Upload folder using huggingface_hub
Browse files- .gitignore +23 -0
- README.md +195 -0
- __init__.py +4 -0
- chest2vec.py +382 -0
- chest2vec_config.json +8 -0
- contrastive/adapter_config.json +42 -0
- contrastive/adapter_model.safetensors +3 -0
- install_deps.sh +16 -0
- pyproject.toml +23 -0
- requirements.txt +12 -0
- setup.py +43 -0
.gitignore
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# Build artifacts
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dist/
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build/
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*.egg-info/
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__pycache__/
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*.pyc
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*.pyo
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*.pyd
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.Python
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# Testing
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.pytest_cache/
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.coverage
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htmlcov/
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# IDE
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.vscode/
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.idea/
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*.swp
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*.swo
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# Jupyter
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.ipynb_checkpoints/
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README.md
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---
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tags:
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- text-embeddings
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- retrieval
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- radiology
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- chest
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- qwen
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library_name: transformers
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---
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| 10 |
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# chest2vec_4b_chest
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This repository contains the *delta weights* for a global embedding model on top of **Qwen/Qwen3-Embedding-4B**:
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| 14 |
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| 15 |
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- **LoRA Adapter**: Contrastive LoRA adapter trained with multi-positive sigmoid loss under `./contrastive/`
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| 16 |
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- **Inference helper**: `chest2vec.py`
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| 17 |
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|
| 18 |
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Base model weights are **not** included; they are downloaded from Hugging Face at runtime.
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| 19 |
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## Model Architecture
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| 21 |
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Chest2Vec is a two-stage model:
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| 23 |
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1. **Base**: Qwen/Qwen3-Embedding-4B (downloaded at runtime)
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| 24 |
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2. **LoRA Adapter**: Contrastive LoRA adapter trained with multi-positive sigmoid loss
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| 25 |
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3. **Pooling**: Last-token pooling (EOS token) for global embeddings
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| 26 |
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|
| 27 |
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The model produces **global embeddings only** (no section-specific embeddings).
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| 28 |
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| 29 |
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## Installation
|
| 30 |
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| 31 |
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Install the package and all dependencies:
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| 32 |
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| 33 |
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```bash
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| 34 |
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# Install PyTorch with CUDA 12.6 support
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| 35 |
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pip install torch==2.6.0 torchvision==0.21.0 torchaudio==2.6.0 --index-url https://download.pytorch.org/whl/cu126
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| 36 |
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|
| 37 |
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# Install transformers and trl
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| 38 |
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pip install transformers==4.57.3 trl==0.9.3
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| 39 |
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|
| 40 |
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# Install deepspeed
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| 41 |
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pip install deepspeed==0.16.9
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| 42 |
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|
| 43 |
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# Install flash-attention
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| 44 |
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pip install https://github.com/Dao-AILab/flash-attention/releases/download/v2.8.3/flash_attn-2.8.3+cu12torch2.6cxx11abiTRUE-cp310-cp310-linux_x86_64.whl
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| 45 |
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# Install chest2vec package
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| 47 |
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pip install chest2vec
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| 48 |
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```
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| 49 |
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Or use the installation script:
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| 51 |
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|
| 52 |
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```bash
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| 53 |
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bash install_deps.sh
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| 54 |
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```
|
| 55 |
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|
| 56 |
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## Requirements
|
| 57 |
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|
| 58 |
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This model **requires FlashAttention-2** (CUDA) by default, which is automatically installed with the package.
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| 59 |
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## Quickstart
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| 61 |
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| 62 |
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### Installation + Loading
|
| 63 |
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| 64 |
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```python
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| 65 |
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from chest2vec import Chest2Vec
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| 66 |
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|
| 67 |
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# Load model from Hugging Face Hub
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| 68 |
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m = Chest2Vec.from_pretrained("lukeingawesome/chest2vec_4b_chest", device="cuda:0")
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| 69 |
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```
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| 70 |
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### Instruction + Query Embeddings
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| 72 |
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```python
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instructions = ["Find findings about the lungs."]
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| 75 |
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queries = ["Consolidation in the right lower lobe."]
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| 76 |
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| 77 |
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out = m.embed_instruction_query(instructions, queries, max_len=512, batch_size=8)
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| 78 |
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| 79 |
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# Global embedding (last-token pooling)
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| 80 |
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emb = out.embedding # [N, H]
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| 81 |
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```
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| 82 |
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|
| 83 |
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### Candidate Embeddings (Retrieval Bank)
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| 84 |
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|
| 85 |
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```python
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| 86 |
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candidates = [
|
| 87 |
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"Lungs are clear. No focal consolidation.",
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| 88 |
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"Pleural effusion on the left.",
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| 89 |
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"Cardiomediastinal silhouette is normal."
