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arxiv: 2505.20535 · v3 · submitted 2025-05-26 · 💻 cs.LG

Rotary Masked Autoencoders are Versatile Learners

Uros Zivanovic , Serafina Di Gioia , Andre Scaffidi , Mart\'in de los Rios , Gabriella Contardo , Roberto Trotta This is my paper

Pith reviewed 2026-05-19 12:28 UTC · model grok-4.3

classification 💻 cs.LG
keywords Rotary Positional EmbeddingsMasked AutoencodersTime SeriesRepresentation LearningIrregular SamplingMultimodal Learning
0
0 comments X p. Extension

The pith

RoMAE applies rotary positional embeddings to masked autoencoders for continuous positions across modalities without time-series customizations.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper presents RoMAE as an extension of the standard Masked Autoencoder that replaces usual positional encodings with rotary embeddings adapted to continuous multidimensional inputs. This setup targets irregular time-series and similar data where positions are not on a fixed grid. A sympathetic reader would care because the method claims to avoid the extra architectural changes and computational costs that usually come with handling uneven sampling or multivariate continuous signals. The work shows RoMAE matching or exceeding specialized models on challenging benchmarks while preserving baseline MAE behavior on images and audio.

Core claim

RoMAE utilizes Rotary Positional Embedding for continuous positions in the MAE framework, enabling interpolation and representation learning with multidimensional continuous positional information while avoiding any time-series-specific architectural specializations. It surpasses specialized time-series architectures on difficult datasets such as the DESC ELAsTiCC Challenge while maintaining MAE's usual performance across other modalities. Including learned embeddings in the input sequence breaks RoPE's relative position property.

What carries the argument

Rotary Positional Embedding (RoPE) adapted for continuous positions, inserted directly into the Masked Autoencoder pipeline to encode relative positional information that supports interpolation without grid assumptions.

If this is right

  • RoMAE performs representation learning on irregular and multivariate time-series without added complexity.
  • The same model maintains standard MAE reconstruction quality on images and audio.
  • Learned embeddings in the sequence interfere with RoPE's relative position encoding.
  • RoMAE can interpolate across continuous positional dimensions in the input sequence.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • The approach may extend naturally to other continuous-valued domains such as spatial sensor grids or scientific measurement series.
  • Direct substitution of rotary embeddings could reduce the need for modality-specific positional modules in future transformer variants.

Load-bearing premise

Rotary positional embeddings can be directly substituted into the masked autoencoder framework for continuous positions without introducing hidden limitations or needing further adjustments.

What would settle it

An experiment where RoMAE is tested on irregular time-series data with known gaps and shows clear degradation compared to specialized architectures, or fails to reconstruct positions while preserving relative properties.

Figures

Figures reproduced from arXiv: 2505.20535 by Andre Scaffidi, Gabriella Contardo, Mart\'in de los Rios, Roberto Trotta, Serafina Di Gioia, Uros Zivanovic.

Figure 1
Figure 1. Figure 1: Overview of the RoMAE pipeline. Left: Visualisation of data embedding via multi￾dimensional (ND) patchification for illustrative data realisations in 1, 2 and 3D. Centre: Full depiction of RoMAE architecture. The optional [CLS] token is omitted from the input sequence for simplicity. Right: The RoMAE encoder/decoder with ROPE operations denoted by rotational arrows. Masked Autoencoders: Architectures such … view at source ↗
Figure 2
Figure 2. Figure 2: RoMAE position reconstruction MSE across two positional ranges. [PITH_FULL_IMAGE:figures/full_fig_p019_2.png] view at source ↗
Figure 3
Figure 3. Figure 3: Average MSE obtained from the interpolation task using RoMAE-tiny for time-series with [PITH_FULL_IMAGE:figures/full_fig_p020_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Same as above but now for time-series with two frequency modes present in the signal. [PITH_FULL_IMAGE:figures/full_fig_p021_4.png] view at source ↗
Figure 5
Figure 5. Figure 5: Illustrative realisation from the evaluation of RoMAE on a the bi-frequency time series. [PITH_FULL_IMAGE:figures/full_fig_p021_5.png] view at source ↗
Figure 6
Figure 6. Figure 6: A training example from the ELAsTiCC dataset. The flux difference of each band has [PITH_FULL_IMAGE:figures/full_fig_p026_6.png] view at source ↗
Figure 7
Figure 7. Figure 7: Two sample realisations of differing chirality from the test set of spirals. The green line is [PITH_FULL_IMAGE:figures/full_fig_p027_7.png] view at source ↗
Figure 8
Figure 8. Figure 8: Samples from interpolation tests using n = 3, 10 and 20 observations. D.9 PhysioNet We adopt the pre–processed release of the PHYSIONET/CinC 2012 Challenge [50], comprising multivariate clinical time–series collected during the 48h window following intensive–care–unit (ICU) admission. Static covariates (Age, Gender, Height, ICU type) occupy feature indices 0–3 and are always observed, whereas the remaining… view at source ↗
read the original abstract

