experiments-binding-affinity's People
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jchodera sukritsingh glass-w ijpulidos andreavolkamer schallerdavid jiayeguo bbyun28 rnaimehaomexperiments-binding-affinity's Issues
Add CI badge to README
We should add a CI badge so we can easily see and access the state of the nightly CI tests.
Training tests do not work
Both training tests in tests/test_examples.sh
do not work with the current kinoml master.
They both report the same error:
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [10]":
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-10-c525cb273784> in <module>
6 a_dataloader = dataloaders[next(iter(dataloaders.keys()))]["train"]
7 x_sample, _ = next(iter(a_dataloader))
----> 8 MODEL_KWARGS["input_shape"] = ModelCls.estimate_input_shape(x_sample)
9
10 nn_model = ModelCls(**MODEL_KWARGS)
~/miniconda3/envs/experiments-binding-affinity/lib/python3.9/site-packages/kinoml/ml/torch_models.py in estimate_input_shape(input_sample)
23 than a Tensor, please adapt this method accordingly.
24 """
---> 25 return input_sample.shape[1]
26
27
Issue with testing example for kinoml and experiments-binding-affinity
As requested by @jaimergp - Running an example notebook on kinoml (as dictated by his presented slides) resulted in the Papermill errors on both MacOS and Linux systems:
In both cases the command run was:
python run_notebook.py features/featurize-template.ipynb features/example-ligand-only-chembl28-morgan512-1k-subsample.py --overwrite
Error stack trace for MacOS:
(experiments-binding-affinity) 31 sukrit@pillarofautumn:~/work/postdoc/kinoml-tutorial/experiments-binding-affinity$ python run_notebook.py \
> features/featurize-template.ipynb \
> features/example-ligand-only-chembl28-morgan512-1k-subsample.py \
>
Executing: 45%|████████████████████████▏ | 13/29 [00:07<00:09, 1.63cell/s]
Traceback (most recent call last):
File "run_notebook.py", line 51, in <module>
main()
File "run_notebook.py", line 47, in main
pm.execute_notebook(str(nbin), str(nbout), parameters)
File "/Users/sukrit/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 118, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/Users/sukrit/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [7]":
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-7-56f51f7ca191> in <module>
----> 1 dataset = import_object(DATASET_CLS).from_source(**DATASET_KWARGS)
2 dataset
~/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/kinoml/datasets/chembl.py in from_source(cls, filename, measurement_types, sample, **kwargs)
66 zf.extractall(tmpdir)
67 cached_path.parent.mkdir(parents=True, exist_ok=True)
---> 68 shutil.copyfile(Path(tmpdir) / csv_filename, cached_path)
69
70 df = pd.read_csv(cached_path)
~/miniconda3/envs/experiments-binding-affinity/lib/python3.8/shutil.py in copyfile(src, dst, follow_symlinks)
262 os.symlink(os.readlink(src), dst)
263 else:
--> 264 with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
265 # macOS
266 if _HAS_FCOPYFILE:
FileNotFoundError: [Errno 2] No such file or directory: '/var/folders/3q/r0xmt3qn6xq02b3p08xbr54r0000gn/T/tmpcilygxcr/activities-chembl27_v0.2.csv'
Error stack trace for linux:
(experiments-binding-affinity) 12 singhs15@lt22:~/kinoml-workshop/openkinome/experiments-binding-affinity$ python run_notebook.py features/featurize-template.ipynb features/example-ligand-only-chembl28-morgan512-1k-subsample.py
Executing: 28%|███████████████████▊ | 8/29 [00:05<00:14, 1.48cell/s]
Traceback (most recent call last):
File "run_notebook.py", line 51, in <module>
main()
File "run_notebook.py", line 47, in main
pm.execute_notebook(str(nbin), str(nbout), parameters)
File "/home/singhs15/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 118, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/home/singhs15/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [4]":
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-4-baec478d6de7> in <module>
19 OUT.mkdir(parents=True, exist_ok=True)
20
---> 21 print(f"This notebook: HERE = ~/{HERE.relative_to(Path.home())}")
22 print(f"This repo: REPO = ~/{REPO.relative_to(Path.home())}")
23 print(f"Outputs in: OUT = ~/{OUT.relative_to(Path.home())}")
~/miniconda3/envs/experiments-binding-affinity/lib/python3.8/pathlib.py in relative_to(self, *other)
905 if (root or drv) if n == 0 else cf(abs_parts[:n]) != cf(to_abs_parts):
906 formatted = self._format_parsed_parts(to_drv, to_root, to_parts)
--> 907 raise ValueError("{!r} does not start with {!r}"
908 .format(str(self), str(formatted)))
909 return self._from_parsed_parts('', root if n == 1 else '',
ValueError: '/lila/home/singhs15/kinoml-workshop/openkinome/experiments-binding-affinity/features/example-ligand-only-chembl28-morgan512-1k-subsample' does not start with '/home/singhs15'
add installation instructions to README
Add installation instructions to README
Composite tests fail
The composite tests fail with the following error:
Traceback (most recent call last):
File "/home/david/github/experiments-binding-affinity/run_notebook.py", line 51, in <module>
main()
File "/home/david/github/experiments-binding-affinity/run_notebook.py", line 47, in main
pm.execute_notebook(str(nbin), str(nbout), parameters)
File "/home/david/miniconda3/envs/test_eba/lib/python3.9/site-packages/papermill/execute.py", line 118, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/home/david/miniconda3/envs/test_eba/lib/python3.9/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [13]":
---------------------------------------------------------------------------
ArrowNotImplementedError Traceback (most recent call last)
/tmp/ipykernel_4232/462024357.py in <module>
8 path = OUT / f"{'__'.join([g for g in group if g != 'valid'])}.parquet"
9 parquets.append(path)
---> 10 ak.to_parquet(parquet, path)
11 # TODO: Missing indices?
