Bio-Inspired Self-Supervised Learning for Wrist-worn Accelerometer Data
Authors: Prithviraj Tarale, Kiet Chu, Abhishek Varghese, Kai-Chun Liu, Maxwell A. Xu, Mohit Iyyer, Sunghoon I. Lee
Organizations: College of Information and Computer Sciences, University of Massachusetts, Amherst, United States · Stevens Institute of Technology, Hoboken, United States · Google Health, Seattle, United States · Department of Computer Science, University of Maryland, College Park, United States
Wearable accelerometers enable large-scale health monitoring, yet learning robust human-activity representations has been constrained by scarce labeled data. While self-supervised learning offers a remedy, existing methods treat sensor streams as unstructured time series, overlooking the underlying biological structure of human movement, a factor we argue is critical for effective Human Activity Recognition (HAR). We introduce a novel tokenization strategy grounded in the submovement theory of motor control, which posits that continuous wrist motion is composed of elementary basis functions called submovements. We define our token as the movement segment, a computationally tractable unit of motion composed of a finite sequence of submovements. By pretraining a Transformer encoder via masked reconstruction of these tokens, we shift the learning focus from local waveform morphology to high-level structural and temporal organization. Pretrained on the NHANES corpus (approximately 28k hours; 11k participants), our representations outperform strong wearable SSL baselines across six subject-disjoint HAR benchmarks. Code and pretrained weights are available at https://prithvitarale.github.io/biopm-site/.
Figures & tables
Figure 1: Bio-PM Representation Learning. We (i) tokenize accelerometry into movement-aligned segments, (ii) pretrain by modeling temporal relation across segments with a Transformer under masked reconstruction, and (iii) transfer the frozen encoder to downstream HAR for linear probing.
Figure 2: Illustration of the proposed tokenization strategy, which uses “type 2” movement segments defined via acceleration zero-crossings.
Model
UMH
PAMAP
WISDM
MHEALTH
WHARF
HAD
Avg.
Generic Time Series FMs
Chronos (8.3M)
0.23±0.02
0.56±0.04
0.53±0.02
0.63±0.05
0.25±0.04
0.34±0.07
0.42 (n=6)
Moment (35M)
0.48±0.04
0.64±0.07
0.68±0.03
0.66±0.06
0.37±0.14
0.72±0.04
0.59 (n=6)
Controlled (NHANES pretrained)
Mask-Recon (1.4M)
0.39±0.04
0.61±0.05
0.58±0.02
0.62±0.06
0.30±0.09
0.33±0.07
0.47 (n=6)
AugPred (10.5M)
0.40±0.03
0.59±0.07
0.60±0.02
0.67±0.08
0.31±0.07
0.69±0.03
0.54 (n=6)
Table 1: Macro-F1 (mean ± std) on six subject-disjoint HAR benchmarks using frozen representations and multinomial logistic regression. All wearable SSL baselines are pretrained on the same NHANES upstream corpus under a matched transfer protocol; generic time-series foundation models are included only as contextual reference and are not pretrained on NHANES.
Model
UMH
PAMAP
WISDM
MHEALTH
WHARF
HAD
Avg.
Bio-PM
0.57±0.05
0.69±0.16
0.70±0.03
0.80±0.08
0.41±0.03
0.75±0.06
0.65±0.07
Bio-PM w/o Gravity
0.48±0.04
0.60±0.04
0.67±0.02
0.70±0.04
0.33±0.08
0.55±0.05
0.56±0.05
Bio-PM w. Naive Tokenization
0.39±0.04
0.61±0.05
0.58±0.02
0.62±0.06
0.30±0.09
0.33±0.07
0.47±0.06
Bio-PM w/o Pretraining
0.45±0.13
0.59±0.14
0.58±0.02
0.67±0.12
0.41±0.11
0.61±0.09
0.55±0.10
Table 2: Macro-F1 (mean ± std. dev.) under controlled ablations isolating key design choices: gravity, tokenization, and pretraining.
Figure 3: Downstream Macro-F1 across varying labeled-subject budgets. Bio-PM maintains strong performance in low-resource regimes and scales more effectively than controlled SSL baselines as training data increases.
Figure 4: Next-token prediction accuracy on unseen token transitions using Bio-PM embeddings. HAD instability reflects its much smaller transition set ( ≈ 250 vs. 2.3k–27k).
Figure 5: Robustness analyses of Bio-PM against (a) additive sensor noise and (b) high-pass cutoff frequency for gravity separation.
Appendix figures & tables17 assets
Supplementary material from the paper’s appendix.
Appendix
Figure 6: End-to-end conversion from raw wrist accelerometer signals to fixed-length movement-segment tokens: gravity separation via filtering, zero-crossing boundary detection, segmentation, and resampling to a common token length, along with token metadata used for sequence modeling.