Applying Transformers to irregular time-series typically requires specializations to their baseline architecture, which can result in additional computational overhead and increased method complexity. We present the Rotary Masked Autoencoder (RoMAE), which utilizes the popular Rotary Positional Embedding (RoPE) method for continuous positions. RoMAE is an extension to the Masked Autoencoder (MAE) that enables interpolation and representation learning with multidimensional continuous positional information while avoiding any time-series-specific architectural specializations. We showcase RoMAE's performance on a variety of modalities including irregular and multivariate time-series, images, and audio, demonstrating that RoMAE surpasses specialized time-series architectures on difficult datasets such as the DESC ELAsTiCC Challenge while maintaining MAE's usual performance across other modalities. In addition, we investigate RoMAE's ability to reconstruct the embedded continuous positions, demonstrating that including learned embeddings in the input sequence breaks RoPE's relative position property.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 1 minor

Summary. The manuscript introduces Rotary Masked Autoencoder (RoMAE), an extension of the standard Masked Autoencoder that incorporates Rotary Positional Embeddings (RoPE) for multidimensional continuous positions. It claims this enables interpolation and representation learning on irregular/multivariate time-series (and other modalities) without any time-series-specific architectural changes to masking, encoder, decoder, or loss, while surpassing specialized time-series models on the DESC ELAsTiCC Challenge and preserving MAE performance on images and audio; an additional investigation shows that learned embeddings break RoPE's relative-position property.

Significance. If the empirical results hold after full verification, the work would be significant for providing a parameter-light, specialization-free route to continuous positional modeling in transformers, potentially reducing complexity for irregular time-series and related modalities while retaining MAE's reconstruction-based pretraining benefits.

major comments (2)
  1. [Abstract] Abstract: the claim that RoMAE 'surpasses specialized time-series architectures on difficult datasets such as the DESC ELAsTiCC Challenge' is unsupported by any quantitative metrics, error bars, ablation tables, or dataset statistics, leaving the central performance claim unevaluable.
  2. [Abstract] Abstract: no equations, pseudocode, or implementation details are supplied for the direct substitution of RoPE into the MAE pipeline for continuous multidimensional positions, so it is impossible to confirm that no auxiliary mechanisms (e.g., custom normalization or adjusted masking) were introduced that would contradict the 'avoiding any time-series-specific architectural specializations' claim.
minor comments (1)
  1. [Abstract] Abstract: the final sentence on reconstructing embedded continuous positions would benefit from a brief statement of the observed outcome rather than only the negative finding about learned embeddings.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their constructive feedback on our manuscript. We address each major comment below and have revised the manuscript to strengthen the support for our claims while preserving the core contributions.

read point-by-point responses

  1. Referee: [Abstract] Abstract: the claim that RoMAE 'surpasses specialized time-series architectures on difficult datasets such as the DESC ELAsTiCC Challenge' is unsupported by any quantitative metrics, error bars, ablation tables, or dataset statistics, leaving the central performance claim unevaluable.

    Authors: We agree that the abstract would be strengthened by including key quantitative results to make the central claim immediately evaluable without requiring the reader to consult the full experiments section. The manuscript contains detailed results on the DESC ELAsTiCC Challenge, including performance metrics, comparisons against specialized time-series baselines, error bars from multiple random seeds, and dataset statistics. We have revised the abstract to incorporate concise quantitative highlights from those experiments. revision: yes

  2. Referee: [Abstract] Abstract: no equations, pseudocode, or implementation details are supplied for the direct substitution of RoPE into the MAE pipeline for continuous multidimensional positions, so it is impossible to confirm that no auxiliary mechanisms (e.g., custom normalization or adjusted masking) were introduced that would contradict the 'avoiding any time-series-specific architectural specializations' claim.

    Authors: The body of the manuscript (Section 3) provides the equations for adapting RoPE to continuous multidimensional positions, along with a description confirming that the substitution uses only standard MAE masking, encoder, decoder, and loss components with no auxiliary mechanisms or modality-specific changes. To improve accessibility from the abstract, we have added a brief clarifying sentence and a reference to the relevant section in the revised abstract, and we have included a short pseudocode block in the main text for the integration step. revision: yes

Circularity Check

0 steps flagged

No derivation chain or equations present; claims are empirical

full rationale

The provided document consists solely of the abstract, which introduces RoMAE as an extension of the standard Masked Autoencoder that applies Rotary Positional Embeddings to continuous multidimensional positions. No equations, derivations, fitted parameters, or self-citations are shown that could reduce any result to its inputs by construction. Performance claims on datasets such as DESC ELAsTiCC are presented as empirical outcomes rather than first-principles predictions, and the investigation of position reconstruction is described without technical steps that invite circularity analysis. Because no load-bearing derivation chain exists in the available text, the paper is self-contained against external benchmarks with no detectable circularity.

Axiom & Free-Parameter Ledger

0 free parameters · 0 axioms · 0 invented entities

Abstract-only review yields no explicit free parameters, axioms, or invented entities beyond the standard components of MAE and RoPE.

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