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Model: northenlab/soilfm-qwen2.5-14b-literature-cpt Source: Original Platform
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---
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license: apache-2.0
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base_model: Qwen/Qwen2.5-14B-Instruct
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library_name: transformers
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tags:
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- soil-science
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- soil-microbiome
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- domain-adaptation
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- continued-pretraining
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- qlora
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- qwen2
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pipeline_tag: text-generation
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language:
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- en
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model-index:
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- name: soilfm-qwen2.5-14b-literature-cpt
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results: []
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---
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# SoilFM Language Tower — Qwen2.5-14B Literature CPT
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A domain-adapted large language model for **soil science and soil microbiology**, created by continued pretraining of [Qwen2.5-14B-Instruct](https://huggingface.co/Qwen/Qwen2.5-14B-Instruct) on 200,000 curated soil science text passages.
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This model is the **Language Tower** component of [SoilFM2](https://github.com/northenlab), a multi-modal foundation model for soil microbiome analysis developed at Lawrence Berkeley National Laboratory.
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## Model Details
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| | |
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|---|---|
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| **Base model** | Qwen/Qwen2.5-14B-Instruct (14.2B parameters) |
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| **Method** | Continued pretraining via QLoRA (4-bit NF4) |
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| **Format** | Full merged model (LoRA weights merged into base) |
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| **Precision** | BF16 |
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| **Context length** | 32,768 tokens |
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| **Size on disk** | ~28 GB |
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| **LoRA adapter** | Also available at [northenlab/soilfm-qwen2.5-14b-qlora](https://huggingface.co/northenlab/soilfm-qwen2.5-14b-qlora) (263 MB) |
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## Intended Uses
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- Generating explanations of soil microbial processes, rhizosphere ecology, and plant-microbe interactions
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- Providing domain-grounded context within the SoilFM2 multi-modal pipeline (prebiotic recommendation, substrate preference prediction)
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- Serving as a soil-science-aware backbone for downstream fine-tuning or RAG systems
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- Research and educational applications in soil microbiology
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## Training Data
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The training corpus was assembled from four sources of soil science domain knowledge, stratified-sampled to 200,000 training examples and 10,000 validation examples (seed = 42):
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| Source | Description | Proportion | Train | Val |
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|--------|-------------|:----------:|------:|----:|
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| **PubMed Central** | Full-text soil microbiology papers (39,853 articles) | 55% | 110,000 | 5,500 |
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| **Wikipedia** | Soil science articles | 20% | 40,000 | 2,000 |
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| **USDA Soil Survey Manual** | Official USDA technical reference | 10% | 20,000 | 1,000 |
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| **Wikipedia General Biology** | Broad biology context to prevent catastrophic forgetting | 15% | 30,000 | 1,500 |
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| **Total** | | **100%** | **200,000** | **10,000** |
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Text was chunked to 1,024 tokens with 100-token overlap. The full corpus contained 329M tokens across 388,563 chunks; the 200K stratified subsample was used for this training run.
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### Preprocessing
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- PubMed Central articles retrieved via BioC JSON API, cleaned of XML artifacts
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- Soil Survey Manual cleaned of page headers, footers, and index content (57 of 435 chunks removed)
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- All sources standardized to JSONL format with `text` and `source` fields
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## Training Procedure
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### Configuration
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| Parameter | Value |
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|-----------|-------|
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| Quantization | 4-bit NF4 (BitsAndBytes, double quantization) |
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| LoRA rank | 16 |
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| LoRA alpha | 32 |
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| LoRA dropout | 0.05 |
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| Rank-stabilized LoRA (rsLoRA) | Yes |
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| Target modules | q_proj, k_proj, v_proj, o_proj, gate_proj, up_proj, down_proj |
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| Trainable parameters | ~263M (1.85% of total) |
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| Optimizer | PagedAdamW8bit |
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| Learning rate | 2e-5 (cosine schedule, 10% warmup) |
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| Effective batch size | 128 (micro-batch 2, gradient accumulation 64) |
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| Max gradient norm | 1.0 |
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| Weight decay | 0.01 |
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| Precision | BF16 mixed precision |
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| Flash Attention 2 | Enabled |
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| Epochs | 1 |
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| Total steps | 1,500 |
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### Infrastructure
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- **GPU**: NVIDIA A100 PCIe 80GB (RunPod)
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- **Training time**: ~42 hours
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- **Peak VRAM**: 54 GB (67% utilization)
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### Training Script
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A custom manual PyTorch training loop was used (rather than HuggingFace Trainer) for compatibility and control. The script is available in the project repository as `train_soilfm_cpt_MANUAL.py`.
