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Features:
- ISTDataModule: Add alignment_loss, scrna_reference_path parameters
- setup_heterodata: Generate ('tx', 'attracts', 'tx') edges with ME gene labels
- LitISTEncoder: Updated check for alignment edges in batch
- Writer: Post-hoc tx-tx similarity computation for fragment mode
New modules:
- models/alignment_loss.py: Vectorized ME gene constraint loss
- validation/me_genes.py: ME gene discovery from scRNA-seq reference
- prediction/fragment.py: GPU/CPU connected components for unassigned transcripts
Tests:
- test_alignment_loss.py: Unit tests + vectorized vs loop correctness
- test_alignment_loss_integration.py: ME gene discovery integration
- test_fragment_mode.py: Connected components tests
- test_prediction_graph.py: Scale factor shrink/expand tests
- test_xenium_export.py: Xenium Explorer format validation
Documentation:
- CLAUDE.md: Updated with completed features and test coverage
- tests/README.md: Test running instructions
- Docstrings for all TODO methods
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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this PR introduces three major CLI workflows and hardens inference/export reliability.
New CLI features:
segger predict: checkpoint-only inference with strict checkpoint/data compatibility validation (segger_vocab, segger_me_gene_pairs, n_genes).segger export: unified multi-format export (xenium_explorer|merged|spatialdata|anndata) with raw|spatialdata input resolution and boundary strategy controls.segger plot: metrics visualization from Lightning logs (--quickterminal mode or PNG output).New capabilities:
Stability/performance changes: