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doctor-dignity's Introduction

Doctor Dignity

DISCLAIMER - Do not take any advice from Doctor Dignity seriously yet. This is a work in progress and taking any advice seriously could result in serious injury or even death.

Overview

Doctor Dignity is a Large Language Model that can pass the US Medical Licensing Exam. This is an open-source project with a mission to provide everyone their own private doctor. Doctor Dignity is a version of Meta's Llama2 7 billion parameter Large Language Model that was fine-tuned on a Medical Dialogue Dataset, then further improved using Reinforcement Learning & Constitutional AI. Since the model is only 3 Gigabytes in size, it fits on any local device, so there is no need to pay an API to use it. It's free, made for offline usage which preserves patient confidentiality, and it's available on iOS, Android, and Web. Pull requests for feature additions and improvements are encouraged.

Dependencies

  • Numpy (Use matrix math operations)
  • PyTorch (Build Deep Learning models)
  • Datasets (Access datasets from huggingface hub)
  • Huggingface_hub (access huggingface data & models)
  • Transformers (Access models from HuggingFace hub)
  • Trl (Transformer Reinforcement Learning. And fine-tuning.)
  • Bitsandbytes (makes models smaller, aka 'quantization')
  • Sentencepiece (Byte Pair Encoding scheme aka 'tokenization')
  • OpenAI (Create synthetic fine-tuning and reward model data)
  • TVM (Tensor Virtual Machine, converts onnx model to efficient cross-platform use)
  • Peft (Parameter Efficient Fine Tuning, use low rank adaption (LoRa) to fine-tune)
  • Onnx (Convert trained model to universal format)

Installation

Install all dependencies in one line using pip

pip install numpy torch datasets huggingface_hub transformers trl bitsandbytes sentencepiece openai tvm peft onnx

iOS QuickStart v2

  1. Clone this repository
git clone https://github.com/llSourcell/Doctor-Dignity
  1. Download the Weights
mkdir -p dist/prebuilt
git clone https://github.com/mlc-ai/binary-mlc-llm-libs.git dist/prebuilt/lib
cd dist/prebuilt
git lfs install
wget --no-check-certificate 'https://drive.google.com/file/d/1MLy8BDhuTTcXqagzLFMA07JDzqjQYUTB/view?pli=1'
cd ../..
  1. Build the Tensor Virtual Machine Runtime
git submodule update --init --recursive
pip install apache-tvm
cd ./ios
pip install --pre --force-reinstall mlc-ai-nightly mlc-chat-nightly -f https://mlc.ai/wheels 
./prepare_libs.sh

** Find the right version of MLC LLM for your system here 4. Add Weights to Xcode

cd ./ios
open ./prepare_params.sh # make sure builtin_list only contains "RedPajama-INCITE-Chat-3B-v1-q4f16_1"
./prepare_params.sh
  1. Open Xcode Project and run!

DIY Training

In order to train the model, you can run the training.ipynb notebook locally or remotely via a cloud service like Google Colab Pro. The training process requires a GPU, and if you don't have one then the most accessible option i found was using Google Colab Pro which costs $10/month. The total training time for Doctor Dignity including supervised fine-tuning of the initial LLama model on custom medical data, as well as further improving it via Reinforcement Learning from Constitional AI Feedback took 24 hours on a paid instance of Google Colab. If you're interested in learning more about how this process works, details are in the training.ipynb notebook.

Cloud Training

Open In Colab click here: https://colab.research.google.com/github/llSourcell/Doctor-Dignity/blob/main/llama2.ipynb

Local Training

git clone https://github.com/llSourcell/Doctor-Dignity.git
jupyter training.ipynb

Get jupyter here

There are 2 huggingface repos, one which is quantized for mobile and one that is not.

Old iOS app

Android app (TODO)

  • Step 1: Download the Android Machine Learning Compilation Chat Repository
  • Step 2: Follow the installation steps
  • Step 3: Tap "add model variant"
  • Step 4: Enter the URL for the latest Doctor Dignity model to download it: https://huggingface.co/llSourcell/doctorGPT_mini
  • Step 5: Tap 'Add Model' and start chatting locally! No internet needed.