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## Results
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### Validation Loss
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| Step | Validation Loss |
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|-----:|:---------------:|
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| 500 | 1.7369 |
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| 1,000 | 1.6281 |
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| 1,500 | **1.6130** |
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**Total improvement: 7.2%** over the course of training. Loss was still decreasing at the end of training with no signs of overfitting. Gradient norms remained stable in the 0.2–0.8 range throughout.
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### Qualitative Evaluation
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**Prompt:** *"The role of root exudates in shaping rhizosphere microbial communities involves"*
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**Output:** The model produces coherent, technically accurate continuations using appropriate domain terminology (root exudates, rhizosphere, primary/secondary metabolites, phytohormones), demonstrating successful domain adaptation.
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## Usage
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### Direct Loading (Recommended)
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```python
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import torch
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from transformers import AutoModelForCausalLM, AutoTokenizer
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model = AutoModelForCausalLM.from_pretrained(
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"northenlab/soilfm-qwen2.5-14b-literature-cpt",
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torch_dtype=torch.bfloat16,
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device_map="auto",
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)
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tokenizer = AutoTokenizer.from_pretrained(
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"northenlab/soilfm-qwen2.5-14b-literature-cpt"
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)
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prompt = "The role of mycorrhizal fungi in soil nutrient cycling"
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inputs = tokenizer(prompt, return_tensors="pt").to(model.device)
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outputs = model.generate(**inputs, max_new_tokens=256)
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print(tokenizer.decode(outputs[0], skip_special_tokens=True))
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```
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### With vLLM (Production)
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```bash
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python3 -m vllm.entrypoints.openai.api_server \
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--model northenlab/soilfm-qwen2.5-14b-literature-cpt \
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--host 0.0.0.0 --port 8001
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```
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### LoRA Adapter Only
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If you prefer to load the adapter separately (e.g., for 4-bit inference):
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```python
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from transformers import AutoModelForCausalLM
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from peft import PeftModel
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base = AutoModelForCausalLM.from_pretrained(
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"Qwen/Qwen2.5-14B-Instruct",
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load_in_4bit=True,
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device_map="auto",
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)
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model = PeftModel.from_pretrained(base, "northenlab/soilfm-qwen2.5-14b-qlora")
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```
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## Part of SoilFM2
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This Language Tower works alongside other SoilFM2 components:
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| Component | Description | HuggingFace |
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|-----------|-------------|-------------|
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| **Language Tower** (this model) | Domain-adapted LLM | [northenlab/soilfm-qwen2.5-14b-literature-cpt](https://huggingface.co/northenlab/soilfm-qwen2.5-14b-literature-cpt) |
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| **Graph Tower** | Heterogeneous GNN on 2.39M-node knowledge graph | [northenlab/soilfm2-graph-tower-joint-v0.1](https://huggingface.co/northenlab/soilfm2-graph-tower-joint-v0.1) |
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| **BSPR** | Bayesian substrate preference model (AUC 0.94) | — |
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Together these components power a prebiotic recommendation pipeline that takes 16S microbiome profiles as input and suggests soil amendments to steer community function.
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## Use Restrictions
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This model is intended for **research and non-commercial use only**. The training corpus includes PubMed Central Open Access articles under various Creative Commons licenses, some of which may carry non-commercial (CC BY-NC) terms. Users should ensure their use complies with the underlying data licenses.
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The base model (Qwen2.5-14B-Instruct) is released under the Apache 2.0 license.
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## Limitations
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- Trained for 1 epoch on a 200K subsample of the full 667K corpus; additional training may further improve performance
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- Domain adaptation was evaluated primarily via validation loss and qualitative generation; systematic benchmarking on soil science Q&A tasks is ongoing
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- The model inherits the base Qwen2.5-14B-Instruct capabilities and limitations
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- Not intended for medical, agricultural, or regulatory decision-making without expert review
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## Citation
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```bibtex
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@misc{soilfm-language-tower-2025,
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title={SoilFM Language Tower: Domain Adaptation of Qwen2.5-14B for Soil Science},
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author={Northen Lab, Lawrence Berkeley National Laboratory},
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year={2025},
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publisher={HuggingFace},
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url={https://huggingface.co/northenlab/soilfm-qwen2.5-14b-literature-cpt},
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note={Continued pretraining on 200K soil science literature examples via QLoRA}
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}
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```
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## License
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Apache 2.0 (inherited from the base Qwen2.5-14B-Instruct model). Training data includes PubMed Central Open Access articles under various CC licenses — see **Use Restrictions** above.
