saberhq.com / sidechain
Virtual Cell Challenge · 2026

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.

Best overall
0.1091
SER-6aefn · 2026-09-12
Best rank when scored
#2
of 42 teams · 2026-08-21
Scored submissions
12
1 calibration run · since 2026-08-21
Deadline
Nov 5
final test set Oct 22
Overall score · 0 = the context mean, 1 = a biological replicate
00.2
SER-1 0.0788
SER-1p 0.0730
SER-1n 0.0822
SER-2 0.0937
SER-3n 0.0963
SER-3fn 0.1034
SER-3afgn 0.0992
SER-3afn 0.1071
SER-4afn 0.1078
SER-5acfnt 0.1075
SER-6aefn 0.1091
Calibration runs · what this means →
PHE-2 below zero · off this scale -0.9807
date (UTC)submissionoverallrank when scored
2026-08-21SER-10.0788#2 of 42
model card sidechain r1-delta-even v1

Rung 1': per-gene log2FC pooled (inverse-variance) over K562 genome-wide + H1 2025 for the targets they cover, gene-wise positive-part shrinkage, re-anchored on each context's control profile; minimum-variance (even-spread) integer cells at control depth; 28 uncovered targets get the H1 mean shift.

2026-08-21SER-1p0.0730#10 of 95
model card Sidechain SER-1p

Same transferred log2FCs as SER-1 (K562 genome-wide + H1, inverse-variance pooled, gene-wise shrinkage, alpha=1), emitted as independent Poisson cells at control depth instead of minimum-variance cells. Controlled experiment on emission dispersion.

2026-08-22SER-1n0.0822#9 of 97
model card Sidechain SER-1n

SER-1 with the transferred log2FCs left unshrunk (no gene-wise positive-part shrinkage); minimum-variance cells. Probe: does shrinkage remove small true signals that cosine-PDS needs?

2026-08-24SER-20.0937#25 of 216
model card Sidechain SER-2

SER-2 = cross-line delta transfer, model 2 (named before the knob letters; shrinkage off, as in SER-1n). Borrows each gene's knockdown effect from K562, H1 and the challenge-panel slice of two genome-wide screens in colon and kidney lines — the first entry to cover all 300 targets — and re-anchors it on the new line's resting state. All models: saberhq.com/sidechain/models/ (card written here — this entry reached the board before cards shipped with every submission)

2026-08-27SER-3n0.0963#54 of 301
model card Sidechain SER-3n

SER-3n = cross-line delta transfer, model 3 (n = no shrinkage). The same four sources as SER-2, with the two genome-wide screens read in full — every gene they measured rather than the challenge panel alone — re-anchored on the new line's resting state. All models: saberhq.com/sidechain/models/ (card written here — this entry reached the board before cards shipped with every submission)

2026-08-27SER-3fn0.1034#58 of 362
model card Sidechain SER-3fn

SER-3fn = cross-line delta transfer, model 3 (f = floored source weights, n = no shrinkage). Borrows each gene's knockdown response from K562, H1 and two genome-wide screens in colon and kidney lines, trusts each source only as far as its cell counts justify, and re-anchors it on the new line's resting state. All models: saberhq.com/sidechain/models/

2026-08-30SER-3afgn0.0992#101 of 476
on the board as Sidechain SER-3afgn
2026-08-30SER-3afn0.1071#86 of 476
model card Sidechain SER-3afn

SER-3afn = cross-line delta transfer, model 3 (a = amplified transfer, f = floored source weights, n = no shrinkage). Borrows each gene's knockdown response from K562, H1 and two genome-wide screens in colon and kidney lines, and scales it up to reference strength, because those screens silenced their targets only partially. All models: saberhq.com/sidechain/models/

2026-08-31SER-4afn0.1078#85 of 481
model card Sidechain SER-4afn

SER-4afn = cross-line delta transfer, model 4 (a = amplified transfer, f = floored source weights, n = no shrinkage). Borrows each gene's knockdown response from K562, H1 and two genome-wide screens in colon and kidney lines, and scales it up to reference strength, because those screens silenced their targets only partially. All models: saberhq.com/sidechain/models/

2026-09-01SER-5acfnt0.1075#114 of 533
model card Sidechain SER-5acfnt

SER-5acfnt = weights each source's vote by how well it actually predicts a new cell line, not by how confident it sounds. All models: saberhq.com/sidechain/models/

2026-09-07PHE-2 calibration-0.9807#746
model card Sidechain PHE-2

PHE-2 = a neural network trained on two cancer cell lines, asked to predict each knockdown's cells directly from an unseen line's untouched controls. All models: saberhq.com/sidechain/models/

2026-09-12SER-6aefn0.1091#245 of 903
model card Sidechain SER-6aefn

SER-6aefn = cross-line delta transfer, model 6 (a = amplified transfer, e = emission dial at lambda 0.5, f = floored source weights, n = no shrinkage). Borrows each gene's knockdown response from K562, H1 and two genome-wide screens in colon and kidney lines, scales it to reference strength, and emits cells with half the Poisson spread instead of identical ones -- the one change from SER-4afn. All models: saberhq.com/sidechain/models/

02

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.

Perturb-seqzero-shot cell lineshuman + Claude Code Virtual Cell Challenge 2026
03

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.

seriesside chainwhat it names
GLYnone — the simplest residuenulls and baselines
ALAa single methyla single statistical shift
SERa hydroxyl — small, reactive, transfers a groupcross-line delta transfer (today's models)
CYSforms bridges between chainscontext-aware models
HIS / LYS / ARGlong and charged — act at a distancegraph and prior heads
PHE / TYR / TRPthe aromatic heavyweightsdeep generative models
PRObends the backbonefusion

For the chemistry behind the pun: Compound Interest's 20 common amino acids poster.