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TabRet: Pre-training Transformer-based Tabular Models for Unseen Columns (ICLR 2023 Workshop on ME-FoMo)

This repository contains the code for our machine learning paper titled "TabRet: Pre-training Transformer-based Tabular Models for Unseen Columns" (link). In this README, we provide information about the environment we used and instructions on how to run the code to reproduce our experiments.

Feel free to report issues.

Environment

The experiments in our paper were conducted using the following environment:

  • Operating System: Ubuntu 22.04.1 LTS
  • CUDA compiler version: 11.7
  • Python 3.9.12

Installation

To install the dependencies for this project, please run the following command:

pip install -r requirements.txt

Preparing the Data

Before running the experiment, you need to prepare the data that will be used for pre-training and fine-tuning the model. The data can be placed under any folder, and you can specify the folder with the data_dir option. By default, the data directory is set to datasets/.

For more information on data types and detailed data placement, please refer to the files for each type of data under data/datasets/.

How to create data for pre-training

Download the data from https://www.kaggle.com/datasets/cdc/behavioral-risk-factor-surveillance-system. After unzipping, rename the folder to raw and move it directly under data/. Then, run data/BRFSS.ipynb accordingly to generate all.csv. Put this file in the data_dir before running the pre-training script.

Running the Experiments

The learning execution phase is divided into pre-training and fine-tuning. Here's how to run each phase:

Pre-training

To run the pre-training phase, please run the following command:

python main_pre.py

This will create a {date}/{time} directory under outputs/ where the trained model will be stored. Note that you can specify any output directory by specifying hydra.run.dir.

You can modify the configurations for the pre-training phase in the conf/pre.yaml file.

A specific example is shown below.

[Click to expand] 
python main_pre.py data=BRFSS \
pre_conf=tabret model=tabret \
model/encoder=dropout_01_6blocks \
pre_conf.mask_ratio=0.7 \
batch_size=8192 eval_batch_size=8192 \
mixed_fp16=true num_workers=15 \
hydra.run.dir=output/Pre/BRFSS/tabret/dropout_01_6blocks/0.7

Fine-tuning

To run the fine-tuning phase, please run the following command:

python main_fine.py fine_conf.pre_path={pre-trained model path} seed={n}

Make sure to replace {pre-trained model path} with the path to the previously trained model. You can modify the configurations for the fine-tuning phase in the conf/fine.yaml file.

Alternatively, you can run optimization during fine-tuning using Optuna by running the following command:

python main_optuna.py fine_conf.pre_path={pre-trained model path} seed={n}

Again, make sure to replace {pre-trained model path} with the path to the previously trained model.

A specific example is shown below.

[Click to expand] 
python main_optuna.py data=Diabetes \
model=tabret model/encoder=dropout_01_6blocks \
fine_conf=ret/tabret \
fine_conf.pre_path=output/Pre/BRFSS/tabret/dropout_01_6blocks/0.7/checkpoints_pre/best_model \
study_name=Diabetes/tabret/1 seed=1 \
hydra.run.dir=outputs/Fine/Diabetes/tabret/1