002. We also [support](https://qdrant.github.io/fastembed/examples/Supported_Models/) an ever-expanding set of models, including a few multilingual models.
+
+## 🚀 Installation
+
+To install the FastEmbed library, pip works best. You can install it with or without GPU support:
+
+```bash
+pip install fastembed
+
+# or with GPU support
+
+pip install fastembed-gpu
+```
+
+## 📖 Quickstart
+
+```python
+from fastembed import TextEmbedding
+
+
+# Example list of documents
+documents: list[str] = [
+    "This is built to be faster and lighter than other embedding libraries e.g. Transformers, Sentence-Transformers, etc.",
+    "fastembed is supported by and maintained by Qdrant.",
+]
+
+# This will trigger the model download and initialization
+embedding_model = TextEmbedding()
+print("The model BAAI/bge-small-en-v1.5 is ready to use.")
+
+embeddings_generator = embedding_model.embed(documents)  # reminder this is a generator
+embeddings_list = list(embedding_model.embed(documents))
+  # you can also convert the generator to a list, and that to a numpy array
+len(embeddings_list[0]) # Vector of 384 dimensions
+```
+
+Fastembed supports a variety of models for different tasks and modalities.
+The list of all the available models can be found [here](https://qdrant.github.io/fastembed/examples/Supported_Models/)
+### 🎒 Dense text embeddings
+
+```python
+from fastembed import TextEmbedding
+
+model = TextEmbedding(model_name="BAAI/bge-small-en-v1.5")
+embeddings = list(model.embed(documents))
+
+# [
+#   array([-0.1115,  0.0097,  0.0052,  0.0195, ...], dtype=float32),
+#   array([-0.1019,  0.0635, -0.0332,  0.0522, ...], dtype=float32)
+# ]
+
+```
+
+Dense text embedding can also be extended with models which are not in the list of supported models.
+
+```python
+from fastembed import TextEmbedding
+from fastembed.common.model_description import PoolingType, ModelSource
+
+TextEmbedding.add_custom_model(
+    model="intfloat/multilingual-e5-small",
+    pooling=PoolingType.MEAN,
+    normalization=True,
+    sources=ModelSource(hf="intfloat/multilingual-e5-small"),  # can be used with an `url` to load files from a private storage
+    dim=384,
+    model_file="onnx/model.onnx",  # can be used to load an already supported model with another optimization or quantization, e.g. onnx/model_O4.onnx
+)
+model = TextEmbedding(model_name="intfloat/multilingual-e5-small")
+embeddings = list(model.embed(documents))
+```
+
+
+### 🔱 Sparse text embeddings
+
+* SPLADE++
+
+```python
+from fastembed import SparseTextEmbedding
+
+model = SparseTextEmbedding(model_name="prithivida/Splade_PP_en_v1")
+embeddings = list(model.embed(documents))
+
+# [
+#   SparseEmbedding(indices=[ 17, 123, 919, ... ], values=[0.71, 0.22, 0.39, ...]),
+#   SparseEmbedding(indices=[ 38,  12,  91, ... ], values=[0.11, 0.22, 0.39, ...])
+# ]
+```
+
+<!--
+* BM42 - ([link](ToDo))
+
+```
+from fastembed import SparseTextEmbedding
+
+model = SparseTextEmbedding(model_name="Qdrant/bm42-all-minilm-l6-v2-attentions")
+embeddings = list(model.embed(documents))
+
+# [
+#   SparseEmbedding(indices=[ 17, 123, 919, ... ], values=[0.71, 0.22, 0.39, ...]),
+#   SparseEmbedding(indices=[ 38,  12,  91, ... ], values=[0.11, 0.22, 0.39, ...])
+# ]
+```
+-->
+
+### 🦥 Late interaction models (aka ColBERT)
+
+
+```python
+from fastembed import LateInteractionTextEmbedding
+
+model = LateInteractionTextEmbedding(model_name="colbert-ir/colbertv2.0")
+embeddings = list(model.embed(documents))
+
+# [
+#   array([
+#       [-0.1115,  0.0097,  0.0052,  0.0195, ...],
+#       [-0.1019,  0.0635, -0.0332,  0.0522, ...],
+#   ]),
+#   array([
+#       [-0.9019,  0.0335, -0.0032,  0.0991, ...],
+#       [-0.2115,  0.8097,  0.1052,  0.0195, ...],
+#   ]),  
+# ]
+```
+
+### 🖼️ Image embeddings
+
+```python
+from fastembed import ImageEmbedding
+
+images = [
+    "./path/to/image1.jpg",
+    "./path/to/image2.jpg",
+]
+
+model = ImageEmbedding(model_name="Qdrant/clip-ViT-B-32-vision")
+embeddings = list(model.embed(images))
+
+# [
+#   array([-0.1115,  0.0097,  0.0052,  0.0195, ...], dtype=float32),
+#   array([-0.1019,  0.0635, -0.0332,  0.0522, ...], dtype=float32)
+# ]
+```
+
+### 🧬 Protein embeddings
+
+```python
+from fastembed import ProteinEmbedding
+
+sequences = [
+    "MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGG",
+    "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK",
+]
+
+model = ProteinEmbedding(model_name="facebook/esm2_t12_35M_UR50D")
+embeddings = list(model.embed(sequences))
+
+# [
+#   array([-0.0055, -0.0144,  0.0355, -0.0049, ...], dtype=float32),
+#   array([ 0.0114,  0.0020, -0.0247,  0.0060, ...], dtype=float32)
+# ]
+```
+
+### Late interaction multimodal models (ColPali)
+
+```python
+from fastembed import LateInteractionMultimodalEmbedding
+
+doc_images = [
+    "./path/to/qdrant_pdf_doc_1_screenshot.jpg",
+    "./path/to/colpali_pdf_doc_2_screenshot.jpg",
+]
+
+query = "What is Qdrant?"
+
+model = LateInteractionMultimodalEmbedding(model_name="Qdrant/colpali-v1.3-fp16")
+doc_images_embeddings = list(model.embed_image(doc_images))
+# shape (2, 1030, 128)
+# [array([[-0.03353882, -0.02090454, ..., -0.15576172, -0.07678223]], dtype=float32)]
+query_embedding = model.embed_text(query)
+# shape (1, 20, 128)
+# [array([[-0.00218201,  0.14758301, ...,  -0.02207947,  0.16833496]], dtype=float32)]
+```
+
+### 🔄 Rerankers
+```python
+from fastembed.rerank.cross_encoder import TextCrossEncoder
+
+query = "Who is maintaining Qdrant?"
+documents: list[str] = [
+    "This is built to be faster and lighter than other embedding libraries e.g. Transformers, Sentence-Transformers, etc.",
+    "fastembed is supported by and maintained by Qdrant.",
+]
+encoder = TextCrossEncoder(model_name="Xenova/ms-marco-MiniLM-L-6-v2")
+scores = list(encoder.rerank(query, documents))
+
+# [-11.48061752319336, 5.472434997558594]
+```
+
+Text cross encoders can also be extended with models which are not in the list of supported models.
+
+```python
+from fastembed.rerank.cross_encoder import TextCrossEncoder 
+from fastembed.common.model_description import ModelSource
+
+TextCrossEncoder.add_custom_model(
+    model="Xenova/ms-marco-MiniLM-L-4-v2",
+    model_file="onnx/model.onnx",
+    sources=ModelSource(hf="Xenova/ms-marco-MiniLM-L-4-v2"),
+)
+model = TextCrossEncoder(model_name="Xenova/ms-marco-MiniLM-L-4-v2")
+scores = list(model.rerank_pairs(
+    [("What is AI?", "Artificial intelligence is ..."), ("What is ML?", "Machine learning is ..."),]
+))
+```
+
+## ⚡️ FastEmbed on a GPU
+
+FastEmbed supports running on GPU devices.
+It requires installation of the `fastembed-gpu` package.
+
+```bash
+pip install fastembed-gpu
+```
+
+Check our [example](https://qdrant.github.io/fastembed/examples/FastEmbed_GPU/) for detailed instructions, CUDA 12.x support and troubleshooting of the common issues.
+
+```python
+from fastembed import TextEmbedding
+
+embedding_model = TextEmbedding(
+    model_name="BAAI/bge-small-en-v1.5", 
+    providers=["CUDAExecutionProvider"]
+)
+print("The model BAAI/bge-small-en-v1.5 is ready to use on a GPU.")
+
+```
+
+## Usage with Qdrant
+
+Installation with Qdrant Client in Python:
+
+```bash
+pip install qdrant-client[fastembed]
+```
+
+or 
+
+```bash
+pip install qdrant-client[fastembed-gpu]
+```
+
+You might have to use quotes ```pip install 'qdrant-client[fastembed]'``` on zsh.
+
+```python
+from qdrant_client import QdrantClient, models
+
+# Initialize the client
+client = QdrantClient("localhost", port=6333) # For production
+# client = QdrantClient(":memory:") # For experimentation
+
+model_name = "sentence-transformers/all-MiniLM-L6-v2"
+payload = [
+    {"document": "Qdrant has Langchain integrations", "source": "Langchain-docs", },
+    {"document": "Qdrant also has Llama Index integrations", "source": "LlamaIndex-docs"},
+]
+docs = [models.Document(text=data["document"], model=model_name) for data in payload]
+ids = [42, 2]
+
+client.create_collection(
+    "demo_collection",
+    vectors_config=models.VectorParams(
+        size=client.get_embedding_size(model_name), distance=models.Distance.COSINE)
+)
+
+client.upload_collection(
+    collection_name="demo_collection",
+    vectors=docs,
+    ids=ids,
+    payload=payload,
+)
+
+search_result = client.query_points(
+    collection_name="demo_collection",
+    query=models.Document(text="This is a query document", model=model_name)
+).points
+print(search_result)
+```

