Promoting cross-modal representations to improve multimodal foundation models for physiological signals

Many healthcare applications are inherently multimodal, involving several physiological signals. As sensors for these signals become more common, improving machine learning methods for multimodal healthcare data is crucial. Pretraining foundation models is a promising avenue for success. However, methods for developing foundation models in healthcare are still in early exploration and it is unclear which pretraining strategies are most effective given the diversity of physiological signals. This is partly due to challenges in multimodal health data: obtaining data across many patients is difficult and costly, there is a lot of inter-subject variability, and modalities are often heterogeneously informative across downstream tasks. Here, we explore these challenges in the PhysioNet 2018 dataset. We use a masked autoencoding objective to pretrain a multimodal model. We show that the model learns representations that can be linearly probed for a diverse set of downstream tasks. We hypothesize that cross-modal reconstruction objectives are important for successful multimodal training, as they encourage the model to integrate information across modalities. We demonstrate that modality dropout in the input space improves performance across downstream tasks. We also find that late-fusion models pretrained with contrastive learning objectives are less effective across multiple tasks. Finally, we analyze the model's representations, showing that attention weights become more cross-modal and temporally aligned with our pretraining strategy. The learned embeddings also become more distributed in terms of the modalities encoded by each unit. Overall, our work demonstrates the utility of multimodal foundation models with health data, even across diverse physiological data sources. We further argue that explicit methods for inducing cross-modality may enhance multimodal pretraining strategies.

Generalizable autoregressive modeling of time series through functional narratives

Time series data are inherently functions of time, yet current transformers often learn time series by modeling them as mere concatenations of time periods, overlooking their functional properties. In this work, we propose a novel objective for transformers that learn time series by re-interpreting them as temporal functions. We build an alternative sequence of time series by constructing degradation operators of different intensity in the functional space, creating augmented variants of the original sample that are abstracted or simplified to different degrees. Based on the new set of generated sequence, we train an autoregressive transformer that progressively recovers the original sample from the most simplified variant. Analogous to the next word prediction task in languages that learns narratives by connecting different words, our autoregressive transformer aims to learn the Narratives of Time Series (NoTS) by connecting different functions in time. Theoretically, we justify the construction of the alternative sequence through its advantages in approximating functions. When learning time series data with transformers, constructing sequences of temporal functions allows for a broader class of approximable functions (e.g., differentiation) compared to sequences of time periods, leading to a 26\% performance improvement in synthetic feature regression experiments. Experimentally, we validate NoTS in 3 different tasks across 22 real-world datasets, where we show that NoTS significantly outperforms other pre-training methods by up to 6\%. Additionally, combining NoTS on top of existing transformer architectures can consistently boost the performance. Our results demonstrate the potential of NoTS as a general-purpose dynamic learner, offering a viable alternative for developing foundation models for time series analysis.

Efficient Source-Free Time-Series Adaptation via Parameter Subspace Disentanglement

In this paper, we propose a framework for efficient Source-Free Domain Adaptation (SFDA) in the context of time-series, focusing on enhancing both parameter efficiency and data-sample utilization. Our approach introduces an improved paradigm for source-model preparation and target-side adaptation, aiming to enhance training efficiency during target adaptation. Specifically, we reparameterize the source model's weights in a Tucker-style decomposed manner, factorizing the model into a compact form during the source model preparation phase. During target-side adaptation, only a subset of these decomposed factors is fine-tuned, leading to significant improvements in training efficiency. We demonstrate using PAC Bayesian analysis that this selective fine-tuning strategy implicitly regularizes the adaptation process by constraining the model's learning capacity. Furthermore, this re-parameterization reduces the overall model size and enhances inference efficiency, making the approach particularly well suited for resource-constrained devices. Additionally, we demonstrate that our framework is compatible with various SFDA methods and achieves significant computational efficiency, reducing the number of fine-tuned parameters and inference overhead in terms of MACs by over 90% while maintaining model performance.

