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Merged
vict0rsch merged 36 commits into from
Dec 7, 2022
Merged

Integrate QM7-X dataset #32

vict0rsch merged 36 commits into from
Dec 7, 2022

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@vict0rsch
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@vict0rsch vict0rsch commented Dec 6, 2022 •
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ENV UPDATES

$ git clone https://github.com/icanswim/cosmosis.git cosmosis
$ pip install torchvision==0.12.0

@vict0rsch
ignore cloned cosmosis repo
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@vict0rsch
Create 3 layers of QM7-X dataset:
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* Original `qchem` dataset `BaseQM7X`
* In-memory version compatible with `torch_geometric` (slow) `InMemoryQM7X`
* File-based `torch_geometric` `QM7X`
@vict0rsch
script to create 1 .pt file per molecule to be ingested by the `QM7…
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…X` class
@vict0rsch
handle set_id specification
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@vict0rsch
Handle slurm tasks
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@vict0rsch
sort fiels
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@vict0rsch
pre-comptued samples mapping (idmol, iconf)
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@vict0rsch
describe file
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@vict0rsch
Using LMDBs: 300x faster
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@vict0rsch
handle lmdb-stored data
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@vict0rsch
use multiprocessing
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@vict0rsch
add stats computations to main
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@vict0rsch
change folder name
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@vict0rsch
save per-property stats
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@vict0rsch
add qm7x stats setting
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@vict0rsch
eval_all_val_splits
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@vict0rsch
adapt evaluator
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@vict0rsch
remap attributes
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@vict0rsch
adapt compute_loss and compute_metrics
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@vict0rsch
add v0 conf
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@vict0rsch
default qm7x confs
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@vict0rsch
use orjson
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@vict0rsch
add tests
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@vict0rsch
towards tests
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@vict0rsch
handle qm7x data in data_list_collater
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@vict0rsch
no otf graph
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@vict0rsch
don't close envs in 1k mode
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@vict0rsch
handle absent graph rewiring param
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@vict0rsch
filter out rewiring for qm7x and 9
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@vict0rsch
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vict0rsch commented Dec 6, 2022 

🎉 `python scripts/test_all.py` finished testing 155/155 configs in 27.87m on commit 8af995c. 155 succeeded. [2022-12-06 18:38:16]

Base automatically changed from qm9-formation-energy to dev December 7, 2022 17:41
@vict0rsch vict0rsch merged commit 4bd12f0 into dev Dec 7, 2022
@vict0rsch vict0rsch deleted the qm7x branch December 7, 2022 17:43
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@vict0rsch