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Add Geneformer#6

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rcannood merged 24 commits intomainopenproblems-bio/task_batch_integration:mainfrom feature/no-ref/add-Geneformeropenproblems-bio/task_batch_integration:feature/no-ref/add-GeneformerCopy head branch name to clipboardNov 8, 2024

+215-1

Commits

Commits on Oct 2, 2024

• Add cxg_immune_cell_atlas as a test resource

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• Add SCimilarity component

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• Add SCimiliarity to benchmark workflow

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Commits on Oct 8, 2024

• Update script to extract model

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• Add SCimilarity model path to benchmark workflow

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• Add base_method API to disable tests for SCimilarity

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• Replace cxg_mouse_pancreas_atlas with cxg_immune_cell_atlas

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• Style SCimiliarity script

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• Remove test resources from SCimiliarity config

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Commits on Oct 11, 2024

• Fix file names in test resources state.yaml

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• Add scimilarity as dependency to benchmark workflow

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Commits on Oct 16, 2024

• Update compute environment

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Commits on Oct 21, 2024

• Update model file path

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Commits on Oct 22, 2024

• Create geneformer files

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• Set SCimilarity name in Python script

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• Adjust container settings

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• Download dictionary files in script

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• Merge remote-tracking branch 'origin/main' into feature/no-ref/add-Geneformer

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Commits on Oct 23, 2024

• Prepare and tokenize data, attempt to embed

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Commits on Oct 28, 2024

• Store and output embedding

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Commits on Oct 29, 2024

• Add Geneformer to benchmark workflow

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• Add argument to select model version to use

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• Style Geneformer script

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Commits on Oct 30, 2024

• Make Geneformer inherit from base_method for tests

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