Transferable Models for Bioacoustics with Human Language Supervision

Passive acoustic monitoring offers a scalable, non-invasive method for tracking global biodiversity and anthropogenic impacts on species. Although deep learning has become a vital tool for processing this data, current models are inflexible, typically cover only a handful of species, and are limited by data scarcity. In this work, we propose BioLingual, a new model for bioacoustics based on contrastive language-audio pretraining. We first aggregate bioacoustic archives into a language-audio dataset, called AnimalSpeak, with over a million audio-caption pairs holding information on species, vocalization context, and animal behavior. After training on this dataset to connect language and audio representations, our model can identify over a thousand species' calls across taxa, complete bioacoustic tasks zero-shot, and retrieve animal vocalization recordings from natural text queries. When fine-tuned, BioLingual sets a new state-of-the-art on nine tasks in the Benchmark of Animal Sounds. Given its broad taxa coverage and ability to be flexibly queried in human language, we believe this model opens new paradigms in ecological monitoring and research, including free-text search on the world's acoustic monitoring archives. We open-source our models, dataset, and code.

Interpreting multi-variate models with setPCA

Principal Component Analysis (PCA) and other multi-variate models are often used in the analysis of "omics" data. These models contain much information which is currently neither easily accessible nor interpretable. Here we present an algorithmic method which has been developed to integrate this information with existing databases of background knowledge, stored in the form of known sets (for instance genesets or pathways). To make this accessible we have produced a Graphical User Interface (GUI) in Matlab which allows the overlay of known set information onto the loadings plot and thus improves the interpretability of the multi-variate model. For each known set the optimal convex hull, covering a subset of elements from the known set, is found through a search algorithm and displayed. In this paper we discuss two main topics; the details of the search algorithm for the optimal convex hull for this problem and the GUI interface which is freely available for download for academic use.

Efficient Learning of Optimal Markov Network Topology with k-Tree Modeling

The seminal work of Chow and Liu (1968) shows that approximation of a finite probabilistic system by Markov trees can achieve the minimum information loss with the topology of a maximum spanning tree. Our current paper generalizes the result to Markov networks of tree width $\leq k$, for every fixed $k\geq 2$. In particular, we prove that approximation of a finite probabilistic system with such Markov networks has the minimum information loss when the network topology is achieved with a maximum spanning $k$-tree. While constructing a maximum spanning $k$-tree is intractable for even $k=2$, we show that polynomial algorithms can be ensured by a sufficient condition accommodated by many meaningful applications. In particular, we prove an efficient algorithm for learning the optimal topology of higher order correlations among random variables that belong to an underlying linear structure.