Understanding Subsystems in Biology through Dimensionality Reduction, Graph Partitioning and Analytical Modeling

Biological systems exhibit rich and complex behavior through the orchestrated interplay of a large array of components. It is hypothesized that separable subsystems with some degree of functional autonomy exist; deciphering their independent behavior and functionality would greatly facilitate understanding the system as a whole. Discovering and analyzing such subsystems are hence pivotal problems in the quest to gain a quantitative understanding of complex biological systems. In this work, using approaches from machine learning, physics and graph theory, methods for the identification and analysis of such subsystems were developed. A novel methodology, based on a recent machine learning algorithm known as non-negative matrix factorization (NMF), was developed to discover such subsystems in a set of large-scale gene expression data. This set of subsystems was then used to predict functional relationships between genes, and this approach was shown to score significantly higher than conventional methods when benchmarking them against existing databases. Moreover, a mathematical treatment was developed to treat simple network subsystems based only on their topology (independent of particular parameter values). Application to a problem of experimental interest demonstrated the need for extentions to the conventional model to fully explain the experimental data. Finally, the notion of a subsystem was evaluated from a topological perspective. A number of different protein networks were examined to analyze their topological properties with respect to separability, seeking to find separable subsystems. These networks were shown to exhibit separability in a nonintuitive fashion, while the separable subsystems were of strong biological significance. It was demonstrated that the separability property found was not due to incomplete or biased data, but is likely to reflect biological structure.

Image-Based View Synthesis

We present a new method for rendering novel images of flexible 3D objects from a small number of example images in correspondence. The strength of the method is the ability to synthesize images whose viewing position is significantly far away from the viewing cone of the example images ("view extrapolation"), yet without ever modeling the 3D structure of the scene. The method relies on synthesizing a chain of "trilinear tensors" that governs the warping function from the example images to the novel image, together with a multi-dimensional interpolation function that synthesizes the non-rigid motions of the viewed object from the virtual camera position. We show that two closely spaced example images alone are sufficient in practice to synthesize a significant viewing cone, thus demonstrating the ability of representing an object by a relatively small number of model images --- for the purpose of cheap and fast viewers that can run on standard hardware.

Model-Based Matching by Linear Combinations of Prototypes

We describe a method for modeling object classes (such as faces) using 2D example images and an algorithm for matching a model to a novel image. The object class models are "learned'' from example images that we call prototypes. In addition to the images, the pixelwise correspondences between a reference prototype and each of the other prototypes must also be provided. Thus a model consists of a linear combination of prototypical shapes and textures. A stochastic gradient descent algorithm is used to match a model to a novel image by minimizing the error between the model and the novel image. Example models are shown as well as example matches to novel images. The robustness of the matching algorithm is also evaluated. The technique can be used for a number of applications including the computation of correspondence between novel images of a certain known class, object recognition, image synthesis and image compression.

The Individual is Nothing, the Class Everything: Psychophysics and Modeling of Recognition in Obect Classes

Most psychophysical studies of object recognition have focussed on the recognition and representation of individual objects subjects had previously explicitely been trained on. Correspondingly, modeling studies have often employed a 'grandmother'-type representation where the objects to be recognized were represented by individual units. However, objects in the natural world are commonly members of a class containing a number of visually similar objects, such as faces, for which physiology studies have provided support for a representation based on a sparse population code, which permits generalization from the learned exemplars to novel objects of that class. In this paper, we present results from psychophysical and modeling studies intended to investigate object recognition in natural ('continuous') object classes. In two experiments, subjects were trained to perform subordinate level discrimination in a continuous object class - images of computer-rendered cars - created using a 3D morphing system. By comparing the recognition performance of trained and untrained subjects we could estimate the effects of viewpoint-specific training and infer properties of the object class-specific representation learned as a result of training. We then compared the experimental findings to simulations, building on our recently presented HMAX model of object recognition in cortex, to investigate the computational properties of a population-based object class representation as outlined above. We find experimental evidence, supported by modeling results, that training builds a viewpoint- and class-specific representation that supplements a pre-existing repre-sentation with lower shape discriminability but possibly greater viewpoint invariance.