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| 90 |
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]
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| 91 |
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cand_out = m.embed_texts(candidates, max_len=512, batch_size=16)
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| 93 |
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| 94 |
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cand_emb = cand_out.embedding # [N, H]
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| 95 |
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```
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| 96 |
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|
| 97 |
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### Retrieval Example (Cosine Top-K)
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| 98 |
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| 99 |
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```python
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| 100 |
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# Query embeddings
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| 101 |
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q = out.embedding # [Nq, H]
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| 102 |
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| 103 |
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# Document embeddings
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| 104 |
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d = cand_out.embedding # [Nd, H]
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| 105 |
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|
| 106 |
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# Compute top-k cosine similarities
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| 107 |
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scores, idx = Chest2Vec.cosine_topk(q, d, k=5, device="cuda")
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| 108 |
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# scores: [Nq, k] - similarity scores
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| 109 |
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# idx: [Nq, k] - indices of top-k candidates
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| 110 |
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|
| 111 |
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print(f"Top-5 scores: {scores[0]}")
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| 112 |
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print(f"Top-5 indices: {idx[0]}")
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| 113 |
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```
|
| 114 |
+
|
| 115 |
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## API Reference
|
| 116 |
+
|
| 117 |
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### `Chest2Vec.from_pretrained()`
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| 118 |
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|
| 119 |
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Load the model from Hugging Face Hub or local path.
|
| 120 |
+
|
| 121 |
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```python
|
| 122 |
+
m = Chest2Vec.from_pretrained(
|
| 123 |
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repo_id_or_path: str, # Hugging Face repo ID or local path
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| 124 |
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device: str = "cuda:0", # Device to load model on
|
| 125 |
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use_4bit: bool = False, # Use 4-bit quantization
|
| 126 |
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force_flash_attention_2: bool = True
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| 127 |
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)
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| 128 |
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```
|
| 129 |
+
|
| 130 |
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### `embed_instruction_query()`
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| 131 |
+
|
| 132 |
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Embed instruction-query pairs. Returns `EmbedOutput` with:
|
| 133 |
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- `embedding`: `[N, H]` - global embeddings (L2-normalized, last-token pooling)
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| 134 |
+
|
| 135 |
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```python
|
| 136 |
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out = m.embed_instruction_query(
|
| 137 |
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instructions: List[str],
|
| 138 |
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queries: List[str],
|
| 139 |
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max_len: int = 512,
|
| 140 |
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batch_size: int = 16
|
| 141 |
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)
|
| 142 |
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```
|
| 143 |
+
|
| 144 |
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### `embed_texts()`
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| 145 |
+
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| 146 |
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Embed plain texts (for document/candidate encoding).
|
| 147 |
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|
| 148 |
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```python
|
| 149 |
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out = m.embed_texts(
|
| 150 |
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texts: List[str],
|
| 151 |
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max_len: int = 512,
|
| 152 |
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batch_size: int = 16
|
| 153 |
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)
|
| 154 |
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```
|
| 155 |
+
|
| 156 |
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Returns `EmbedOutput` with:
|
| 157 |
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- `embedding`: `[N, H]` - global embeddings (L2-normalized, last-token pooling)
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| 158 |
+
|
| 159 |
+
### `cosine_topk()`
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| 160 |
+
|
| 161 |
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Static method for efficient top-k cosine similarity search.
|
| 162 |
+
|
| 163 |
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```python
|
| 164 |
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scores, idx = Chest2Vec.cosine_topk(
|
| 165 |
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query_emb: torch.Tensor, # [Nq, H]
|
| 166 |
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cand_emb: torch.Tensor, # [Nd, H]
|
| 167 |
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k: int = 10,
|
| 168 |
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device: str = "cuda"
|
| 169 |
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)
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| 170 |
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```
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| 171 |
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|
| 172 |
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## Model Files
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| 173 |
+
|
| 174 |
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- `chest2vec.py` - Model class and inference utilities
|
| 175 |
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- `chest2vec_config.json` - Model configuration
|
| 176 |
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- `contrastive/` - LoRA adapter directory
|
| 177 |
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- `adapter_config.json` - LoRA adapter configuration
|
| 178 |
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- `adapter_model.safetensors` - LoRA adapter weights
|
| 179 |
+
|
| 180 |
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## Citation
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| 181 |
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|
| 182 |
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If you use this model, please cite:
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| 183 |
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|
| 184 |
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```bibtex
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| 185 |
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@misc{chest2vec_4b_chest,
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| 186 |
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title={Chest2Vec: Global Embeddings for Chest X-Ray Reports},
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| 187 |
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author={Your Name},
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| 188 |
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year={2024},
|
| 189 |
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howpublished={\url{https://huggingface.co/lukeingawesome/chest2vec_4b_chest}}
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| 190 |
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}
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| 191 |
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```
|
| 192 |
+
|
| 193 |
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## License
|
| 194 |
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|
| 195 |
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[Specify your license here]
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__init__.py
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from chest2vec import Chest2Vec, EmbedOutput
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__all__ = ["Chest2Vec", "EmbedOutput"]
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__version__ = "4.0.0"
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chest2vec.py
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|
| 1 |
+
import os
|
| 2 |
+
import json
|
| 3 |
+
from dataclasses import dataclass
|
| 4 |
+
from typing import Any, Dict, List, Optional, Tuple
|
| 5 |
+
|
| 6 |
+
import torch
|
| 7 |
+
import torch.nn.functional as F
|
| 8 |
+
|
| 9 |
+
from transformers import AutoTokenizer, AutoModel, BitsAndBytesConfig
|
| 10 |
+
|
| 11 |
+
try:
|
| 12 |
+
from peft import PeftModel
|
| 13 |
+
_HAS_PEFT = True
|
| 14 |
+
except Exception:
|
| 15 |
+
PeftModel = None
|
| 16 |
+
_HAS_PEFT = False
|
| 17 |
+
|
| 18 |
+
try:
|
| 19 |
+
from huggingface_hub import snapshot_download
|
| 20 |
+
_HAS_HUB = True
|
| 21 |
+
except Exception:
|
| 22 |
+
snapshot_download = None
|
| 23 |
+
_HAS_HUB = False
|
| 24 |
+
|
| 25 |
+
|
| 26 |
+
def require_flash_attention_2() -> str:
|
| 27 |
+
if not torch.cuda.is_available():
|
| 28 |
+
raise RuntimeError("FlashAttention-2 requires CUDA, but torch.cuda.is_available() is False.")
