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Model: RehanaHasin/mistral-7b-instruct-v0.3-adjuvant-extractor Source: Original Platform
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README.md
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---
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license: apache-2.0
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language:
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- en
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library_name: transformers
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pipeline_tag: text-generation
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tags:
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- biomedical
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- infectious-disease
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- vaccine-adjuvant
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- information-extraction
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- evidence-grounded
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base_model: mistralai/Mistral-7B-Instruct-v0.3
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---
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# mistral-7b-instruct-v0.3-adjuvant-extractor
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This model is a task-specific fine-tuned version of **Mistral 7B Instruct v0.3** for extracting **vaccine adjuvant concepts** and associated **evidence snippets** from infectious disease biomedical abstracts.
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## Model Summary
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- **Model name:** `mistral-7b-instruct-v0.3-adjuvant-extractor`
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- **Base model:** `mistralai/Mistral-7B-Instruct-v0.3`
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- **Fine-tuning method:** LoRA adapter training, merged into full model weights
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- **Primary task:** Evidence-linked adjuvant extraction from title+abstract text
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## Prompt Used for Inference
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### System prompt
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```text
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You are a biomedical information extraction assistant.
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```
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### User instruction template
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```text
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Extract infectious-disease adjuvants from the text and provide evidence snippets.
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Return ONLY valid JSON in this format:
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[{"adjuvant": "<string>", "evidence": "<string>"}, ...]
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Do not include any extra keys or explanation.
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```
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### Input format
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```text
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Title: <paper title>
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Abstract: <paper abstract>
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```
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The model receives the user instruction template followed by the title/abstract text.
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## Actual Output Format Target
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The model is prompted to return a JSON array of objects with exactly two keys:
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```json
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[
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{
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"adjuvant": "<string>",
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"evidence": "<string>"
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}
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]
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```
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Expected behavior:
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- Return a JSON array (can be empty: `[]`).
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- Each object must contain:
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- `adjuvant`: normalized or near-normalized adjuvant name
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- `evidence`: supporting text snippet from the same input abstract
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- No extra keys and no explanatory text outside JSON.
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## Input/Output Example
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### Example Input
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```text
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Title: Intranasal vaccination study using alum and MPLA adjuvants in a murine influenza model.
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Abstract: Mice immunized with antigen formulated with alum showed increased IgG titers. A separate group receiving MPLA-adjuvanted vaccine demonstrated stronger IFN-gamma responses and reduced viral load after challenge.
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```
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### Expected Output
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```json
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[
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{
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"adjuvant": "alum",
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"evidence": "Mice immunized with antigen formulated with alum showed increased IgG titers."
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},
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{
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"adjuvant": "MPLA",
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"evidence": "A separate group receiving MPLA-adjuvanted vaccine demonstrated stronger IFN-gamma responses and reduced viral load after challenge."
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}
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]
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```
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### Notes on Output Validity
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- Output must be valid JSON.
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- Output must be a JSON array (use `[]` if no supported adjuvant is found).
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- Each item should include only `adjuvant` and `evidence`.
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- Evidence text should come from the provided input abstract.
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## Working Inference Code (Validated)
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```python
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import torch
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import json
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from transformers import AutoTokenizer, AutoModelForCausalLM
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repo_id = "RehanaHasin/mistral-7b-instruct-v0.3-adjuvant-extractor"
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SYS_PROMPT = "You are a biomedical information extraction assistant."
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PROMPT_INSTRUCTION = (
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"Extract infectious-disease adjuvants from the text and provide evidence snippets.\n"
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"Return ONLY valid JSON in this format:\n"
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"[{\"adjuvant\": \"<string>\", \"evidence\": \"<string>\"}, ...]\n"
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"Do not include any extra keys or explanation."
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)
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title = "Protective immune response against Streptococcus pyogenes in mice after intranasal vaccination with the fibronectin-binding protein SfbI."
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abstract = (
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"Despite the significant impact on human health caused by Streptococcus pyogenes, "
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"there is currently no vaccine available. Intranasal immunization of mice with either "
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"SfbI alone or coupled to cholera toxin B subunit (CTB) triggered efficient SfbI-specific responses."
