Unicast-based Characterization of Network Loss Topologies

Current Internet transport protocols make end-to-end measurements and maintain per-connection state to regulate the use of shared network resources. When a number of such connections share a common endpoint, that endpoint has the opportunity to correlate these end-to-end measurements to better diagnose and control the use of shared resources. A valuable characterization of such shared resources is the "loss topology". From the perspective of a server with concurrent connections to multiple clients, the loss topology is a logical tree rooted at the server in which edges represent lossy paths between a pair of internal network nodes. We develop an end-to-end unicast packet probing technique and an associated analytical framework to: (1) infer loss topologies, (2) identify loss rates of links in an existing loss topology, and (3) augment a topology to incorporate the arrival of a new connection. Correct, efficient inference of loss topology information enables new techniques for aggregate congestion control, QoS admission control, connection scheduling and mirror site selection. Our extensive simulation results demonstrate that our approach is robust in terms of its accuracy and convergence over a wide range of network conditions.

Typed Abstraction of Complex Network Compositions

The heterogeneity and open nature of network systems make analysis of compositions of components quite challenging, making the design and implementation of robust network services largely inaccessible to the average programmer. We propose the development of a novel type system and practical type spaces which reflect simplified representations of the results and conclusions which can be derived from complex compositional theories in more accessible ways, essentially allowing the system architect or programmer to be exposed only to the inputs and output of compositional analysis without having to be familiar with the ins and outs of its internals. Toward this end we present the TRAFFIC (Typed Representation and Analysis of Flows For Interoperability Checks) framework, a simple flow-composition and typing language with corresponding type system. We then discuss and demonstrate the expressive power of a type space for TRAFFIC derived from the network calculus, allowing us to reason about and infer such properties as data arrival, transit, and loss rates in large composite network applications.

Type Systems for a Network Specification Language With Multiple-Choice Let

When analysing the behavior of complex networked systems, it is often the case that some components within that network are only known to the extent that they belong to one of a set of possible "implementations" – e.g., versions of a specific protocol, class of schedulers, etc. In this report we augment the specification language considered in BUCSTR-2004-021, BUCS-TR-2005-014, BUCS-TR-2005-015, and BUCS-TR-2005-033, to include a non-deterministic multiple-choice let-binding, which allows us to consider compositions of networking subsystems that allow for looser component specifications.

Extending snBench to Support a Graphical Programming Interface for a Sensor Network Tasking Language (STEP)

The purpose of this project is the creation of a graphical "programming" interface for a sensor network tasking language called STEP. The graphical interface allows the user to specify a program execution graphically from an extensible pallet of functionalities and save the results as a properly formatted STEP file. Moreover, the software is able to load a file in STEP format and convert it into the corresponding graphical representation. During both phases a type-checker is running on the background to ensure that both the graphical representation and the STEP file are syntactically correct. This project has been motivated by the Sensorium project at Boston University. In this technical report we present the basic features of the software, the process that has been followed during the design and implementation. Finally, we describe the approach used to test and validate our software.

Integrating Sensor-Network Research and Development into a Software Engineering Curriculum

The emergence of a sensor-networked world produces a clear and urgent need for well-planned, safe and secure software engineering. It is the role of universities to prepare graduates with the knowledge and experience to enter the work-force with a clear understanding of software design and its application to the future safety of computing. The snBench (Sensor Network WorkBench) project aims to provide support to the programming and deployment of Sensor Network Applications, enabling shared sensor embedded spaces to be easily tasked with various sensory applications by different users for simultaneous execution. In this report we discus our experience using the snBench research project as the foundation for semester-long project in a graduate level software engineering class at Boston University (CS511).

Safe Compositional Specification of Network Systems With Polymorphic, Constrained Types

In the framework of iBench research project, our previous work created a domain specific language TRAFFIC [6] that facilitates specification, programming, and maintenance of distributed applications over a network. It allows safety property to be formalized in terms of types and subtyping relations. Extending upon our previous work, we add Hindley-Milner style polymorphism [8] with constraints [9] to the type system of TRAFFIC. This allows a programmer to use for-all quantifier to describe types of network components, escalating power and expressiveness of types to a new level that was not possible before with propositional subtyping relations. Furthermore, we design our type system with a pluggable constraint system, so it can adapt to different application needs while maintaining soundness. In this paper, we show the soundness of the type system, which is not syntax-directed but is easier to do typing derivation. We show that there is an equivalent syntax-directed type system, which is what a type checker program would implement to verify the safety of a network flow. This is followed by discussion on several constraint systems: polymorphism with subtyping constraints, Linear Programming, and Constraint Handling Rules (CHR) [3]. Finally, we provide some examples to illustrate workings of these constraint systems.

