Shuangjia Zheng, Zichen Wang, Zhijian Wei, Runze Ma, Zhongmin Li, Shuotong Song
We lifted 14 functions out of this paper's own repositories and ran 0 of them in a sandbox. "Ran" means the function executed on a synthesized input and returned a value. It is not a reproduction of the paper's results.
| Repository | Role | Ran |
|---|---|---|
| theislab/cpa | canonical | 0 of 8 |
| GENTEL-lab/VCWorld | canonical | 0 of 6 |
| Function | Status | Where it lives |
|---|---|---|
| build_seen_structures | Not yet run | GENTEL-lab/VCWorld/src/cli_pipeline/stages/retrieve.py pointer only (licence: NONE) · get_code("979ed1f7ce650afe") |
| entropy_batch_mixing | Not yet run | theislab/cpa/cpa/_metrics.py code served (permissive licence) · get_code("a097de2c5ee5703a") |
| evaluate_r2_benchmark | Not yet run | theislab/cpa/cpa/_api.py code served (permissive licence) · get_code("7884dc6fe2db998a") |
| fast_dimred | Not yet run | theislab/cpa/cpa/_plotting.py code served (permissive licence) · get_code("1d04de8baa8067c6") |
| get_description | Not yet run | GENTEL-lab/VCWorld/src/cli_pipeline/stages/prompt.py pointer only (licence: NONE) · get_code("6d18c722c8734c08") |
| get_palette | Not yet run | theislab/cpa/cpa/_plotting.py code served (permissive licence) · get_code("7c73c81f20db72ff") |
| get_reference_from_combo | Not yet run | theislab/cpa/cpa/_api.py code served (permissive licence) · get_code("04e7a3ac4c778291") |
| knn_purity | Not yet run | theislab/cpa/cpa/_metrics.py code served (permissive licence) · get_code("d20076190239a46e") |
| linear_interp | Not yet run | theislab/cpa/cpa/_api.py code served (permissive licence) · get_code("b74b8f3ae9fbcf97") |
| load_drug_data | Not yet run | GENTEL-lab/VCWorld/src/cli_pipeline/stages/retrieve.py pointer only (licence: NONE) · get_code("2cd78d65a0e02fe4") |
| load_json | Not yet run | GENTEL-lab/VCWorld/src/cli_pipeline/stages/prompt.py pointer only (licence: NONE) · get_code("581e1a3430c33f5f") |
| load_similarity_json | Not yet run | GENTEL-lab/VCWorld/src/cli_pipeline/stages/retrieve.py pointer only (licence: NONE) · get_code("b4c67b07ba135ccc") |
| load_template_vars | Not yet run | GENTEL-lab/VCWorld/src/cli_pipeline/stages/prompt.py pointer only (licence: NONE) · get_code("2f527d54bf7044a8") |
| log10_with0 | Not yet run | theislab/cpa/cpa/_plotting.py code served (permissive licence) · get_code("a2338578129cfbb5") |
Some links come from the archived Papers with Code dataset (CC BY-SA 4.0): attribution and licence.
Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent models attempt to incorporate multi-source biological information, their generalization remains constrained by data quality, coverage, and batch effects. More critically, these models often function as black boxes, offering predictions without interpretability or consistency with biological principles, which undermines their credibility in scientific research. To address these challenges, we present VCWorld, a cell-level white-box simulator that integrates structured biological knowledge with the iterative reasoning capabilities of large language models to instantiate a biological world model. VCWorld operates in a data-efficient manner to reproduce perturbationinduced signaling cascades and generates interpretable, stepwise predictions alongside explicit mechanistic hypotheses. In drug perturbation benchmarks, VCWorld achieves state-of-the-art predictive performance, and the inferred mechanistic pathways are consistent with publicly available biological evidence. Our code is publicly available at https://github.com/GENTEL-lab/VCWorld.
The same record, over MCP at https://syntology.ai/mcp:
get_harvested_code_for_paper("2512.00306")
get_code_for_paper("2512.00306")
have("2512.00306")
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