Featured Publications
A look at the topology of convolutional neural networks
The problem of understanding how convolutional neural nets (CNN’s) work and learn is one of the fundamental problems in machine learning. It is important to study both the weights and the activations, as these roughly…
Publications
Quantifying similarity of pore-geometry in nanoporous materials
In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture…
Publications
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development
Transcriptional programs control cellular lineage commitment and differentiation during development. Understanding of cell fate has been advanced by studying single-cell RNA-sequencing (RNA-seq) but is limited…
Publications
Syria Polio Vaccination Analyses
SumAll.org used Ayasdi software to perform a quick systemic cluster analysis of a Polio vaccination campaign in Syria for children, with data provided by HumanitarianTracker.org. This humanitarian effort in a…
Publications
MRI and Biomechanics Multidimensional Data Analysis Reveals R2-R1q as an Early Predictor of Cartilage Lesion Progression in Knee Osteoarthritis
Osteoarthritis (OA) is a complex and multifactorial disorder and a leading cause of chronic disability. OA prevalence in the United States is conservatively estimated at 26.9 million US adults,1 with estimated annual…
Publications
Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is an unexplained, chronic debilitating disorder that in the USA alone is estimated to affect up to 2.5 million people, with annual costs of $24 billion…
Publications
Machine learning algorithm for automatic detection of CT-identifiable hyperdense lesions associated with traumatic brain injury
Traumatic brain injury (TBI) is a major cause of death and disability in the United States. Time to treatment is often related to patient outcome. Access to cerebral imaging data in a timely manner is a vital component of patient…
Publications
Spatiotemporal genomic architecture informs precision oncology in glioblastoma
Most clinical trials for targeted therapy in GBM have shown limited clinical success. Although recent genome-wide studies evaluating regional heterogeneity and longitudinal GBM pairs have suggested potential…
Publications
Identification of Topological Network Modules in Perturbed Protein Interaction Networks
Biological networks consist of functional modules, however detecting and characterizing such modules in networks remains challenging. Perturbing networks is one strategy for identifying modules. Here we used an advanced…
Publications
Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis
Mutation of highly conserved residues in transcription factors may affect protein-protein or proteinDNA interactions, leading to gene network dysregulation and human disease. Human mutations in…