NETEMBED: A Network Resource Mapping Service for Distributed Applications

Emerging configurable infrastructures such as large-scale overlays and grids, distributed testbeds, and sensor networks comprise diverse sets of available computing resources (e.g., CPU and OS capabilities and memory constraints) and network conditions (e.g., link delay, bandwidth, loss rate, and jitter) whose characteristics are both complex and time-varying. At the same time, distributed applications to be deployed on these infrastructures exhibit increasingly complex constraints and requirements on resources they wish to utilize. Examples include selecting nodes and links to schedule an overlay multicast file transfer across the Grid, or embedding a network experiment with specific resource constraints in a distributed testbed such as PlanetLab. Thus, a common problem facing the efficient deployment of distributed applications on these infrastructures is that of "mapping" application-level requirements onto the network in such a manner that the requirements of the application are realized, assuming that the underlying characteristics of the network are known. We refer to this problem as the network embedding problem. In this paper, we propose a new approach to tackle this combinatorially-hard problem. Thanks to a number of heuristics, our approach greatly improves performance and scalability over previously existing techniques. It does so by pruning large portions of the search space without overlooking any valid embedding. We present a construction that allows a compact representation of candidate embeddings, which is maintained by carefully controlling the order via which candidate mappings are inserted and invalid mappings are removed. We present an implementation of our proposed technique, which we call NETEMBED – a service that identify feasible mappings of a virtual network configuration (the query network) to an existing real infrastructure or testbed (the hosting network). We present results of extensive performance evaluation experiments of NETEMBED using several combinations of real and synthetic network topologies. Our results show that our NETEMBED service is quite effective in identifying one (or all) possible embeddings for quite sizable queries and hosting networks – much larger than what any of the existing techniques or services are able to handle.

Emergence of Tri-Phasic Muscle Activation from the Non-linear Interactions of Central and Spinal Neural Network Circuits

The origin of the tri-phasic burst pattern, observed in the EMGs of opponent muscles during rapid self-terminated movements, has been controversial. Here we show by computer simulation that the pattern emerges from interactions between a central neural trajectory controller (VITE circuit) and a peripheral neuromuscularforce controller (FLETE circuit). Both neural models have been derived from simple functional constraints that have led to principled explanations of a wide variety of behavioral and neurobiological data, including, as shown here, the generation of tri-phasic bursts.

A Neural Network of Adaptively Timed Reinforcement Learning and Hippocampal Dynamics

A neural model is described of how adaptively timed reinforcement learning occurs. The adaptive timing circuit is suggested to exist in the hippocampus, and to involve convergence of dentate granule cells on CA3 pyramidal cells, and NMDA receptors. This circuit forms part of a model neural system for the coordinated control of recognition learning, reinforcement learning, and motor learning, whose properties clarify how an animal can learn to acquire a delayed reward. Behavioral and neural data are summarized in support of each processing stage of the system. The relevant anatomical sites are in thalamus, neocortex, hippocampus, hypothalamus, amygdala, and cerebellum. Cerebellar influences on motor learning are distinguished from hippocampal influences on adaptive timing of reinforcement learning. The model simulates how damage to the hippocampal formation disrupts adaptive timing, eliminates attentional blocking, and causes symptoms of medial temporal amnesia. It suggests how normal acquisition of subcortical emotional conditioning can occur after cortical ablation, even though extinction of emotional conditioning is retarded by cortical ablation. The model simulates how increasing the duration of an unconditioned stimulus increases the amplitude of emotional conditioning, but does not change adaptive timing; and how an increase in the intensity of a conditioned stimulus "speeds up the clock", but an increase in the intensity of an unconditioned stimulus does not. Computer simulations of the model fit parametric conditioning data, including a Weber law property and an inverted U property. Both primary and secondary adaptively timed conditioning are simulated, as are data concerning conditioning using multiple interstimulus intervals (ISIs), gradually or abruptly changing ISis, partial reinforcement, and multiple stimuli that lead to time-averaging of responses. Neurobiologically testable predictions are made to facilitate further tests of the model.

