arXiv subjects

Christian O'Reilly

Publications and source records attributed to Christian O'Reilly.

4 recordsLinked to original sources

arXiv2026

AMICA-Python: Adaptive Mixture Independent Component Analysis with Anderson Acceleration

Adaptive Mixture Independent Component Analysis (AMICA) is widely used in EEG research and has long been associated with strong empirical performance for blind source separation. Despite its impact, practical use has historically depended on a single Fortran implementation, accessed via the EEGLAB toolbox for MATLAB, limiting its accessibility for analytical pipelines not designed within the MATLAB ecosystem. Here we present AMICA-Python, a Python implementation of the AMICA algorithm, with a scikit-learn-conformant API designed for integration with existing scientific Python pipelines. The implementation follows the reference algorithm closely while adopting modern software engineering practices and an interface familiar to Python users. Additionally, we introduce an optional Anderson acceleration scheme that can dramatically reduce the time to convergence for this relatively slow algorithm. To evaluate numerical agreement and practical performance, we benchmarked AMICA-Python against the reference Fortran implementation on 14 open EEG recordings. After averaging 3 runs of each implementation on all 14 recordings, AMICA-Python closely matched the reference, with a median final normalized log-likelihoods of 11.572 for both the Fortran and Python implementations, and a negligible median relative absolute difference of only $1.07\times10^{-8}$ when normalized by the absolute Fortran value. Runtime was also competitive. Relative to the reference implementation, AMICA-Python was 17.7\% faster, while the Anderson-accelerated variant was 34.1\% faster. AMICA-Python reproduces the reference implementation to high numerical precision with competitive runtime, while making AMICA available through a more accessible and extensible Python interface.

cs.LG↗

arXiv2025

SACA: Selective Attention-Based Clustering Algorithm

Clustering algorithms are fundamental tools across many fields, with density-based methods offering particular advantages in identifying arbitrarily shaped clusters and handling noise. However, their effectiveness is often limited by the requirement of critical parameter tuning by users, which typically requires significant domain expertise. This paper introduces a novel density-based clustering algorithm loosely inspired by the concept of selective attention, designed to minimize reliance on parameter tuning for most applications. The proposed method computes an adaptive threshold to exclude sparsely distributed points and outliers, constructs an initial cluster framework, and subsequently reintegrates the filtered points to refine the final results. Extensive experiments on diverse benchmark datasets demonstrate the robustness, accuracy, and ease of use of the proposed approach, establishing it as a powerful alternative to conventional density-based clustering techniques.

cs.LG↗

arXiv2025

A Reliable and Efficient Detection Pipeline for Rodent Ultrasonic Vocalizations

Analyzing ultrasonic vocalizations (USVs) is crucial for understanding rodents' affective states and social behaviors, but the manual analysis is time-consuming and prone to errors. Automated USV detection systems have been developed to address these challenges. Yet, these systems often rely on machine learning and fail to generalize effectively to new datasets. To tackle these shortcomings, we introduce ContourUSV, an efficient automated system for detecting USVs from audio recordings. Our pipeline includes spectrogram generation, cleaning, pre-processing, contour detection, post-processing, and evaluation against manual annotations. To ensure robustness and reliability, we compared ContourUSV with three state-of-the-art systems using an existing open-access USV dataset (USVSEG) and a second dataset we are releasing publicly along with this paper. On average, across the two datasets, ContourUSV outperformed the other three systems with a 1.51x improvement in precision, 1.17x in recall, 1.80x in F1 score, and 1.49x in specificity while achieving an average speedup of 117.07x.

cs.SD↗

arXiv2025

Deep Jansen-Rit Parameter Inference for Model-Driven Analysis of Brain Activity

Accurately modeling effective connectivity (EC) is critical for understanding how the brain processes and integrates sensory information. Yet, it remains a formidable challenge due to complex neural dynamics and noisy measurements such as those obtained from the electroencephalogram (EEG). Model-driven EC infers local (within a brain region) and global (between brain regions) EC parameters by fitting a generative model of neural activity onto experimental data. This approach offers a promising route for various applications, including investigating neurodevelopmental disorders. However, current approaches fail to scale to whole-brain analyses and are highly noise-sensitive. In this work, we employ three deep-learning architectures--a transformer, a long short-term memory (LSTM) network, and a convolutional neural network and bidirectional LSTM (CNN-BiLSTM) network--for inverse modeling and compare their performance with simulation-based inference in estimating the Jansen-Rit neural mass model (JR-NMM) parameters from simulated EEG data under various noise conditions. We demonstrate a reliable estimation of key local parameters, such as synaptic gains and time constants. However, other parameters like local JR-NMM connectivity cannot be evaluated reliably from evoked-related potentials (ERP). We also conduct a sensitivity analysis to characterize the influence of JR-NMM parameters on ERP and evaluate their learnability. Our results show the feasibility of deep-learning approaches to estimate the subset of learnable JR-NMM parameters.

q-bio.NC↗