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Update core utils: paths config, SMILES encoder, data processing and … #31

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25 changes: 19 additions & 6 deletions src/molgen3D/config/paths.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,8 +112,13 @@ def _resolve_path_value(value: str | Path | Sequence[str | Path]) -> Path:
continue
seen.add(candidate_path)
resolved.append(candidate_path)
if candidate_path.exists():
return candidate_path
try:
if candidate_path.exists():
return candidate_path
except OSError:
# Some shared mounts are present but not traversable for this user;
# skip them and continue through the configured fallbacks.
continue

return resolved[0]

Expand Down Expand Up @@ -389,8 +394,12 @@ def _base_candidate_values(base_key: str) -> list[str | Path]:
if rel_path.is_absolute():
if default_path is None:
default_path = rel_path
if rel_path.exists():
return rel_path
try:
if rel_path.exists():
return rel_path
except OSError:
# Shared mounts may be present but not accessible for this user.
continue
continue

rel_str = str(rel_candidate)
Expand All @@ -405,8 +414,12 @@ def _base_candidate_values(base_key: str) -> list[str | Path]:
candidate_path = base_path / rel_path
if default_path is None:
default_path = candidate_path
if candidate_path.exists():
return candidate_path
try:
if candidate_path.exists():
return candidate_path
except OSError:
# Skip unreadable fallback roots and keep trying the rest.
continue

if default_path is not None:
return default_path
Expand Down
136 changes: 130 additions & 6 deletions src/molgen3D/config/paths.yaml
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Original file line number Diff line number Diff line change
@@ -1,45 +1,62 @@
base_paths:
project_root: "."
data_root:
- "/mnt/weka/vtarasov"
- "/data/vtarasov"
- "/data/molgen"
- "data"
geom_data_root:
- "/data/vtarasov"
- "/data/molgen"
- "/data/molgen/GEOM_data"
geom_dataset_root:
- "/data/molgen/GEOM_data/torsional_diff_gdrive/extracted"
- "/mnt/weka/vtarasov/torsional_gdrive/extracted"
- "/data/molgen/GEOM_data/torsional_gdrive/extracted"
ckpts_root:
- "/mnt/weka/vtarasov/checkpoints"
- "/data/chem-project/checkpoints"
hf_yerevann_root:
- "/mnt/weka/vtarasov/checkpoints/hf/yerevann"
- "/nfs/h100/raid/chem/checkpoints/hf/yerevann"
- "/data/chem-project/checkpoints/hf/yerevann"
qwen_yerevann_root:
- "/mnt/weka/vtarasov/checkpoints"
- "/mnt/weka/vtarasov/checkpoints/hf/yerevann"
- "/data/chem-project/checkpoints"
- "/mnt/weka/data/chem-project/checkpoints"
- "/home/chem-project/checkpoints"
- "/data/chem-project/checkpoints/yerevann"
- "/nfs/h100/raid/chem/checkpoints/yerevann"
grpo_root:
- "/mnt/weka/vtarasov/conf_grpo"
- "/mnt/weka/vtarasov/checkpoints/grpo"
- "/data/chem-project/checkpoints/conf_grpo"
- "/nfs/h100/raid/chem/checkpoints/conf_grpo"
qwen3_grpo_root:
- "/mnt/weka/vtarasov/conf_grpo"
- "/mnt/weka/vtarasov/checkpoints/grpo"
- "/data/chem-project/checkpoints/conf_grpo"
- "/nfs/h100/raid/chem/checkpoints/conf_grpo"
gen_results_root: "outputs/gen_results"
eval_results_root: "outputs/eval_results"
pretrain_results_root: "outputs/pretrain_results"
pretrain_logs_root: "outputs/pretrain_logs"
gen_results_root: "/mnt/weka/vtarasov/outputs/outputs/gen_results/"
eval_results_root: "/mnt/weka/vtarasov/outputs/outputs/eval_results"
pretrain_results_root: "/mnt/weka/vtarasov/outputs/outputs/pretrain_results"
pretrain_logs_root: "/mnt/weka/vtarasov/outputs/outputs/pretrain_logs"
wandb_root: "wandb_runs"
qwen3_0.6b_base_model:
- "/mnt/weka/vtarasov/Qwen3-0.6B-Base"
- "/data/chem-project/checkpoints/Qwen3-0.6B-Base"
- "/nfs/h100/raid/chem/checkpoints/yerevann/qwen3_06b/Qwen3-0.6B-Base"
- "/data/chem-project/checkpoints/yerevann/qwen3_06b/Qwen3-0.6B-Base"
tokenizers_root: "src/molgen3D/training/tokenizers"