Web (TODO)

As an experiment in Online Learning using actual human feedback, i want to deploy the model as a Flask API with a React front-end. In this case, anyone can chat with the model at this URL. After each query, a human can rate the model's response. This rating is then used to further improve the model's performance through reinforcement learning. to run the app, download flask and then you can run:

flask run

Then visit localhost:3000 to interact with it! You can also deploy to vercel

Credits

Meta, MedAlpaca, Apache, MLC Chat & OctoML

doctor-dignity's People

Contributors

bbuf avatar bowels avatar charliefruan avatar cyx-6 avatar davidpissarra avatar eltociear avatar fubge avatar hzfengsy avatar jakelin avatar jinhongyii avatar junrushao avatar kathryn-cat avatar l0phtg avatar leiwang1999 avatar llsourcell avatar masahi avatar masterjh5574 avatar nverke avatar plateaukao avatar rojotek avatar sbelcmu avatar sing-li avatar spectrometerhbh avatar sudeepag avatar sunggg avatar tqchen avatar twiceyuan avatar ubospica avatar vinx13 avatar yzh119 avatar

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doctor-dignity's Issues

Confused how to run on Linux PC [Question]

โ“ General Questions

Hi,

This looks incredible, thanks for making it available! It will be an awesome addition to my Free Life Planner project, which is undertaken in a similar spirit:

https://github.com/aindilis/flp/blob/main/ReferenceManual.md

However, I am unclear how to run DoctorGPT on Linux PC. The instructions say how to build for Android or iOS. Could you please if possible also either add instructions to run on Linux PC or if they already exists please direct me to the Linux PC installation instructions? I would prefer to download the models and avoid training if possible, and also have instructions how to run inference with it and especially to have the ability to run as a server if possible.

Thanks,

Sincerely,

Andrew

unable to build code is incomplete non working demo

this project is non functional and a clone of the real DoctorGTP and that is a paid Service the copyright code in question is missing

10: fatal error: 'tvm/runtime/relax_vm/memory_manager.h' file not found
#include <tvm/runtime/relax_vm/memory_manager.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.

Its because when the code was copied they didn't copy all the files
I think you will get a copyright trick for stolen code

Missing ethical disclosures

I totally get that your goal is to help people who can't afford a doctor, can't physically get to a doctor right now, etc. But like.

You can't just make a robot that dispenses medical advice with absolutely no disclosures of risk. I do not see anything in the readme, I do not see anything skimming through the notebook - nothing about the fact that LLMs are a highly experimental technology that are highly prone to confabulation.

You need an ethics disclosure in both the readme and the interface and it needs to be EXTREMELY obvious.

It should be physically impossible to engage with this LLM without being clear on the fact it may just tell you to poison yourself. Right now the only safety net is that you need to be computer-literate enough to run a pip command.

Also it wouldn't surprise me if this thing is just plain illegal in some jurisdictions but I'll let y'all figure that one out.

How to load the saved model after 2.4 Run Fine-Tuning Loop?

The folder does not contain the usual config.json file.

./my_model] ls

adapter_config.json README.md tokenizer_config.json tokenizer.model
adapter_model.bin special_tokens_map.json tokenizer.json training_args.bin

cat adapter_config.json 
{
  "auto_mapping": null,
  "base_model_name_or_path": "meta-llama/Llama-2-7b-chat-hf",
  "bias": "none",
  "fan_in_fan_out": false,
  "inference_mode": true,
  "init_lora_weights": true,
  "layers_pattern": null,
  "layers_to_transform": null,
  "lora_alpha": 16,
  "lora_dropout": 0.1,
  "modules_to_save": null,
  "peft_type": "LORA",
  "r": 64,
  "revision": null,
  "target_modules": [
    "q_proj",
    "v_proj"
  ],
  "task_type": "CAUSAL_LM"
}

out of memory on AWS ec2 p3.2xlarge, any ideas?

Hi, not a bug, but I tried to run this on AWS with 16G of memory on a Tesla V100-SXM2-16GB GPU and I couldn't load the model. It ran out of memory. Anyone know what might be going on? I ran it in colab just fine (at least loading the model) on 16GB memory. Thanks!
.

Unable to Load Pretrained Model Due to Missing config.json

Issue Description:
I encountered an issue while attempting to load a pretrained model using the provided code snippet. It seems that the error is related to the absence of the config.json file in the model directory. I'm seeking guidance on how to properly load the model and perform inference on a Linux system.
Deployment Steps:

Create a conda environment and install required packages:

conda create -n doc python=3.8
conda activate doc
pip install numpy torch datasets huggingface_hub transformers trl bitsandbytes sentencepiece openai tvm peft onnx jupyter
git clone https://github.com/llSourcell/DoctorGPT.git

Download the pretrained model from https://huggingface.co/llSourcell/medllama2_7b and save it locally.
Attempt to debug using the provided code snippet:

from transformers import (
    AutoModelForCausalLM,
    AutoTokenizer,
    BitsAndBytesConfig,
    HfArgumentParser,
    AutoTokenizer,
    TrainingArguments,
)

local_model_path = "/data/gitclone/text-generation-webui/models/llSourcell_medllama2_7b"
model = AutoModelForCausalLM.from_pretrained(local_model_path)

Error Details:
The error arises because the config.json file is missing in the model directory.

