Cluster analysis and display of genome-wide expression patterns
A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according ...
Publications
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1,678 publications
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...
Inference from Iterative Simulation Using Multiple Sequences
The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, ho...
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...
Embryonic Stem Cell Lines Derived from Human Blastocysts
Human blastocyst-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express cell surface markers that cha...
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 ...
Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift
Training Deep Neural Networks is complicated by the fact that the distribution of each layer's inputs changes during training, as the parameters of the previous layers change. T...
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...
Definition, diagnosis and classification of diabetes mellitus and its complications. Part 1: diagnosis and classification of diabetes mellitus. Provisional report of a WHO Consultation
The classification of diabetes mellitus and the tests used for its diagnosis were brought into order by the National Diabetes Data Group of the USA and the second World Health O...
UCHIME improves sensitivity and speed of chimera detection
Abstract Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Interna...
An Analysis of Transformations
Summary In the analysis of data it is often assumed that observations y 1, y 2, …, yn are independently normally distributed with constant variance and with expectations specifi...
Minimap2: pairwise alignment for nucleotide sequences
Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic cont...