GeneMamba / examples

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Update examples/3_pretrain_from_scratch.py
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Upload train-from-scratch next-token example script
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Update Phase 3 to next-token train-from-scratch with checkpoint auto-resume
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Remove continue pretraining example
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Use next-token training and checkpoint resume in train-from-scratch
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Update continue pretraining docs and tokenizer details
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Remove stale file: examples/README.md
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Remove stale file: examples/21_pretrain_from_scratch_reference.py
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Remove stale file: examples/20_continue_pretraining_reference.py
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Remove stale file: examples/12_batch_integration_eval.py
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Remove stale file: examples/11_zero_shot_logreg.py
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Remove stale file: examples/10_finetune_classification.py
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Remove stale file: examples/01_extract_embeddings.py
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Remove stale file: examples/00_preprocess_to_input_ids.py
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Upload GeneMamba model
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Remove stale path: examples/legacy_from_gene_mamba/mamba2_classification_finetune_without_label_zero_shot.py
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Remove stale path: examples/legacy_from_gene_mamba/mamba2_classification_finetune_without_label.py
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Remove stale path: examples/legacy_from_gene_mamba/mamba2_classification_finetune_with_label.py
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Remove stale path: examples/downstream/legacy_from_gene_mamba/mamba2_classification_finetune_without_label_zero_shot.py
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Remove stale path: examples/downstream/legacy_from_gene_mamba/mamba2_classification_finetune_without_label.py
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Remove stale path: examples/downstream/legacy_from_gene_mamba/mamba2_classification_finetune_with_label.py
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Remove stale path: examples/downstream/README.md
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Remove stale path: examples/downstream/21_pretrain_from_scratch_reference.py
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Remove stale path: examples/downstream/20_continue_pretraining_reference.py
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Remove stale path: examples/downstream/12_batch_integration_eval.py
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Remove stale path: examples/downstream/11_zero_shot_logreg.py
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Remove stale path: examples/downstream/10_finetune_classification.py
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Remove downstream and legacy_from_gene_mamba folders
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Flatten examples: move downstream files to examples root
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Unify repo: default 24l-512d at root, add size variants via subfolder
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