Request for Assistance:
Could you please provide guidance on the correct approach to load the pretrained model without encountering the missing config.json error? Additionally, I would appreciate instructions on how to perform inference using the loaded model on a Linux system.

Error Screenshot:
image

Thank you for your help!

[Question] how to "Web (TODO)" ?

โ“ General Questions

I would like to follow the Web (TODO) in the "read me", it is just indicated "flask run".

I looked for a solution, and it's not easy to find :-)

Can you give more details ?
Do we need to run this command in a specific folder ? If yes which one ?
What do we need to do ?

Thanks for your help.

RuntimeError: probability tensor contains either `inf`, `nan` or element < 0

After 2.4 Run Fine-Tuning Loop, I got the following error when running 2.6 Evaluate Performance (USMLE):

Traceback (most recent call last):
File "llama2.py", line 450, in
accuracy = evaluate_model(model, tokenizer, dataset,"")
File "llama2.py", line 284, in evaluate_model
output = model.generate(input_ids, num_beams=4)
File ". pytorch/1.13.1/lib/python3.9/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File ".local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/generation/utils.py", line 1665, in generate
return self.beam_sample(
File ".local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/generation/utils.py", line 3309, in beam_sample
next_tokens = torch.multinomial(probs, num_samples=2 * num_beams)
RuntimeError: probability tensor contains either inf, nan or element < 0

A token is already saved on your machine

Hi there. I'm getting this message. I've tested with both huggingface-cli login and huggingface-cli logout. There's a file where I can set the huggingface token? Because even logged stop there.

image

I'm already logged:

image

Thank you.

1.8 Performance Boost via Soft Prompting - dataset['train'] - KeyError: "Column train not in the dataset. Current columns in the dataset: ['question', 'answer', 'options', 'meta_info', 'answer_idx', 'metamap_phrases']"

I'm getting

KeyError: "Column train not in the dataset. Current columns in the dataset: ['question', 'answer', 'options', 'meta_info', 'answer_idx', 'metamap_phrases']"

When running 1.8 Performance Boost via Soft Prompting on colab

def evaluate_model(model, tokenizer, dataset, conversation_history):
    correct = 0
    total = 0

    # Iterate through the dataset
    for example in dataset['train']: # Fixed from get_split to dictionary-style access
        try:
            question = example["question"]
            options = example["options"]
            correct_answer_idx = example["answer_idx"]

            # Combine the question with the options
            input_text = conversation_history + question + " " + " ".join([f"{k}: {v}" for k, v in options.items()]) + 'only respond with a single alphabetical character.'

            # Generate model's answer
            input_ids = tokenizer.encode(input_text, return_tensors="pt").to('cuda')
            output = model.generate(input_ids, num_beams=4)
            generated_text = tokenizer.decode(output[0]).strip()

            # Extract the selected option from the generated text
            predicted_answer_idx = generated_text[0]  # Assuming the generated text starts with the selected option letter

            # Compare with the correct answer
            if correct_answer_idx == predicted_answer_idx:
                correct += 1

            total += 1

        except KeyError as e:
            print("KeyError encountered for example:", example)
            raise e  # To see the full traceback and understand the origin of the error.

    return correct / total

Full message

User:
['question', 'answer', 'options', 'meta_info', 'answer_idx', 'metamap_phrases']
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-28-bb8bf40a3938> in <cell line: 83>()
     81 
     82 # Evaluate the model
---> 83 accuracy = evaluate_model(model, tokenizer, dataset, conversation_history)
     84 print(f"Accuracy: {accuracy * 100:.2f}%")

4 frames
/usr/local/lib/python3.10/dist-packages/datasets/formatting/formatting.py in _check_valid_column_key(key, columns)
    518 def _check_valid_column_key(key: str, columns: List[str]) -> None:
    519     if key not in columns:
--> 520         raise KeyError(f"Column {key} not in the dataset. Current columns in the dataset: {columns}")
    521 
    522 

KeyError: "Column train not in the dataset. Current columns in the dataset: ['question', 'answer', 'options', 'meta_info', 'answer_idx', 'metamap_phrases']"

[Question] No module named 'tvm'

