Confidence of a k-Nearest Neighbors Python Algorithm for the 3D Visualization of Sedimentary Porous Media

In a previous paper, the authors implemented a machine learning k-nearest neighbors (KNN) algorithm and Python libraries to create two 3D interactive models of the stratigraphic architecture of the Quaternary onshore Llobregat River Delta (NE Spain) for groundwater exploration purposes. The main limitation of this previous paper was its lack of routines for evaluating the confidence of the 3D models. Building from the previous paper, this paper refines the programming code and introduces an additional algorithm to evaluate the confidence of the KNN predictions. A variant of the Similarity Ratio method was used to quantify the KNN prediction confidence. This variant used weights that were inversely proportional to the distance between each grain-size class and the inferred point to work out a value that played the role of similarity. While the KNN algorithm and Python libraries demonstrated their efficacy for obtaining 3D models of the stratigraphic arrangement of sedimentary porous media, the KNN prediction confidence verified the certainty of the 3D models. In the Llobregat River Delta, the KNN prediction confidence at each prospecting depth was a function of the available data density at that depth. As expected, the KNN prediction confidence decreased according to the decreasing data density at lower depths. The obtained average-weighted confidence was in the 0.44−0.53 range for gravel bodies at prospecting depths in the 12.7−72.4 m b.s.l. range and was in the 0.42−0.55 range for coarse sand bodies at prospecting depths in the 4.6−83.9 m b.s.l. range. In a couple of cases, spurious average-weighted confidences of 0.29 in one gravel body and 0.30 in one coarse sand body were obtained. These figures were interpreted as the result of the quite different weights of neighbors from different grain-size classes at short distances. The KNN algorithm confidence has proven its suitability for identifying these anomalous results in the supposedly well-depurated grain-size database used in this study. The introduced KNN algorithm confidence quantifies the reliability of the 3D interactive models, which is a necessary stage to make decisions in economic and environmental geology. In the Llobregat River Delta, this quantification clearly improves groundwater exploration predictability.Research Project PID2020-114381GB-100 of the Spanish Ministry of Science and Innovation, Research Project 101086497 of the Horizon Europe Framework Programme HORIZON-CL6-2022-GOVERNANCE-01-07, Research Groups and Projects of the Generalitat Valenciana from the University of Alicante (CTMA-IGA), and Research Groups FQM-343 and RNM-188 of the Junta de Andalucía

Enhancing the functional content of protein interaction networks

Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we explore the use of the concept of common neighborhood similarity (CNS), which is a form of local structure in networks, to address these issues. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of S. cerevisiae interactions, and a set of 136 GO terms, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the $HC.cont$ measure proposed here performs particularly well for this task. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures, especially $HC.cont$, to prune out noisy edges and introduce new links between functionally related proteins

A mechanistic model of connector hubs, modularity, and cognition

The human brain network is modular--comprised of communities of tightly interconnected nodes. This network contains local hubs, which have many connections within their own communities, and connector hubs, which have connections diversely distributed across communities. A mechanistic understanding of these hubs and how they support cognition has not been demonstrated. Here, we leveraged individual differences in hub connectivity and cognition. We show that a model of hub connectivity accurately predicts the cognitive performance of 476 individuals in four distinct tasks. Moreover, there is a general optimal network structure for cognitive performance--individuals with diversely connected hubs and consequent modular brain networks exhibit increased cognitive performance, regardless of the task. Critically, we find evidence consistent with a mechanistic model in which connector hubs tune the connectivity of their neighbors to be more modular while allowing for task appropriate information integration across communities, which increases global modularity and cognitive performance