ckpts:
qwen3_06b:
- "/mnt/weka/vtarasov/qwen3_06b"
- "/data/chem-project/checkpoints/qwen3_06b"
- "/nfs/h100/raid/chem/checkpoints/yerevann/qwen3_06b"
- "/data/chem-project/checkpoints/yerevann/qwen3_06b"
qwen3_grpo:
- "/mnt/weka/vtarasov/conf_grpo"
- "/data/chem-project/checkpoints/conf_grpo"
- "/nfs/h100/raid/chem/checkpoints/conf_grpo"

Expand All @@ -48,6 +65,7 @@ data:
distinct_smi: "tmp/distinct_smi_filtered_13.pickle"
xl_smi: "xl_smi.pickle"
qm9_smi: "qm9_smi.pickle"
revisited_smi: "/home/vtarasov/code/3DMolGen/data/revisited_smi.pickle"
icl_5_smi: "icl_5_smi.pickle"
icl_10_smi: "icl_10_smi.pickle"
icl_20_smi: "icl_20_smi.pickle"
Expand Down Expand Up @@ -117,11 +135,80 @@ data:
- "3DMolGen_data/binned_filtered/processed_strings/test"
- "binned_filtered/processed_strings/test"

revisited_cartesian_train:
- "geom_revisited_cartesian/processed_strings/train"
revisited_cartesian_valid:
- "geom_revisited_cartesian/processed_strings/valid"
revisited_cartesian_test:
- "geom_revisited_cartesian/processed_strings/test"

revisited_quantile_binned_train:
- "geom_revisited_quantile_binned/processed_strings/train"
revisited_quantile_binned_valid:
- "geom_revisited_quantile_binned/processed_strings/valid"
revisited_quantile_binned_test:
- "geom_revisited_quantile_binned/processed_strings/test"

revisited_uniform_binned_train:
- "geom_revisited_uniform_binned/processed_strings/train"
revisited_uniform_binned_valid:
- "geom_revisited_uniform_binned/processed_strings/valid"
revisited_uniform_binned_test:
- "geom_revisited_uniform_binned/processed_strings/test"

revisited_cartesian_isomeric_grouped_train:
- "geom_revisited_cartesian_isomeric_grouped/processed_strings/train"
revisited_cartesian_isomeric_grouped_valid:
- "geom_revisited_cartesian_isomeric_grouped/processed_strings/valid"
revisited_cartesian_isomeric_grouped_test:
- "geom_revisited_cartesian_isomeric_grouped/processed_strings/test"

revisited_quantile_binned_isomeric_grouped_train:
- "geom_revisited_quantile_binned_isomeric_grouped/processed_strings/train"
revisited_quantile_binned_isomeric_grouped_valid:
- "geom_revisited_quantile_binned_isomeric_grouped/processed_strings/valid"
revisited_quantile_binned_isomeric_grouped_test:
- "geom_revisited_quantile_binned_isomeric_grouped/processed_strings/test"

revisited_uniform_binned_isomeric_grouped_train:
- "geom_revisited_uniform_binned_isomeric_grouped/processed_strings/train"
revisited_uniform_binned_isomeric_grouped_valid:
- "geom_revisited_uniform_binned_isomeric_grouped/processed_strings/valid"
revisited_uniform_binned_isomeric_grouped_test:
- "geom_revisited_uniform_binned_isomeric_grouped/processed_strings/test"


