Biology subjects

Lehmann, B.

Publications and source records attributed to Lehmann, B..

3 recordsLinked to original sources

bioRxiv2025

Power-to-power cross-frequency coupling as a novel approach for temporal lobe seizure detection and analysis

ObjectivePower-to-power cross-frequency coupling (CFC) is a novel method to index the dynamic spatio-temporal interactions between brain rhythms, including high frequency oscillations (HFOs). This research evaluates this promising methods capacity for seizure detection with intracranial EEG. Seizures can be conceptualized as composites of different electrographic patterns including (1) spike, (2) ripple-on-spike, and (3) ripple-on-oscillation. This study also performs a basic CFC analysis of each of these components which has potential to further the understanding of epileptogenic processes. MethodsIn this study, deep learning networks including Stacked Sparse Autoencoder (SSAE) and Long Short Term Memory (LSTM) are trained to detect seizures and help characterize CFC patterns for these three common seizure components. The analysis uses intracranial EEG (iEEG) records from the ieeg.org (Mayo Clinic files) database. Temporal Lobe Epilepsy (TLE) seizures (n = 120) from 26 patients were analyzed along with segments of background activity. Power-to-power coupling was calculated between all frequencies 1-250 Hz pairwise using the EEGLAB toolbox. CFC matrices of seizure and background activity were used as training or testing inputs to the autoencoder. ResultsThe trained network was able to recognize background and seizure segments (not used in training) with a sensitivity of 90.2%, specificity of 96.8% and overall accuracy of 93.4%. The three seizure components (spike, ripple-on-spike, ripple-on-oscillation) were also observed to have unique CFC signatures. ConclusionsThe results provide evidence both for (1) the relevance of power-to-power coupling (PPC) for TLE seizure detection in iEEG, as well as (2) there existing unique PPC signatures of three common seizure components.

neuroscience↗

bioRxiv2025

On ARGs, pedigrees, and genetic relatedness matrices

Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant settings. It is typically stored as a genetic relatedness matrix (GRM), whose elements are pairwise relatedness values between individuals. This relatedness has been defined in various contexts based on pedigree, genotype, phylogeny, coalescent times, and, recently, ancestral recombination graph (ARG). ARG-based GRMs have been found to better capture the structure of a population and improve association studies relative to the genotype GRM. However, calculating GRMs and further operations with them is fundamentally challenging due to inherent quadratic time and space complexity. Here, we first discuss the different definitions of relatedness in a unifying context, making use of the additive model of a quantitative trait to provide a definition of "branch relatedness" and the corresponding "branch GRM". We explore the relationship between branch relatedness and pedigree relatedness through a case study of French-Canadian individuals that have a known pedigree. Through the tree sequence encoding of an ARG, we then derive an efficient algorithm for computing products between the branch GRM and a general vector, without explicitly forming the branch GRM. This algorithm leverages the sparse encoding of genomes with the tree sequence and hence enables large-scale computations with the branch GRM. We demonstrate the power of this algorithm by developing a randomized principal components algorithm for tree sequences that easily scales to millions of genomes. All algorithms are implemented in the open source tskit Python package. Taken together, this work consolidates the different notions of relatedness as branch relatedness and by leveraging the tree sequence encoding of an ARG it provides efficient algorithms that enable computations with the branch GRM that scale to mega-scale genomic datasets.

genomics↗

bioRxiv2018

SciReader*: A Cloud-based Recommender System for Biomedical Literature

With the growing number of biomedical papers published each year, keeping up with relevant literature has become increasingly important, and yet more challenging. SciReader (www.scireader.com) is a cloud-based personalized recommender system that specifically aims to assist biomedical researchers and clinicians identify publications of interest to them. SciReader uses topic modeling and other machine learning algorithms to provide users with recommendations that are recent, relevant, and of high quality1.

scientific communication and education↗