โ“ General Questions

When I run the python prepare_model_lib.py script, an error occurs:

Traceback (most recent call last):
  File "/Users/wyh/Desktop/Programs/DoctorGPT/ios/prepare_model_lib.py", line 3, in <module>
    from tvm.contrib import cc
ModuleNotFoundError: No module named 'tvm'

I tried :

pip install --pre --force-reinstall mlc-ai-nightly mlc-chat-nightly -f https://mlc.ai/wheels

and got this:

WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x10d1ca4b0>, 'Connection to mlc.ai timed out. (connect timeout=15)')': /wheels
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x10df43470>, 'Connection to mlc.ai timed out. (connect timeout=15)')': /wheels
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x10df43680>, 'Connection to mlc.ai timed out. (connect timeout=15)')': /wheels
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x10df438c0>, 'Connection to mlc.ai timed out. (connect timeout=15)')': /wheels
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x10df43ad0>, 'Connection to mlc.ai timed out. (connect timeout=15)')': /wheels
ERROR: Could not find a version that satisfies the requirement mlc-ai-nightly (from versions: none)
ERROR: No matching distribution found for mlc-ai-nightly

python version:

python --version
pip --version
which python
which pip3

Python 3.11.4
pip 23.2.1 from /Users/wyh/anaconda3/lib/python3.11/site-packages/pip (python 3.11)
/Users/wyh/anaconda3/bin/python
/Users/wyh/anaconda3/bin/pip3

MacOS Ventura 13.5.2

[Bug] rwkv-raven-3b-q4f16_2 not found when compiling the iOS project

๐Ÿ› Bug

To Reproduce

In the DoctorGPT project, following the compilation documentation for mlc-llm, I get an error when executing the script.

sh ./prepare_libs.sh
Traceback (most recent call last):
  File "/Users/wyh/Desktop/Programs/DoctorGPT/ios/prepare_model_lib.py", line 29, in <module>
    main()
  File "/Users/wyh/Desktop/Programs/DoctorGPT/ios/prepare_model_lib.py", line 19, in main
    raise RuntimeError(
RuntimeError: Cannot find lib for rwkv-raven-3b-q4f16_2 in the following candidate path: ['/Users/wyh/Desktop/Programs/DoctorGPT/dist/rwkv-raven-3b-q4f16_2/rwkv-raven-3b-q4f16_2-iphone.tar', '/Users/wyh/Desktop/Programs/DoctorGPT/dist/prebuilt/lib/rwkv-raven-3b-q4f16_2-iphone.tar']

But after I modified /ios/MLCChat/app-config.json, the prepare_libs.sh script executed successfully, and Xcode was able to compile successfully.

IMG_9084B58BB2C7-1

However, the program crashes when running.

ๆˆชๅฑ2023-09-13 22 58 41

Issue with ppo_trainer.generate()

Thank you for the clear-cut amazing video tutorial and repo. I have been working on this repo and faced the following issue on 8 GPU A100 with OS disk space of 100GB and 5TB external. Could you kindly help me with this!!

Traceback (most recent call last):
File "rl_finetuning.py", line 175, in
response_tensor = ppo_trainer.generate(query_tensor, pad_token_id=tokenizer.eos_token_id, max_new_tokens=20)
File "/data-mount/trl/trl/trainer/ppo_trainer.py", line 450, in generate
response = self.accelerator.unwrap_model(self.model).generate(
File "/data-mount/trl/trl/models/modeling_value_head.py", line 198, in generate
return self.pretrained_model.generate(*args, **kwargs)
File "/home/aishu/.local/lib/python3.8/site-packages/peft/peft_model.py", line 977, in generate
outputs = self.base_model.generate(**kwargs)
File "/home/aishu/.local/lib/python3.8/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
File "/home/aishu/.local/lib/python3.8/site-packages/transformers/generation/utils.py", line 1642, in generate
return self.sample(
File "/home/aishu/.local/lib/python3.8/site-packages/transformers/generation/utils.py", line 2724, in sample
outputs = self(
File "/home/aishu/.local/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
return forward_call(*args, **kwargs)
File "/home/aishu/.local/lib/python3.8/site-packages/transformers/models/llama/modeling_llama.py", line 809, in forward
outputs = self.model(
File "/home/aishu/.local/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
return forward_call(*args, **kwargs)
File "/home/aishu/.local/lib/python3.8/site-packages/transformers/models/llama/modeling_llama.py", line 628, in forward
batch_size, seq_length = input_ids.shape
ValueError: too many values to unpack (expected 2)

Usage

You say it is possible to use it with MLC Chat, but I think it needs a config file that is missing ! mlc-chat-config.json ...
Here is the screenshot :
Screenshot_20230813-010309_MLCChat.jpg

RuntimeError: shape '[-1, 32]' is invalid for input of size 1

The modeling_llama.py code is too buggy. I am debugging a common pattern of error. the input_ids has one additional dimension added in front. Then many other places in the code do not know this and get the wrong dimension information.