|
| 29 |
+
try:
|
| 30 |
+
import flash_attn # noqa: F401
|
| 31 |
+
ver = getattr(flash_attn, "__version__", "0.0.0")
|
| 32 |
+
major = int(str(ver).split(".")[0])
|
| 33 |
+
if major < 2:
|
| 34 |
+
raise RuntimeError(f"flash-attn version {ver} < 2.0.0")
|
| 35 |
+
except Exception as e:
|
| 36 |
+
raise RuntimeError(
|
| 37 |
+
"FlashAttention-2 is REQUIRED but not available/importable.\n"
|
| 38 |
+
"Install flash-attn>=2 and ensure it matches your torch/CUDA.\n"
|
| 39 |
+
f"Import/Version error: {repr(e)}"
|
| 40 |
+
)
|
| 41 |
+
return "flash_attention_2"
|
| 42 |
+
|
| 43 |
+
|
| 44 |
+
def build_qwen_query(instruction: str, query: str) -> str:
|
| 45 |
+
instruction = str(instruction).strip()
|
| 46 |
+
query = str(query).strip()
|
| 47 |
+
return f"Instruct: {instruction}\nQuery: {query}"
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
def get_pool_token_id(tok) -> int:
|
| 51 |
+
eod_id = tok.convert_tokens_to_ids("<|endoftext|>")
|
| 52 |
+
if eod_id is None or eod_id < 0:
|
| 53 |
+
eod_id = tok.pad_token_id
|
| 54 |
+
return eod_id
|
| 55 |
+
|
| 56 |
+
|
| 57 |
+
def encode_with_eos_ids(tok, texts: List[str], max_len: int) -> Dict[str, torch.Tensor]:
|
| 58 |
+
"""
|
| 59 |
+
Encode texts with guaranteed <|endoftext|> at the end for Qwen3-Embedding pooling.
|
| 60 |
+
Reserves 1 slot for <|endoftext|>, left-pads to batch max length.
|
| 61 |
+
Must match the training tokenization exactly.
|
| 62 |
+
"""
|
| 63 |
+
pad_id = tok.pad_token_id if tok.pad_token_id is not None else tok.eos_token_id
|
| 64 |
+
eod_id = get_pool_token_id(tok)
|
| 65 |
+
|
| 66 |
+
# Reserve 1 position for <|endoftext|>
|
| 67 |
+
enc = tok(
|
| 68 |
+
[str(t) for t in texts],
|
| 69 |
+
add_special_tokens=False,
|
| 70 |
+
truncation=True,
|
| 71 |
+
max_length=max_len - 1,
|
| 72 |
+
padding=False,
|
| 73 |
+
return_attention_mask=False,
|
| 74 |
+
)
|
| 75 |
+
|
| 76 |
+
input_ids = [ids + [eod_id] for ids in enc["input_ids"]]
|
| 77 |
+
attn_mask = [[1] * len(ids) for ids in input_ids]
|
| 78 |
+
|
| 79 |
+
# Left-pad to batch max length
|
| 80 |
+
T = max(len(ids) for ids in input_ids) if input_ids else 1
|
| 81 |
+
input_ids = [[pad_id] * (T - len(ids)) + ids for ids in input_ids]
|
| 82 |
+
attn_mask = [[0] * (T - len(m)) + m for m in attn_mask]
|
| 83 |
+
|
| 84 |
+
return {
|
| 85 |
+
"input_ids": torch.tensor(input_ids, dtype=torch.long),
|
| 86 |
+
"attention_mask": torch.tensor(attn_mask, dtype=torch.long),
|
| 87 |
+
}
|
| 88 |
+
|
| 89 |
+
|
| 90 |
+
def last_token_pool(last_hidden_states: torch.Tensor, attention_mask: torch.Tensor) -> torch.Tensor:
|
| 91 |
+
"""
|
| 92 |
+
Left-padding aware last-token pooling (extracts EOS token embedding).
