HPP-Voice: A Large-Scale Evaluation of Speech Embeddings for Multi-Phenotypic Classification

Human speech contains paralinguistic cues that reflect a speaker's physiological and neurological state, potentially enabling non-invasive detection of various medical phenotypes. We introduce the Human Phenotype Project Voice corpus (HPP-Voice): a dataset of 7,188 recordings in which Hebrew-speaking adults count for 30 seconds, with each speaker linked to up to 15 potentially voice-related phenotypes spanning respiratory, sleep, mental health, metabolic, immune, and neurological conditions. We present a systematic comparison of 14 modern speech embedding models, where modern speech embeddings from these 30-second counting tasks outperform MFCCs and demographics for downstream health condition classifications. We found that embedding learned from a speaker identification model can predict objectively measured moderate to severe sleep apnea in males with an AUC of 0.64 $\pm$ 0.03, while MFCC and demographic features led to AUCs of 0.56 $\pm$ 0.02 and 0.57 $\pm$ 0.02, respectively. Additionally, our results reveal gender-specific patterns in model effectiveness across different medical domains. For males, speaker identification and diarization models consistently outperformed speech foundation models for respiratory conditions (e.g., asthma: 0.61 $\pm$ 0.03 vs. 0.56 $\pm$ 0.02) and sleep-related conditions (insomnia: 0.65 $\pm$ 0.04 vs. 0.59 $\pm$ 0.05). For females, speaker diarization models performed best for smoking status (0.61 $\pm$ 0.02 vs 0.55 $\pm$ 0.02), while Hebrew-specific models performed best (0.59 $\pm$ 0.02 vs. 0.58 $\pm$ 0.02) in classifying anxiety compared to speech foundation models. Our findings provide evidence that a simple counting task can support large-scale, multi-phenotypic voice screening and highlight which embedding families generalize best to specific conditions, insights that can guide future vocal biomarker research and clinical deployment.

Improving Diseases Predictions Utilizing External Bio-Banks

Machine learning has been successfully used in critical domains, such as medicine. However, extracting meaningful insights from biomedical data is often constrained by the lack of their available disease labels. In this research, we demonstrate how machine learning can be leveraged to enhance explainability and uncover biologically meaningful associations, even when predictive improvements in disease modeling are limited. We train LightGBM models from scratch on our dataset (10K) to impute metabolomics features and apply them to the UK Biobank (UKBB) for downstream analysis. The imputed metabolomics features are then used in survival analysis to assess their impact on disease-related risk factors. As a result, our approach successfully identified biologically relevant connections that were not previously known to the predictive models. Additionally, we applied a genome-wide association study (GWAS) on key metabolomics features, revealing a link between vascular dementia and smoking. Although being a well-established epidemiological relationship, this link was not embedded in the model's training data, which validated the method's ability to extract meaningful signals. Furthermore, by integrating survival models as inputs in the 10K data, we uncovered associations between metabolic substances and obesity, demonstrating the ability to infer disease risk for future patients without requiring direct outcome labels. These findings highlight the potential of leveraging external bio-banks to extract valuable biomedical insights, even in data-limited scenarios. Our results demonstrate that machine learning models trained on smaller datasets can still be used to uncover real biological associations when carefully integrated with survival analysis and genetic studies.