Multi-layer attentive probing improves transfer of audio representations for bioacoustics

Pretrained audio embeddings are standard in bioacoustics, yet little is known about which acoustic features these models encode, nor which are useful for a given task. This hinders transparency and limits extension to rare species or data-scarce domains. Here we reveal which speech-like features are encoded in bioacoustic representations. Using the 88~eGeMAPS features across six taxonomic groups, we apply linear and nonlinear regression probes to quantify which acoustic properties each model captures. Results confirm a ``no free lunch'' pattern: no single model captures the full feature space. A concatenated embedding achieves the highest performance, suggesting complementary acoustic space coverage across models. Loudness features are best encoded ($R^2 = 0.76$) while F0 is hardest to recover ($R^2 = 0.33$). By cross-referencing recoverability with per-species feature salience (NMI), we derive data-driven model selection guidance for bioacoustics.

Probing is widely used to study which features can be decoded from language model representations. However, the common decoding probe approach has two limitations that we aim to solve with our new encoding probe approach: contributions of different features to model representations cannot be directly compared, and feature correlations can affect probing results. We present an Encoding Probe that reverses this direction and reconstructs internal representations of models using interpretable features. We evaluate this method on text and speech transformer models, using feature sets spanning acoustics, phonetics, syntax, lexicon, and speaker identity. Our results suggest that speaker-related effects vary strongly across different training objectives and datasets, while syntactic and lexical features contribute independently to reconstruction. These results show that the Encoding Probe provides a complementary perspective on interpreting model representations beyond decodability.

Masked token prediction has emerged as a powerful pre-training objective across language, vision, and speech, offering the potential to unify these diverse modalities through a single pre-training task. However, its application for general audio understanding remains underexplored, with BEATs being the only notable example. BEATs has seen limited modifications due to the absence of open-source pre-training code. Furthermore, BEATs was trained only on AudioSet, restricting its broader downstream applicability. To address these gaps, we present OpenBEATs, an open-source framework that extends BEATs via multi-domain audio pre-training. We conduct comprehensive evaluations across six types of tasks, twenty five datasets, and three audio domains, including audio reasoning tasks such as audio question answering, entailment, and captioning. OpenBEATs achieves state-of-the-art performance on six bioacoustics datasets, two environmental sound datasets and five reasoning datasets, performing better than models exceeding a billion parameters at one-fourth their parameter size. These results demonstrate the effectiveness of multi-domain datasets and masked token prediction task to learn general-purpose audio representations. To promote further research and reproducibility, we release all pre-training and evaluation code, pretrained and fine-tuned checkpoints, and training logs at https://github.com/Shikhar-S/OpenBEATs