|
| 93 |
+
"""
|
| 94 |
+
left_padding = (attention_mask[:, -1].sum() == attention_mask.shape[0])
|
| 95 |
+
if left_padding:
|
| 96 |
+
return last_hidden_states[:, -1]
|
| 97 |
+
idx = attention_mask.sum(dim=1) - 1
|
| 98 |
+
return last_hidden_states[torch.arange(last_hidden_states.size(0), device=last_hidden_states.device), idx]
|
| 99 |
+
|
| 100 |
+
|
| 101 |
+
def get_last_hidden_state(model, input_ids, attention_mask):
|
| 102 |
+
"""
|
| 103 |
+
Get final hidden state from the model.
|
| 104 |
+
Provide position_ids for left padding (FlashAttention-2).
|
| 105 |
+
"""
|
| 106 |
+
m = model.module if hasattr(model, "module") else model
|
| 107 |
+
|
| 108 |
+
# Compute position_ids for left-padded sequences (required for flash_attention_2)
|
| 109 |
+
position_ids = attention_mask.long().cumsum(-1) - 1
|
| 110 |
+
position_ids.masked_fill_(attention_mask == 0, 0)
|
| 111 |
+
|
| 112 |
+
out = m(
|
| 113 |
+
input_ids=input_ids,
|
| 114 |
+
attention_mask=attention_mask,
|
| 115 |
+
position_ids=position_ids,
|
| 116 |
+
use_cache=False,
|
| 117 |
+
return_dict=True,
|
| 118 |
+
)
|
| 119 |
+
if hasattr(out, "last_hidden_state"):
|
| 120 |
+
return out.last_hidden_state
|
| 121 |
+
|
| 122 |
+
out = m(
|
| 123 |
+
input_ids=input_ids,
|
| 124 |
+
attention_mask=attention_mask,
|
| 125 |
+
position_ids=position_ids,
|
| 126 |
+
output_hidden_states=True,
|
| 127 |
+
use_cache=False,
|
| 128 |
+
return_dict=True,
|
| 129 |
+
)
|
| 130 |
+
return out.hidden_states[-1]
|
| 131 |
+
|
| 132 |
+
|
| 133 |
+
def _read_json(path: str) -> Dict[str, Any]:
|
| 134 |
+
with open(path, "r", encoding="utf-8") as f:
|
| 135 |
+
return json.load(f)
|
| 136 |
+
|
| 137 |
+
|
| 138 |
+
def _resolve_repo_path(repo_id_or_path: str) -> str:
|
| 139 |
+
# If it's a local directory, use it as-is.
|
| 140 |
+
if os.path.isdir(repo_id_or_path):
|
| 141 |
+
return repo_id_or_path
|
| 142 |
+
# Otherwise treat as HF repo_id and download snapshot.
|
| 143 |
+
if not _HAS_HUB:
|
| 144 |
+
raise RuntimeError(
|
| 145 |
+
"huggingface_hub is required to load by repo_id. "
|
| 146 |
+
"Install it: pip install huggingface_hub"
|
| 147 |
+
)
|
| 148 |
+
return snapshot_download(repo_id_or_path)
|
| 149 |
+
|
| 150 |
+
|
| 151 |
+
@dataclass
|
| 152 |
+
class EmbedOutput:
|
| 153 |
+
"""
|
| 154 |
+
Simplified output: only global embeddings (no section embeddings).
|
| 155 |
+
"""
|
| 156 |
+
embedding: torch.Tensor # [N,H], float32 on CPU by default
|
| 157 |
+
|
| 158 |
+
|
| 159 |
+
class Chest2Vec:
|
| 160 |
+
"""
|
| 161 |
+
Simplified wrapper for global embeddings only:
|
| 162 |
+
- loads base Qwen3-Embedding
|
| 163 |
+
- applies LoRA adapter
|
| 164 |
+
- returns global embeddings via last-token pooling
|
| 165 |
+
"""
|
| 166 |
+
def __init__(self, tokenizer, model, device: torch.device):
|
| 167 |
+
self.tokenizer = tokenizer
|
| 168 |
+
self.model = model
|
| 169 |
+
self.device = device
|
| 170 |
+
|
| 171 |
+
self.model.eval()
|
| 172 |
+
|
| 173 |
+
@classmethod
|
| 174 |
+
def from_pretrained(
|
| 175 |
+
cls,
|
| 176 |
+
repo_id_or_path: str,
|
| 177 |
+
*,
|
| 178 |
+
device: str = "cuda:0",
|
| 179 |
+
use_4bit: bool = False,
|
| 180 |
+
force_flash_attention_2: bool = True,
|
| 181 |
+
) -> "Chest2Vec":
|
| 182 |
+
