Joseph T. Chang

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A Markov model of evolution of characters on a phylogenetic tree consists of a tree topology together with a specification of probability transition matrices on the edges of the tree. Previous work has shown that, under mild conditions, the tree topology may be reconstructed, in the sense that the topology is identifiable from knowledge of the joint(More)
Global analyses of RNA expression levels are useful for classifying genes and overall phenotypes. Often these classification problems are linked, and one wants to find "marker genes" that are differentially expressed in particular sets of "conditions." We have developed a method that simultaneously clusters genes and conditions, finding distinctive(More)
A fundamental problem in reconstructing the evolutionary history of a set of species is to infer the topology of the evolutionary tree that relates those species. A statistical method for estimating such a topology from character data is called consistent if, given data from more and more characters, the method is sure to converge to the true topology. A(More)
Stochastic gradient descent is a general algorithm that includes LMS, on-line backpropagation, and adaptive k-means clustering as special cases. The standard choices of the learning rate (both adap-tive and xed functions of time) often perform quite poorly. In contrast, our recently proposed class of \search then converge" (STC) learning rate schedules(More)
If a common ancestor of all living humans is defined as an individual who is a genealogical ancestor of all present-day people, the most recent common ancestor (MRCA) for a randomly mating population would have lived in the very recent past. However, the random mating model ignores essential aspects of population substructure, such as the tendency of(More)
BACKGROUND Autism spectrum disorders (ASD) are neurodevelopmental disorders of complex etiology, with a recognized substantial contribution of heterogeneous genetic factors; one of the core features of ASD is a lack of affiliative behaviors. METHODS On the basis of the existing literature, in this study we examined the hypothesis of allelic associations(More)