-
at `/LINCS/instances`
and
`/LINCS/pert`
respectively
ghost updated
2 years ago
-
I'm not happy with the results of the large sweep that we ran on LINCS. Mainly:
- We should fix the latent space dimension to 64 (or 32?). This also restricts the number of parameters for the Vanilla…
-
## Idea:
Observing how the transformed drug embeddings cluster, and comparing the clustering to Vanilla, to the clustering of Trapnell gene expressions (supp figure in Sciplex paper), to the cluster…
-
I am running into some issues when using with `constraints = all-angles` for a box of ethanol in GROMACS (with the LINCS algorithm). The simulation ran fine with `constraints = all-bonds`, so I am jus…
-
https://mp.weixin.qq.com/s/KyqJfWW7MDoFHT70mXLpeA
-
requires update of REST server and possible lincs module
ghost updated
2 years ago
-
Reminder for @MxMstrmn to check how the LINCS train / test split was calculated (column `split1` in `lincs_full_smiles.h5ad`) and whether it should be adjusted.
-
Looking at the results in `chemical_CPA/simon/plot_sweep_results.ipynb`
**Hypothesis**: The drug disentanglement might be easier for NN based embeddings as these are chemically motivated.
**Poten…
-
I started writing the code that does the transfer learning (loads the model pretrained on LINCS for finetuning on Trapnell) and ran into a stumbling block: LINCS has 978 genes, one of which isn't part…
-
Node attributes on chemical compounds indicate drug approval status. Clearly we could filter based on these attributes post-query, and a helper tool to do this may be quite useful in the short term. …