Criminal networks analysis in missing data scenarios through graph distances.
Ontology highlight
ABSTRACT:
SUBMITTER: Ficara A
PROVIDER: S-EPMC8357088 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Compared to other types of social networks, criminal networks present particularly hard challenges, due to their strong resilience to disruption, which poses severe hurdles to Law-Enforcement Agencies (LEAs). Herein, we borrow methods and tools from Social Network Analysis (SNA) to (i) unveil the structure and organization of Sicilian Mafia gangs, based on two real-world datasets, and (ii) gain insights as to how to efficiently reduce the Largest Connected Component (LCC) of two networks derived from them. Mafia networks have peculiar features in terms of the links distribution and strength, which makes them very different from other social networks, and extremely robust to exogenous perturbations. Analysts also face difficulties in collecting reliable datasets that accurately describe the gangs' internal structure and their relationships with the external world, which is why earlier studies are largely qualitative, elusive and incomplete. An added value of our work is the generation of two real-world datasets, based on raw data extracted from juridical acts, relating to a Mafia organization that operated in Sicily during the first decade of 2000s. We created two different networks, capturing phone calls and physical meetings, respectively. Our analysis simulated different intervention procedures: (i) arresting one criminal at a time (sequential node removal); and (ii) police raids (node block removal). In both the sequential, and the node block removal intervention procedures, the Betweenness centrality was the most effective strategy in prioritizing the nodes to be removed. For instance, when targeting the top 5% nodes with the largest Betweenness centrality, our simulations suggest a reduction of up to 70% in the size of the LCC. We also identified that, due the peculiar type of interactions in criminal networks (namely, the distribution of the interactions' frequency), no significant differences exist between weighted and unweighted network analysis. Our work has significant practical applications for perturbing the operations of criminal and terrorist networks.
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Project description:BackgroundEpigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias downstream results.ResultsWe show that accounting for genetic variation using a modified reference genome or a de novo assembled genome can alter histone H3K4me1 and H3K27ac ChIP-seq peak calls either by creating new personal peaks or by the loss of reference peaks. Using permissive cutoffs, modified reference genomes are found to alter approximately 1% of peak calls while de novo assembled genomes alter up to 5% of peaks. We also show statistically significant differences in the amount of reads observed in regions associated with the new, altered, and unchanged peaks. We report that short insertions and deletions (indels), followed by single nucleotide variants (SNVs), have the highest probability of modifying peak calls. We show that using a graph personalized genome represents a reasonable compromise between modified reference genomes and de novo assembled genomes. We demonstrate that altered peaks have a genomic distribution typical of other peaks.ConclusionsAnalyzing epigenomic datasets with personalized and graph genomes allows the recovery of new peaks enriched for indels and SNVs. These altered peaks are more likely to differ between individuals and, as such, could be relevant in the study of various human phenotypes.
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Project description:Missing data are frequently encountered in molecular phylogenetics, but there has been no accurate distance imputation method available for distance-based phylogenetic reconstruction. The general framework for distance imputation is to explore tree space and distance values to find an optimal combination of output tree and imputed distances. Here I develop a least-square method coupled with multivariate optimization to impute multiple missing distance in a distance matrix or from a set of aligned sequences with missing genes so that some sequences share no homologous sites (whose distances therefore need to be imputed). I show that phylogenetic trees can be inferred from distance matrices with about 10% of distances missing, and the accuracy of the resulting phylogenetic tree is almost as good as the tree from full information. The new method has the advantage over a recently published one in that it does not assume a molecular clock and is more accurate (comparable to maximum likelihood method based on simulated sequences). I have implemented the function in DAMBE software, which is freely available at http://dambe.bio.uottawa.ca.
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Project description:Missing data are often problematic when analyzing complete longitudinal social network data. We review approaches for accommodating missing data when analyzing longitudinal network data with stochastic actor-based models. One common practice is to restrict analyses to participants observed at most or all time points, to achieve model convergence. We propose and evaluate an alternative, more inclusive approach to sub-setting and analyzing longitudinal network data, using data from a school friendship network observed at four waves (N =694). Compared to standard practices, our approach retained more information from partially observed participants, generated a more representative analytic sample, and led to less biased model estimates for this case study. The implications and potential applications for longitudinal network analysis are discussed.
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Project description:This manuscript describes the experimental observation of vasculogenesis in chick embryos by means of network analysis. The formation of the vascular network was observed in the area opaca of embryos from 40 to 55 h of development. In the area opaca endothelial cell clusters self-organize as a primitive and approximately regular network of capillaries. The process was observed by bright-field microscopy in control embryos and in embryos treated with Bevacizumab (Avastin®), an antibody that inhibits the signalling of the vascular endothelial growth factor (VEGF). The sequence of images of the vascular growth were thresholded, and used to quantify the forming network in control and Avastin-treated embryos. This characterization is made by measuring vessels density, number of cell clusters and the largest cluster density. From the original images, the topology of the vascular network was extracted and characterized by means of the usual network metrics such as: the degree distribution, average clustering coefficient, average short path length and assortativity, among others. This analysis allows to monitor how the largest connected cluster of the vascular network evolves in time and provides with quantitative evidence of the disruptive effects that Avastin has on the tree structure of vascular networks.
