Merge branch 'main' into 313-update-readme-components

README.md

@@ -237,7 +237,7 @@ This repository has been used in at least the following research articles:
 
 Bibtex Format
 
-```txt
+```text
 @misc{hernandez-garcia2024,
   author = {Hernandez-Garcia, Alex and Saxena, Nikita and Volokhova, Alexandra and Koziarski, Michał and Sharma, Divya and Viviano, Joseph D and Carrier, Pierre Luc and Schmidt, Victor},
   title  = {gflownet},

config/env/alaninedipeptide.yaml

@@ -26,5 +26,3 @@ buffer:
   test:
     type: grid
     n: 1000
-    output_csv: alaninedipeptide_test.csv
-    output_pkl: alaninedipeptide_test.pkl

config/env/ccube.yaml

@@ -5,7 +5,6 @@ _target_: gflownet.envs.cube.ContinuousCube
 
 id: ccube
 continuous: True
-func: corners
 # Dimensions of hypercube
 n_dim: 2
 # Constant to restrict interval of test sets
@@ -35,5 +34,3 @@ buffer:
   test:
     type: grid
     n: 900
-    output_csv: ccube_test.csv
-    output_pkl: ccube_test.pkl

config/env/crystals/composition.yaml

@@ -20,7 +20,5 @@ buffer:
   data_path: null
   train:
     type: all
-    output_csv: composition_train.csv
   test:
     type: all
-    output_csv: composition_test.csv

config/env/crystals/crystal.yaml

@@ -3,27 +3,25 @@ defaults:
 
 _target_: gflownet.envs.crystals.crystal.Crystal
 
-# Composition parameters
+# Composition config
 id: crystal
 composition_kwargs:
   elements: 89
-  max_atoms: 20
-  max_atom_i: 16
+# Lattice parameters config
 lattice_parameters_kwargs:
   min_length: 1.0
-  max_length: 5.0
-  min_angle: 30.0
+  max_length: 350.0
+  min_angle: 50.0
   max_angle: 150.0
-  grid_size: 10
+# Space group config
+space_group_kwargs:
+  space_groups_subset: null
 # Stoichiometry <-> space group check
-do_stoichiometry_sg_check: False
+do_composition_to_sg_constraints: True
+self.do_sg_to_lp_constraints: True
 
 # Buffer
 buffer:
   data_path: null
-  train:
-    type: all
-    output_csv: crystal_train.csv
-  test:
-    type: all
-    output_csv: crystal_test.csv
+  train: null
+  test: null

config/env/crystals/lattice_parameters.yaml

@@ -5,24 +5,37 @@ _target_: gflownet.envs.crystals.lattice_parameters.LatticeParameters
 
 id: lattice_parameters
 
+# Lattice system
 lattice_system: triclinic
+# Allowed ranges of size and angles
 min_length: 1.0
 max_length: 350.0
 min_angle: 50.0
 max_angle: 150.0
-grid_size: 10
-max_increment: 1
+
+# Policy
+min_incr: 0.1
+n_comp: 2
+epsilon: 1e-6
+beta_params_min: 0.1
+beta_params_max: 100.0
+fixed_distribution:
+  beta_weights: 1.0
+  beta_alpha: 10.0
+  beta_beta: 10.0
+  bernoulli_bts_prob: 0.1
+  bernoulli_eos_prob: 0.1
+random_distribution:
+  beta_weights: 1.0
+  beta_alpha: 10.0
+  beta_beta: 10.0
+  bernoulli_bts_prob: 0.1
+  bernoulli_eos_prob: 0.1
 
 # Buffer
 buffer:
   data_path: null
-  train:
-    type: random
-    n: 2000
-    output_csv: lattice_parameters_train.csv
-    output_pkl: lattice_parameters_train.pkl
+  train: null
   test:
-    type: random
-    n: 2000
-    output_csv: lattice_parameters_test.csv
-    output_pkl: lattice_parameters_test.pkl
+    type: grid
+    n: 900

config/env/crystals/spacegroup.yaml

@@ -15,9 +15,5 @@ buffer:
   data_path: null
   train:
     type: all
-    output_csv: spacegroup_train.csv
-    output_pkl: spacegroup_train.pkl
   test:
     type: all
-    output_csv: spacegroup_test.csv
-    output_pkl: spacegroup_test.pkl

config/env/ctorus.yaml

@@ -4,7 +4,6 @@ defaults:
 _target_: gflownet.envs.ctorus.ContinuousTorus
 
 id: ctorus
-func: sincos
 # Dimensions of hypertorus
 n_dim: 2
 policy_encoding_dim_per_angle: null
@@ -27,5 +26,3 @@ buffer:
   test:
     type: grid
     n: 1000
-    output_csv: ctorus_test.csv
-    output_pkl: ctorus_test.pkl

