feat: embeddings

[awmulyadi]

For authors

Description

I have developed a set of codes for performing embedding using textual and protein sequences as a pair of examples on StarkQA-PrimeKG and BioBridge-PrimeKG dataset.

Following are several detailed key updates:

1. Source Code: Within the folder of aiagents4pharma/talk2knowledgegraphs/utils/embeddings, I included an abstract class of Embeddings followed by a set of implementation classes of EmbeddingWithSentenceTransformer and EmbeddingWithHuggingFace for embeddings.
2. Pytest: I included test cases of the above classes under the folder of aiagents4pharma/talk2knowledgegraphs/tests/*
3. Tutorial Notebooks: I added an interactive notebook for showcasing the use cases of the embedding classes under docs/notebooks/talk2knowledgegraphs/*. In addition, I also included a tutorial for evaluating StarQA-PrimeKG with Vector Similarity Search (VSS) model using textual embeddings. Finally, there is a dedicated tutorial for multimodal embedding alignment tutorial using linear regression and neural network as examples.
4. Documentation: Finally, I updated the related documentation using mkdocs, which is available in docs/talk2knowledgegraphs/*.

Note: There is an issue related to the sentence-transformer library that caused failing tests on macos-latest. For the time being, I set the tests on macOS-13 instead and opened a separate issue for this one at #59 .

Fixes #33

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)
• This change requires a documentation update

How Has This Been Tested?

Please describe the tests you conducted to verify your changes. These may involve creating new test scripts or updating existing ones.

• Added new test(s) in the tests folder
• Added new function(s) to an existing test(s) (i.e., aiagents4pharma/talk2knowledgegraphs/tests/*)

Checklist

• My code follows the style guidelines mentioned in the Code/DevOps guides
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation (e.g. MkDocs)
• My changes generate no new warnings
• I have added or updated tests (in the tests folder) that prove my fix is effective or that my feature works
• New and existing tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

For reviewers

Checklist pre-approval

• Is there enough documentation?
• If a new feature has been added, or a bug fixed, has a test been added to confirm good behavior?
• Does the test(s) successfully test edge/corner cases?
• Does the PR pass the tests? (if the repository has continuous integration)

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• Does this PR close an issue? If so, please make sure to descriptively close this issue when the PR is merged.

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[dmccloskey]

Please double check the notebooks for typos. The corrections can be added to a separate PR.

[github-actions]

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