This paper explores two aspects of social network modeling. First, we generalize a successful static model of relationships into a dynamic model that accounts for friendships drifting over time. Second, we show how to make it tractable to learn such models from data, even as the number of entities n gets large.

We describe a hierarchy of motif-based kernels for multiple alignments of biological sequences, particularly suitable to process regulatory regions ofgenes. The kernels incorporate progressively more information, with the most complex kernel accounting for a multiple alignment of orthologous regions, the phylogenetic tree relating the species, and the prior knowledge that relevant sequence patterns occur in conserved motif blocks.These kernels can be used in the presence of a library of known transcription factor binding sites, or de novo by iterating over all k-mers of a given length. In the latter mode, a discriminative classifier builtfrom such a kernel not only recognizes a given class of promoter regions,but as a side effect simultaneously identifies a collection of relevant, discriminative sequence motifs. We demonstrate the utility of the motif-based multiple alignment kernels by using a collection ofaligned promoter regions from five yeast species to recognize classes of cell-cycle regulated genes.

Let x E RIXI be a Visible pattern7 and y E {3/1, . . .

Nonnegative matrix approximation (NNMA) is a recent technique for dimensionality reductionand data analysis that yields a parts based, sparse nonnegative representation for nonnegative input data. NNMA has found a wide variety of applications, including text analysis, document clustering, face/imagerecognition, language modeling, speech processing and many others. Despite these numerous applications, the algorithmic development forcomputing the NNMA factors has been relatively deficient. This paper makes algorithmic progress by modeling and solving (using multiplicative updates) new generalized NNMA problems that minimize Bregman divergences between the input matrix and its lowrank approximation.The multiplicative update formulae in the pioneering work by Lee and Seung [11] arise as a special case of our algorithms. In addition, the paper shows how to use penalty functions for incorporating constraintsother than nonnegativity into the problem. Further, some interesting extensions to the use of "link" functions for modeling nonlinear relationshipsare also discussed.

We present a novel cochlear model implemented in analog very large scale integration (VLSI) technology that emulates nonlinear active cochlear behavior. This silicon cochlea includes outer hair cell (OHC) electromotility through active bidirectional coupling (ABC), a mechanism weproposed in which OHC motile forces, through the microanatomical organizationof the organ of Corti, realize the cochlear amplifier. Our chip measurements demonstrate that frequency responses become larger and more sharply tuned when ABC is turned on; the degree ofthe enhancement decreases with input intensity as ABC includes saturation of OHC forces.

We present a probabilistic generative model of entity relationships and their attributes that simultaneously discovers groups among the entities and topics among the corresponding textual attributes. Block-models of relationship data have been studied in social network analysis for some time. Here we simultaneously cluster in several modalities at once, incorporating the attributes (here, words) associated with certain relationships. Significantly, joint inference allows the discovery of topics to be guided by the emerging groups, and vice-versa. We present experimental results on two large data sets: sixteen years of bills put before the U.S. Senate, comprising their corresponding text and voting records, and thirteen years of similar data from the United Nations. We show that in comparison with traditional, separate latent-variable models for words, or Block-structures for votes, the Group-Topic model's joint inference discovers more cohesive groups and improved topics.

We present a nonlinear, simple, yet effective, feature subset selection method for regression and use it in analyzing cortical neural activity. Our algorithm involves a feature-weighted version of the k-nearest-neighbor algorithm. It is able to capture complex dependency of the target function onits input and makes use of the leave-one-out error as a natural regularization. We explain the characteristics of our algorithm on synthetic problemsand use it in the context of predicting hand velocity from spikes recorded in motor cortex of a behaving monkey. By applying feature selectionwe are able to improve prediction quality and suggest a novel way of exploring neural data.

In multi-agent systems, individuals within a group coordinate and interact to achieve a goal.

The network topology of neurons in the brain exhibits an abundance of feedback connections, but the computational function of these feedback connections is largely unknown. We present a computational theory that characterizes the gain in computational power achieved through feedback in dynamical systems with fading memory. It implies that many such systems acquire through feedback universal computational capabilities for analog computing with a non-fading memory. In particular, we show that feedback enables such systems to process time-varying input streams in diverse ways according to rules that are implemented through internal states of the dynamical system. In contrast to previous attractor-based computational models for neural networks, these flexible internal states are high-dimensional attractors of the circuit dynamics, that still allow the circuit state to absorb new information from online input streams. In this way one arrives at novel models for working memory, integration of evidence, and reward expectation in cortical circuits. We show that they are applicable to circuits of conductance-based Hodgkin-Huxley (HH) neurons with high levels of noise that reflect experimental data on invivo conditions.

Predictive state representations (PSRs) are a method of modeling dynamical systemsusing only observable data, such as actions and observations, to describe their model. PSRs use predictions about the outcome of future teststo summarize the system state.