We provide preliminary evidence that eXlstmg algorithms for inferring small-scale gene regulation networks from gene expression data can be adapted to large-scale gene expression data coming from hybridization microarrays. The essential steps are (1) clustering many genes by their expression time-course data into a minimal set of clusters of co-expressed genes, (2) theoretically modeling the various conditions under which the time-courses are measured using a continious-time analog recurrent neural network for the cluster mean time-courses, (3) fitting such a regulatory model to the cluster mean time courses by simulated annealing with weight decay, and (4) analysing several such fits for commonalities in the circuit parameter sets including the connection matrices. This procedure can be used to assess the adequacy of existing and future gene expression time-course data sets for determ ining transcriptional regulatory relationships such as coregulation.

In this paper, we present Committee, a new multi-class learning algorithm related to the Winnow family of algorithms. Committee is an algorithm for combining the predictions of a set of sub-experts in the online mistake-bounded model oflearning. A sub-expert is a special type of attribute that predicts with a distribution over a finite number of classes. Committee learns a linear function of sub-experts and uses this function to make class predictions. We provide bounds for Committee that show it performs well when the target can be represented by a few relevant sub-experts. We also show how Committee can be used to solve more traditional problems composed of attributes. This leads to a natural extension that learns on multi-class problems that contain both traditional attributes and sub-experts.

Dual estimation refers to the problem of simultaneously estimating the state of a dynamic system and the model which gives rise to the dynamics. Algorithms include expectation-maximization (EM), dual Kalman filtering, and joint Kalman methods. These methods have recently been explored in the context of nonlinear modeling, where a neural network is used as the functional form of the unknown model. Typically, an extended Kalman filter (EKF) or smoother is used for the part of the algorithm that estimates the clean state given the current estimated model. An EKF may also be used to estimate the weights of the network. This paper points out the flaws in using the EKF, and proposes an improvement based on a new approach called the unscented transformation (UT) [3]. A substantial performance gain is achieved with the same order of computational complexity as that of the standard EKF. The approach is illustrated on several dual estimation methods.

The Karush-Kuhn-Tucker Theorem is used to derive conditions for determining whether or not a given working set is optimal. These conditions become the algorithm)s termination criteria) as an alternative to Osuna)s criteria (also used by Joachims without modification) which used conditions for individual points. The advantage of the new conditions is that knowledge of the hyperplane)s constant factor b) which in some cases is difficult to compute) is not required. Further investigation of the new termination conditions allows to form the strategy for selecting an optimal working set. The new algorithm is applicable to the pattern recognition SVM) and is provably equivalent to Joachims) algorithm. One can also interpret the new algorithm in the sense of the method of feasible directions. Experimental results presented in the last section demonstrate superior performance of the new method in comparison with traditional training of regression SVM. 2 General Principles of Regression SVM Decomposition The original decomposition algorithm proposed for the pattern recognition SVM in [2] has been extended to the regression SVM in [4]. For the sake of completeness I will repeat the main steps of this extension with the aim of providing terse and streamlined notation to lay the ground for working set selection.

Suppose you are given some dataset drawn from an underlying probability distribution P and you want to estimate a "simple" subset S of input space such that the probability that a test point drawn from P lies outside of S equals some a priori specified

This question was recently shown in [9] to be a special case of a much more fundamental problem: What are the features of the variable X that are relevant for the prediction of another, relevance, variable Y?

We present a new learning architecture: the Decision Directed Acyclic Graph (DDAG), which is used to combine many two-class classifiers into a multiclass classifier. For an N -class problem, the DDAG contains N(N - 1)/2 classifiers, one for each pair of classes. We present a VC analysis of the case when the node classifiers are hyperplanes; the resulting bound on the test error depends on N and on the margin achieved at the nodes, but not on the dimension of the space. This motivates an algorithm, DAGSVM, which operates in a kernel-induced feature space and uses two-class maximal margin hyperplanes at each decision-node of the DDAG. The DAGSVM is substantially faster to train and evaluate than either the standard algorithm or Max Wins, while maintaining comparable accuracy to both of these algorithms. 1 Introduction The problem of multiclass classificatIon, especially for systems like SVMs, doesn't present an easy solution. It is generally simpler to construct classifier theory and algorithms for two mutually-exclusive classes than for N mutually-exclusive classes.

Local linear regression performs very well in many low-dimensional forecasting problems. In high-dimensional spaces, its performance typically decays due to the well-known "curse-of-dimensionality". A possible way to approach this problem is by varying the "shape" of the weighting kernel. In this work we suggest a new, data-driven method to estimating the optimal kernel shape. Experiments using an artificially generated data set and data from the UC Irvine repository show the benefits of kernel shaping. 1 Introduction Local linear regression has attracted considerable attention in both statistical and machine learning literature as a flexible tool for nonparametric regression analysis [Cle79, FG96, AMS97]. Like most statistical smoothing approaches, local modeling suffers from the so-called "curse-of-dimensionality", the well-known fact that the proportion of the training data that lie in a fixed-radius neighborhood of a point decreases to zero at an exponential rate with increasing dimension of the input space.

Suppose there exists a function y* fo(x) from which we observe the measurements corrupted with noise ((Xl, YI),".

We present a new technique for time series analysis based on dynamic probabilistic networks. In this approach, the observed data are modeled in terms of unobserved, mutually independent factors, as in the recently introduced technique of Independent Factor Analysis (IFA). However, unlike in IFA, the factors are not Li.d.; each factor has its own temporal statistical characteristics. We derive a family of EM algorithms that learn the structure of the underlying factors and their relation to the data. These algorithms perform source separation and noise reduction in an integrated manner, and demonstrate superior performance compared to IFA. 1 Introduction The technique of independent factor analysis (IFA) introduced in [1] provides a tool for modeling L'-dim data in terms of L unobserved factors. These factors are mutually independent and combine linearly with added noise to produce the observed data.