fastembed_bio-0.1.0.dist-info/RECORD

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+fastembed_bio-0.1.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+fastembed_bio-0.1.0.dist-info/licenses/NOTICE,sha256=cReuFIFnRtulaJjqzwufwt_0fQukX2-A768Lyh4zIVc,883
+fastembed_bio-0.1.0.dist-info/RECORD,,

fastembed_bio-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: poetry-core 2.3.0
+Root-Is-Purelib: true
+Tag: py3-none-any

fastembed_bio-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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fastembed_bio-0.1.0.dist-info/licenses/NOTICE

@@ -0,0 +1,22 @@
+Copyright 2024 Qdrant
+
+This product includes software developed by Qdrant
+
+This distribution includes the following Jina AI models, each with its respective license:
+- jinaai/jina-colbert-v2
+    - License: cc-by-nc-4.0
+- jinaai/jina-reranker-v2-base-multilingual
+    - License: cc-by-nc-4.0
+- jinaai/jina-embeddings-v3
+    - License: cc-by-nc-4.0
+
+These models are developed by Jina (https://jina.ai/) and are subject to Jina AI's licensing terms.
+
+This distribution includes the following Google models, each with its respective license:
+- vidore/colpali-v1.3
+    - License: gemma
+
+Gemma is provided under and subject to the Gemma Terms of Use found at ai.google.dev/gemma/terms
+
+Additional Notes:
+This project also includes third-party libraries with their respective licenses. Please refer to the documentation of each library for details regarding its usage and licensing terms.