Beyond receptive fields: sequence-pooled normalization can supply most of a sequence labeler's context
Organizations: Department of Computer Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Abstract
A convolutional sequence labeler's receptive field is routinely treated as the extent of the model's usable context: it sets dilation schedules, bounds streaming horizons, and underwrites locality claims. However, we show that this can be false: when a normalization layer computes statistics from the current input along the sequence at inference, those statistics open a sequence-spanning path that bypasses the convolutional receptive field to provide global context. We derive this from the layer's Jacobian (the criterion needs no experiment), and what the path carries has a closed form. On a synthetic labeling process with computable optima, the global summary that a sequence-spanning normalization encodes already supplies almost all of what a larger receptive field would buy where labels come in long runs: a network reaching 9 positions comes within 0.009 of the whole-sequence optimum, against a near-chance bound for its reach. Closing the path, by taking the same statistics per position, multiplies what enlarging the receptive field is worth by up to an order of magnitude on simulated genomes at every difficulty level tested and on real 1000 Genomes haplotypes. The same path also confounds attribution: ablating a trained network's receptive-field-enlarging blocks severs part of the path, overstating their contribution 8.3-16.1-fold relative to retraining from scratch. The substitution of normalization for receptive field fades as labels switch more often. Where labels run long, neither the receptive-field justification nor the ablation is wrong about its numbers, but both credit the wrong component.
Figures & tables
| normalization | statistics pooled over | path at inference | reach worth |
|---|---|---|---|
| none | — | no | +0.3740 0.0052 |
| per position | channels | no | +0.3741 0.0052 |
| instance | length | yes | +0.0424 0.0080 |
| group | channels and length | yes | +0.0452 0.0107 |
| batch | batch and length; running at eval | no | +0.3687 0.0046 |
| normalization | statistics pooled over | by ablation | by retraining | ratio |
|---|---|---|---|---|
| none | — | |||
| per position | channels | |||
| batch | batch and length, running at eval | |||
| instance | length | |||
| group | channels and length |
Appendix figures & tables11 assets
Supplementary material from the paper’s appendix.
Appendix
| normalization | ||||||
|---|---|---|---|---|---|---|
| pooled over length | 0.2405 | 0.9631 | 0.9817 | 0.9962 | 0.9982 | 0.9983 |
| 0.0719 | 0.9353 | 0.9478 | 0.9686 | 0.9836 | 0.9877 | |
| 0.0380 | 0.9158 | 0.9250 | 0.9381 | 0.9532 | 0.9610 | |
| 0.0199 | 0.8502 | 0.8649 | 0.8745 | 0.8907 | 0.8969 | |
| 0.0096 | 0.7272 | 0.7339 | 0.7399 | 0.7507 | 0.7592 | |
| per position | 0.2405 | 0.7228 | 0.8786 | 0.9849 | 0.9980 | 0.9983 |
| pooled over length | per position | ratio | |
|---|---|---|---|
| 0.2405 | 7.8 | ||
| 0.0719 | 7.0 | ||
| 0.0380 | 8.3 | ||