repo_path = _resolve_repo_path(repo_id_or_path)
|
| 183 |
+
|
| 184 |
+
cfg_path = os.path.join(repo_path, "chest2vec_config.json")
|
| 185 |
+
if not os.path.isfile(cfg_path):
|
| 186 |
+
raise FileNotFoundError(f"Missing chest2vec_config.json in {repo_path}")
|
| 187 |
+
cfg = _read_json(cfg_path)
|
| 188 |
+
|
| 189 |
+
base_model = str(cfg["base_model"])
|
| 190 |
+
adapter_subdir = str(cfg.get("adapter_subdir", "contrastive"))
|
| 191 |
+
|
| 192 |
+
if force_flash_attention_2 or bool(cfg.get("require_flash_attention_2", False)):
|
| 193 |
+
attn_impl = require_flash_attention_2()
|
| 194 |
+
else:
|
| 195 |
+
attn_impl = "sdpa"
|
| 196 |
+
|
| 197 |
+
if not _HAS_PEFT:
|
| 198 |
+
raise RuntimeError("peft is required. Install: pip install peft")
|
| 199 |
+
|
| 200 |
+
device_t = torch.device(device)
|
| 201 |
+
|
| 202 |
+
tokenizer = AutoTokenizer.from_pretrained(base_model, padding_side="left", trust_remote_code=True)
|
| 203 |
+
if tokenizer.pad_token_id is None:
|
| 204 |
+
tokenizer.pad_token = tokenizer.eos_token
|
| 205 |
+
|
| 206 |
+
device_map = {"": str(device_t)}
|
| 207 |
+
|
| 208 |
+
# Load base model with FlashAttention-2
|
| 209 |
+
if use_4bit:
|
| 210 |
+
qconf = BitsAndBytesConfig(
|
| 211 |
+
load_in_4bit=True,
|
| 212 |
+
bnb_4bit_quant_type="nf4",
|
| 213 |
+
bnb_4bit_use_double_quant=True,
|
| 214 |
+
bnb_4bit_compute_dtype=torch.bfloat16,
|
| 215 |
+
)
|
| 216 |
+
try:
|
| 217 |
+
base = AutoModel.from_pretrained(
|
| 218 |
+
base_model,
|
| 219 |
+
trust_remote_code=True,
|
| 220 |
+
attn_implementation=attn_impl,
|
| 221 |
+
quantization_config=qconf,
|
| 222 |
+
device_map=device_map,
|
| 223 |
+
)
|
| 224 |
+
except TypeError as e:
|
| 225 |
+
raise RuntimeError(
|
| 226 |
+
"Your transformers version does not support attn_implementation=... "
|
| 227 |
+
"Upgrade transformers to use FlashAttention-2."
|
| 228 |
+
) from e
|
| 229 |
+
else:
|
| 230 |
+
try:
|
| 231 |
+
base = AutoModel.from_pretrained(
|
| 232 |
+
base_model,
|
| 233 |
+
trust_remote_code=True,
|
| 234 |
+
attn_implementation=attn_impl,
|
| 235 |
+
torch_dtype=torch.bfloat16,
|
| 236 |
+
device_map=device_map,
|
| 237 |
+
)
|
| 238 |
+
except TypeError as e:
|
| 239 |
+
raise RuntimeError(
|
| 240 |
+
"Your transformers version does not support attn_implementation=... "
|
| 241 |
+
"Upgrade transformers to use FlashAttention-2."
|
| 242 |
+
) from e
|
| 243 |
+
|
| 244 |
+
# Load adapter from this repo folder
|
| 245 |
+
adapter_dir = os.path.join(repo_path, adapter_subdir)
|
| 246 |
+
if not os.path.isfile(os.path.join(adapter_dir, "adapter_config.json")):
|
| 247 |
+
raise FileNotFoundError(f"adapter_config.json not found under: {adapter_dir}")
|
| 248 |
+
|
| 249 |
+
model = PeftModel.from_pretrained(base, adapter_dir)
|
| 250 |
+
model.eval()
|
| 251 |
+
|
| 252 |
+
return cls(tokenizer=tokenizer, model=model, device=device_t)
|
| 253 |
+
|
| 254 |
+
@torch.inference_mode()
|
| 255 |
+
def embed_texts(
|
| 256 |
+
self,
|
| 257 |
+
texts: List[str],
|
| 258 |
+
*,
|
| 259 |
+
max_len: int = 512,
|
| 260 |
+
batch_size: int = 16,
|
| 261 |
+
return_cpu_float32: bool = True,
|
| 262 |
+
) -> EmbedOutput:
|
| 263 |
+
"""
|
| 264 |
+
Encodes arbitrary texts and returns global embeddings via last-token pooling.
