Corrigendum: Building an open source classifier for the neonatal EEG background: a systematic feature-based approach from expert scoring to clinical visualization.

[This corrects the article DOI: 10.3389/fnhum.2021.675154.].

Building an Open Source Classifier for the Neonatal EEG Background: A Systematic Feature-Based Approach From Expert Scoring to Clinical Visualization.

Neonatal brain monitoring in the neonatal intensive care units (NICU) requires a continuous review of the spontaneous cortical activity, i.e., the electroencephalograph (EEG) background activity. This needs development of bedside methods for an automated assessment of the EEG background activity. In this paper, we present development of the key components of a neonatal EEG background classifier, starting from the visual background scoring to classifier design, and finally to possible bedside visualization of the classifier results. A dataset with 13,200 5-minute EEG epochs (8-16 channels) from 27 infants with birth asphyxia was used for classifier training after scoring by two independent experts. We tested three classifier designs based on 98 computational features, and their performance was assessed with respect to scoring system, pre- and post-processing of labels and outputs, choice of channels, and visualization in monitor displays. The optimal solution achieved an overall classification accuracy of 97% with a range across subjects of 81-100%. We identified a set of 23 features that make the classifier highly robust to the choice of channels and missing data due to artefact rejection. Our results showed that an automated bedside classifier of EEG background is achievable, and we publish the full classifier algorithm to allow further clinical replication and validation studies.

Explicit Correlation Amplifiers for Finding Outlier Correlations in Deterministic Subquadratic Time.

We derandomize Valiant's (J ACM 62, Article 13, 2015) subquadratic-time algorithm for finding outlier correlations in binary data. This demonstrates that it is possible to perform a deterministic subquadratic-time similarity join of high dimensionality. Our derandomized algorithm gives deterministic subquadratic scaling essentially for the same parameter range as Valiant's randomized algorithm, but the precise constants we save over quadratic scaling are more modest. Our main technical tool for derandomization is an explicit family of correlation amplifiers built via a family of zigzag-product expanders by Reingold et al. (Ann Math 155(1):157-187, 2002). We say that a function f : { - 1 , 1 } d → { - 1 , 1 } D is a correlation amplifier with threshold 0 ≤ τ ≤ 1 , error γ ≥ 1 , and strength p an even positive integer if for all pairs of vectors x , y ∈ { - 1 , 1 } d it holds that (i) | ⟨ x , y ⟩ | < τ d implies | ⟨ f ( x ) , f ( y ) ⟩ | ≤ ( τ γ ) p D ; and (ii) | ⟨ x , y ⟩ | ≥ τ d implies ⟨ x , y ⟩ γ d p D ≤ ⟨ f ( x ) , f ( y ) ⟩ ≤ γ ⟨ x , y ⟩ d p D .

Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.

A Naive Bayes classifier for protein function prediction.

A Naive Bayes classifier tool is presented for annotating proteins on the basis of amino acid motifs, cellular localization and protein-protein interactions. Annotations take the form of posterior probabilities within the Molecular Function hierarchy of the Gene Ontology (GO). Experiments with the data available for yeast, Saccharomyces cerevisiae, show that our prediction method can yield a relatively high level of accuracy. Several apparent challenges and possibilities for future developments are also discussed. A common approach to functional characterization is to use sequence similarities at varying levels, by utilizing several existing databases and local alignment/identification algorithms. Such an approach is typically quite labor-intensive when performed by an expert in a manual fashion. Integration of several sources of information is in this context generally considered as the only possibility to obtain valuable predictions with practical implications. However, some improvements in the prediction accuracy of the molecular functions, and thereby also savings in the computational effort, can be achieved by restricting attention to only those data sources that involve a higher degree of specificity. We employ here a Naive Bayes model in order to provide probabilistic predictions, and to enable a computationally efficient approach to data integration.