. We introduce, analyze and demonstrate a recursive hierarchical generalization of the widely used hidden Markov models, which we name Hierarchical Hidden Markov Models (HHMM). Our model is motivated by the complex multi-scale structure which appears in many natural sequences, particularly in language, handwriting and speech. We seek a systematic unsupervised approach to the modeling of such structures. By extendingthe standard forward-backward(BaumWelch) algorithm, we derive an efficient procedure for estimating the model parameters from unlabeled data. We then use the trained model for automatic hierarchical parsing of observation sequences. We describe two applications of our model and its parameter estimation procedure. In the first application we show how to construct hierarchical models of natural English text. In these models different levels of the hierarchy correspond to structures on different length scales in the text. In the second application we demonstrate how HHMMs can b...

The brain is perhaps the most complex system to have ever been subjected to rigorous scientific investigation. The scale is staggering: over 1011 neurons, each making an average of 10 3 synapses, with computation occurring on scales ranging from a single dendritic spine, to an entire cortical area. Slowly, we are beginning to acquire experimental tools that can gather the massive amounts of data needed to characterize this system. However, to understand and interpret these data will also require substantial strides in inferential and statistical techniques. This dissertation attempts to meet this need, extending and applying the modern tools of latent variable modeling to problems in neural data analysis. It is divided

Determining the relationship between the activity of a single nerve cell to that of an entire population is a fundamental question that bears on the basic neural computation paradigms. In this paper we apply an information theoretic approach to quantify the level of cooperative activity among cells in a behavioral context. It is possible to discriminate between synergetic activity of the cells vs. redundant activity, depending on the difference between the information they provide when measured jointly and the information they provide independently. We define a synergy value that is positive in the first case and negative in the second and show that the synergy value can be measured by detecting the behavioral mode of the animal from simultaneously recorded activity of the cells. We observe that among cortical cells positive synergy can be found, while cells from the basal ganglia, active during the same task, do not exhibit similar synergetic activity. fitay,tishbyg@cs.huji.ac.il y...

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1.1 Example: the switching Poisson model is a simple model for spike trains which flip between a few distinct firing states...................... 5 1.2 Example: ion channels are often modeled as HMMs............... 7

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