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--- |
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library_name: transformers |
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tags: |
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- biology |
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- chemistry |
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- biological materials |
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- materials science |
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- engineering |
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- materials informatics |
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- scientific AI |
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- AI4science |
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--- |
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## Inference example |
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``` |
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model_name='lamm-mit/BioinspiredLlama-3-1-8B-128k' |
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model = AutoModelForCausalLM.from_pretrained( |
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model_name, |
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trust_remote_code=True, |
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device_map="auto", |
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torch_dtype =torch.bfloat16, |
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attn_implementation="flash_attention_2" |
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) |
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model.config.use_cache = True |
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tokenizer = AutoTokenizer.from_pretrained(model_name) |
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``` |
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Check https://huggingface.co/lamm-mit/BioinspiredLlama-3-1-8B-128k-dominant-protein-SS-structure for further examples use of the model for protein structural features prediction, including a fine-tuning script. |
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#### Function to interact with the model |
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``` |
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def generate_response (text_input="What is spider silk?", |
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system_prompt='', |
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num_return_sequences=1, |
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temperature=1., #the higher the temperature, the more creative the model becomes |
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max_new_tokens=127,device='cuda', |
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add_special_tokens = False, #since tokenizer.apply_chat_template adds <|begin_of_text|> template already, set to False |
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num_beams=1,eos_token_id= [ |
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128001, |
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128008, |
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128009 |
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], verbatim=False, |
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top_k = 50, |
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top_p = 0.9, |
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repetition_penalty=1.1, |
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messages=[], |
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): |
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if messages==[]: #start new messages dictionary |
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if system_prompt != '': #include system prompt if provided |
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messages.extend ([ {"role": "system", "content": system_prompt}, ]) |
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messages.extend ( [ {"role": "user", "content": text_input}, ]) |
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else: #if messages provided, will extend (make sure to add previous response as assistant message) |
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messages.append ({"role": "user", "content": text_input}) |
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text_input = tokenizer.apply_chat_template( |
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messages, |
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tokenize=False, |
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add_generation_prompt=True |
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) |
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inputs = tokenizer([text_input], add_special_tokens = add_special_tokens, return_tensors ='pt' ).to(device) |
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if verbatim: |
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print (inputs) |
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with torch.no_grad(): |
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outputs = model.generate(**inputs, |
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max_new_tokens=max_new_tokens, |
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temperature=temperature, |
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num_beams=num_beams, |
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top_k = top_k,eos_token_id=eos_token_id, |
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top_p =top_p, |
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num_return_sequences = num_return_sequences, |
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do_sample =True, repetition_penalty=repetition_penalty, |
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) |
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outputs=outputs[:, inputs["input_ids"].shape[1]:] |
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return tokenizer.batch_decode(outputs.detach().cpu().numpy(), skip_special_tokens=True), messages |
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``` |
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Usage: |
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``` |
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res,_= generate_response (text_input = "What is collagen?", system_prompt = 'You are a materials scientist.', |
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num_return_sequences=1, |
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temperature=1., #the higher the temperature, the more creative the model becomes |
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max_new_tokens=127, |
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num_beams=1, |
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top_k = 50, top_p =0.9, repetition_penalty=1.1, |
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) |
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print (res[0]) |
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``` |
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To realize multi-turn interactions, see this example: |
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``` |
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res, messages = generate_response (text_input="What is spider silk?", messages=[]) |
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messages.append ({"role": "assistant", "content": res[0]}, ) #append result to messages dict |
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print (res) |
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res, messages = generate_response (text_input="Explain this result in detail.", messages=messages) |
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messages.append ({"role": "assistant", "content": res[0]}, ) #append result to messages dict |
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print (res) |
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res, messages = generate_response (text_input="Provide this in JSON format.", messages=messages) |
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messages.append ({"role": "assistant", "content": res[0]}) #append result to messages dict |
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print (res) |
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``` |
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## Fine-tuning script |
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See (https://huggingface.co/lamm-mit/BioinspiredLlama-3-1-8B-128k-dominant-protein-SS-structure) for a Colab fine-tuning script. |