Masking Rate
PAMAP
MHEALTH
WHARF
HAD
Avg
25%
0.69±0.12
0.80±0.08
0.40±0.02
0.71±0.06
0.65 (n=4)
50%
0.71±0.12
0.80±0.08
0.42±0.03
0.73±0.06
0.67 (n=4)
75%
0.69±0.13
0.79±0.10
0.41±0.05
0.71±0.07
0.65 (n=4)
Appendix
Table 3: Effect of masking rate on linear-probe Macro-F1 for Bio-PM
Model Size
PAMAP
MHEALTH
WHARF
HAD
Avg
1.4M
0.71±0.12
0.80±0.08
0.42±0.03
0.73±0.06
0.67 (n=4)
6M
0.69±0.13
0.82±0.1
0.43±0.05
0.71±0.08
0.66 (n=4)
13M
0.69±0.13
0.82±0.09
0.44±0.05
0.76±0.04
0.68 (n=4)
Appendix
Table 4: Effect of model size on linear-probe Macro-F1 for Bio-PM
Figure 7: Upstream masked-region reconstruction quality under different masking rates. Violin plots show the distribution of reconstruction performance evaluated only on masked regions for MR25/50/75 using MSE, RMSE, MAE, Pearson r , and NRMSE. Boxes indicate median and interquartile range (whiskers: 1.5 × IQR). Numbers below each subplot report mean μ , standard deviation σ , and outlier fraction. Increasing masking increases error (MSE 0.085→0.145 , MAE 0.128→0.177 ) and reduces correlation ( r=0.760→0.518 ), while NRMSE stays roughly constant ( ≈0.081 – 0.083 ).
Figure 8: Qualitative masked-region reconstruction examples. Each panel visualizes the masked-movement-segment pretraining task on a representative 1D channel: the top subplot shows the input with masked spans removed (gray bands denote masked regions), and the bottom subplot overlays the ground-truth signal with the model reconstruction. Pearson r (shown in titles where available) summarizes agreement between reconstruction and ground truth on masked movement segments. These examples illustrate the range of outcomes from near-perfect recovery (e.g., r≈0.99 ) to clear failure modes ( r≈0.12 ), where the model under-reconstructs sharp transients and high-amplitude bursts within masked segments.
Dataset
Setting
#Sub
#Classes
Hz
References
NHANES Accelerometer
Free-living
≈ 11k
–
80
( Centers for Disease Control and Prevention (CDC), 2010 )
UMH
Semi-natural
25
29
100
( Casilari et al., 2024 )
PAMAP
Lab protocol
8
8
100
( Reiss, 2012 )
WISDM (Actitracker)
Semi-natural
51
18
20
( Weiss, 2019 )
MHEALTH
Scripted protocol
10
11
50
( Banos et al., 2014b ; Banos et al., 2014a ; Banos et al., 2015 )
WHARF
In-home scripted
17
14
32
( Bruno et al., 2014 )
Appendix
Table 5: Summary of downstream HAR datasets.
Dataset
Classes
AugPred
TF-C
Transformer
Bio-PM
( K )
(1024-d)
(512-d)
(128-d)
(1028-d)
UMH
29
29,725
14,877
3,741
29,841
PAMAP
8
8,200
4,104
1,032
8,232
MHEALTH
11
11,275
5,643
1,419
11,319
HAD
27
27,675
13,851
3,483
27,783
Appendix
Table 6: Number of learned parameters in linear probing. Only logistic regression weights are trained; encoder weights remain frozen.
Figure 9: Confusion matrices for Bio-PM (left) vs TF-C (right) on the Mhealth dataset.
Figure 10: Confusion matrices for Bio-PM (left) vs TF-C (right) on the WISDM dataset.
Figure 11: Confusion matrices for Bio-PM (left) vs TF-C (right) on the UMAHand dataset.
Figure 12: Confusion matrices for Bio-PM (left) vs TF-C (right) on the HAD dataset.
Figure 13: Confusion matrices for Bio-PM (left) vs TF-C (right) on the WHARF dataset.
Figure 14: Confusion matrices for Bio-PM (left) vs Bio-PM without gravity (right) on the Mhealth dataset.
Figure 15: Confusion matrices for Bio-PM (left) vs Bio-PM without gravity (right) on the WISDM dataset.
Figure 16: Confusion matrices for Bio-PM (left) vs Bio-PM without gravity (right) on the UMAHand dataset.
Figure 17: Confusion matrices for Bio-PM (left) vs Bio-PM without gravity (right) on the HAD dataset.
Figure 18: Confusion matrices for Bio-PM (left) vs Bio-PM without gravity (right) on the WHARF dataset.
