Technology
From Coexpression to Coregulation: An Approach to Inferring Transcriptional Regulation among Gene Classes from Large-Scale Expression Data
Mjolsness, Eric, Mann, Tobias, Castaรฑo, Rebecca, Wold, Barbara J.
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.
Constructing Heterogeneous Committees Using Input Feature Grouping: Application to Economic Forecasting
Liao, Yuansong, Moody, John E.
Yuansong Liao and John Moody Department of Computer Science, Oregon Graduate Institute, P.O.Box 91000, Portland, OR 97291-1000 Abstract The committee approach has been proposed for reducing model uncertainty and improving generalization performance. The advantage of committees depends on (1) the performance of individual members and (2) the correlational structure of errors between members. This paper presents an input grouping technique for designing a heterogeneous committee. With this technique, all input variables are first grouped based on their mutual information. Statistically similar variables are assigned to the same group.
Learning the Similarity of Documents: An Information-Geometric Approach to Document Retrieval and Categorization
The project pursued in this paper is to develop from first information-geometric principles a general method for learning the similarity between text documents. Each individual document is modeled as a memoryless information source. Based on a latent class decomposition of the term-document matrix, a lowdimensional (curved) multinomial subfamily is learned. From this model a canonical similarity function - known as the Fisher kernel - is derived. Our approach can be applied for unsupervised and supervised learning problems alike.
Kirchoff Law Markov Fields for Analog Circuit Design
Three contributions to developing an algorithm for assisting engineers in designing analog circuits are provided in this paper. First, a method for representing highly nonlinear and noncontinuous analog circuits using Kirchoff current law potential functions within the context of a Markov field is described. Second, a relatively efficient algorithm for optimizing the Markov field objective function is briefly described and the convergence proof is briefly sketched. And third, empirical results illustrating the strengths and limitations of the approach are provided within the context of a JFET transistor design problem. The proposed algorithm generated a set of circuit components for the JFET circuit model that accurately generated the desired characteristic curves. 1 Analog circuit design using Markov random fields
Learning Informative Statistics: A Nonparametnic Approach
III, John W. Fisher, Ihler, Alexander T., Viola, Paul A.
We discuss an information theoretic approach for categorizing and modeling dynamic processes. The approach can learn a compact and informative statistic which summarizes past states to predict future observations. Furthermore, the uncertainty of the prediction is characterized nonparametrically by a joint density over the learned statistic and present observation. We discuss the application of the technique to both noise driven dynamical systems and random processes sampled from a density which is conditioned on the past. In the first case we show results in which both the dynamics of random walk and the statistics of the driving noise are captured. In the second case we present results in which a summarizing statistic is learned on noisy random telegraph waves with differing dependencies on past states. In both cases the algorithm yields a principled approach for discriminating processes with differing dynamics and/or dependencies. The method is grounded in ideas from information theory and nonparametric statistics.
Image Representations for Facial Expression Coding
Bartlett, Marian Stewart, Donato, Gianluca, Movellan, Javier R., Hager, Joseph C., Ekman, Paul, Sejnowski, Terrence J.
The Facial Action Coding System (FACS) (9) is an objective method for quantifying facial movement in terms of component actions. This system is widely used in behavioral investigations of emotion, cognitive processes, and social interaction. The coding is presently performed by highly trained human experts. This paper explores and compares techniques for automatically recognizing facial actions in sequences of images. These methods include unsupervised learning techniques for finding basis images such as principal component analysis, independent component analysis and local feature analysis, and supervised learning techniques such as Fisher's linear discriminants.
Robust Learning of Chaotic Attractors
Bakker, Rembrandt, Schouten, Jaap C., Coppens, Marc-Olivier, Takens, Floris, Giles, C. Lee, Bleek, Cor M. van den
A fundamental problem with the modeling of chaotic time series data is that minimizing short-term prediction errors does not guarantee a match between the reconstructed attractors of model and experiments. We introduce a modeling paradigm that simultaneously learns to short-tenn predict and to locate the outlines of the attractor by a new way of nonlinear principal component analysis. Closed-loop predictions are constrained to stay within these outlines, to prevent divergence from the attractor. Learning is exceptionally fast: parameter estimation for the 1000 sample laser data from the 1991 Santa Fe time series competition took less than a minute on a 166 MHz Pentium PC.
Managing Uncertainty in Cue Combination
Yang, Zhiyong, Zemel, Richard S.
We develop a hierarchical generative model to study cue combination. The model maps a global shape parameter to local cuespecific parameters, which in tum generate an intensity image. Inferring shape from images is achieved by inverting this model. Inference produces a probability distribution at each level; using distributions rather than a single value of underlying variables at each stage preserves information about the validity of each local cue for the given image. This allows the model, unlike standard combination models, to adaptively weight each cue based on general cue reliability and specific image context.
A SNoW-Based Face Detector
Yang, Ming-Hsuan, Roth, Dan, Ahuja, Narendra
A novel learning approach for human face detection using a network of linear units is presented. The SNoW learning architecture is a sparse network of linear functions over a predefined or incrementally learned feature space and is specifically tailored for learning in the presence of a very large number of features. A wide range of face images in different poses, with different expressions and under different lighting conditions are used as a training set to capture the variations of human faces. Experimental results on commonly used benchmark data sets of a wide range of face images show that the SNoW-based approach outperforms methods that use neural networks, Bayesian methods, support vector machines and others. Furthermore, learning and evaluation using the SNoW-based method are significantly more efficient than with other methods. 1 Introduction Growing interest in intelligent human computer interactions has motivated a recent surge in research on problems such as face tracking, pose estimation, face expression and gesture recognition. Most methods, however, assume human faces in their input images have been detected and localized.