~/miniconda3/envs/test_eba/lib/python3.9/site-packages/awkward/operations/convert.py in to_parquet(array, where, explode_records, list_to32, string_to32, bytestring_to32, **options)
3028 options["schema"] = first.schema
3029
-> 3030 writer = pyarrow.parquet.ParquetWriter(**options)
3031 writer.write_table(pyarrow.Table.from_batches([first]))
3032
~/miniconda3/envs/test_eba/lib/python3.9/site-packages/pyarrow/parquet.py in __init__(self, where, schema, filesystem, flavor, version, use_dictionary, compression, write_statistics, use_deprecated_int96_timestamps, compression_level, use_byte_stream_split, writer_engine_version, data_page_version, use_compliant_nested_type, **options)
653 self._metadata_collector = options.pop('metadata_collector', None)
654 engine_version = 'V2'
--> 655 self.writer = _parquet.ParquetWriter(
656 sink, schema,
657 version=version,
~/miniconda3/envs/test_eba/lib/python3.9/site-packages/pyarrow/_parquet.pyx in pyarrow._parquet.ParquetWriter.__cinit__()
~/miniconda3/envs/test_eba/lib/python3.9/site-packages/pyarrow/error.pxi in pyarrow.lib.check_status()
ArrowNotImplementedError: Unhandled type for Arrow to Parquet schema conversion: dense_union<0: bool not null=0, 1: int64 not null=1>
Can not create environment from environment.yaml
Using the following command fails to create an environment:
mamba env create -f environment.yml -n experiments-binding-affinity
I got the following error about missing torch modules in the pip installation step:
....
import torch
ModuleNotFoundError: No module named 'torch'
----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/29/96/566ac314e796d4b07209a3b88cc7a8d2e8582d55819e33f72e6c0e8d8216/torch_scatter-0.3.0.tar.gz#sha256=9e5e5a6efa4ef45f584e8611f83690d799370dd122b862646751ae112b685b50 (from https://pypi.org/simple/torch-scatter/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement torch-scatter (from versions: 0.3.0, 1.0.2, 1.0.3, 1.0.4, 1.1.0, 1.1.1, 1.1.2, 1.2.0, 1.3.0, 1.3.1, 1.3.2, 1.4.0, 2.0.2, 2.0.3, 2.0.4, 2.0.5, 2.0.6, 2.0.7)
ERROR: No matching distribution found for torch-scatter
I will check what I can find about this but let me know if you have an easy fix.
Protect master branch
Should we protect the master branch? I accidentally pushed something to master this morning instead of to a new branch.
Tests/examples
The ligand-based only tests are not ligand-based, grouper per kinases should be added to the associated python scripts.
Create CI badge in README
We should add a CI badge so we can easily see and access the state of the nightly CI tests.
KLIFS binding site
Features and models KLIFS' binding site sequence, and not the full kinase sequence.
🚧 WIP , see #45 PR in kinoml
- morgan + composition binding site sequence
- smiles + sequence binding site sequence
Graph Convolutional Neural Network
Ligand-based model
Graph
Featurization:
- Running
Model:
- Running
Models not running
The aim of this PR is to have scripts that are running for featurization schemes and associated machine learning models on the latest ChEMBL (v.28) data set.
Models
Ligand-based
To run these models, type:
(experiments-binding-affinity) $ bash tests/test_model_ligand_only.sh
- Morgan & Fully connected neural network
- One-hot SMILES & Convolutional neural network
- Graph & Graph neural network
Kinase-informed
To run these models, type:
(experiments-binding-affinity) $ bash tests/test_model_kinase_informed.sh
- morgan + hash & Fully connected neural network
- morgan + composition & Fully connected neural network
- smiles + sequence & Convolutional neural network
Status
-
Models Running
-
Ready to go
Features missing
Ligand features to be tested in notebook template
- graph featurizer
- check per node features
- onehot smiles
- check pipeline and max length padding
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