Human Activity Recognition (HAR) from wearable sensors supports broad healthcare and behavior science applications. However, data heterogeneity and the scarcity of labeled data limit its real-world generalization. Recent advances in self-supervised learning (SSL) in vision and language domains have shown strong capability for learning generalizable representations from unlabeled data. Yet, few studies have systematically compared the generalization performance of SSL methods or explored how to adapt them for generalizable HAR. To address these gaps, we present BenchHAR, a unified framework for evaluating the generalization capability of SSL methods for sensor-based HAR on unseen target distributions. BenchHAR curates a large-scale dataset (~258K samples) and evaluates eight representative SSL methods across 12 encoder-classifier architectures. Our results reveal that existing SSL methods struggle to achieve satisfactory generalization performance. We find that: (1) For HAR models, the hybrid paradigm (combining reconstruction and contrastive pretraining) achieves the best overall performance. The CNN encoder exhibits the strongest ability to learn generalizable representations, while more expressive classifier architectures further improve generalization. (2) For data scale, increasing the amount of pretraining data from downstream activity classes consistently improves generalization, while adding more labeled data yields limited gains. Interestingly, incorporating unlabeled data from non-downstream activity classes does not improve generalization. (3) Sensor data collected from custom-grade devices generalizes better than that from research-grade devices, and data from limb transfers more effectively to trunk positions. BenchHAR provides a unified benchmark and actionable insights for generalizable sensor-based HAR systems. Our code is available at https://github.com/saiketa/HAR-Bench.
Yize Cai, Rui Feng, Anlan Yu +2
The Hong Kong University of Science and Technology (Guangzhou) · Peking University · Singapore-MIT Alliance for Research and Technology
A major challenge in wearable device activity recognition is the heterogeneity across datasets in sensor placement, channel count, sampling rate and subjects. Moreover, the motion patterns that distinguish activities often appear as subtle, scale-specific variations within otherwise similar waveforms. As a result, raw signals are often ambiguous, and models trained on them tend to rely on cues specific to a particular sensor setup or participant, which limits both cross-dataset transfer and generalization to unseen participants. Addressing this requires representations that preserve such activity-relevant, scale-specific variation. We introduce W-JEPA, a self-supervised framework that exploits the multiscale structure of inertial motion and leverages a joint-embedding predictive architecture, by organizing windows into a fixed grid of wavelet tokens indexed by scale, sensor axis, and time. These wavelet tokens help expose activity-specific detail within broadly similar raw signals, and serve as the units of masked latent prediction. W-JEPA predicts masked token representations supplied by an exponential-moving-average (EMA) target encoder. Because recovering a masked token requires relating motion at one scale and axis to motion at other scales and axes, the model learns the cross-scale, cross-axis structure of human movement. Across six wearable activity benchmarks, W-JEPA outperforms state-of-the-art methods under random-window splits and remains the strongest when subjects are held out, improving average macro-F1 by 8.7 percentage points over the strongest published baseline. These results indicate that physically grounded multiscale tokenization, combined together with latent predictive learning, provides a promising foundation for transferable representations of heterogeneous wearable inertial data.
Yogesh Prabhu, Loki Natarajan, Jingjing Zou
Department of Computer Science and Engineering, University of California San Diego (UCSD). · Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego (UCSD). · UCSD Shiley-Marcos Alzheimer’s Disease Research Center. +1
Despite the ubiquity of sensors in wearable and mobile devices and the abundance of human movement data they generate, translating unlabeled recordings into foundational motion models remains an open challenge. Self-supervised learning (SSL) has alleviated the need for costly annotations, yet existing approaches leave the global structure of large-scale motion data largely untapped, relying on randomly sampled batches and local comparisons that become particularly problematic for in-the-wild inertial data dominated by stationary, low-variance behaviors. Here we introduce Morphological Contrastive Learning (MorphCL), a self-supervised pretraining framework that uses structure-aware grouping to inject explicit modeling of global structure into inertial-based SSL approaches. Building on two well-established pillars of motion analysis, the discovery of motion primitives, or motifs, and domain-specific feature descriptors, we show that MorphCL substantially improves linear probing and finetuning results of learned encoders by up to 15 percentage points in F1-score. In a comparison with existing foundation models, we demonstrate that MorphCL-pretrained encoders match or surpass them models in linear probing performance while trained on 4600× less data. Qualitative analysis of the resulting embedding spaces further reveals morphologically meaningful cluster structure, with improved separation of kinematically similar activity classes.
Marius Bock, Yuwei Zhang, Juergen Gall +3
University of Bonn · University of Cambridge · Lamarr Institute for Machine Learning and Artificial Intelligence +1