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)
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user_input = f"{PROMPT_INSTRUCTION}\n\nTitle: {title}\nAbstract: {abstract}"
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tokenizer = AutoTokenizer.from_pretrained(repo_id, use_fast=True)
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model = AutoModelForCausalLM.from_pretrained(
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repo_id,
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dtype=torch.float16,
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device_map="auto",
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)
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model.eval()
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chat = tokenizer.apply_chat_template(
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[
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{"role": "system", "content": SYS_PROMPT},
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{"role": "user", "content": user_input},
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],
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tokenize=False,
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add_generation_prompt=True,
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)
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inputs = tokenizer(chat, return_tensors="pt", truncation=True, max_length=1024)
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inputs = {k: v.to(model.get_input_embeddings().weight.device) for k, v in inputs.items()}
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with torch.no_grad():
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outputs = model.generate(
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**inputs,
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max_new_tokens=200,
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do_sample=False,
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pad_token_id=tokenizer.eos_token_id,
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)
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prediction = tokenizer.decode(
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outputs[0][inputs["input_ids"].shape[1]:],
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skip_special_tokens=True
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).strip()
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print(json.dumps(json.loads(prediction), indent=2, ensure_ascii=False))
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```
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## Intended Use
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This model is intended for research workflows in biomedical literature mining, especially:
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- infectious disease vaccine literature curation
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- vaccine adjuvant concept extraction
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- evidence-linked information extraction for downstream manual review
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This model is not intended for clinical decision-making.
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## Training Data and Split Context
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The model was trained on a curated infectious disease adjuvant corpus derived from VIOLIN ecosystem resources.
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- Corpus size used in workflow: 298 abstracts
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- Fixed split framework used across models:
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- 256 train
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- 13 validation
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- 29 test
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## Training Configuration (Fixed Manuscript Setting)
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- LoRA rank (`r`): 8
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- Learning rate: `2e-4`
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- Epochs: `5`
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- Quantization during fine-tuning: 4-bit NF4 with double quantization
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- Compute dtype: float16
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- Per-device batch size and gradient accumulation were configured for stable updates across model families.
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## Usage
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```python
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from transformers import AutoTokenizer, AutoModelForCausalLM
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import torch
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repo_id = "RehanaHasin/mistral-7b-instruct-v0.3-adjuvant-extractor"
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tokenizer = AutoTokenizer.from_pretrained(repo_id)
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model = AutoModelForCausalLM.from_pretrained(
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repo_id,
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torch_dtype=torch.float16,
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device_map="auto",
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)
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```
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## Prompting Recommendation
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Use prompts that explicitly request structured JSON output containing only:
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- `adjuvant`
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- `evidence`
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and restrict extra commentary to reduce parsing errors.
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## Limitations
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- Evaluated on a focused infectious-disease adjuvant corpus; broader-domain generalization is not guaranteed.
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- Performance depends on abstract quality and terminology variation.
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- Structured output may still require post-processing and manual validation.
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## Ethical and Safety Notes
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- Outputs can contain extraction errors or unsupported predictions.
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- Human review is required before downstream knowledge integration.
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- Not for diagnosis, treatment, or direct patient-care decisions.
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## Reproducibility Resources
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Code, notebooks, and workflow details are available at:
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https://github.com/hurlab/Infectious-Disease-Adjuvant-LLM-Fine-tuning
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## Citation
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If you use this model, please cite the associated manuscript and project repository.
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## Contact
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For questions, please contact hasin.rehana@und.edu.
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87
chat_template.jinja
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{%- if messages[0]["role"] == "system" %}
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{%- set system_message = messages[0]["content"] %}
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{%- set loop_messages = messages[1:] %}
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{%- else %}
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{%- set loop_messages = messages %}
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{%- endif %}
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{%- if not tools is defined %}
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{%- set tools = none %}
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{%- endif %}
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{%- set user_messages = loop_messages | selectattr("role", "equalto", "user") | list %}
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{#- This block checks for alternating user/assistant messages, skipping tool calling messages #}
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{%- set ns = namespace() %}
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{%- set ns.index = 0 %}
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{%- for message in loop_messages %}