|
| 265 |
+
|
| 266 |
+
Returns:
|
| 267 |
+
- embedding: [N,H] - global embeddings (L2-normalized)
|
| 268 |
+
"""
|
| 269 |
+
# Determine AMP
|
| 270 |
+
device = self.device
|
| 271 |
+
if device.type == "cuda":
|
| 272 |
+
amp_dtype = torch.bfloat16 if torch.cuda.is_bf16_supported() else torch.float16
|
| 273 |
+
use_amp = True
|
| 274 |
+
else:
|
| 275 |
+
amp_dtype = torch.float32
|
| 276 |
+
use_amp = False
|
| 277 |
+
|
| 278 |
+
outs = []
|
| 279 |
+
for i in range(0, len(texts), batch_size):
|
| 280 |
+
chunk = [str(t) for t in texts[i:i + batch_size]]
|
| 281 |
+
enc = encode_with_eos_ids(self.tokenizer, chunk, max_len)
|
| 282 |
+
input_ids = enc["input_ids"].to(device, non_blocking=True)
|
| 283 |
+
attention_mask = enc["attention_mask"].to(device, non_blocking=True)
|
| 284 |
+
|
| 285 |
+
with torch.autocast(device_type=("cuda" if device.type == "cuda" else "cpu"),
|
| 286 |
+
dtype=amp_dtype, enabled=use_amp):
|
| 287 |
+
h = get_last_hidden_state(self.model, input_ids, attention_mask) # [B,T,H]
|
| 288 |
+
|
| 289 |
+
# Global embedding: extract EOS token embedding via last-token pooling
|
| 290 |
+
emb = last_token_pool(h, attention_mask) # [B,H]
|
| 291 |
+
emb = F.normalize(emb.float(), p=2, dim=-1)
|
| 292 |
+
|
| 293 |
+
outs.append(emb.detach())
|
| 294 |
+
|
| 295 |
+
embeddings = torch.cat(outs, dim=0) # on device, dtype ~ bf16
|
| 296 |
+
|
| 297 |
+
# Move to CPU float32 if requested (recommended for retrieval stability)
|
| 298 |
+
if return_cpu_float32:
|
| 299 |
+
embeddings_cpu = embeddings.float().cpu()
|
| 300 |
+
# re-normalize to fix any numerical drift
|
| 301 |
+
embeddings_cpu = F.normalize(embeddings_cpu, p=2, dim=-1)
|
| 302 |
+
else:
|
| 303 |
+
embeddings_cpu = embeddings
|
| 304 |
+
|
| 305 |
+
return EmbedOutput(embedding=embeddings_cpu)
|
| 306 |
+
|
| 307 |
+
@torch.inference_mode()
|
| 308 |
+
def embed_instruction_query(
|
| 309 |
+
self,
|
| 310 |
+
instructions: List[str],
|
| 311 |
+
queries: List[str],
|
| 312 |
+
*,
|
| 313 |
+
max_len: int = 512,
|
| 314 |
+
batch_size: int = 16,
|
| 315 |
+
return_cpu_float32: bool = True,
|
| 316 |
+
) -> EmbedOutput:
|
| 317 |
+
"""
|
| 318 |
+
Embed instruction-query pairs.
|
| 319 |
+
|
| 320 |
+
Returns:
|
| 321 |
+
- embedding: [N,H] - global embeddings (L2-normalized)
|
| 322 |
+
"""
|
| 323 |
+
if len(instructions) != len(queries):
|
| 324 |
+
raise ValueError("instructions and queries must have the same length.")
|
| 325 |
+
q_texts = [build_qwen_query(i, q) for i, q in zip(instructions, queries)]
|
| 326 |
+
return self.embed_texts(
|
| 327 |
+
q_texts,
|
| 328 |
+
max_len=max_len,
|
| 329 |
+
batch_size=batch_size,
|
| 330 |
+
return_cpu_float32=return_cpu_float32,
|
| 331 |
+
)
|
| 332 |
+
|
| 333 |
+
@staticmethod
|
| 334 |
+
def cosine_topk(
|
| 335 |
+
query_emb: torch.Tensor, # [Nq,H] CPU float32 recommended
|
| 336 |
+
cand_emb: torch.Tensor, # [Nd,H] CPU float32 recommended
|
| 337 |
+
k: int = 10,
|
| 338 |
+
*,
|
| 339 |
+
device: str = "cuda",
|
| 340 |
+
query_batch_size: int = 256,
|
| 341 |
+
doc_chunk_size: int = 8192,
|
| 342 |
+
) -> Tuple[torch.Tensor, torch.Tensor]:
|
| 343 |
+
"""
|
| 344 |
+
Chunked cosine top-k, stable in float32.
|
| 345 |
+
Returns (top_scores [Nq,k], top_indices [Nq,k]) on CPU.
