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Merging recent changes into main#89

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mmcdermott merged 161 commits intomainmmcdermott/EventStreamGPT:mainfrom devmmcdermott/EventStreamGPT:devCopy head branch name to clipboardDec 14, 2023

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Commits

Commits on Jul 27, 2023

• Added a (yet untested) learnable TPE layer.

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• Merge branch 'dev' into learnable_frequency_ATEs

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Commits on Jul 31, 2023

• Added a unihpf style linearization / new HF dataset output prelim notebook example.

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Commits on Aug 1, 2023

• Adding flat summarization methods to dataset; yet untested.

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• tested FT baseline data generation.

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• Some small bug fixes.

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• Merged dev.

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• Merge pull request #48 from mmcdermott/learnable_frequency_ATEs

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• Merge branch 'dev' into fine_tuning_task_baselines

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Commits on Aug 2, 2023

• Improved param revisions and fixed current loading method (though saving should be further modified as well.

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• Added starter for modeling code (commented out for now)

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• Merge branch 'fine_tuning_task_baselines' of github.com:mmcdermott/EventStreamGPT into fine_tuning_task_baselines

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Commits on Aug 3, 2023

• Add streaming flag to collect operations

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• Add flag for using pyarrow when writing parquets

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• Added flat representations and sklearn modeling examples.

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Commits on Aug 4, 2023

• Merge branch 'dev' into streaming

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• Merge branch 'dev' into write_parquet_pyarrow

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• Got flat data sklearn pipes working.

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Commits on Aug 6, 2023

• Added some documentation to FT code.

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• Merge pull request #50 from juancq/streaming

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• Merge branch 'dev' into write_parquet_pyarrow

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• Merge pull request #51 from juancq/write_parquet_pyarrow

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• Add missing type to train_subset_size.

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• Added documentation on how to control max threadpool size to address #47

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Commits on Aug 7, 2023

• Support for measurements with '/'s in them.

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Commits on Aug 8, 2023

• Added train set subsampling.

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Commits on Aug 10, 2023

• Partial work in progress.

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• Added script.

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Commits on Aug 11, 2023

• Correcting small typo.

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• Initial files; not yet working.

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• Re-structured fine-tuning config to better enable FT hyperparameter search. Untested.

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Commits on Aug 14, 2023

• Fixing documentation error.

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• Small change to ensure project is carried over.

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• Merge branch 'dev' into hyperparameter_tune_FT_runs

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• Fixed errors with FT changes.

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• Updated parameters configs.

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• Re-arranged num_dataloader_workers

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Commits on Aug 15, 2023

• Updated hyperparameter default search distribution.

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• Made a bunch of small modifications so hyperparameter tuning works.

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• Removed pre-built synthetic dataset as path errors preclude usage. Users will need to reproduce it themselves (as is noted in the notebook).

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• Corrected small typo in example synthetic notebook.

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• Updated synthetic tutorial to be runnable from jupyter notebook and to fix loading dataset from a new directory issue.

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Commits on Aug 16, 2023

• Numpy doesn't work like that, so removed it.

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• Merge branch 'dev' into unihpf_support

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• Tentative new schema.

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• merged dev.

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• Merge branch 'dev' into hyperparameter_tune_FT_runs

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• Formatted files.

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• Added module docstring for embedding.py

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Commits on Aug 17, 2023

• Improved load flat rep to be faster / more memory efficient.

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• SHouldn't have overused n_samples.

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• Added poetry build setup and installation dependencies. May be working. Also updated to later versions of dependencies.

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• Updated things so that after pip install and installation of jupyter notebooks, the synthetic experiment can be run successfully.

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Commits on Aug 18, 2023

• Adding support for a different approach.

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• Made wandb sklearn stuff runnable.

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• Merge branch 'hyperparameter_tune_FT_runs' into fine_tuning_task_baselines

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• Merging.

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• Starting to set-up for hyperparameter tuning.

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• Trying to get a wandb sweep working with sklearn models.

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• Updated install instructions to use poetry, not conda.

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• Attempt #2

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• Added pytest-cov

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• Attempt #3 to get workflows working again.

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• Added missing dependency.

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• Updated lock.

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• one more time.

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• Attempting to set-up installation options for multiple versions.

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• Merge pull request #55 from mmcdermott/hyperparameter_tune_FT_runs

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• Merge remote-tracking branch 'origin/dev' into simpler_install_environment

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• Trying a different approach.

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• Added wandb

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• Merge pull request #56 from mmcdermott/simpler_install_environment

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• Updated install instructions.

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Commits on Aug 19, 2023

• Got sklearn hyperparameter tuning working-ish

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Commits on Aug 20, 2023

• Merge branch 'dev' into fine_tuning_task_baselines

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• Removed old erroneous script.

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• Removed old erroneous script and fixing pre-commit issues.

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Commits on Aug 21, 2023

• Added scipy and scikit-learn.

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• Added content to the tutorial about when data is dropped.

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• Extending pytorch batch documentation.

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• Trying to fix doc generation env.

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• Using bibliography for link for Learnable sinsuoidal embeddings.