Stimulus Simplification and Object Representation: A Modeling Study

Tsunoda et al. (2001) recently studied the nature of object representation in monkey inferotemporal cortex using a combination of optical imaging and extracellular recordings. In particular, they examined IT neuron responses to complex natural objects and "simplified" versions thereof. In that study, in 42% of the cases, optical imaging revealed a decrease in the number of activation patches in IT as stimuli were "simplified". However, in 58% of the cases, "simplification" of the stimuli actually led to the appearance of additional activation patches in IT. Based on these results, the authors propose a scheme in which an object is represented by combinations of active and inactive columns coding for individual features. We examine the patterns of activation caused by the same stimuli as used by Tsunoda et al. in our model of object recognition in cortex (Riesenhuber 99). We find that object-tuned units can show a pattern of appearance and disappearance of features identical to the experiment. Thus, the data of Tsunoda et al. appear to be in quantitative agreement with a simple object-based representation in which an object's identity is coded by its similarities to reference objects. Moreover, the agreement of simulations and experiment suggests that the simplification procedure used by Tsunoda (2001) is not necessarily an accurate method to determine neuronal tuning.

Modeling Stock Order Flows and Learning Market-Making from Data

Stock markets employ specialized traders, market-makers, designed to provide liquidity and volume to the market by constantly supplying both supply and demand. In this paper, we demonstrate a novel method for modeling the market as a dynamic system and a reinforcement learning algorithm that learns profitable market-making strategies when run on this model. The sequence of buys and sells for a particular stock, the order flow, we model as an Input-Output Hidden Markov Model fit to historical data. When combined with the dynamics of the order book, this creates a highly non-linear and difficult dynamic system. Our reinforcement learning algorithm, based on likelihood ratios, is run on this partially-observable environment. We demonstrate learning results for two separate real stocks.

Towards Grid-Wide Modeling and Simulation

Modeling and simulation permeate all areas of business, science and engineering. With the increase in the scale and complexity of simulations, large amounts of computational resources are required, and collaborative model development is needed, as multiple parties could be involved in the development process. The Grid provides a platform for coordinated resource sharing and application development and execution. In this paper, we survey existing technologies in modeling and simulation, and we focus on interoperability and composability of simulation components for both simulation development and execution. We also present our recent work on an HLA-based simulation framework on the Grid, and discuss the issues to achieve composability.

Differential epipolar constraint in mobile robot egomotion estimation

The estimation of camera egomotion is a well established problem in computer vision. Many approaches have been proposed based on both the discrete and the differential epipolar constraint. The discrete case is mainly used in self-calibrated stereoscopic systems, whereas the differential case deals with a unique moving camera. The article surveys several methods for mobile robot egomotion estimation covering more than 0.5 million samples using synthetic data. Results from real data are also given

Modeling and Classifying Breast Tissue Density in Mammograms

We present a new approach to model and classify breast parenchymal tissue. Given a mammogram, first, we will discover the distribution of the different tissue densities in an unsupervised manner, and second, we will use this tissue distribution to perform the classification. We achieve this using a classifier based on local descriptors and probabilistic Latent Semantic Analysis (pLSA), a generative model from the statistical text literature. We studied the influence of different descriptors like texture and SIFT features at the classification stage showing that textons outperform SIFT in all cases. Moreover we demonstrate that pLSA automatically extracts meaningful latent aspects generating a compact tissue representation based on their densities, useful for discriminating on mammogram classification. We show the results of tissue classification over the MIAS and DDSM datasets. We compare our method with approaches that classified these same datasets showing a better performance of our proposal

Experimental Modeling and Control Strategies on an Open Mobile Robot Platform PRIM