|
| 346 |
+
"""
|
| 347 |
+
device_t = torch.device(device)
|
| 348 |
+
q = F.normalize(query_emb.float(), p=2, dim=-1)
|
| 349 |
+
d = F.normalize(cand_emb.float(), p=2, dim=-1)
|
| 350 |
+
Nq, H = q.shape
|
| 351 |
+
Nd = d.shape[0]
|
| 352 |
+
k = min(int(k), Nd)
|
| 353 |
+
|
| 354 |
+
top_scores_all = torch.empty((Nq, k), dtype=torch.float32)
|
| 355 |
+
top_indices_all = torch.empty((Nq, k), dtype=torch.long)
|
| 356 |
+
|
| 357 |
+
for qs in range(0, Nq, query_batch_size):
|
| 358 |
+
qe = q[qs:qs + query_batch_size].to(device_t, non_blocking=True)
|
| 359 |
+
bq = qe.size(0)
|
| 360 |
+
|
| 361 |
+
top_scores = torch.full((bq, k), -1e9, device=device_t, dtype=torch.float32)
|
| 362 |
+
top_indices = torch.full((bq, k), -1, device=device_t, dtype=torch.long)
|
| 363 |
+
|
| 364 |
+
for ds in range(0, Nd, doc_chunk_size):
|
| 365 |
+
de = d[ds:ds + doc_chunk_size].to(device_t, non_blocking=True)
|
| 366 |
+
scores = (qe @ de.T).float()
|
| 367 |
+
|
| 368 |
+
chunk = scores.size(1)
|
| 369 |
+
idx_chunk = torch.arange(ds, ds + chunk, device=device_t, dtype=torch.long).unsqueeze(0).expand(bq, -1)
|
| 370 |
+
|
| 371 |
+
comb_scores = torch.cat([top_scores, scores], dim=1)
|
| 372 |
+
comb_idx = torch.cat([top_indices, idx_chunk], dim=1)
|
| 373 |
+
|
| 374 |
+
new_scores, new_pos = torch.topk(comb_scores, k, dim=1)
|
| 375 |
+
new_idx = comb_idx.gather(1, new_pos)
|
| 376 |
+
|
| 377 |
+
top_scores, top_indices = new_scores, new_idx
|
| 378 |
+
|
| 379 |
+
top_scores_all[qs:qs + bq] = top_scores.cpu()
|
| 380 |
+
top_indices_all[qs:qs + bq] = top_indices.cpu()
|
| 381 |
+
|
| 382 |
+
return top_scores_all, top_indices_all
|
chest2vec_config.json
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"name": "chest2vec_4b_chest",
|
| 3 |
+
"base_model": "Qwen/Qwen3-Embedding-4B",
|
| 4 |
+
"adapter_subdir": "contrastive",
|
| 5 |
+
"require_flash_attention_2": true,
|
| 6 |
+
"default_max_len": 512,
|
| 7 |
+
"pooling": "last_token"
|
| 8 |
+
}
|
contrastive/adapter_config.json
ADDED
|
@@ -0,0 +1,42 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"alpha_pattern": {},
|
| 3 |
+
"auto_mapping": {
|
| 4 |
+
"base_model_class": "Qwen3Model",
|
| 5 |
+
"parent_library": "transformers.models.qwen3.modeling_qwen3"
|
| 6 |
+
},
|
| 7 |
+
"base_model_name_or_path": "Qwen/Qwen3-Embedding-4B",
|
| 8 |
+
"bias": "none",
|
| 9 |
+
"corda_config": null,
|
| 10 |
+
"eva_config": null,
|
| 11 |
+
"exclude_modules": null,
|
| 12 |
+
"fan_in_fan_out": false,
|
| 13 |
+
"inference_mode": true,
|
| 14 |
+
"init_lora_weights": true,
|
| 15 |
+
"layer_replication": null,
|
| 16 |
+
"layers_pattern": null,
|
| 17 |
+
"layers_to_transform": null,
|
| 18 |
+
"loftq_config": {},
|
| 19 |
+
"lora_alpha": 32,
|
| 20 |
+
"lora_bias": false,
|
| 21 |
+
"lora_dropout": 0.1,
|
| 22 |
+
"megatron_config": null,
|
| 23 |
+
"megatron_core": "megatron.core",
|
| 24 |
+
"modules_to_save": null,
|
| 25 |
+
"peft_type": "LORA",
|
| 26 |
+
"r": 16,
|
| 27 |
+
"rank_pattern": {},
|
| 28 |
+
"revision": null,
|
| 29 |
+
"target_modules": [
|
| 30 |
+
"o_proj",
|
| 31 |
+
"v_proj",
|
| 32 |
+
"q_proj",
|
| 33 |
+
"up_proj",
|
| 34 |
+
"down_proj",
|
| 35 |
+
"gate_proj",
|
| 36 |
+
"k_proj"
|
| 37 |
+
],
|
| 38 |
+
"task_type": null,
|
| 39 |
+
"trainable_token_indices": null,
|
| 40 |
+
"use_dora": false,
|
| 41 |
+
"use_rslora": false
|
| 42 |
+
}
|
contrastive/adapter_model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:dd8ad38ebccd46fa13e2522e8ef23dc80aef48d29f70a780418cf5a1019d7243
|
| 3 |
+
size 66124752
|
install_deps.sh
ADDED
|
@@ -0,0 +1,16 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/bash
|
| 2 |
+
# Installation script for chest2vec dependencies
|
| 3 |
+
# This script installs PyTorch and flash-attention with the correct versions
|
| 4 |
+
|
| 5 |
+
set -e
|
| 6 |
+
|
| 7 |
+
echo "Installing PyTorch packages from custom index..."
