Datasets, transformations, and pretrained models for biological cellular systems.
Command Claude Code
Relevant files: experiments/005-kuzmin2018-tmi/scripts/GOgraphdatefiltercomparison.py experiments/005-kuzmin2018-tmi/scripts/dcellgoperturbationvisualization.py torchcell/graph/graphanalysis.py /Users/michaelvolk/Documents/projects/torchcell/notes/assets/images/gographunfilteredvisualization2025-05-13-17-54-25.png…
Command Claude Code
We are writing a pipeline for training the Dango Model. The way they set lambda is based on the difference.
Command Claude Code
The torchcell project is migrating from a label-based data format to a COO (Coordinate) format for phenotype data. In the old format, phenotype values were stored as data["gene"]["fitness"] or data["gene"]["geneinteraction"]. In the new COO format, all phenotype values are stored in a single tensor with accompanying…
Command Claude Code
We are writing the experimental pipeline for Dcell. It is very similar to the pipeline for the Dango model. We want to keep it similar to the Dango pipeline as possible. We want to record all of the same metrics, use the same code structure, etc.
Command Claude Code
We are writing the experimental pipeline for Dcell. It is very similar to the pipeline for the Dango model. We want to keep it similar to the Dango pipeline as possible. We want to record all of the same metrics, use the same code structure, etc.
Command Claude Code
We have written the experimental pipeline for Dcell. It is very similar to the pipeline for the Dango model. have kept it similar to the Dango pipeline as possible. We kept a record or all of the same metrics, use the same code structure, etc.
Command Claude Code
We're working on improving the Gene Ontology (GO) term handling in TorchCell, specifically focusing on properly integrating GO annotations from multiple sources within the graph representation module. The goal is to ensure that the Ggo graph in TorchCell correctly incorporates GO terms from both raw SGD (Saccharomyces…
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Command "hetero_cell_bipartite_dango_gi_refactor" from Mjvolk3/torchcell, covering heterocellbipartitedangogi model refactoring plan, current status summary, context, key files and completed tasks.
Command Claude Code
The GeneInteractionDango model experiences NaN values during training when using ICLoss in the Lightning training pipeline, but works fine with LogCosh loss and also works fine with ICLoss when run standalone (outside the Lightning pipeline).
Command Claude Code
A general-purpose dataset class for inference that follows the Neo4jCellDataset pattern but removes the complexity of database queries, conversion, deduplication, and aggregation. This dataset uses LMDB for efficient storage and retrieval of experiments, following the same format as Neo4jCellDataset. Put the new class…
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Command "load_coo_context" from Mjvolk3/torchcell, covering new data, old transforms with named phenotypes and old test results.
Command Claude Code
We are riding a pipeline for training the Dango Model.
Command Claude Code
@/Users/michaelvolk/Documents/projects/torchcell/torchcell/data/experimentdataset.py @/Users/michaelvolk/Documents/projects/torchcell/torchcell/datasets/scerevisiae/kuzmin2018.py @/Users/michaelvolk/Documents/projects/torchcell/torchcell/datasets/scerevisiae/costanzo2016.py…
Command Claude Code
We are refactoring pipeline for training the Dcell Model. We want to base it off the structure of the recent Dango Model Pipeline. The issue is that we have had a decent amount of updates since working with this code.
Command Claude Code
We have refactored the pipeline for training the Dcell Model. We have based it off the recent Dango Model Pipeline.