Adaptive Loss Balancing for Multi-Task Bioacoustic Classification of Bird Species and Call Types
Authors: Paria Vali Zadeh, Sven Tomforde
Organizations: Kiel University, Kiel, Germany
Abstract
Reliable analysis of bird vocalisations in passive acoustic monitoring requires models handling multiple, imbalanced annotation targets. We extend BirdCallNet for joint species and call-type classification on the long-tailed WiWa dataset and investigate how task-loss balancing interacts with pretrained representations and adaptation depth. We evaluate four bird-domain encoders, ConvNeXtBS, EAT, BirdMAE, and ProtoCLR, with separate species and call-type heads under linear probing, attentive probing, and full fine-tuning. A manually tuned fixed objective is compared with homoscedastic uncertainty weighting and Dynamic Weight Averaging across all three adaptation regimes, while GradNorm is evaluated only under full fine-tuning. Results indicate that the factorised multi-task formulation yields the most consistent improvements over the combined single-task baseline for call-type recognition, while its effect on species recognition depends on the adaptation regime. Full fine-tuning is not consistently optimal: ConvNeXtBS achieves the highest mean species performance under linear probing, whereas BirdMAE provides the strongest call-type performance under attentive probing. Adaptive weighting benefits species recognition more consistently than call-type recognition. Uncertainty weighting is particularly effective for species recognition under attentive probing, whereas Dynamic Weight Averaging is generally stronger for the same task under full fine-tuning. GradNorm achieves competitive call-type performance for selected backbones but consistently underperforms other weighting strategies for species recognition and incurs higher computational and memory costs. Overall, the preferred loss-balancing strategy depends on the backbone, adaptation regime, and target task, while frozen-backbone adaptation can provide a more favourable performance-efficiency trade-off than end-to-end fine-tuning.
Passive acoustic monitoring enables large-scale observation of wildlife, but most bioacoustic classifiers only predict species presence in a time window without localizing vocalizations precisely in time or frequency, limiting downstream analyses. We formulate bird vocalization detection as an object detection task on spectrograms and train YOLO11 models to localize bird calls in dense tropical soundscapes from Singapore. We additionally introduce an open-source browser-based annotation tool and propose Intersection over Minimum (IoMin), an evaluation metric that better handles ambiguous acoustic boundaries than standard IoU and is better suited to the problem at hand. The best YOLO model nearly doubles baseline performance on in-distribution soundscapes from Singapore (81.8% vs. 42.1% IoMin@50 F1-score) while still outperforming the baseline on unseen out-of-distribution recordings from Hawaii (58.6% vs. 48.6%). These results suggest that object detection frameworks are a promising approach to time-frequency localization of animal vocalizations in complex soundscapes.
Passive acoustic monitoring is an important tool for biodiversity assessment and wildlife conservation because it supports continuous and non-invasive monitoring of species across large spatial and temporal scales. Robust monitoring remains challenging because many datasets contain sparse positive labels, where species presences may be confirmed while unannotated species cannot be assumed absent. In this work, we study transfer learning under sparse positive labels using BirdCLEF+ 2026 as a target benchmark and BirdCLEF 2021, iNatSounds, WABAD, and BirdSet as external bioacoustic sources. We introduce a multi-source reliability framework that models heterogeneous bioacoustic datasets as distinct supervision sources with differing reliability. Our approach achieves 0.584 macro average precision and 0.860 macro AUC on public BirdCLEF+ 2026 validation labels while outperforming naive source pooling strategies. The strongest gains arise from passive acoustic monitoring datasets and biologically informed source selection. Our findings suggest that transfer learning in bioacoustics is fundamentally a weak supervision and negative transfer problem.
Bioacoustic call-type classification relies on costly expert annotation. Active learning can reduce this burden by selecting a small batch of segments for expert annotation and using the labeled segments for training the classifier. The setting is hard: the target calls are extremely sparse and the call-type distribution is long-tailed, so a tight budget must be spent on the few rare, informative segments. We propose BADGE-Greedy-DPP, a deterministic batch selector that greedily adds the segment whose BADGE gradient embedding most enlarges the volume spanned by the batch; because this log-volume objective is submodular, the greedy rule guarantees a batch value at least a (1-1/e) fraction of the optimum of this objective, a guarantee not provided by BADGE's existing k-means++ and MCMC DPP sampling heuristics. There is also a temporal granularity mismatch in the task. The acquisition function scores whole segments, yet the informative frames inside them are few. Uniform averaging therefore washes them out. We show that the BADGE construction naturally addresses this mismatch when applied frame-wise, as prediction residuals weight the aggregated pseudo-gradient, so confidently predicted no-call frames contribute little while a single uncertain rare-call frame can still set the segment's direction. Across 10 runs on a sparse, imbalanced hyena call-type dataset, BADGE-Greedy-DPP achieves the best overall and rare-call-type performance among all compared query strategies, including MFFT, the strongest non-BADGE baseline, and the two vanilla BADGE traversals.
Shiqi Zhang, Marius Faiß, Ariana Strandburg-Peshkin +1