BioSEN: A Bio-acoustic Signal Enhancement Network for Animal Vocalizations

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.

Animals hear and vocalize across frequency ranges that differ substantially from humans, often extending into the ultrasonic domain. Yet most computational bioacoustics systems rely on audio models pre-trained at 16 kHz, restricting their usable bandwidth to the 0-8 kHz baseband and discarding higher-frequency information present in many bioacoustic recordings. We investigate a multi-band encoding framework that decomposes the full spectrum of animal calls into band features and fuses them into a unified representation. Similarity analyses on models show that certain encoders produce decorrelated band embeddings that improve class separation after fusion. Classification experiments on three bioacoustic datasets using eight pre-trained models and five fusion strategies show that fused representations consistently outperform the baseband and time-expansion baselines on two datasets, showing the potential of multi-band methods for full-spectrum encoding of animal calls.

Bioacoustic recordings are often degraded by ambient noise, which complicates the analysis of weak or noise-overlapped vocalizations. Convolutional neural networks, particularly U-Net architectures, have shown a strong denoising performance in speech and music processing. However, their direct application to bioacoustic signals is limited by the scarcity of clean training data. To address this issue, we propose a training set synthesis approach and develop a supervised denoising model that predicts a complex ratio mask in the time-frequency domain. The model leverages ridges, or frequency contours, that represent the fundamental frequency together with one or more harmonic partial components of vocalizations. These ridges are used both for the synthesis of training sets and to design a loss function that assigns higher weights to the ridge regions (ridge-guided loss function). This weighting step helps the network better preserve vocalization details during denoising. As a case study, we evaluate our approach using ultrasonic vocalizations (USVs) recordings of house mice, which are widely studied in behavioral biology and neuroscience. In actual field recordings, the proposed method enhances fundamental and harmonic partial ridge tracking compared to our previous signal-processing approach. In addition, a classifier trained on denoised data improves USV classification on out-of-sample, noisy recordings from wild and domesticated mice compared to classifiers trained on noisy recordings. Our proposed method also substantially improves the scale-invariant signal-to-distortion ratio on synthetic testing data across a wide range of input signal-to-noise ratios. Although we focus on USVs, the proposed approach should be broadly applicable to other bioacoustic signals with trackable ridges, and thus enables ridgebased training set synthesis and denoising.