MEDIQA-shared-tasks

This is our repo for MEDIQA-Sum shared tasks, 2023 (Website: https://www.imageclef.org/2023/medical/mediqa)

Tasks

• Subtask A - Dialogue2Topic Classification. Given a conversation snippet between a doctor and patient, participants are tasked with identifying the topic (associated section header). Topics/Section headers will be one of twenty normalized common section labels (e.g. Assessment, Diagnosis, Exam, Medications, Past Medical History).
• Subtask B - Dialogue2Note Summarization. Given a conversation snippet between a doctor and patient and a section header, participants are tasked with producing a clinical note section text summarizing the conversation.
• Subtask C - Full-Encounter Dialogue2Note Summarization. Given a full encounter conversation between a doctor and patient, participants are tasked with producing a full clinical note summarizing the conversation

Inference

To run our model on the test dataset, do the following:

1. To set up the environment, clone this repo and do the following cmd lines:

## install.sh creates the environment & install all packages
source ./install.sh
## activate.sh activates the environment
source ./activate.sh

2. To run Task A, do the following cmd lines:

cd taskA
source ./decode_taskA_run1.sh

The output will be a .csv file: "taskA_HuskyScribe_run1_mediqaSum.csv"

3. To run Task B, do the following cmd lines:

cd taskB
source ./decode_taskB_run1.sh

The output will be a .csv file: "taskB_HuskyScribe_run1_mediqaSum.csv"

4. To run Task C, do the following cmd lines:

cd taskC
source ./decode_taskC_run1.sh
source ./decode_taskC_run2.sh

There will be two output .csv files: "taskC_HuskyScribe_run1_mediqaSum.csv", "taskC_HuskyScribe_run2_mediqaSum.csv"