We lifted 4 functions out of this paper's own repositories and ran 4 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 |
|---|---|---|
| eliasventre/ltreweighting | canonical | 4 of 4 |
| Function | Status | Where it lives |
|---|---|---|
| RMS | Ran | eliasventre/ltreweighting/Figure2.py code served (permissive licence) · get_code("0c35454400d8f399") |
| barcode_distances | Ran | eliasventre/ltreweighting/lineageot_files/inference.py code served (permissive licence) · get_code("ea48c4cbe31cb341") |
| rate_estimator | Ran | eliasventre/ltreweighting/lineageot_files/inference.py code served (permissive licence) · get_code("6e62aeb3917117f0") |
| scaled_Hamming_distance | Ran | eliasventre/ltreweighting/lineageot_files/inference.py code served (permissive licence) · get_code("80ca6c3965ef859f") |
Some links come from the archived Papers with Code dataset (CC BY-SA 4.0): attribution and licence.
A core challenge for modern biology is how to infer the trajectories of individual cells from population-level time courses of high-dimensional gene expression data. Birth and death of cells present a particular difficulty: existing trajectory inference methods cannot distinguish variability in net proliferation from cell differentiation dynamics, and hence require accurate prior knowledge of the proliferation rate. Building on Global Waddington-OT (gWOT), which performs trajectory inference with rigorous theoretical guarantees when birth and death can be neglected, we show how to use lineage trees available with recently developed CRISPR-based measurement technologies to disentangle proliferation and differentiation. In particular, when there is neither death nor subsampling of cells, we show that we extend gWOT to the case with proliferation with similar theoretical guarantees and computational cost, without requiring any prior information. In the case of death and/or subsampling, our method introduces a bias, that we describe explicitly and argue to be inherent to these lineage tracing data. We demonstrate in both cases the ability of this method to reliably reconstruct the landscape of a branching SDE from time-courses of simulated datasets with lineage tracing, outperforming even a benchmark using the experimentally unavailable true branching rates.
The same record, over MCP at https://syntology.ai/mcp:
get_harvested_code_for_paper("2307.07687")
get_code_for_paper("2307.07687")
have("2307.07687")
Connect an agent — have() is free.