Update ovarian_xenium/heldout_split/README.md
Browse files
ovarian_xenium/heldout_split/README.md
CHANGED
|
@@ -109,20 +109,6 @@ Pearson r. The masks are fixed (seed 2026), so other models can be compared on t
|
|
| 109 |
| 50 % of (cell, gene) entries masked | 0.165 | 0.167 |
|
| 110 |
| no masking (what `get_model_output` returns) | 0.175 | 0.160 |
|
| 111 |
|
| 112 |
-
As a reference, a truncated SVD of the same matrix at the same width (256) reaches median gene r =
|
| 113 |
-
0.317. That is the ceiling for any linear encoder–decoder, and the model reaches about half of it.
|
| 114 |
-
|
| 115 |
-
## Limitations
|
| 116 |
-
|
| 117 |
-
* **One tissue section.** The test windows come from the same slide as the training windows, and
|
| 118 |
-
neighbouring windows are spatially autocorrelated. The scores measure generalisation to unseen
|
| 119 |
-
*regions of this section*, not to new donors or new slides.
|
| 120 |
-
* **Cell masking** was chosen because it forces the model to predict a hidden cell from its
|
| 121 |
-
neighbours, and that neighbourhood dependence is what the attention read-out interprets. A
|
| 122 |
-
gene-masking model fills in missing genes of a visible cell better (r ≈ 0.25) but predicts a fully
|
| 123 |
-
hidden cell worse (r ≈ 0.13).
|
| 124 |
-
* Attention-based net flow is a model read-out, not a measurement of ligand–receptor signalling.
|
| 125 |
-
|
| 126 |
## Citation
|
| 127 |
|
| 128 |
Drummer, F., Jiménez, S. *et al.* InterScale. bioRxiv (2026). Code:
|
|
|
|
| 109 |
| 50 % of (cell, gene) entries masked | 0.165 | 0.167 |
|
| 110 |
| no masking (what `get_model_output` returns) | 0.175 | 0.160 |
|
| 111 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 112 |
## Citation
|
| 113 |
|
| 114 |
Drummer, F., Jiménez, S. *et al.* InterScale. bioRxiv (2026). Code:
|