Adaptive Resonance Associative Map: A Hierarchical ART System for Fast Stable Associative Learning

This paper introduces a new class of predictive ART architectures, called Adaptive Resonance Associative Map (ARAM) which performs rapid, yet stable heteroassociative learning in real time environment. ARAM can be visualized as two ART modules sharing a single recognition code layer. The unit for recruiting a recognition code is a pattern pair. Code stabilization is ensured by restricting coding to states where resonances are reached in both modules. Simulation results have shown that ARAM is capable of self-stabilizing association of arbitrary pattern pairs of arbitrary complexity appearing in arbitrary sequence by fast learning in real time environment. Due to the symmetrical network structure, associative recall can be performed in both directions.

Integration of relational and hierarchical network information for protein function prediction

BACKGROUND:In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.RESULTS:We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing.CONCLUSION:A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased positive predictive value), and that this increase is consistent uniformly with GO-term depth. Additional in silico validation on a collection of new annotations recently added to GO confirms the advantages suggested by the cross-validation study. Taken as a whole, our results show that a hierarchical approach to network-based protein function prediction, that exploits the ontological structure of protein annotation databases in a principled manner, can offer substantial advantages over the successive application of 'flat' network-based methods.

Structural Analysis of Network Traffic Flows

Network traffic arises from the superposition of Origin-Destination (OD) flows. Hence, a thorough understanding of OD flows is essential for modeling network traffic, and for addressing a wide variety of problems including traffic engineering, traffic matrix estimation, capacity planning, forecasting and anomaly detection. However, to date, OD flows have not been closely studied, and there is very little known about their properties. We present the first analysis of complete sets of OD flow timeseries, taken from two different backbone networks (Abilene and Sprint-Europe). Using Principal Component Analysis (PCA), we find that the set of OD flows has small intrinsic dimension. In fact, even in a network with over a hundred OD flows, these flows can be accurately modeled in time using a small number (10 or less) of independent components or dimensions. We also show how to use PCA to systematically decompose the structure of OD flow timeseries into three main constituents: common periodic trends, short-lived bursts, and noise. We provide insight into how the various constituents contribute to the overall structure of OD flows and explore the extent to which this decomposition varies over time.

On the Relationship Between File Sizes, Transport Protocols, and Self-Similar Network Traffic

Recent measurements of local-area and wide-area traffic have shown that network traffic exhibits variability at a wide range of scales self-similarity. In this paper, we examine a mechanism that gives rise to self-similar network traffic and present some of its performance implications. The mechanism we study is the transfer of files or messages whose size is drawn from a heavy-tailed distribution. We examine its effects through detailed transport-level simulations of multiple TCP streams in an internetwork. First, we show that in a "realistic" client/server network environment i.e., one with bounded resources and coupling among traffic sources competing for resources the degree to which file sizes are heavy-tailed can directly determine the degree of traffic self-similarity at the link level. We show that this causal relationship is not significantly affected by changes in network resources (bottleneck bandwidth and buffer capacity), network topology, the influence of cross-traffic, or the distribution of interarrival times. Second, we show that properties of the transport layer play an important role in preserving and modulating this relationship. In particular, the reliable transmission and flow control mechanisms of TCP (Reno, Tahoe, or Vegas) serve to maintain the long-range dependency structure induced by heavy-tailed file size distributions. In contrast, if a non-flow-controlled and unreliable (UDP-based) transport protocol is used, the resulting traffic shows little self-similar characteristics: although still bursty at short time scales, it has little long-range dependence. If flow-controlled, unreliable transport is employed, the degree of traffic self-similarity is positively correlated with the degree of throttling at the source. Third, in exploring the relationship between file sizes, transport protocols, and self-similarity, we are also able to show some of the performance implications of self-similarity. We present data on the relationship between traffic self-similarity and network performance as captured by performance measures including packet loss rate, retransmission rate, and queueing delay. Increased self-similarity, as expected, results in degradation of performance. Queueing delay, in particular, exhibits a drastic increase with increasing self-similarity. Throughput-related measures such as packet loss and retransmission rate, however, increase only gradually with increasing traffic self-similarity as long as reliable, flow-controlled transport protocol is used.

A Neural Network Architecture for Autonomous Learning, Recognition, and Prediction in a Nonstationary World

In a constantly changing world, humans are adapted to alternate routinely between attending to familiar objects and testing hypotheses about novel ones. We can rapidly learn to recognize and narne novel objects without unselectively disrupting our memories of familiar ones. We can notice fine details that differentiate nearly identical objects and generalize across broad classes of dissimilar objects. This chapter describes a class of self-organizing neural network architectures--called ARTMAP-- that are capable of fast, yet stable, on-line recognition learning, hypothesis testing, and naming in response to an arbitrary stream of input patterns (Carpenter, Grossberg, Markuzon, Reynolds, and Rosen, 1992; Carpenter, Grossberg, and Reynolds, 1991). The intrinsic stability of ARTMAP allows the system to learn incrementally for an unlimited period of time. System stability properties can be traced to the structure of its learned memories, which encode clusters of attended features into its recognition categories, rather than slow averages of category inputs. The level of detail in the learned attentional focus is determined moment-by-moment, depending on predictive success: an error due to over-generalization automatically focuses attention on additional input details enough of which are learned in a new recognition category so that the predictive error will not be repeated. An ARTMAP system creates an evolving map between a variable number of learned categories that compress one feature space (e.g., visual features) to learned categories of another feature space (e.g., auditory features). Input vectors can be either binary or analog. Computational properties of the networks enable them to perform significantly better in benchmark studies than alternative machine learning, genetic algorithm, or neural network models. Some of the critical problems that challenge and constrain any such autonomous learning system will next be illustrated. Design principles that work together to solve these problems are then outlined. These principles are realized in the ARTMAP architecture, which is specified as an algorithm. Finally, ARTMAP dynamics are illustrated by means of a series of benchmark simulations.

A Neural Network Model of Spatio-Temporal Pattern Recognition, Recall and Timing

This paper describes the design of a self~organizing, hierarchical neural network model of unsupervised serial learning. The model learns to recognize, store, and recall sequences of unitized patterns, using either short-term memory (STM) or both STM and long-term memory (LTM) mechanisms. Timing information is learned and recall {both from STM and from LTM) is performed with a learned rhythmical structure. The network, bearing similarities with ART (Carpenter & Grossberg 1987a), learns to map temporal sequences to unitized patterns, which makes it suitable for hierarchical operation. It is therefore capable of self-organizing codes for sequences of sequences. The capacity is only limited by the number of nodes provided. Selected simulation results are reported to illustrate system properties.