Classifying bioacoustic data without individual call annotations using temporal convolutional networks and feature extractors

Passive Acoustic Monitoring (PAM) is an efficient and non-invasive method for surveying ecosystems at a reduced cost. Typically, autonomous recorders allow the acquisition of vast bioacoustic datasets which are then analyzed. However, power consumption and data storage are both scarce and limit the duration of acquisition campaigns. To address this issue, we propose a smart PAM system which allows the in-situ analysis of the soundscape by embedding a classifier directly onto an AudioMoth microcontroller. Specifically, we propose an optimized yet simple 1D Convolutional Neural Network (1D-CNN) to classify the raw audio. The model focuses on the specific call of Scopoli Shearwater seabirds (endangered species) and is trained on a real-world dataset with a classification accuracy of 91% (balanced accuracy of 89%). We also propose a process to optimize the model to fit the severe resource constraints of the AudioMoth, achieving a ~10kB RAM memory footprint and 20ms inference time. Finally, we present an open-source tutorial of our model optimization and export strategy which can be used for embedding models beyond the scope of our study. Our modified version of the AudioMoth firmware adds two functions: (F1) which selectively records data when the target species has been detected and (F2) which logs the continuous classification results in real time. This work intends to facilitate the conception of intelligent sensors, enhancing the efficiency and scalability of bioacoustic monitoring campaigns.

Bioacoustic recognition requires fine-grained acoustic understanding to distinguish similar-sounding species. However, many large-scale data repositories such as iNaturalist are weakly annotated, often with only a single positive species label per recording, making supervised learning particularly challenging. Inspired by advances in computer vision, recent approaches have shifted toward self-supervised learning to capture the underlying structure of audio without relying on exhaustive annotations. In particular, masked autoencoders (MAE) have shown strong transferability on massive audio corpora, yet their effectiveness in more modest bioacoustic settings remains underexplored. In this work, we conduct a systematic study of MAE pretraining for species classification on iNatSounds, analyzing the impacts of pretraining data scale, domain specificity, data curation, and transfer strategies. Consistent with prior work, we find that models pretrained on diverse general audio data achieve the best transfer performance on iNatSounds. Contrary to observations from large-scale audio benchmarks, we find that (1) additional masked reconstruction pretraining on domain-specific data provides limited benefits and may even degrade performance relative to off-the-shelf models, and (2) selective data filtering offers a negligible advantage when the overall data scale is limited. Our results indicate that, in moderate-sized fine-grained bioacoustic settings, pretraining scale dominates objective design. These findings further clarify when MAE-based pretraining is effective and provide practical guidance for model selection under limited supervision.

Passive acoustic monitoring can measure biodiversity at larger scales, but time--frequency annotation of animal vocalizations is expensive, site-specific, and difficult to sustain at scale. We present a label-efficient sound detection framework that combines masked audio pretraining with a lightweight detector on mel spectrograms, then further improves robustness through iterative self-training on unlabeled audio. We first pretrain a ViT-based encoder on unlabeled recordings via masked reconstruction and transfer the encoder to a detection backbone. To better separate animal sounds from confounding background, we add a box-level contrastive loss that pulls matched event regions together while pushing noisy negatives apart. We then apply a two-stage pseudo-labeling curriculum to exploit large unlabeled pools without additional annotation. We evaluate the performance on two ecologically distinct domains: tropical rainforest soundscapes (Indonesia) and bird vocalizations in Mediterranean habitats (Spain). On both domains, masked audio pretraining and contrastive learning consistently improve time--frequency detection under temporal and cross-site distribution shift, and self-training yields further gains in out-of-distribution performance. On the rainforest domain, MAST with self-training achieves +0.22 mAP and +0.24 F1 over the strongest baseline under cross-site shift. On the bird domain, self-training achieves +0.12 mAP and +0.10 F1 over the strongest baseline under cross-site shift. Overall, our results show that MAST can effectively extend self-supervised audio representations from clip-level tasks to robust box-level localization across diverse bioacoustic settings, providing a practical path for biodiversity monitoring with limited labels.