Abstract
Do learned audio embeddings encode structure that nobody told them to encode? We probe four large pretrained audio models (AST, CLAP, BEATs-bio and BirdNET) with a downstream task none of them saw during training: recovering phylogenetic distance from species vocalizations. If the geometry of the embedding space tracks the tree of life, the representation is picking up something deeper than the labels the model was optimized for. We run Mantel tests across two independent radiations. In 32 marine mammal species (1,754 recordings from the Watkins Marine Mammal Sound Database) the foundation models recover strong phylogenetic signal within the 26 cetaceans (CLAP r=0.82, BEATs-bio r=0.82, AST r=0.74; all p<0.001), among the highest acoustic-phylogenetic correlations reported for any taxon. Hand-crafted MFCC features (105d) find nothing (r=0.040, p=0.338). The gap survives after PCA-projecting every embedding down to 105 dimensions, so it is not an artefact of representation size. It also survives a partial Mantel test controlling for dominant frequency (partial Mantel r=0.404, keeping 97% of the variance explained), so it is not just pitch in disguise. We repeat the analysis on 20 bird species using the Jetz et al. (2012) phylogeny, and this time add BirdNET, a classifier trained end-to-end on around 6,000 bird species. The general-purpose foundation models recover the signal again (AST r=0.55, CLAP r=0.52). The unexpected result is that neither BirdNET nor the bioacoustic BEATs-bio beat them (r around 0.32 to 0.36). Matching the training domain to the target taxon does not, by itself, help. Pretrained audio embeddings carry evolutionary information across two independent radiations, and domain-specific pretraining is not required for it to emerge.
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Sep 14, 2026cs.SD
What did an ancestral bird species sound like? Existing ancestral state reconstruction methods can infer low-dimensional traits such as morphological characters at internal nodes of a phylogenetic tree, but no one has tried to produce rich perceptual signals such as audio. Some of the challenges include inferred representations that are either too low-dimensional to decode or lie in non-generative feature spaces, so no method to date can produce ancestral audio. We introduce the first framework that generates plausible ancestral vocalizations. Our pipeline encodes bird recordings into a VAE latent space, learns a low-dimensional trait projection aligned with phylogenetic distances, performs ancestral inference in this trait space, and recovers decodable latents through an anchored inverse lift before emitting novel waveforms for each ancestral node. Because the entire pipeline stays within a decodable latent space, every internal node receives a genuinely new audio output representing plausible intermediate ancestral sounds unavailable to retrieval-based alternatives. Experiments on two phylogenetically distant bird clades, 21-species Tyrannidae and 19-species Paridae, show that our method is the only approach that simultaneously achieves genuine generation, phylogenetic consistency, and naturalistic audio quality across both datasets.
Tianyi Xu, Shrinaath Narasimhan, Evan Gorstein +3
Jun 12, 2026cs.LG
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 (
R2=0.76) while F0 is hardest to recover (
R2=0.33). By cross-referencing recoverability with per-species feature salience (NMI), we derive data-driven model selection guidance for bioacoustics.
Ines Nolasco, Jules Cauzinille, Marius Miron +8
Apr 30, 2026eess.AS
We show that pretrained acoustic embeddings classify elephant vocalisations at a level approaching that of end-to-end supervised neural networks, without any fine-tuning of the embedding model. This result is of practical importance because annotated bioacoustic data are scarce and costly to obtain, leaving conventional supervised approaches prone to overfitting and to poor generalisation under domain shift. A broad range of embedding models drawn from general audio, speech, and bioacoustic domains is evaluated, all of which are either out-of-domain (containing no bioacoustic data) or out-of-species (containing no elephant call data). The embedding networks themselves remain fixed; only the lightweight downstream classifiers, which include a linear model and several small neural networks, are trained. Among the models considered, Perch 2.0 achieves the best cross-validated classification performance, attaining AUCs of 0.849 on African bush elephant (Loxodonta africana) calls and 0.936 on Asian elephant (Elephas maximus) calls, with Perch 1.0 close behind. The best-performing system is within 2.2 % of an end-to-end supervised elephant call classification system. A layerwise analysis of pretrained transformer encoders, considered as embedding models, shows that intermediate representations outperform final-layer outputs. The second layer of both wav2vec2.0 and HuBERT encodes sufficient information for effective elephant call classification; truncation at this layer therefore preserves classification performance whilst retaining only approximately 10 % of the parameters of the full network. Such compact embedding networks are well suited to on-device processing where computational resources are limited.
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