Applications of node-based resilience graph theoretic framework to clustering autism spectrum disorders phenotypes.

With the growing ubiquity of data in network form, clustering in the context of a network, represented as a graph, has become increasingly important. Clustering is a very useful data exploratory machine learning tool that allows us to make better sense of heterogeneous data by grouping data with similar attributes based on some criteria. This paper investigates the application of a novel graph theoretic clustering method, Node-Based Resilience clustering (NBR-Clust), to address the heterogeneity of Autism Spectrum Disorder (ASD) and identify meaningful subgroups. The hypothesis is that analysis of these subgroups would reveal relevant biomarkers that would provide a better understanding of ASD phenotypic heterogeneity useful for further ASD studies. We address appropriate graph constructions suited for representing the ASD phenotype data. The sample population is drawn from a very large rigorous dataset: Simons Simplex Collection (SSC). Analysis of the results performed using graph quality measures, internal cluster validation measures, and clinical analysis outcome demonstrate the potential usefulness of resilience measure clustering for biomedical datasets. We also conduct feature extraction analysis to characterize relevant biomarkers that delineate the resulting subgroups. The optimal results obtained favored predominantly a 5-cluster configuration.

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine.

The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)-an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM's autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies.

Simulating retrieval from a highly clustered network: implications for spoken word recognition.

Network science describes how entities in complex systems interact, and argues that the structure of the network influences processing. Clustering coefficient, C - one measure of network structure - refers to the extent to which neighbors of a node are also neighbors of each other. Previous simulations suggest that networks with low C dissipate information (or disease) to a large portion of the network, whereas in networks with high C information (or disease) tends to be constrained to a smaller portion of the network (Newman, 2003). In the present simulation we examined how C influenced the spread of activation to a specific node, simulating retrieval of a specific lexical item in a phonological network. The results of the network simulation showed that words with lower C had higher activation values (indicating faster or more accurate retrieval from the lexicon) than words with higher C. These results suggest that a simple mechanism for lexical retrieval can account for the observations made in Chan and Vitevitch (2009), and have implications for diffusion dynamics in other fields.