Fast Computation of Latent Correlations

Atlas-based structural disconnectomes are associated to cognitive performance in brain tumors

BACKGROUND

Brain tumors are associated with impaired cognitive functioning, which may result from disruptions in brain structural connectivity. Estimating structural disconnections is a more advantageous representation of tumor impact and can be performed indirectly through normative brain atlases.

MATERIALS AND METHODS

Using a publicly available dataset of glioma and meningioma patient MRI scans and tumor masks, latent correlations were estimated between measures of structural disconnection and attention-based cognitive functioning. These measures included gray matter (GM) parcel damage, white matter tract (WMT) damage, GM parcel-to-parcel disconnections, and reaction time (RTI) as part of the Cambridge Neuropsychological Test Automated Battery (CANTAB) to assess attention.

RESULTS

Preprocessing pipelines with two different methods of minimizing the pathology impact on MRI normalization were utilized: cost function masking and lesion filling. The results across both pipelines were nearly consistent, with significant correlations mainly found between RTI measures and the damage to left inferior fronto-occipital and uncinate fasciculus, as well as the left prefrontal-visual disconnections.

CONCLUSIONS

This alludes to the importance of left-hemispheric prefrontal-visual coupling in attention-based tasks, particularly those involving object- and feature-based attention.

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering

In recent years, unsupervised analysis of microbiome data, such as microbial network analysis and clustering, has increased in popularity. Many new statistical and computational methods have been proposed for these tasks. This multiplicity of analysis strategies poses a challenge for researchers, who are often unsure which method(s) to use and might be tempted to try different methods on their dataset to look for the "best" ones. However, if only the best results are selectively reported, this may cause over-optimism: the "best" method is overly fitted to the specific dataset, and the results might be non-replicable on validation data. Such effects will ultimately hinder research progress. Yet so far, these topics have been given little attention in the context of unsupervised microbiome analysis. In our illustrative study, we aim to quantify over-optimism effects in this context. We model the approach of a hypothetical microbiome researcher who undertakes four unsupervised research tasks: clustering of bacterial genera, hub detection in microbial networks, differential microbial network analysis, and clustering of samples. While these tasks are unsupervised, the researcher might still have certain expectations as to what constitutes interesting results. We translate these expectations into concrete evaluation criteria that the hypothetical researcher might want to optimize. We then randomly split an exemplary dataset from the American Gut Project into discovery and validation sets multiple times. For each research task, multiple method combinations (e.g., methods for data normalization, network generation, and/or clustering) are tried on the discovery data, and the combination that yields the best result according to the evaluation criterion is chosen. While the hypothetical researcher might only report this result, we also apply the "best" method combination to the validation dataset. The results are then compared between discovery and validation data. In all four research tasks, there are notable over-optimism effects; the results on the validation data set are worse compared to the discovery data, averaged over multiple random splits into discovery/validation data. Our study thus highlights the importance of validation and replication in microbiome analysis to obtain reliable results and demonstrates that the issue of over-optimism goes beyond the context of statistical testing and fishing for significance.