相关论文: OrfMapper: A Web-Based Application for Visualizing…
Metal-organic frameworks (MOFs) have been widely investigated for challenging catalytic transformations due to their well-defined structures and high degree of synthetic tunability. These features, at least in principle, make MOFs ideally…
We propose a new approach to querying graph databases. Our approach balances competing goals of expressive power, language clarity and computational complexity. A distinctive feature of our approach is the ability to express properties of…
We present the Open Graph Benchmark (OGB), a diverse set of challenging and realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine learning (ML) research. OGB datasets are large-scale, encompass multiple…
We propose a method for gene expression based analysis of cancer phenotypes incorporating network biology knowledge through unsupervised construction of computational graphs. The structural construction of the computational graphs is driven…
Motivation: In transcriptomic and proteomics-based studies, the abundance of genes is often compared to functional pathways such as the Kyoto Encyclopaedia at Genes and Genomes (KEGG) to identify active metabolic processes. Even though a…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…
Clustering is a popular data mining technique that aims to partition an input space into multiple homogeneous regions. There exist several clustering algorithms in the literature. The performance of a clustering algorithm depends on its…
A GraphMaps is a system that visualizes a graph using zoom levels, which is similar to a geographic map visualization. GraphMaps reveals the structural properties of the graph and enables users to explore the graph in a natural way by using…
Background: Understanding the relationship between the Omics and the phenotype is a central problem in precision medicine. The high dimensionality of metabolomics data challenges learning algorithms in terms of scalability and…
We propose a topological mapping and localization system able to operate on real human colonoscopies, despite significant shape and illumination changes. The map is a graph where each node codes a colon location by a set of real images,…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
In mass spectrometry-based proteomics, experts usually project data onto a single set of reference sequences, overlooking the influence of common haplotypes (combinations of genetic variants inherited together from a parent). We recently…
We propose a method for demonstrating sub community structure in scientific networks of relatively small size from analyzing databases of publications. Research relationships between the network members can be visualized as a graph with…
We propose an algorithm for clustering high dimensional data. If $P$ features for $N$ objects are represented in an $N\times P$ matrix ${\bf X}$, where $N\ll P$, the method is based on exploiting the cluster-dependent structure of the…
Discovery of novel protein biomarkers for clinical applications is an active research field across a manifold of diseases. Despite some successes and progress, the biomarker development pipeline still frequently ends in failure as biomarker…
We present and review Coupled Two Way Clustering, a method designed to mine gene expression data. The method identifies submatrices of the total expression matrix, whose clustering analysis reveals partitions of samples (and genes) into…
Conjugated organic molecules represent an important area of materials chemistry for both fundamental scientific exploration and technological applications. Using a genetic algorithm to computationally screen up to ~25-50 million molecules…
Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To…
Identifying the genes and mutations that drive the emergence of tumors is a major step to improve understanding of cancer and identify new directions for disease diagnosis and treatment. Despite the large volume of genomics data, the…