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• Added more MIMIC FT examples.

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• Added more MIMIC FT examples.

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• Fixed pre-commit.

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Commits on Aug 22, 2023

• Added some more tests and doctests.

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• Attempting to test the running of the sample notebook.

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• Merge pull request #57 from mmcdermott/fine_tuning_task_baselines

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• Merge branch 'dev' into test_sample_notebook

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• Merged with dev.

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• Removed pre-built unihpf sample data.

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• Re-setting the labs sample data.

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• Added the ability to test sample notebook tutorial code.

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• Merge pull request #59 from mmcdermott/test_sample_notebook

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• Updating config to handle cases where outliers or normalizers are null.

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• Modified finetuning so that it loads the best model (lowest tuning loss) for testing. Brought prepare_pretrain_subsets.py configuration generation up to speed with current configs

  

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Commits on Aug 23, 2023

• Update README.md

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• Merge branch 'dev' into unihpf_support

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• Fixed tests and lint errors.

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• Fixed doctest error.

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• Added more test cases for caching/uncaching measurement configs.

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• fix valid_loss to tuning loss in model checkpointingand config path type error

  

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Commits on Aug 25, 2023

• Added another collect-lazy step and removed dtype shrinking to eliminate errors in materializing flat representations.

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• Fixed small bug in task baseline numbers.

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• Merge branch 'dev' of github.com:mmcdermott/EventStreamML into dev

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• Added missing comma.

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• Adding some missing documentation.

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• Corrected small error in link syntax.

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Commits on Aug 26, 2023

• Merge branch 'dev' into fine_tuning_task_baselines

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• Some small revisions.

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• Adjusted one other thing in prepare pretrain subsets.

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Commits on Aug 27, 2023

• Made AUC compute on CPU, fixed do_compute_only_loss, made pre-training not default to skipping all metrics in hyperparameter search (it should report loss parts), and made it easier to overwrite ba…

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Commits on Aug 28, 2023

• Added e2e tests through the script endpoints.

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• Updated gitignore.

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• Merge pull request #63 from mmcdermott/e2e_tests

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• Adding package to workflow.

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• Merge branch 'e2e_tests' into fine_tuning_task_baselines

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• Merge pull request #62 from mmcdermott/fine_tuning_task_baselines

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Commits on Aug 30, 2023

• Added more e2e tests.

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• Fixed some pre-commit issues.

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• Updated pre-commit action version.

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• Updated pre-commit action version.

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• New pre-commit versions.

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• Adding explicit typing throughout flat representation.

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• Hopefully fixed test and pre-commit error.

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• Merge pull request #64 from mmcdermott/e2e_tests

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• Partial changes. Merging dev changes into this branch next.

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• Merge branch 'dev' into flat_representation_types

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• Re-worked the flat representation storage stuff a fair bit for better type safety, and re-worked the sample notebooks to clean that section up.

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Commits on Aug 31, 2023

• Fixed tests.

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• Merge pull request #65 from mmcdermott/flat_representation_types

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• Merged.

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• Corrected a test.

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• Merge pull request #58 from mmcdermott/unihpf_support

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• Added intermediate size to default PT hyperparameter search config.

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Commits on Sep 3, 2023

• Made some small deviations to further speed things up. Is mostly working.

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Commits on Sep 4, 2023

• Address any settings where there are no static events for #66.

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Commits on Sep 5, 2023

• Fixed a small bug with compiling flat representations.

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Commits on Sep 6, 2023

• pre-commit lint changes.

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• Merge branch 'dev' into faster_flat_reps

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• Fixed a small bug with feature existence in computing mean/var features.

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• Re-arranged some things, and added capability to cache task specific FT flat datasets.

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• Fixed a small bug with update rules for loading flat data and improved test coverage via synthetic notebook.

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• Made cell not raise exception as nbmake was still failing the test.

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• Merge pull request #69 from mmcdermott/cache_task_flat_reps

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• Merge branch 'dev' into fix_static_data_bug

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• Forgot to uncomment some test lines.

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• Merge pull request #67 from mmcdermott/fix_static_data_bug

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• Updated docs theme to use sphinx immaterial.

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Commits on Sep 7, 2023

• Allow the exception to be raised naturally; fixed the error with cell metadata.

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• Changed dependency management structure to use pip for installing docs requirements to streamline readthedocs setup and remove deprecated env files.

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• Added missing build tool to readthedocs config.

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Commits on Sep 18, 2023

• Updated synthetic tutorial notebook.

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Commits on Sep 20, 2023

• Fixed mutable defaults.

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Commits on Oct 16, 2023

• Fixes #72 by correcting spelling of measurement

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• Merge branch 'py311' into dev

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Commits on Oct 24, 2023

• Fixed bug causing the system to ignore cached files for task representations.

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• Fixed one more error with the same thing.

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• ... fixed a third bug associated with the second bug fix related to missing format specifiers.

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Commits on Oct 25, 2023

• Fixed broken nbmake test. Not sure why the raises-exception was not working.

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Commits on Dec 14, 2023

• Added some basic model tutorial informaiton and video about model architectures.

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