arXiv subjects

Panu Somervuo

Publications and source records attributed to Panu Somervuo.

3 recordsLinked to original sources

arXiv2026

ForestIR: Physics-Informed Forest Sound Simulation for Array-Based Bioacoustic Remote Sensing

Microphone array-based passive acoustic monitoring is increasingly used for biodiversity sensing in forests. However, design and evaluation of array systems and configurations remains difficult since field recordings are costly, difficult to reproduce, and provide limited control over forest and atmospheric conditions. We present ForestIR, a physics-informed and reproducible simulation framework that links forest and environmental conditions to microphone-array recordings for bioacoustic remote sensing. Through a more realistic sound propagation method and a systematic control over array design and environmental factors, ForestIR provides a practical simulation framework for optimizing array-based monitoring systems, especially for sound source localization purposes. ForestIR generates source-microphone impulse responses (IRs) under user-controlled forest and atmospheric conditions, and renders synthetic array recordings by convolving test signals with controlled background noise. We evaluate and demonstrate realistic features of ForestIR through experiments based on localization sensitivity to forest layout and atmospheric conditions, and also comparison between simulated IRs with sine-sweep IR measurements from a field experiment. ForestIR provides a practical way to test how forest and ground conditions, atmospheric state, and array geometry affect bioacoustic localization, and can support microphone-array design, robustness testing, and synthetic-data generation for passive acoustic monitoring.

eess.AS↗

arXiv2026

Mixture-Constrained Max Pooling Improves Separation-Based Bird Species Classification

Bird species classification from field recordings remains challenging due to overlapping vocalizations and incomplete species labels. We study source separation as a preprocessing for bird species classification to improve multi-species detection. Specifically, we employ an ensemble of two separators, FTRNN and TF-Locoformer, both trained with mixture invariant training (MixIT). To address the false positive gain caused by separation errors in separated outputs, we propose mixture-constrained max pooling (MCM), which clips the predicted probability from each separated channel based on the corresponding species probability in the original mixture. The classifier is applied to each separated output and the original mixture independently, and MCM aggregates the predictions into a final per-species probability. Experiments on two real-world datasets show that the ensemble outperforms individual separators and MCM outperforms standard max pooling across multiple metrics, and reveal that separation leads to both true positive gain for present species and false positive gain for absent species.

eess.AS↗

arXiv2025

OptimOTU: Taxonomically aware OTU clustering with optimized thresholds and a bioinformatics workflow for metabarcoding data

To turn environmentally derived metabarcoding data into community matrices for ecological analysis, sequences must first be clustered into operational taxonomic units (OTUs). This task is particularly complex for data including large numbers of taxa with incomplete reference libraries. OptimOTU offers a taxonomically aware approach to OTU clustering. It uses a set of taxonomically identified reference sequences to choose optimal genetic distance thresholds for grouping each ancestor taxon into clusters which most closely match its descendant taxa. Then, query sequences are clustered according to preliminary taxonomic identifications and the optimized thresholds for their ancestor taxon. The process follows the taxonomic hierarchy, resulting in a full taxonomic classification of all the query sequences into named taxonomic groups as well as placeholder "pseudotaxa" which accommodate the sequences that could not be classified to a named taxon at the corresponding rank. The OptimOTU clustering algorithm is implemented as an R package, with computationally intensive steps implemented in C++ for speed, and incorporating open-source libraries for pairwise sequence alignment. Distances may also be calculated externally, and may be read from a UNIX pipe, allowing clustering of large datasets where the full distance matrix would be inconveniently large to store in memory. The OptimOTU bioinformatics pipeline includes a full workflow for paired-end Illumina sequencing data that incorporates quality filtering, denoising, artifact removal, taxonomic classification, and OTU clustering with OptimOTU. The OptimOTU pipeline is developed for use on high performance computing clusters, and scales to datasets with millions of reads per sample, and tens of thousands of samples.

q-bio.QM↗