Publications

Cancer statistics, 2018

Abstract Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States and compiles the most recent data on ca...

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction metho...

A Fast Learning Algorithm for Deep Belief Nets

We show how to use “complementary priors” to eliminate the explaining-away effects that make inference difficult in densely connected belief nets that have many hidden layers. U...

The psychological impact of quarantine and how to reduce it: rapid review of the evidence

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Molecular portraits of human breast tumours

Regularization Paths for Generalized Linear Models via Coordinate Descent

We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multi- nom...

Detecting Functionality-Specific Vulnerabilities via Retrieving Individual Functionality-Equivalent APIs in Open-Source Repositories

Functionality-specific vulnerabilities, which mainly occur in Application Programming Interfaces (APIs) with specific functionalities, are crucial for software developers to det...

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies ...

Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information

This paper considers the model problem of reconstructing an object from incomplete frequency samples. Consider a discrete-time signal f ∈ C N and a randomly chosen set of freque...

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

The cBioPortal enables integration, visualization, and analysis of multidimensional cancer genomic and clinical data.

Parallel Distributed Processing

What makes people smarter than computers? These volumes by a pioneering neurocomputing group suggest that the answer lies in the massively parallel architecture of the human min...