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Project description:Networks play a crucial role in computational biology, yet their analysis and representation is still an open problem. Power Graph Analysis is a lossless transformation of biological networks into a compact, less redundant representation, exploiting the abundance of cliques and bicliques as elementary topological motifs. We demonstrate with five examples the advantages of Power Graph Analysis. Investigating protein-protein interaction networks, we show how the catalytic subunits of the casein kinase II complex are distinguishable from the regulatory subunits, how interaction profiles and sequence phylogeny of SH3 domains correlate, and how false positive interactions among high-throughput interactions are spotted. Additionally, we demonstrate the generality of Power Graph Analysis by applying it to two other types of networks. We show how power graphs induce a clustering of both transcription factors and target genes in bipartite transcription networks, and how the erosion of a phosphatase domain in type 22 non-receptor tyrosine phosphatases is detected. We apply Power Graph Analysis to high-throughput protein interaction networks and show that up to 85% (56% on average) of the information is redundant. Experimental networks are more compressible than rewired ones of same degree distribution, indicating that experimental networks are rich in cliques and bicliques. Power Graphs are a novel representation of networks, which reduces network complexity by explicitly representing re-occurring network motifs. Power Graphs compress up to 85% of the edges in protein interaction networks and are applicable to all types of networks such as protein interactions, regulatory networks, or homology networks.
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Project description:BackgroundMissing data is a pervasive problem in clinical research. Generative adversarial imputation nets (GAIN), a novel machine learning data imputation approach, has the potential to substitute missing data accurately and efficiently but has not yet been evaluated in empirical big clinical datasets.ObjectivesThis study aimed to evaluate the accuracy of GAIN in imputing missing values in large real-world clinical datasets with mixed-type variables. The computation efficiency of GAIN was also evaluated. The performance of GAIN was compared with other commonly used methods, MICE and missForest.MethodsTwo real world clinical datasets were used. The first was that of a cohort study on the long-term outcomes of patients with diabetes (50,000 complete cases), and the second was of a cohort study on the effectiveness of a risk assessment and management programme for patients with hypertension (10,000 complete cases). Missing data (missing at random) to independent variables were simulated at different missingness rates (20, 50%). The normalized root mean square error (NRMSE) between imputed values and real values for continuous variables and the proportion of falsely classified (PFC) for categorical variables were used to measure imputation accuracy. Computation time per imputation for each method was recorded. The differences in accuracy of different imputation methods were compared using ANOVA or non-parametric test.ResultsBoth missForest and GAIN were more accurate than MICE. GAIN showed similar accuracy as missForest when the simulated missingness rate was 20%, but was more accurate when the simulated missingness rate was 50%. GAIN was the most accurate for the imputation of skewed continuous and imbalanced categorical variables at both missingness rates. GAIN had a much higher computation speed (32 min on PC) comparing to that of missForest (1300 min) when the sample size is 50,000.ConclusionGAIN showed better accuracy as an imputation method for missing data in large real-world clinical datasets compared to MICE and missForest, and was more resistant to high missingness rate (50%). The high computation speed is an added advantage of GAIN in big clinical data research. It holds potential as an accurate and efficient method for missing data imputation in future big data clinical research.Trial registrationClinicalTrials.gov ID: NCT03299010 ; Unique Protocol ID: HKUCTR-2232.
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Project description:Quantitative Structure-Activity Relationship (QSAR) modeling is a common computational technique for predicting chemical toxicity, but a lack of new methodological innovations has impeded QSAR performance on many tasks. We show that contemporary QSAR modeling for predictive toxicology can be substantially improved by incorporating semantic graph data aggregated from open-access public databases, and analyzing those data in the context of graph neural networks (GNNs). Furthermore, we introspect the GNNs to demonstrate how they can lead to more interpretable applications of QSAR, and use ablation analysis to explore the contribution of different data elements to the final models' performance.
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Project description:The current gold standard for the localization of the cortical regions responsible for the initiation and propagation of the ictal activity is through the use of invasive electrocorticography (ECoG). This method is utilized to guide surgical intervention in cases of medically intractable epilepsy by identifying the location and extent of the epileptogenic focus. Recent studies have proposed mechanisms in which the activity of epileptogenic cortical networks, rather than discrete focal sources, contributes to the generation of the ictal state. If true, selective modulation of key network components could be employed for the prevention and termination of the ictal state.Here, we have applied graph theory methods as a means to identify critical network nodes in cortical networks during both ictal and interictal states. ECoG recordings were obtained from a cohort of 25 patients undergoing presurgical monitoring for the treatment of intractable epilepsy at the Mayo Clinic (Rochester, MN, U.S.A.).One graph measure, the betweenness centrality, was found to correlate with the location of the resected cortical regions in patients who were seizure-free following surgical intervention. Furthermore, these network interactions were also observed during random nonictal periods as well as during interictal spike activity. These network characteristics were found to be frequency dependent, with high frequency gamma band activity most closely correlated with improved postsurgical outcome as has been reported in previous literature.These findings could lead to improved understanding of epileptogenesis. In addition, this theoretically allows for more targeted therapeutic interventions through the selected modulation or disruption of these epileptogenic networks.
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