Traceback (most recent call last):
  File "/global/cfs/cdirs/m2956/workspace-cfs/openmp-qa/reinforcement_learning.py", line 140, in <module>
    response_tensor = ppo_trainer.generate(query_tensor, pad_token_id=tokenizer.eos_token_id, max_new_tokens=20)
  File "/global/homes/l/liaoch/.local/unknown/pytorch1.13.1/lib/python3.9/site-packages/trl/trainer/ppo_trainer.py", line 454, in generate
    response = self.accelerator.unwrap_model(self.model).generate(
  File "/global/homes/l/liaoch/.local/unknown/pytorch1.13.1/lib/python3.9/site-packages/trl/models/modeling_value_head.py", line 198, in generate
    return self.pretrained_model.generate(*args, **kwargs)
  File "/global/common/software/nersc/pm-2022q4/sw/pytorch/1.13.1/lib/python3.9/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
    return func(*args, **kwargs)
  File "/global/homes/l/liaoch/.local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/generation/utils.py", line 1538, in generate
    return self.greedy_search(
  File "/global/homes/l/liaoch/.local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/generation/utils.py", line 2362, in greedy_search
    outputs = self(
  File "/global/common/software/nersc/pm-2022q4/sw/pytorch/1.13.1/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1194, in _call_impl
    return forward_call(*input, **kwargs)
  File "/global/homes/l/liaoch/.local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py", line 806, in forward
    outputs = self.model(
  File "/global/common/software/nersc/pm-2022q4/sw/pytorch/1.13.1/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1194, in _call_impl
    return forward_call(*input, **kwargs)
  File "/global/homes/l/liaoch/.local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py", line 643, in forward
    position_ids = position_ids.view(-1, seq_length).long()
RuntimeError: shape '[-1, 32]' is invalid for input of size 1

the size of position_ids should be the same as the input_ids's last dimension (1x1x32 ).
But it has 1x1 shape.

(Pdb) p position_ids

tensor([[0]], device='cuda:0')

def prepare_inputs_for_generation () sets position_ids, based on the shape of attention_mask, which in turn is set by _prepare_attention_mask_for_generation () from .. pytorch1.13.1/lib/python3.9/site-packages/transformers/generation/utils.py

return torch.ones(inputs.shape[:2], dtype=torch.long, device=inputs.device)

I changed it to inputs.shape[1:3] instead the code can proceed.

But it then get another similar error later.

  File ".local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py", line 287, in forward
    bsz, q_len, _ = hidden_states.size()
ValueError: too many values to unpack (expected 3)
Uncaught exception. Entering post mortem debugging
Running 'cont' or 'step' will restart the program
> ...local/unknown/pytorch1.13.1/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py(287)forward()
-> bsz, q_len, _ = hidden_states.size()
(Pdb) p hidden_states.size()
torch.Size([1, 1, 32, 4096])

LLM Bros the next Crypto Bros?

Speculations arise that the new AI fad is being pushed by the same people who lead us down the failed path of crypto currency, altcoins, and web 3.0.

A wolf in sheep's clothing would pass as a human to this "doctor" of yours.

You're going to get people killed. And then get sued. Then you'll go to jail. Then I will laugh at the absurdity of your idiocy.

Model URL fails to import into MLCChat for Android

It just says "Add model failed: " and then the URL. Sorry I can't be more help here, but will be happy to confirm that the URL works if/when it gets fixed. Seems like all Android users will be unable to use this unless there's something presumed to be obvious missing from the instructions. URL specified by the instructions is: https://huggingface.co/llSourcell/doctorGPT_mini

Asus ROG Phone 6
Tramisu (13)
Qualcomm SM8475 Snapdragon 8+ Gen 1
Adreno 730
18GB RAM

[Question] Impossible to reproduce results, model performs poorly

โ“ General Questions

I evaluated the model using lm-evaluation-harness on MedMCQA, MedQA-USMLE and PubMedQA and the model performs barely above llama2 7b with only 38% on the USMLE, 36% on MedMCQa and 73.9% on PubMedQA.

Could you describe how you got your results?

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