Sara Keen

Jiacheng Shen, Masato Hagiwara, Milad Alizadeh et al.

Large language models have shown strong performance on broad-domain knowledge and reasoning benchmarks, but it remains unclear how well language models handle specialized animal-related knowledge under a unified closed-book evaluation protocol. We introduce BAGEL, a benchmark for evaluating animal knowledge expertise in language models. BAGEL is constructed from diverse scientific and reference sources, including bioRxiv, Global Biotic Interactions, Xeno-canto, and Wikipedia, using a combination of curated examples and automatically generated closed-book question-answer pairs. The benchmark covers multiple aspects of animal knowledge, including taxonomy, morphology, habitat, behavior, vocalization, geographic distribution, and species interactions. By focusing on closed-book evaluation, BAGEL measures animal-related knowledge of models without external retrieval at inference time. BAGEL further supports fine-grained analysis across source domains, taxonomic groups, and knowledge categories, enabling a more precise characterization of model strengths and systematic failure modes. Our benchmark provides a new testbed for studying domain-specific knowledge generalization in language models and for improving their reliability in biodiversity-related applications.

David Robinson, Marius Miron, Masato Hagiwara et al.

Large language models (LLMs) prompted with text and audio have achieved state-of-the-art performance across various auditory tasks, including speech, music, and general audio, showing emergent abilities on unseen tasks. However, their potential has yet to be fully demonstrated in bioacoustics tasks, such as detecting animal vocalizations in large recordings, classifying rare and endangered species, and labeling context and behavior -- tasks that are crucial for conservation, biodiversity monitoring, and animal behavior studies. In this work, we present NatureLM-audio, the first audio-language foundation model specifically designed for bioacoustics. Our training dataset consists of carefully curated text-audio pairs spanning bioacoustics, speech, and music, designed to address the field's limited availability of annotated data. We demonstrate successful transfer of learned representations from music and speech to bioacoustics, and our model shows promising generalization to unseen taxa and tasks. We evaluate NatureLM-audio on a novel benchmark (BEANS-Zero) and it sets a new state of the art on several bioacoustics tasks, including zero-shot classification of unseen species. To advance bioacoustics research, we release our model weights, benchmark data, and open-source the code for training and benchmark data generation and model training.

Marius Miron, David Robinson, Masato Hagiwara et al.

Probing heads map the representations learned from audio by a machine learning model to downstream task labels and are a key component in evaluating representation learning. Most bioacoustic benchmarks use a fixed, low-capacity probe, such as a linear layer on the final encoder layer. While this standardization enables model comparisons, it may bias results by overlooking the interaction between encoder features and probe design. In this work, we systematically study different probing strategies across two bioacoustic benchmarks, BEANs and BirdSet. We evaluate last- and multi-layer probing, across linear and attention probes. We show that larger probe heads that leverage time information have superior performance. Our results suggest that current benchmarks may misrepresent encoder quality when relying on a last-layer probing setup. Multi-layer probing improves downstream task performance across all tested models, while attention probing has superior performance to linear probing for transformer models.

Louis Mahon, Benjamin Hoffman, Logan James et al.

We propose a method for accurately detecting bioacoustic sound events that is robust to overlapping events, a common issue in domains such as ethology, ecology and conservation. While standard methods employ a frame-based, multi-label approach, we introduce an onset-based detection method which we name Voxaboxen. It takes inspiration from object detection methods in computer vision, but simultaneously takes advantage of recent advances in self-supervised audio encoders. For each time window, Voxaboxen predicts whether it contains the start of a vocalization and how long the vocalization is. It also does the same in reverse, predicting whether each window contains the end of a vocalization, and how long ago it started. The two resulting sets of bounding boxes are then fused using a graph-matching algorithm. We also release a new dataset designed to measure performance on detecting overlapping vocalizations. This consists of recordings of zebra finches annotated with temporally-strong labels and showing frequent overlaps. We test Voxaboxen on seven existing data sets and on our new data set. We compare Voxaboxen to natural baselines and existing sound event detection methods and demonstrate SotA results. Further experiments show that improvements are robust to frequent vocalization overlap.

Marius Miron, David Robinson, Milad Alizadeh et al.

Bioacoustics, the study of sounds produced by living organisms, plays a vital role in conservation, biodiversity monitoring, and behavioral studies. Many tasks in this field, such as species, individual, and behavior classification and detection, are well-suited to machine learning. However, they often suffer from limited annotated data, highlighting the need for a general-purpose bioacoustic encoder capable of extracting useful representations for diverse downstream tasks. Such encoders have been proposed before, but are often limited in scope due to a focus on a narrow range of species (typically birds), and a reliance on a single model architecture or training paradigm. Moreover, they are usually evaluated on a small set of tasks and datasets. In this work, we present a large-scale empirical study that covers aspects of bioacoustics that are relevant to research but have previously been scarcely considered: training data diversity and scale, model architectures and training recipes, and the breadth of evaluation tasks and datasets. We obtain encoders that are state-of-the-art on the existing and proposed benchmarks. We also identify what matters for training these encoders, such that this work can be extended when more data are available or better architectures are proposed. Specifically, across 26 datasets with tasks including species classification, detection, individual ID, and vocal repertoire discovery, we find self-supervised pre-training followed by supervised post-training on a mixed bioacoustics + general-audio corpus yields the strongest in- and out-of-distribution performance. We show the importance of data diversity in both stages. To support ongoing research and application, we will release the model checkpoints.