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{%- if not (message.role == "tool" or message.role == "tool_results" or (message.tool_calls is defined and message.tool_calls is not none)) %}
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{%- if (message["role"] == "user") != (ns.index % 2 == 0) %}
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{{- raise_exception("After the optional system message, conversation roles must alternate user/assistant/user/assistant/...") }}
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{%- endif %}
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{%- set ns.index = ns.index + 1 %}
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{%- endif %}
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{%- endfor %}
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{{- bos_token }}
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{%- for message in loop_messages %}
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{%- if message["role"] == "user" %}
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{%- if tools is not none and (message == user_messages[-1]) %}
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{{- "[AVAILABLE_TOOLS] [" }}
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{%- for tool in tools %}
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{%- set tool = tool.function %}
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{{- '{"type": "function", "function": {' }}
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{%- for key, val in tool.items() if key != "return" %}
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{%- if val is string %}
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{{- '"' + key + '": "' + val + '"' }}
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{%- else %}
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{{- '"' + key + '": ' + val|tojson }}
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{%- endif %}
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{%- if not loop.last %}
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{{- ", " }}
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{%- endif %}
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{%- endfor %}
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{{- "}}" }}
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{%- if not loop.last %}
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{{- ", " }}
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{%- else %}
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{{- "]" }}
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{%- endif %}
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{%- endfor %}
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{{- "[/AVAILABLE_TOOLS]" }}
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{%- endif %}
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{%- if loop.last and system_message is defined %}
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{{- "[INST] " + system_message + "\n\n" + message["content"] + "[/INST]" }}
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{%- else %}
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{{- "[INST] " + message["content"] + "[/INST]" }}
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{%- endif %}
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{%- elif message.tool_calls is defined and message.tool_calls is not none %}
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{{- "[TOOL_CALLS] [" }}
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{%- for tool_call in message.tool_calls %}
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{%- set out = tool_call.function|tojson %}
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||||
{{- out[:-1] }}
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{%- if not tool_call.id is defined or tool_call.id|length != 9 %}
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||||
{{- raise_exception("Tool call IDs should be alphanumeric strings with length 9!") }}
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||||
{%- endif %}
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||||
{{- ', "id": "' + tool_call.id + '"}' }}
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||||
{%- if not loop.last %}
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{{- ", " }}
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||||
{%- else %}
|
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{{- "]" + eos_token }}
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{%- endif %}
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||||
{%- endfor %}
|
||||
{%- elif message["role"] == "assistant" %}
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||||
{{- " " + message["content"]|trim + eos_token}}
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{%- elif message["role"] == "tool_results" or message["role"] == "tool" %}
|
||||
{%- if message.content is defined and message.content.content is defined %}
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||||
{%- set content = message.content.content %}
|
||||
{%- else %}
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{%- set content = message.content %}
|
||||
{%- endif %}
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||||
{{- '[TOOL_RESULTS] {"content": ' + content|string + ", " }}
|
||||
{%- if not message.tool_call_id is defined or message.tool_call_id|length != 9 %}
|
||||
{{- raise_exception("Tool call IDs should be alphanumeric strings with length 9!") }}
|
||||
{%- endif %}
|
||||
{{- '"call_id": "' + message.tool_call_id + '"}[/TOOL_RESULTS]' }}
|
||||
{%- else %}
|
||||
{{- raise_exception("Only user and assistant roles are supported, with the exception of an initial optional system message!") }}
|
||||
{%- endif %}
|
||||
{%- endfor %}
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26
config.json
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config.json
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{
|
||||
"architectures": [
|
||||
"MistralForCausalLM"
|
||||
],
|
||||
"attention_dropout": 0.0,
|
||||
"bos_token_id": 1,
|
||||
"dtype": "float16",
|
||||
"eos_token_id": 2,
|
||||
"head_dim": null,
|
||||
"hidden_act": "silu",
|
||||
"hidden_size": 4096,
|
||||
"initializer_range": 0.02,
|
||||
"intermediate_size": 14336,
|
||||
"max_position_embeddings": 32768,
|
||||
"model_type": "mistral",
|
||||
"num_attention_heads": 32,
|
||||
"num_hidden_layers": 32,
|
||||
"num_key_value_heads": 8,
|
||||
"rms_norm_eps": 1e-05,
|
||||
"rope_theta": 1000000.0,
|
||||
"sliding_window": null,
|
||||
"tie_word_embeddings": false,
|
||||
"transformers_version": "4.57.5",
|
||||
"use_cache": true,
|
||||
"vocab_size": 32768
|
||||
}
|
||||
6
generation_config.json
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generation_config.json
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|
||||
{
|
||||
"_from_model_config": true,
|
||||
"bos_token_id": 1,
|
||||
"eos_token_id": 2,
|
||||
"transformers_version": "4.57.5"
|
||||
}
|
||||
8
merge_metadata.json
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merge_metadata.json
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|
||||
{
|
||||
"base_model": "mistralai/Mistral-7B-Instruct-v0.3",
|
||||
"adapter_dir": "results/hparam_runs_mistral_7B_instruct_v0.3_GRID1_V2/run_8",
|
||||
"output_dir": "finetuned_models/mistral-7b-instruct-v0.3-adjuvant-extractor",
|
||||
"dtype": "float16",
|
||||
"device_map": "cpu",
|
||||
"tokenizer_source": "base_model"
|
||||
}
|
||||
3
model-00001-of-00003.safetensors
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model-00001-of-00003.safetensors
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299
model.safetensors.index.json
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299
model.safetensors.index.json
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|
||||
{
|
||||
"metadata": {
|
||||
"total_parameters": 7248023552,
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23
special_tokens_map.json
Normal file
23
special_tokens_map.json
Normal file
@@ -0,0 +1,23 @@
|
||||
{
|
||||
"bos_token": {
|
||||
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||||
}
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||||
275733
tokenizer.json
Normal file
275733
tokenizer.json
Normal file
File diff suppressed because it is too large
Load Diff
3
tokenizer.model
Normal file
3
tokenizer.model
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:37f00374dea48658ee8f5d0f21895b9bc55cb0103939607c8185bfd1c6ca1f89
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||||
size 587404
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||||
6187
tokenizer_config.json
Normal file
6187
tokenizer_config.json
Normal file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user