Model-driven Heart Rate Estimation and Heart Murmur Detection based on Phonocardiogram

Acoustic signals are crucial for health monitoring, particularly heart sounds which provide essential data like heart rate and detect cardiac anomalies such as murmurs. This study utilizes a publicly available phonocardiogram (PCG) dataset to estimate heart rate using model-driven methods and extends the best-performing model to a multi-task learning (MTL) framework for simultaneous heart rate estimation and murmur detection. Heart rate estimates are derived using a sliding window technique on heart sound snippets, analyzed with a combination of acoustic features (Mel spectrogram, cepstral coefficients, power spectral density, root mean square energy). Our findings indicate that a 2D convolutional neural network (\textbf{\texttt{2dCNN}}) is most effective for heart rate estimation, achieving a mean absolute error (MAE) of 1.312 bpm. We systematically investigate the impact of different feature combinations and find that utilizing all four features yields the best results. The MTL model (\textbf{\texttt{2dCNN-MTL}}) achieves accuracy over 95% in murmur detection, surpassing existing models, while maintaining an MAE of 1.636 bpm in heart rate estimation, satisfying the requirements stated by Association for the Advancement of Medical Instrumentation (AAMI).

Pre-Trained Foundation Model representations to uncover Breathing patterns in Speech

The process of human speech production involves coordinated respiratory action to elicit acoustic speech signals. Typically, speech is produced when air is forced from the lungs and is modulated by the vocal tract, where such actions are interspersed by moments of breathing in air (inhalation) to refill the lungs again. Respiratory rate (RR) is a vital metric that is used to assess the overall health, fitness, and general well-being of an individual. Existing approaches to measure RR (number of breaths one takes in a minute) are performed using specialized equipment or training. Studies have demonstrated that machine learning algorithms can be used to estimate RR using bio-sensor signals as input. Speech-based estimation of RR can offer an effective approach to measure the vital metric without requiring any specialized equipment or sensors. This work investigates a machine learning based approach to estimate RR from speech segments obtained from subjects speaking to a close-talking microphone device. Data were collected from N=26 individuals, where the groundtruth RR was obtained through commercial grade chest-belts and then manually corrected for any errors. A convolutional long-short term memory network (Conv-LSTM) is proposed to estimate respiration time-series data from the speech signal. We demonstrate that the use of pre-trained representations obtained from a foundation model, such as Wav2Vec2, can be used to estimate respiration-time-series with low root-mean-squared error and high correlation coefficient, when compared with the baseline. The model-driven time series can be used to estimate $RR$ with a low mean absolute error (MAE) ~ 1.6 breaths/min.

Investigating salient representations and label Variance in Dimensional Speech Emotion Analysis

Representations derived from models such as BERT (Bidirectional Encoder Representations from Transformers) and HuBERT (Hidden units BERT), have helped to achieve state-of-the-art performance in dimensional speech emotion recognition. Despite their large dimensionality, and even though these representations are not tailored for emotion recognition tasks, they are frequently used to train large speech emotion models with high memory and computational costs. In this work, we show that there exist lower-dimensional subspaces within the these pre-trained representational spaces that offer a reduction in downstream model complexity without sacrificing performance on emotion estimation. In addition, we model label uncertainty in the form of grader opinion variance, and demonstrate that such information can improve the models generalization capacity and robustness. Finally, we compare the robustness of the emotion models against acoustic degradations and observed that the reduced dimensional representations were able to retain the performance similar to the full-dimensional representations without significant regression in dimensional emotion performance.