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207
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|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151644": {
|
||||
"content": "<|im_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151645": {
|
||||
"content": "<|im_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151646": {
|
||||
"content": "<|object_ref_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151647": {
|
||||
"content": "<|object_ref_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151648": {
|
||||
"content": "<|box_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151649": {
|
||||
"content": "<|box_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151650": {
|
||||
"content": "<|quad_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151651": {
|
||||
"content": "<|quad_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151652": {
|
||||
"content": "<|vision_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151653": {
|
||||
"content": "<|vision_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151654": {
|
||||
"content": "<|vision_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151655": {
|
||||
"content": "<|image_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151656": {
|
||||
"content": "<|video_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151657": {
|
||||
"content": "<tool_call>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151658": {
|
||||
"content": "</tool_call>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151659": {
|
||||
"content": "<|fim_prefix|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151660": {
|
||||
"content": "<|fim_middle|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151661": {
|
||||
"content": "<|fim_suffix|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151662": {
|
||||
"content": "<|fim_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151663": {
|
||||
"content": "<|repo_name|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151664": {
|
||||
"content": "<|file_sep|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
}
|
||||
},
|
||||
"additional_special_tokens": [
|
||||
"<|im_start|>",
|
||||
"<|im_end|>",
|
||||
"<|object_ref_start|>",
|
||||
"<|object_ref_end|>",
|
||||
"<|box_start|>",
|
||||
"<|box_end|>",
|
||||
"<|quad_start|>",
|
||||
"<|quad_end|>",
|
||||
"<|vision_start|>",
|
||||
"<|vision_end|>",
|
||||
"<|vision_pad|>",
|
||||
"<|image_pad|>",
|
||||
"<|video_pad|>"
|
||||
],
|
||||
"bos_token": null,
|
||||
"chat_template": "{%- if tools %}\n {{- '<|im_start|>system\\n' }}\n {%- if messages[0]['role'] == 'system' %}\n {{- messages[0]['content'] }}\n {%- else %}\n {{- 'You are Qwen, created by Alibaba Cloud. You are a helpful assistant.' }}\n {%- endif %}\n {{- \"\\n\\n# Tools\\n\\nYou may call one or more functions to assist with the user query.\\n\\nYou are provided with function signatures within <tools></tools> XML tags:\\n<tools>\" }}\n {%- for tool in tools %}\n {{- \"\\n\" }}\n {{- tool | tojson }}\n {%- endfor %}\n {{- \"\\n</tools>\\n\\nFor each function call, return a json object with function name and arguments within <tool_call></tool_call> XML tags:\\n<tool_call>\\n{\\\"name\\\": <function-name>, \\\"arguments\\\": <args-json-object>}\\n</tool_call><|im_end|>\\n\" }}\n{%- else %}\n {%- if messages[0]['role'] == 'system' %}\n {{- '<|im_start|>system\\n' + messages[0]['content'] + '<|im_end|>\\n' }}\n {%- else %}\n {{- '<|im_start|>system\\nYou are Qwen, created by Alibaba Cloud. You are a helpful assistant.<|im_end|>\\n' }}\n {%- endif %}\n{%- endif %}\n{%- for message in messages %}\n {%- if (message.role == \"user\") or (message.role == \"system\" and not loop.first) or (message.role == \"assistant\" and not message.tool_calls) %}\n {{- '<|im_start|>' + message.role + '\\n' + message.content + '<|im_end|>' + '\\n' }}\n {%- elif message.role == \"assistant\" %}\n {{- '<|im_start|>' + message.role }}\n {%- if message.content %}\n {{- '\\n' + message.content }}\n {%- endif %}\n {%- for tool_call in message.tool_calls %}\n {%- if tool_call.function is defined %}\n {%- set tool_call = tool_call.function %}\n {%- endif %}\n {{- '\\n<tool_call>\\n{\"name\": \"' }}\n {{- tool_call.name }}\n {{- '\", \"arguments\": ' }}\n {{- tool_call.arguments | tojson }}\n {{- '}\\n</tool_call>' }}\n {%- endfor %}\n {{- '<|im_end|>\\n' }}\n {%- elif message.role == \"tool\" %}\n {%- if (loop.index0 == 0) or (messages[loop.index0 - 1].role != \"tool\") %}\n {{- '<|im_start|>user' }}\n {%- endif %}\n {{- '\\n<tool_response>\\n' }}\n {{- message.content }}\n {{- '\\n</tool_response>' }}\n {%- if loop.last or (messages[loop.index0 + 1].role != \"tool\") %}\n {{- '<|im_end|>\\n' }}\n {%- endif %}\n {%- endif %}\n{%- endfor %}\n{%- if add_generation_prompt %}\n {{- '<|im_start|>assistant\\n' }}\n{%- endif %}\n",
|
||||
"clean_up_tokenization_spaces": false,
|
||||
"eos_token": "<|im_end|>",
|
||||
"errors": "replace",
|
||||
"model_max_length": 131072,
|
||||
"pad_token": "<|endoftext|>",
|
||||
"split_special_tokens": false,
|
||||
"tokenizer_class": "Qwen2Tokenizer",
|
||||
"unk_token": null
|
||||
}
|
||||
1
vocab.json
Normal file
1
vocab.json
Normal file
File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user