This research work deals with the problem of modeling and design of low level speed controller for the mobile robot PRIM. The main objective is to develop an effective educational tool. On one hand, the interests in using the open mobile platform PRIM consist in integrating several highly related subjects to the automatic control theory in an educational context, by embracing the subjects of communications, signal processing, sensor fusion and hardware design, amongst others. On the other hand, the idea is to implement useful navigation strategies such that the robot can be served as a mobile multimedia information point. It is in this context, when navigation strategies are oriented to goal achievement, that a local model predictive control is attained. Hence, such studies are presented as a very interesting control strategy in order to develop the future capabilities of the system

Availability analysis of GMPLS connections based on physical network topology

This paper presents a study of connection availability in GMPLS over optical transport networks (OTN) taking into account different network topologies. Two basic path protection schemes are considered and compared with the no protection case. The selected topologies are heterogeneous in geographic coverage, network diameter, link lengths, and average node degree. Connection availability is also computed considering the reliability data of physical components and a well-known network availability model. Results show several correspondences between suitable path protection algorithms and several network topology characteristics

Constraint satisfaction techniques under uncertain conditions for fault diagnosis in nonlinear dynamic systems

The speed of fault isolation is crucial for the design and reconfiguration of fault tolerant control (FTC). In this paper the fault isolation problem is stated as a constraint satisfaction problem (CSP) and solved using constraint propagation techniques. The proposed method is based on constraint satisfaction techniques and uncertainty space refining of interval parameters. In comparison with other approaches based on adaptive observers, the major advantage of the presented method is that the isolation speed is fast even taking into account uncertainty in parameters, measurements and model errors and without the monotonicity assumption. In order to illustrate the proposed approach, a case study of a nonlinear dynamic system is presented

Modeling of hybrid systems by piecewise decomposition

Piecewise linear models systems arise as mathematical models of systems in many practical applications, often from linearization for nonlinear systems. There are two main approaches of dealing with these systems according to their continuous or discrete-time aspects. We propose an approach which is based on the state transformation, more particularly the partition of the phase portrait in different regions where each subregion is modeled as a two-dimensional linear time invariant system. Then the Takagi-Sugeno model, which is a combination of local model is calculated. The simulation results show that the Alpha partition is well-suited for dealing with such a system

Shape complexity based on mutual information

Shape complexity has recently received attention from different fields, such as computer vision and psychology. In this paper, integral geometry and information theory tools are applied to quantify the shape complexity from two different perspectives: from the inside of the object, we evaluate its degree of structure or correlation between its surfaces (inner complexity), and from the outside, we compute its degree of interaction with the circumscribing sphere (outer complexity). Our shape complexity measures are based on the following two facts: uniformly distributed global lines crossing an object define a continuous information channel and the continuous mutual information of this channel is independent of the object discretisation and invariant to translations, rotations, and changes of scale. The measures introduced in this paper can be potentially used as shape descriptors for object recognition, image retrieval, object localisation, tumour analysis, and protein docking, among others

A proposal for the diagnosis of uncertain dynamic systems based on interval models

The performance of a model-based diagnosis system could be affected by several uncertainty sources, such as,model errors,uncertainty in measurements, and disturbances. This uncertainty can be handled by mean of interval models.The aim of this thesis is to propose a methodology for fault detection, isolation and identification based on interval models. The methodology includes some algorithms to obtain in an automatic way the symbolic expression of the residual generators enhancing the structural isolability of the faults, in order to design the fault detection tests. These algorithms are based on the structural model of the system. The stages of fault detection, isolation, and identification are stated as constraint satisfaction problems in continuous domains and solved by means of interval based consistency techniques. The qualitative fault isolation is enhanced by a reasoning in which the signs of the symptoms are derived from analytical redundancy relations or bond graph models of the system. An initial and empirical analysis regarding the differences between interval-based and statistical-based techniques is presented in this thesis. The performance and efficiency of the contributions are illustrated through several application examples, covering different levels of complexity.