An Empirical Audit of Input Encoders for Multi-Channel Signal Transformers

📅 2026-06-03
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🤖 AI Summary
This study addresses the challenge of channel embedding for multivariate time series inputs in Transformer-based models by systematically evaluating eight input encoding strategies on both synthetic and real-world data (ETTh1), using negative log-likelihood as the primary metric. The findings reveal that the standard per-channel linear projection (nn.Linear(C, d_model)) consistently achieves superior and robust performance across most scenarios. While positional encoding with projection shows marginal gains for small channel counts and nonlinear MLP backbones offer slight improvements for large channel counts, these advantages diminish as data volume increases. Through geometric probing and paired significance tests, the work uncovers fundamental limitations in both shared-scalar and channel-independent architectures, demonstrating that mainstream encoders exhibit remarkably similar empirical performance, thereby offering practical guidance for multivariate time series modeling.
📝 Abstract
Transformers consuming multi-channel scalar signals must embed $C$ simultaneous values into one $d_{\text{model}}$-dimensional vector per time step. We empirically audit eight input encoders -- spanning a shared-scalar baseline, per-channel linear projections, an orthogonality regulariser, a nonlinear MLP stem, block-partitioned concatenation, channel-independent and channel-as-token architectures, and a projected positional encoding -- on a synthetic benchmark designed to make channel identity informative and on ETTh1 as a real-data check, measured in next-step negative log-likelihood (NLL). The headline is one of practical near-equivalence within a wide "top tier": the standard per-channel linear projection (nn.Linear(C, $d_{\text{model}}$)) matches every alternative in that tier up to small, statistically real but practically modest, differences. Two encoders lose decisively: the shared-scalar baseline, which collapses for information-theoretic reasons we make explicit, and the channel-independent PatchTST-spirit baseline, which underperforms on both benchmarks and overfits universally on the synthetic one. Paired tests resolve two small gaps: projecting the sinusoidal positional encoding through a learned linear layer edges the rest at small $C$, with a direct geometric probe showing the mechanism is positional-channel orthogonalisation; a nonlinear MLP stem edges them at the largest $C$ we test, with the gap shrinking under more training data. The practical recommendation is to use nn.Linear(C, $d_{\text{model}}$) by default and reach for something more elaborate only when the task at hand gives a real reason to do so. Code and data to reproduce every experiment in this paper are available at https://github.com/OssiLehtinen/channel-encoder-audit
Problem

Research questions and friction points this paper is trying to address.

multi-channel signals
input encoding
Transformers
channel embedding
time series modeling
Innovation

Methods, ideas, or system contributions that make the work stand out.

input encoders
multi-channel signals
empirical audit
channel identity
Transformer architecture
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