bioRxiv Science⌕ Search

Biology subjects

Sidorov, L.

Publications and source records attributed to Sidorov, L..

2 recordsLinked to original sources

Data aggregation strategies for a P300 speller: decoding models, epoch averaging, cross-subject ensembles, and multi-channel models

Accurate detection of P300 event-related potentials from electroencephalography (EEG) re-mains challenging for small numbers of trials due to low signal-to-noise ratios and substantial inter-subject variability. This study presents a systematic comparison of data aggregation strate-gies for improving P300 classification, evaluated on a 10-subject dataset using two convolutional neural network architectures (EEGNet and BaseCNN) and a support vector machine (SVM). We compared: (1) subject-specific and pooled general models for single trials; (2) epoch aver-aging with 5 and 10 stimuli repetitions; (3) multi-channel models where subjects corresponded to different input channels; (4) cross-subject averaging; (5) mixed (uncontrolled) averaging; (6) a combined approach with K trials per subject across all participants; and (7) time-shifted channels from extended single-trial epochs. Decoding performance was quantified using the Information Transfer Rate (ITR), computed for binary classification accuracy. We found that single-trial ITR was unpractical (0.15-0.64 bits/trial), whereas controlled aggregation improved the performance. The combined cross-subject approach with K = 3 trials per participant (30 channels) achieves the highest ITR with multi-channel EEGNet: 0.95 bits/aggregated decision in the no-aperture recordings and 0.97 bits/aggregated decision on Aperture data, approaching the theoretical binary-classification limit for the aggregated decision. Controlled cross-subject averaging consistently outperformed random trial mixing, and multi-channel architectures out-performed simple averaging when inter-subject structure was preserved. These findings con-tribute to improving P300 decoding and implementing multi-subject brain-computer interfaces (BCIs).

neuroscience↗

Chromosome-level genome assembly of the sponge Halisarca dujardinii

Halisarca dujardinii is a marine sponge known for its ability to completely regenerate via cell reaggregation. Here we present the first chromosome-level genome assembly of H. dujardinii, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C data. The final assembly spans 226.5 Mbp and is organized into 21 chromosome-scale scaffolds, representing the full nuclear genome, with an assembly N50 of 10.1 Mbp. In addition, we report the complete mitochondrial genome for H. dujardinii, assembled as a circular molecule and annotated to contain 14 protein-coding genes. We provide a comprehensive genome annotation comprising 14,565 nuclear protein-coding genes, of which 85.6% are functionally annotated, along with repetitive elements and non-coding RNAs. Transcript models were refined using extensive bulk and single-cell RNA sequencing data, enabling accurate annotation of 3' untranslated regions. This new genomic resource provides a valuable foundation for investigating the molecular basis of sponge regeneration, as well as for comparative studies of sponge evolution and marine biology.

genomics↗