| 0.0199 | 6.8 | ||
| 0.0096 | 6.3 |
| process | pooled over length | per position | ratio | ||
|---|---|---|---|---|---|
| genomic | 0.29 | 8.3 | 2.08 | ||
| 0.99 | 3.1 | 2.13 | |||
| 3.00 | 1.7 | 2.08 | |||
| 9.89 | 1.3 | 2.68 | |||
| synthetic | 0.09 | 62.8 | 5.80 | ||
| 0.29 | 15.2 | 4.05 |
| layer | statistics pooled over | |||||
|---|---|---|---|---|---|---|
| gLN | channels and time | 0.9246 | 0.9244 | 0.9245 | 0.9289 | 0.9407 |
| cLN | channels and time up to | 0.8676 | 0.8705 | 0.8740 | 0.8860 | 0.9186 |
| per position | channels | 0.5423 | 0.5681 | 0.6262 | 0.7314 | 0.8745 |
| switches per sequence | pooled over length | per position | difference | exact optimum | shortfall |
|---|---|---|---|---|---|
| 0.27 | 0.9497 | 0.9472 | +0.0025 | 0.9522 | 0.0025 |
| 0.98 | 0.8956 | 0.8932 | +0.0024 | 0.8993 | 0.0037 |
| 2.98 | 0.8146 | 0.8125 | +0.0021 | 0.8194 | 0.0047 |
| 9.79 | 0.7023 | 0.7000 | +0.0022 | 0.7058 | 0.0035 |
| switches/sequence | |||||
|---|---|---|---|---|---|
| 0.09 | -0.0006 | -0.0017 | -0.0050 | -0.0124 | -0.0172 |
| 0.29 | -0.0003 | -0.0016 | -0.0049 | -0.0115 | -0.0119 |
| 0.99 | -0.0008 | -0.0016 | -0.0030 | -0.0049 | -0.0013 |
| 2.98 | -0.0010 | -0.0007 | +0.0012 | +0.0019 | -0.0001 |
| 5.99 | -0.0008 | +0.0005 | +0.0031 | +0.0084 | -0.0009 |
| 9.89 | -0.0003 | +0.0010 | +0.0051 | +0.0091 | -0.0002 |
| switches | full | proportion oracle | |||||
|---|---|---|---|---|---|---|---|
| 0.09 | 0.5479 | 0.5908 | 0.6741 | 0.8165 | 0.9537 | 0.9759 | 0.9760 |
| 0.29 | 0.5479 | 0.5905 | 0.6738 | 0.8110 | 0.9335 | 0.9504 | 0.9348 |
| 0.99 | 0.5482 | 0.5903 | 0.6708 | 0.7951 | 0.8835 | 0.8986 | 0.8390 |
| 2.98 | 0.5493 | 0.5913 | 0.6660 | 0.7666 | 0.8115 | 0.8194 | 0.7239 |
| 5.99 | 0.5474 | 0.5875 | 0.6543 | 0.7211 | 0.7466 | 0.7508 | 0.6567 |
| 9.89 | 0.5466 | 0.5846 | 0.6424 | 0.6869 | 0.7008 | 0.7031 | 0.6290 |
| split time | , ours | , benchmark | difference | accuracy |
|---|---|---|---|---|
| 3200 | 0.2405 | 0.2434 | -0.0029 | 0.9983 |
| 1600 | 0.1366 | 0.1376 | -0.0010 | 0.9955 |
| 800 | 0.0719 | 0.0736 | -0.0017 | 0.9877 |
| 400 | 0.0380 | 0.0384 | -0.0004 | 0.9610 |
| 200 | 0.0199 | 0.0200 | -0.0001 | 0.8969 |
| 100 | 0.0096 | 0.0097 | -0.0001 | 0.7592 |
| switches/sequence | depth | receptive field | pooled over length | per position |
|---|---|---|---|---|
| 0.27 | 1 | 22 | 0.9247 | 0.5730 |
| 2 | 48 | 0.9252 | 0.6060 | |
| 3 | 96 | 0.9255 | 0.6493 | |
| 4 | 192 | 0.9276 | 0.7039 | |
| 5 | 384 | 0.9326 | 0.7756 | |
| 6 | 768 | 0.9417 | 0.8482 |
| normalization | ablated | retrained | ratio | |
|---|---|---|---|---|
| pooled over length | 0.2405 | 0.3117 | 0.0351 | 8.9 |
| 0.0719 | 0.4273 | 0.0524 | 8.2 | |
| 0.0380 | 0.4099 | 0.0452 | 9.1 | |
| 0.0199 | 0.3774 | 0.0467 | 8.1 | |
| 0.0096 | 0.2289 | 0.0320 | 7.2 | |
| per position | 0.2405 | 0.4085 | 0.2754 | 1.5 |
| switches per sequence | computed | error | |
|---|---|---|---|
| 0.09 | 0.4760 | 1.3029 | -63% |
| 0.29 | 0.4348 | 0.7471 | -42% |
| 0.99 | 0.3390 | 0.4001 | -15% |
| 2.98 | 0.2239 | 0.2311 | -3% |
| 5.99 | 0.1567 | 0.1631 | -4% |
| 9.89 | 0.1290 | 0.1269 | +2% |