Geometry Matters in Packed 3D Attention

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Packing a 3D volume into a token sequence is not merely long-sequence modeling. Once the volume is packed, sequence order no longer encodes the geometry of the sample---so a positional mechanism indexed by sequence position can learn the memory layout rather than the object. This is a general failure mode for attention over packed geometric data. We introduce PACK3D, a local-global attention operator that separates memory layout from attention geometry. PACK3D keeps local neighborhood attention exact, compresses only distant context into contiguous 3D block summaries, and indexes every query-key interaction with axial RoPE on true token-grid coordinates rather than packed positions. Because the rotation is applied before a block is summarized, the query-to-summary logit remains a weighted sum of query-relative 3D displacements; compressed global context therefore stays spatially interpretable after packing, instead of collapsing to anonymous pooled content. We measure the failure mode directly. On a controlled synthetic task---train on one packing, change only the memory order of the tokens, hold the physical labeling rule fixed---learned positional embeddings and packed-sequence RoPE solve the training layout perfectly yet collapse under Morton, block-contiguous, and random repacking, while axial grid-coordinate RoPE stays exact throughout. The same coordinate system carries to real data: on Allen WTC-11 hiPSC microscopy, PACK3D improves over a parameter-matched 3D U-Net on the 15-structure joint task and over a matched learned-position local-global baseline, with controls isolating the coordinate system, not encoder capacity, as the source of the gain. A fused Triton implementation matches windowed-attention latency at 65k tokens while supplying the long-range context windowing cannot---so the operator is not only correct but trainable at scale.