Sidechain.
Predicting how a cell's transcriptome shifts when a gene is silenced — a solo entry to the Virtual Cell Challenge 2026, built in the open.
Every submission, as Arc scored it. The live board shows only a team's latest entry, so the rank is the one each entry held when it was scored. An entry's model card is the sentence beside it on the board, and the models page says what each name means and what it borrows.
| date (UTC) | submission | overall | rank when scored |
|---|---|---|---|
| 2026-08-21 | SER-1 | 0.0788 | #2 of 42 |
model card | |||
| 2026-08-21 | SER-1p | 0.0730 | #10 of 95 |
model card | |||
| 2026-08-22 | SER-1n | 0.0822 | #9 of 97 |
model card | |||
| 2026-08-24 | SER-2 | 0.0937 | #25 of 216 |
model card | |||
| 2026-08-27 | SER-3n | 0.0963 | #54 of 301 |
model card | |||
| 2026-08-27 | SER-3fn | 0.1034 | #58 of 362 |
model card | |||
| 2026-08-30 | SER-3afgn | 0.0992 | #101 of 476 |
on the board as Sidechain SER-3afgn | |||
| 2026-08-30 | SER-3afn | 0.1071 | #86 of 476 |
model card | |||
| 2026-08-31 | SER-4afn | 0.1078 | #85 of 481 |
model card | |||
| 2026-09-01 | SER-5acfnt | 0.1075 | #114 of 533 |
model card | |||
| 2026-09-07 | PHE-2 calibration | -0.9807 | #746 |
model card | |||
| 2026-09-12 | SER-6aefn | 0.1091 | #245 of 903 |
model card | |||
What it is
What it is. Given expression data for genes that have been silenced, predict what happens when you silence a gene never seen silenced — in cell lines the model has never seen, given only their resting state. Sidechain is a solo entry that works as a small research group: Saber at the bench, Claude Code at the keyboard, and a ladder of models climbed from the simplest baseline up, keeping only what the metric pays for.
How it’s shared. Code, configs and tests are on GitHub. Progress notes go out on LinkedIn; the longer write-ups live here, and dashboards of the data and the models will join them as they are built.
Why “Sidechain”
A side chain is the part of an amino acid that makes it different from the other canonical nineteen. The models are named the same way: each series is an amino acid whose side chain matches the model's character, and a number counts entries within it. A letter suffix marks a one-knob variant — SER-1p is SER-1 with Poisson cells, SER-1n is SER-1 without shrinkage.
| series | side chain | what it names |
|---|---|---|
| GLY | none — the simplest residue | nulls and baselines |
| ALA | a single methyl | a single statistical shift |
| SER | a hydroxyl — small, reactive, transfers a group | cross-line delta transfer (today's models) |
| CYS | forms bridges between chains | context-aware models |
| HIS / LYS / ARG | long and charged — act at a distance | graph and prior heads |
| PHE / TYR / TRP | the aromatic heavyweights | deep generative models |
| PRO | bends the backbone | fusion |
For the chemistry behind the pun: Compound Interest's 20 common amino acids poster.