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Retrieving Multimodal Prompts for Medical Visual Question Answering

This repository includes the source code for MPR_Gen, a generative model which optionally integrates visual features or retrieved information into T5 via prompting. This enables rapid zero-shot dataset adaptation to unseen data distributions and open-set answer labels across datasets.

How to use

Setup the environment

We use conda version 4.13.0 with python 3.9.12 to conduct our experiments. After creating a fresh anaconda environment with this python version or above, you can install the required libraries to run our code with the following commands:

pip install -r requirements.txt
pip install git+https://github.com/openai/CLIP.git

Obtain the data

To reproduce our results, first clone this repository and download the SLAKE dataset from their website. Also obtain the image folder, trainset.json, and testset.json files for VQA_RAD from the data folder at this github repository. Once the data has been obtained, organize the data into this directory structure (note, VQA_RAD json files should also be renamed to train.json, test.json):

data
|----SLAKE
     |----train.json
     |----validate.json
     |----test.json
     |----imgs
          |----xmlab0
          |----xmlab1
                ⋮
|----VQA_RAD
    |----train.json
    |----test.json
    |----imgs
          |----synpic100132.jpg
          |----synpic100176.jpg
                ⋮

Setup the config file

We provide a sample config file in the config folder. You may edit the various entries within it to customize the experiment. Here is a brief explanation of important settings:

{
    "dataset":                       # The source dataset used for training (SLAKE or VQA_RAD)
    "datafolder":                    # The path to the folder containing the medical VQA datasets
    "use_image_info":                # 0/1 Indicating whether to use the image features in the prompt
    "T5_version":                    # The size of the T5 model: "t5-small" works best
    "vision_encoder":                # The type of CLIP model: "ViT-B/32" works well
    "vision_checkpoint":             # The path to the saved PubMedCLIP weights
    "use_BAN":                       # 0/1 indicating whether to use BAN for feature fusion (only for prediction head models)
    "use_prediction_head":           # 0/1 indicating whether to use a prediction head or generate free-text answers
    "freeze":                        # 0/1 indicating whether the encoder/decoder stack of T5 should be frozen
    "glimpse":                       # A hyperparameter for BAN
    "retrieval":                     # 0/1 indicating whether the model should do retrieval
    "use_additional_retrieval_data": # 0/1 indicating whether additional synthetic data should be used for retrieval
    "transfer_dataset":              # The Target dataset (SLAKE or VQA_RAD)
    "retrieval_dataset":             # Name of the retrieval dataset (SLAKE, VQA_RAD, or ROCO)
    "k": 1,                          # Number of retrieved question-answer pairs during retrieval
    "quantifier":                    # 0/1 indicating if a quantifier should be used in the retrieved prompts
    "further_finetune":              # 0/1 indicating whether model weights should be updated during adaptation
}

Run main.py

To train a model, execute the following command:

python main.py --train --config <path_to_config_file> --gpu_id <ID of GPU>

To test a model, use the following:

python main.py --test --config <path_to_config_file> --gpu_id <ID of GPU>

Advanced Usage

PubMedCLIP Model

We observed mariginal gains for both in-domain and dataset adaptation tasks when using a domain-specific encoder. To reproduce these results, please follow these instructions and download the PubMedCLIP_ViT32.pth checkpoint. You may then supply the path to these weights in the config file under the vision_checkpoint argument.

Synthetic Data

To reproduce the experiments with synthetic data, first download the ROCO dataset following these instructions . Then run the generate_roco_questions script from the root project folder as follows:

python synthetic_data/generate_roco_questions.py <path_to_ROCO_dataset> <path_to_folder_with_SLAKE_and_VQA_RAD_datasets>

This will create a new dataset called ROCO in the same folder as the SLAKE and VQA_RAD datasets. After this step, you can toggle use "ROCO" for the retrieval dataset argument, or optionally toggle the use_additional_data flag in the config file to combine both in-domain and synthetic retrieval data.

Acknowledgement

We make use of the following repositories to help in our experiments: OpenAI CLIP, PubMedCLIP, Medical VQA with Conditional Reasoning

Citation

Please feel free to cite our paper if you use our model or results in your research 😊

@article{ossowski2023multimodal,
  title={Multimodal Prompt Retrieval for Generative Visual Question Answering},
  author={Ossowski, Timothy and Hu, Junjie},
  journal={Findings of the 61st Annual Meeting of the Association for Computational Linguistics},
  year={2023}
}