Organizations: University of Wisconsin–Madison · 2Massachusetts Institute of Technology
Abstract
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.
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.
Brain-to-audio reconstruction is limited by \emph{prior domination}: when a pretrained generator is conditioned on a weak neural signal, it produces realistic but stimulus-inaccurate audio. We introduce RAG-Audio, which decodes fMRI into a semantic audio embedding, retrieves a matching real-audio exemplar, and initializes the frozen generator's sampling trajectory from that exemplar while retaining the decoded embedding as conditioning. On Brain2Music, RAG-Audio improves 10-way stimulus identification from 0.14--0.18 for direct generation, near the 0.10 chance level, to 0.40--0.43, comparable to retrieval. It also reduces Fréchet Audio Distance by roughly an order of magnitude, from 13.49 to 1.25 for AudioLDM. RAG-Audio approaches nearest-neighbor retrieval in identification while remaining generative; its higher FAD is expected because retrieval directly replays real audio. An autoregressive negative control, which lacks an initializable latent trajectory, shows no comparable gain, attributing the improvement to trajectory initialization. These results suggest that retrieval-guided initialization can mitigate prior domination in brain-to-audio generation.
Continuous Variational Autoencoders (VAEs) serve as the fundamental continuous tokenizer for modern neural audio generation systems, enabling high-fidelity reconstruction while providing a compact, smooth latent space for downstream generative priors. However, continuous VAEs face a fundamental conflict among compression rate, reconstruction fidelity, and latent space topology, which we formalize as the Rate-Distortion-Regularity Trilemma. This trilemma stems from a topological mismatch: the isotropic Gaussian prior in standard VAEs imposes a flat latent geometry that fails to accommodate audio's hierarchical nature, where low-frequency components are structured and compressible while high-frequency components are stochastic and incompressible, leading to disordered information packing in which crucial semantic features are interleaved with high-entropy noise. To address this challenge, we propose Structured Topology-Aware Regularization (STAR), a general training strategy that reshapes latent space geometry by imposing a growth-based constraint field, routing structural and textural information into channel subspaces with matching capacities. STAR is applicable to any VAE architecture and effectively resolves the trilemma, as demonstrated in CNN-based VAEs. We further present STAR-VAE, which combines STAR with a hybrid CNN-Mamba architecture for local feature extraction and linear-complexity global context modeling, and STAR-Gen, an LLM-based Flow Matching framework that leverages STAR-VAE's structured latent space for high-fidelity generation without vector quantization artifacts. Experiments across diverse audio domains show that STAR-VAE achieves state-of-the-art reconstruction fidelity and enhanced semantic information preservation, while the structured latent space improves both traditional diffusion models and STAR-Gen for text-to-audio generation.