Frequency-Aware Masked Autoencoders for Multimodal Pretraining on Biosignals

Leveraging multimodal information from biosignals is vital for building a comprehensive representation of people's physical and mental states. However, multimodal biosignals often exhibit substantial distributional shifts between pretraining and inference datasets, stemming from changes in task specification or variations in modality compositions. To achieve effective pretraining in the presence of potential distributional shifts, we propose a frequency-aware masked autoencoder ($\texttt{bio}$FAME) that learns to parameterize the representation of biosignals in the frequency space. $\texttt{bio}$FAME incorporates a frequency-aware transformer, which leverages a fixed-size Fourier-based operator for global token mixing, independent of the length and sampling rate of inputs. To maintain the frequency components within each input channel, we further employ a frequency-maintain pretraining strategy that performs masked autoencoding in the latent space. The resulting architecture effectively utilizes multimodal information during pretraining, and can be seamlessly adapted to diverse tasks and modalities at test time, regardless of input size and order. We evaluated our approach on a diverse set of transfer experiments on unimodal time series, achieving an average of $\uparrow$5.5% improvement in classification accuracy over the previous state-of-the-art. Furthermore, we demonstrated that our architecture is robust in modality mismatch scenarios, including unpredicted modality dropout or substitution, proving its practical utility in real-world applications. Code will be available soon.

Pre-trained Model Representations and their Robustness against Noise for Speech Emotion Analysis

Pre-trained model representations have demonstrated state-of-the-art performance in speech recognition, natural language processing, and other applications. Speech models, such as Bidirectional Encoder Representations from Transformers (BERT) and Hidden units BERT (HuBERT), have enabled generating lexical and acoustic representations to benefit speech recognition applications. We investigated the use of pre-trained model representations for estimating dimensional emotions, such as activation, valence, and dominance, from speech. We observed that while valence may rely heavily on lexical representations, activation and dominance rely mostly on acoustic information. In this work, we used multi-modal fusion representations from pre-trained models to generate state-of-the-art speech emotion estimation, and we showed a 100% and 30% relative improvement in concordance correlation coefficient (CCC) on valence estimation compared to standard acoustic and lexical baselines. Finally, we investigated the robustness of pre-trained model representations against noise and reverberation degradation and noticed that lexical and acoustic representations are impacted differently. We discovered that lexical representations are more robust to distortions compared to acoustic representations, and demonstrated that knowledge distillation from a multi-modal model helps to improve the noise-robustness of acoustic-based models.

Speech Emotion: Investigating Model Representations, Multi-Task Learning and Knowledge Distillation

Estimating dimensional emotions, such as activation, valence and dominance, from acoustic speech signals has been widely explored over the past few years. While accurate estimation of activation and dominance from speech seem to be possible, the same for valence remains challenging. Previous research has shown that the use of lexical information can improve valence estimation performance. Lexical information can be obtained from pre-trained acoustic models, where the learned representations can improve valence estimation from speech. We investigate the use of pre-trained model representations to improve valence estimation from acoustic speech signal. We also explore fusion of representations to improve emotion estimation across all three emotion dimensions: activation, valence and dominance. Additionally, we investigate if representations from pre-trained models can be distilled into models trained with low-level features, resulting in models with a less number of parameters. We show that fusion of pre-trained model embeddings result in a 79% relative improvement in concordance correlation coefficient CCC on valence estimation compared to standard acoustic feature baseline (mel-filterbank energies), while distillation from pre-trained model embeddings to lower-dimensional representations yielded a relative 12% improvement. Such performance gains were observed over two evaluation sets, indicating that our proposed architecture generalizes across those evaluation sets. We report new state-of-the-art "text-free" acoustic-only dimensional emotion estimation $CCC$ values on two MSP-Podcast evaluation sets.

Subject-Aware Contrastive Learning for Biosignals

Datasets for biosignals, such as electroencephalogram (EEG) and electrocardiogram (ECG), often have noisy labels and have limited number of subjects (<100). To handle these challenges, we propose a self-supervised approach based on contrastive learning to model biosignals with a reduced reliance on labeled data and with fewer subjects. In this regime of limited labels and subjects, intersubject variability negatively impacts model performance. Thus, we introduce subject-aware learning through (1) a subject-specific contrastive loss, and (2) an adversarial training to promote subject-invariance during the self-supervised learning. We also develop a number of time-series data augmentation techniques to be used with the contrastive loss for biosignals. Our method is evaluated on publicly available datasets of two different biosignals with different tasks: EEG decoding and ECG anomaly detection. The embeddings learned using self-supervision yield competitive classification results compared to entirely supervised methods. We show that subject-invariance improves representation quality for these tasks, and observe that subject-specific loss increases performance when fine-tuning with supervised labels.