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.
| date (UTC) | submission | on the board as | overall | rank when scored |
|---|---|---|---|---|
| 2026-08-21 | SER-1 | sidechain r1-delta-even v1 | 0.0788 | #2 of 41 |
| 2026-08-21 | SER-1p | Sidechain SER-1p | 0.0730 | — (a probe) |
| 2026-08-22 | SER-1n | Sidechain SER-1n | 0.0822 | #14 of 107 |
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.
SER-1n — shrinkage off — scores 0.0822, the best entry so far.
Aug 21
First entry scored: 0.0788, #2 of 41 teams on day one. It slid within hours — a baseline is there to be overtaken.
Aug 20
The 2026 challenge opens: six unseen cell lines, 300 knockdowns each, no training data from the organisers.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.
Nothing published yet — the first write-up is being written. Until then the running commentary is on LinkedIn ↗, and you can subscribe to the feed so the first post finds you.