config/env/grid.yaml

@@ -4,7 +4,6 @@ defaults:
 _target_: gflownet.envs.grid.Grid
 
 id: grid
-func: corners
 # Dimensions of hypergrid
 n_dim: 2
 # Number of cells per dimension
@@ -22,5 +21,3 @@ buffer:
   train: null
   test:
     type: all
-    output_csv: grid_test.csv
-    output_pkl: grid_test.pkl

config/env/htorus.yaml

@@ -5,7 +5,6 @@ _target_: gflownet.envs.htorus.HybridTorus
 
 id: ctorus
 continuous: True
-func: sincos
 # Dimensions of hypertorus
 n_dim: 2
 policy_encoding_dim_per_angle: null
@@ -27,5 +26,3 @@ buffer:
   test:
     type: grid
     n: 1000
-    output_csv: htorus_test.csv
-    output_pkl: htorus_test.pkl

config/env/scrabble.yaml

@@ -11,5 +11,3 @@ buffer:
   test:
     type: uniform
     n: 10
-    output_csv: scrabble_test.csv
-    output_pkl: scrabble_test.pkl

config/env/tetris.yaml

@@ -20,6 +20,3 @@ buffer:
   test:
     type: random
     n: 10
-    output_csv: tetris_test.csv
-    output_pkl: tetris_test.pkl
-

config/env/torus.yaml

@@ -4,7 +4,6 @@ defaults:
 _target_: gflownet.envs.torus.Torus
 
 id: torus
-func: sincos
 # Dimensions of hypertorus
 n_dim: 2
 # Number of angles per dimension
@@ -20,8 +19,5 @@ buffer:
   data_path: null
   train:
     type: all
-    output_csv: torus_train.csv
   test:
     type: all
-    output_csv: torus_test.csv
-    output_pkl: torus_test.pkl

config/env/tree.yaml

@@ -35,5 +35,3 @@ buffer:
   test:
     type: random
     n: 1000
-    output_csv: tree_test.csv
-    output_pkl: tree_test.pkl

config/evaluator/base.yaml

@@ -0,0 +1,26 @@
+_target_: gflownet.evaluator.base.BaseEvaluator
+
+# config formerly from logger.test
+first_it: True
+period: 100
+n: 100
+kde:
+  bandwidth: 0.1
+  kernel: gaussian
+n_top_k: 5000
+top_k: 100
+top_k_period: -1
+# Number of backward trajectories to estimate the log likelihood of each test data point
+n_trajs_logprobs: 10
+logprobs_batch_size: 100
+logprobs_bootstrap_size: 10000
+# Maximum number of test data points to compute log likelihood probs.
+max_data_logprobs: 1e5
+# Number of points to obtain a grid to estimate the reward density
+n_grid: 40000
+train_log_period: 1
+checkpoints_period: 1000
+# List of metrics as per gflownet/eval/evaluator.py:METRICS_NAMES
+# Set to null for all of them
+# Values must be comma separated like `metrics: "l1, kl, js"` (spaces are optional)
+metrics: all

config/experiments/ccube/branin.yaml

@@ -0,0 +1,76 @@
+# @package _global_
+# A configuration that works well with the Branin proxy.
+# wandb: https://wandb.ai/alexhg/Branin/runs/xlxfdc6k
+
+defaults:
+   - override /env: ccube
+   - override /gflownet: trajectorybalance
+   - override /proxy: box/branin
+   - override /logger: wandb
+
+# Environment
+env:
+  n_dim: 2
+  n_comp: 5
+  beta_params_min: 0.1
+  beta_params_max: 100.0
+  min_incr: 0.1
+  fixed_distr_params:
+    beta_weights: 1.0
+    beta_alpha: 10.0
+    beta_beta: 10.0
+    bernoulli_eos_prob: 0.1
+    bernoulli_bts_prob: 0.1
+  random_distr_params:
+    beta_weights: 1.0
+    beta_alpha: 10.0
+    beta_beta: 10.0
+    bernoulli_eos_prob: 0.1
+    bernoulli_bts_prob: 0.1
+  reward_func: identity
+
+# GFlowNet hyperparameters
+gflownet:
+  random_action_prob: 0.1
+  optimizer:
+    batch_size:
+      forward: 100
+    lr: 0.0001
+    z_dim: 16
+    lr_z_mult: 100
+    n_train_steps: 10000
+
+# Policy
+policy:
+  forward:
+    type: mlp
+    n_hid: 128
+    n_layers: 2
+    checkpoint: forward
+  backward:
+    shared_weights: True
+    checkpoint: backward
+
+# Evaluator
+evaluator:
+  first_it: False
+  period: 500
+  n: 1000
+  checkpoints_period: 500
+
+# WandB
+logger:
+  do:
+    online: true
+  lightweight: True
+  project_name: "branin"
+  tags: 
+    - gflownet
+    - continuous
+    - ccube
+    - branin
+
+# Hydra
+hydra:
+  run:
+    dir: ${user.logdir.root}/ccube/branin/${now:%Y-%m-%d_%H-%M-%S_%f}