|
| 8 |
+
pip install torch==2.6.0 torchvision==0.21.0 torchaudio==2.6.0 --index-url https://download.pytorch.org/whl/cu126
|
| 9 |
+
|
| 10 |
+
echo "Installing flash-attention from GitHub release..."
|
| 11 |
+
pip install https://github.com/Dao-AILab/flash-attention/releases/download/v2.8.3/flash_attn-2.8.3+cu12torch2.6cxx11abiTRUE-cp310-cp310-linux_x86_64.whl
|
| 12 |
+
|
| 13 |
+
echo "Installing chest2vec package..."
|
| 14 |
+
pip install chest2vec
|
| 15 |
+
|
| 16 |
+
echo "Installation complete!"
|
pyproject.toml
ADDED
|
@@ -0,0 +1,23 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[build-system]
|
| 2 |
+
requires = ["setuptools>=61.0", "wheel"]
|
| 3 |
+
build-backend = "setuptools.build_meta"
|
| 4 |
+
|
| 5 |
+
[project]
|
| 6 |
+
name = "chest2vec"
|
| 7 |
+
version = "4.0.0"
|
| 8 |
+
description = "Section-aware embeddings for chest X-ray reports"
|
| 9 |
+
readme = "README.md"
|
| 10 |
+
requires-python = ">=3.8"
|
| 11 |
+
dependencies = [
|
| 12 |
+
"transformers==4.57.3",
|
| 13 |
+
"trl==0.9.3",
|
| 14 |
+
"deepspeed==0.16.9",
|
| 15 |
+
"peft",
|
| 16 |
+
"huggingface_hub",
|
| 17 |
+
"bitsandbytes",
|
| 18 |
+
"accelerate",
|
| 19 |
+
"numpy",
|
| 20 |
+
]
|
| 21 |
+
|
| 22 |
+
[project.urls]
|
| 23 |
+
Homepage = "https://github.com/chest2vec/chest2vec"
|
requirements.txt
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
torch==2.6.0
|
| 2 |
+
torchvision==0.21.0
|
| 3 |
+
torchaudio==2.6.0
|
| 4 |
+
transformers==4.57.3
|
| 5 |
+
trl==0.9.3
|
| 6 |
+
deepspeed==0.16.9
|
| 7 |
+
https://github.com/Dao-AILab/flash-attention/releases/download/v2.8.3/flash_attn-2.8.3+cu12torch2.6cxx11abiTRUE-cp310-cp310-linux_x86_64.whl
|
| 8 |
+
peft
|
| 9 |
+
huggingface_hub
|
| 10 |
+
bitsandbytes
|
| 11 |
+
accelerate
|
| 12 |
+
numpy
|
setup.py
ADDED
|
@@ -0,0 +1,43 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from setuptools import setup, find_packages
|
| 2 |
+
from pathlib import Path
|
| 3 |
+
|
| 4 |
+
# Read README for long description
|
| 5 |
+
readme_file = Path(__file__).parent / "README.md"
|
| 6 |
+
long_description = readme_file.read_text(encoding="utf-8") if readme_file.exists() else ""
|
| 7 |
+
|
| 8 |
+
setup(
|
| 9 |
+
name="chest2vec",
|
| 10 |
+
version="4.0.0",
|
| 11 |
+
description="Section-aware embeddings for chest X-ray reports",
|
| 12 |
+
long_description=long_description,
|
| 13 |
+
long_description_content_type="text/markdown",
|
| 14 |
+
author="Chest2Vec Team",
|
| 15 |
+
url="https://github.com/chest2vec/chest2vec",
|
| 16 |
+
packages=find_packages(),
|
| 17 |
+
py_modules=["chest2vec"],
|
| 18 |
+
include_package_data=True,
|
| 19 |
+
package_data={"": ["__init__.py"]},
|
| 20 |
+
install_requires=[
|
| 21 |
+
"transformers==4.57.3",
|
| 22 |
+
"trl==0.9.3",
|
| 23 |
+
"deepspeed==0.16.9",
|
| 24 |
+
"peft",
|
| 25 |
+
"huggingface_hub",
|
| 26 |
+
"bitsandbytes",
|
| 27 |
+
"accelerate",
|
| 28 |
+
"numpy",
|
| 29 |
+
],
|
| 30 |
+
python_requires=">=3.8",
|
| 31 |
+
classifiers=[
|
| 32 |
+
"Development Status :: 4 - Beta",
|
| 33 |
+
"Intended Audience :: Developers",
|
| 34 |
+
"Intended Audience :: Science/Research",
|
| 35 |
+
"License :: OSI Approved :: Apache Software License",
|
| 36 |
+
"Programming Language :: Python :: 3",
|
| 37 |
+
"Programming Language :: Python :: 3.8",
|
| 38 |
+
"Programming Language :: Python :: 3.9",
|
| 39 |
+
"Programming Language :: Python :: 3.10",
|
| 40 |
+
"Programming Language :: Python :: 3.11",
|
| 41 |
+
"Topic :: Scientific/Engineering :: Artificial Intelligence",
|
| 42 |
+
],
|
| 43 |
+
)
|