LS-GFN

Official Code for Local Search GFlowNets

Note: I find that there are some differences in terms of mode metrics and hyperparameters. Now it is fixed.

Environment Setup

Please first install your conda with yaml file and install the pyg (of pytorch 1.13). (https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html)

conda env create -f environment.yaml

pip install torch_geometric
pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-1.13.0+cu117.html

conda activate ls_gfn

Code references

Our implementation is based on "Towards Understanding and Improving GFlowNet Training" (https://github.com/maxwshen/gflownet).

Our contribution (in terms of codes)

We extend codebase with RNA-binding tasks designed by FLEXS (https://github.com/samsinai/FLEXS)

We implement detailed balance (DB), sub-trajectory balance (SubTB), and our method LS-GFN on top of DB, SubTB, TB, MaxEnt and GTB.

We also implement various state-of-the-art baselines including RL approaches (A2C-Entropy, SQL, PPO) and recent MCMC approaches (MARS)

Large files

To run sehstr task, you should download sehstr_gbtr_allpreds.pkl.gz and block_18_stop6.pkl.gz. Both are available for download at https://figshare.com/articles/dataset/sEH_dataset_for_GFlowNet_/22806671 DOI: 10.6084/m9.figshare.22806671 These files should be placed in datasets/sehstr/.

Main Experiments

We should run all experiments with at least 3 different random seeds. You can see example script in scripts/<task_name>.sh

For QM9 task, you can run experiments by following commands

# TB + LS-GFN
python runexpwb.py --setting qm9str --beta 5 --model tb --ls true --deterministic true --num_active_learning_rounds 2000 --seed 0

# TB
python runexpwb.py --setting qm9str --beta 5 --model tb --num_active_learning_rounds 2000 --seed 0

# MARS
python runexpwb.py --setting qm9str --beta 5 --model mars --num_active_learning_rounds 2000 --seed 0

# A2C
python runexpwb.py --setting qm9str --beta 5 --model a2c --num_active_learning_rounds 2000 --seed 0

# SQL
python runexpwb.py --setting qm9str --beta 5 --model sql --num_active_learning_rounds 2000 --seed 0

# PPO
python runexpwb.py --setting qm9str --beta 5 --model ppo --num_active_learning_rounds 2000 --seed 0

Evaluation

After training, you can run the following commands to evaluate the performance of models.

eval.py returns top-100 reward, diversity, unique fraction of samples generated by trained models

number_of_modes.py returns the total number of modes discovered over the course of training.

python eval.py --setting qm9str --beta 5 --model tb --ls true --deterministic true --seed 0
python number_of_modes.py --setting qm9str --beta 5 --model tb --ls true --deterministic true --seed 0

Different GFN Objectives

If you want to run LS-GFN with different training objectives, you can run following commands:

MaxEnt

# MaxEnt + LS-GFN
python runexpwb.py --setting qm9str --beta 5 --model maxent --ls true --deterministic true --num_active_learning_rounds 2000 --seed 0

# MaxEnt
python runexpwb.py --setting qm9str --beta 5 --model maxent --num_active_learning_rounds 2000 --seed 0

# DB + LS-GFN
python runexpwb.py --setting qm9str --beta 5 --model db --ls true --deterministic true --num_active_learning_rounds 2000 --seed 0

# DB
python runexpwb.py --setting qm9str --beta 5 --model db --num_active_learning_rounds 2000 --seed 0

SubTB

# SubTB + LS-GFN
python runexpwb.py --setting qm9str --beta 5 --model subtb --lamda 0.9 --ls true --deterministic true --num_active_learning_rounds 2000 --seed 0

# SubTB
python runexpwb.py --setting qm9str --beta 5 --model subtb --lamda 0.9 --num_active_learning_rounds 2000 --seed 0

GTB

# GTB + LS-GFN
python runexpwb.py --setting qm9str --beta 5 --model gtb --ls true --deterministic true --num_active_learning_rounds 2000 --seed 0

# GTB
python runexpwb.py --setting qm9str --beta 5 --model gtb --num_active_learning_rounds 2000 --seed 0

Ablations

Filtering Strategies (Deterministic vs Stochastic)

# Deterministic
python runexpwb.py --setting qm9str --model tb --ls true --deterministic true --num_active_learning_rounds 2000 --seed 0

# Stochastic
python runexpwb.py --setting qm9str --model tb --ls true --num_active_learning_rounds 2000 --seed 0

Number of Deconstruction / Reconstruction Steps (K)

python runexpwb.py --setting qm9str --model tb --ls true --deterministic true --k <reconstruction_steps> --num_active_learning_rounds 2000 --seed 0

Number of Revision Steps (I)

python runexpwb.py --setting qm9str --model tb --ls true --deterministic true --i <revision_steps> --num_active_learning_rounds 2000 --seed 0

Different Mode Metrics

# QM9 - Diversity
python number_of_modes.py --setting qm9str --model tb --ls true --deterministic true --mode_metric div_threshold_05 --seed 0
python number_of_modes.py --setting qm9str --model tb --ls true --deterministic true --mode_metric div_threshold_075 --seed 0

# RNA - Distance
python number_of_modes.py --setting rna --rna_task 1 --rna_length 14 --model tb --ls true --deterministic true --mode_metric hamming_ball1 --seed 0
python number_of_modes.py --setting rna --rna_task 1 --rna_length 14 --model tb --ls true --deterministic true --mode_metric hamming_ball2 --seed 0

dbsxodud-11/ls_gfn