# Same Brain, Different Prediction: How Preprocessing Choices Undermine EEG Decoding Reliability

arXiv: https://arxiv.org/abs/2605.07212 · HTML: https://mlsanity.com/paper/2605.07212/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 22 of its 45 references that are in the map.
- First posted on arXiv 8 May 2026.

## Builds on (most cited first, 22 of 22)

- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [Domain-Adversarial Training of Neural Networks](https://mlsanity.com/paper/1505.07818/) (2015)
- [Shortcut Learning in Deep Neural Networks](https://mlsanity.com/paper/2004.07780/) (2020)
- [Invariant Risk Minimization](https://mlsanity.com/paper/1907.02893/) (2019)
- [Distributionally Robust Neural Networks for Group Shifts: On the Importance of Regularization for Worst-Case Generalization](https://mlsanity.com/paper/1911.08731/) (2019)
- [Deep CORAL: Correlation Alignment for Deep Domain Adaptation](https://mlsanity.com/paper/1607.01719/) (2016)
- [In Search of Lost Domain Generalization](https://mlsanity.com/paper/2007.01434/) (2020)
- [A Review of Uncertainty Quantification in Deep Learning: Techniques, Applications and Challenges](https://mlsanity.com/paper/2011.06225/) (2020)
- [Domain Generalization: A Survey](https://mlsanity.com/paper/2103.02503/) (2021)
- [EEGNet: A Compact Convolutional Network for EEG-based Brain-Computer Interfaces](https://mlsanity.com/paper/1611.08024/) (2016)
- [Underspecification Presents Challenges for Credibility in Modern Machine Learning](https://mlsanity.com/paper/2011.03395/) (2020)
- [Large Brain Model for Learning Generic Representations with Tremendous EEG Data in BCI](https://mlsanity.com/paper/2405.18765/) (2024)
- [BENDR: using transformers and a contrastive self-supervised learning task to learn from massive amounts of EEG data](https://mlsanity.com/paper/2101.12037/) (2021)
- [Deep learning-based electroencephalography analysis: a systematic review](https://mlsanity.com/paper/1901.05498/) (2019)
- [MOABB: Trustworthy algorithm benchmarking for BCIs](https://mlsanity.com/paper/1805.06427/) (2018)
- [REVE: A Foundation Model for EEG -- Adapting to Any Setup with Large-Scale Pretraining on 25,000 Subjects](https://mlsanity.com/paper/2510.21585/) (2025)
- [CSBrain: A Cross-scale Spatiotemporal Brain Foundation Model for EEG Decoding](https://mlsanity.com/paper/2506.23075/) (2025)
- [NeurIPT: Foundation Model for Neural Interfaces](https://mlsanity.com/paper/2510.16548/) (2025)
- [How EEG preprocessing shapes decoding performance](https://mlsanity.com/paper/2410.14453/) (2024)
- [The more, the better? Evaluating the role of EEG preprocessing for deep learning applications](https://mlsanity.com/paper/2411.18392/) (2024)
- [Pipeline-Invariant Representation Learning for Neuroimaging](https://mlsanity.com/paper/2208.12909/) (2022)

## Built on by (most cited first, 2 of 2)

- [Subject-Specific Analysis of Self-Initiated Attention Shifts from EEG with Controlled Internal and External Attention Conditions](https://mlsanity.com/paper/2605.18251/) (2026)
- [CogEEGAgent: Toward Autonomous Cognitive EEG Analysis with Grounded Execution and Selection-Aware Verification](https://mlsanity.com/paper/2607.25045/) (2026)

## Abstract (arXiv)

Electroencephalography (EEG) is a cornerstone of brain-computer interfaces and clinical neuroscience, yet deep learning models are typically trained and evaluated under a single, unreported preprocessing pipeline. We formalize preprocessing choices as a counterfactual intervention space and show that EEG predictions are surprisingly unstable under this space: across six datasets spanning four paradigms, up to 42% of trial-level predictions flip when only the preprocessing changes, a variability that standard uncertainty methods do not explicitly quantify because they condition on a fixed preprocessing pipeline. We provide three tools to make this instability measurable, decomposable, and reducible. First, a Walsh-Hadamard decomposition of the 2^7 pipeline space reveals that sensitivity is near-additive in practice under the binary intervention design, enabling efficient step-by-step optimization. Second, we introduce Preprocessing Uncertainty (PU), a per-trial diagnostic that captures a dimension of instability complementary to model-based confidence. Third, we study Normalized Adaptive PGI (NA-PGI), a graph-structured regularizer that exploits the compositional structure of preprocessing interventions as one mitigation strategy with clear scope conditions.