revisited_uniform_binned_isomeric_train:
- "geom_revisited_uniform_binned_isomeric/processed_strings/train"
revisited_uniform_binned_isomeric_valid:
- "geom_revisited_uniform_binned_isomeric/processed_strings/valid"
revisited_uniform_binned_isomeric_test:
- "geom_revisited_uniform_binned_isomeric/processed_strings/test"

revisited_quantile_binned_isomeric_train:
- "geom_revisited_quantile_binned_isomeric/processed_strings/train"
revisited_quantile_binned_isomeric_valid:
- "geom_revisited_quantile_binned_isomeric/processed_strings/valid"
revisited_quantile_binned_isomeric_test:
- "geom_revisited_quantile_binned_isomeric/processed_strings/test"

revisited_cartesian_isomeric_grouped_train:
- "geom_revisited_cartesian_isomeric_grouped/processed_strings/train"
revisited_cartesian_isomeric_grouped_valid:
- "geom_revisited_cartesian_isomeric_grouped/processed_strings/valid"
revisited_cartesian_isomeric_grouped_test:
- "geom_revisited_cartesian_isomeric_grouped/processed_strings/test"

big_data_train:
- "3DBigData_formatted/processed/bigdata_uniform_binned_isomeric/processed_strings/train"


tokenizers:
llama3_chem_v1: "src/molgen3D/training/tokenizers/Llama-3.2-chem-1B-v1"
qwen3_0.6b_custom: "src/molgen3D/training/tokenizers/Qwen3_tokenizer_custom"
qwen3_0.6b_origin: "src/molgen3D/training/tokenizers/Qwen3_tokenizer_original"
qwen3_0.6b_binned: "src/molgen3D/training/tokenizers/Qwen3_tokenizer_binned"
qwen3_0.6b_binned_258: "src/molgen3D/training/tokenizers/Qwen3_tokenizer_binned_258"

models:
# ---------- BASE MODELS ----------
Expand Down Expand Up @@ -277,14 +364,51 @@ models:
"5e": "step-27500-hf"

qw600_pre_binned_paired:
root: "qwen3_06b/260126-1354-3b2e-qwen3_06b_pre_5e_8e-4_binned_grouped"
root: "qwen3_06b/260126-0653-7cf8-qwen3_06b_pre_5e_8e-4_binned_grouped"
steps:
"1e": "step-5500-hf"
"2e": "step-11000-hf"
"3e": "step-16500-hf"
"4e": "step-22000-hf"
"5e": "step-27500-hf"

qw600_pre_binned_revisited_uniform_isomeric:
root: "qwen3_06b/260330-1525-9eef-qwen3_06b_pre_4e_revisited_uniform_binned_isomeric_grouped"
steps:
"1e": "step-6800-hf"
"2e": "step-13600-hf"
"3e": "step-20400-hf"
"4e": "step-27200-hf"

qw600_pre_binned_revisited_quantile_isomeric:
root: "qwen3_06b/260330-1541-7425-qwen3_06b_pre_4e_revisited_quantile_binned_isomeric/"
steps:
"1e": "step-6800-hf"
"2e": "step-13600-hf"
"3e": "step-20400-hf"
"4e": "step-27200-hf"

qw600_pre_binned_revisited_cartesian_isomeric:
root: "qwen3_06b/260308-0316-05c6-qwen3_06b_pre_4e_revisited_cartesian_isomeric/"
steps:
"1e": "step-20500-hf"
"2e": "step-41000-hf"
"3e": "step-61500-hf"
"4e": "step-82000-hf"

qwen600_pre_binned_uniform_bigdata:
root: "qwen3_06b/260507-2158-3956-qwen3_06b_pre_1e_8e-4_bigdata_pairs/"
steps:
"1e": "step-222000-hf"

qw600_pre_binned_uniform_revisited_finetuned_from_bigdata:
root: "qwen3_06b/260508-1740-4135-qwen3_06b_finetuned_4e_uniform_binned_isomeric_from_bigdata/"
steps:
"1e": "step-6800-hf"
"2e": "step-13600-hf"
"3e": "step-20400-hf"
"4e": "step-27200-hf"

# ---------- GRPO / FINETUNED MODELS (same structure) ----------

m380_1e_1xgrpo_100e_100s:
Expand Down
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