A Self-Organizing Neural Network Model for Redundant Sensory-Motor Control, Motor Equivalence, and Tool Use

A neural network is introduced which provides a solution of the classical motor equivalence problem, whereby many different joint configurations of a redundant manipulator can all be used to realize a desired trajectory in 3-D space. To do this, the network self-organizes a mapping from motion directions in 3-D space to velocity commands in joint space. Computer simulations demonstrate that, without any additional learning, the network can generate accurate movement commands that compensate for variable tool lengths, clamping of joints, distortions of visual input by a prism, and unexpected limb perturbations. Blind reaches have also been simulated.

A Spectral Network Model of Pitch Perception

A model of pitch perception, called the Spatial Pitch Network or SPINET model, is developed and analyzed. The model neurally instantiates ideas front the spectral pitch modeling literature and joins them to basic neural network signal processing designs to simulate a broader range of perceptual pitch data than previous spectral models. The components of the model arc interpreted as peripheral mechanical and neural processing stages, which arc capable of being incorporated into a larger network architecture for separating multiple sound sources in the environment. The core of the new model transforms a spectral representation of an acoustic source into a spatial distribution of pitch strengths. The SPINET model uses a weighted "harmonic sieve" whereby the strength of activation of a given pitch depends upon a weighted sum of narrow regions around the harmonics of the nominal pitch value, and higher harmonics contribute less to a pitch than lower ones. Suitably chosen harmonic weighting functions enable computer simulations of pitch perception data involving mistuned components, shifted harmonics, and various types of continuous spectra including rippled noise. It is shown how the weighting functions produce the dominance region, how they lead to octave shifts of pitch in response to ambiguous stimuli, and how they lead to a pitch region in response to the octave-spaced Shepard tone complexes and Deutsch tritones without the use of attentional mechanisms to limit pitch choices. An on-center off-surround network in the model helps to produce noise suppression, partial masking and edge pitch. Finally, it is shown how peripheral filtering and short term energy measurements produce a model pitch estimate that is sensitive to certain component phase relationships.

Neural network analysis identifies scaffold properties necessary for in vitro chondrogenesis in elastin-like polypeptide biopolymer scaffolds.

The successful design of biomaterial scaffolds for articular cartilage tissue engineering requires an understanding of the impact of combinations of material formulation parameters on diverse and competing functional outcomes of biomaterial performance. This study sought to explore the use of a type of unsupervised artificial network, a self-organizing map, to identify relationships between scaffold formulation parameters (crosslink density, molecular weight, and concentration) and 11 such outcomes (including mechanical properties, matrix accumulation, metabolite usage and production, and histological appearance) for scaffolds formed from crosslinked elastin-like polypeptide (ELP) hydrogels. The artificial neural network recognized patterns in functional outcomes and provided a set of relationships between ELP formulation parameters and measured outcomes. Mapping resulted in the best mean separation amongst neurons for mechanical properties and pointed to crosslink density as the strongest predictor of most outcomes, followed by ELP concentration. The map also grouped formulations together that simultaneously resulted in the highest values for matrix production, greatest changes in metabolite consumption or production, and highest histological scores, indicating that the network was able to recognize patterns amongst diverse measurement outcomes. These results demonstrated the utility of artificial neural network tools for recognizing relationships in systems with competing parameters, toward the goal of optimizing and accelerating the design of biomaterial scaffolds for articular cartilage tissue engineering.

Influence of network topology and data collection on network inference.

We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data sampling regime influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops and multiple targets of a regulator with small amounts of data, but required more data to recover multiple regulators of a gene. When collecting the same number of data samples at different intervals from the system, the best recovery was produced by sampling intervals long enough such that sampling covered propagation of regulation through the network but not so long such that intervals missed internal dynamics. These results further elucidate the possibilities and limitations of network inference based on biological data.

Evaluating functional network inference using simulations of complex biological systems.

MOTIVATION: Although many network inference algorithms have been presented in the bioinformatics literature, no suitable approach has been formulated for evaluating their effectiveness at recovering models of complex biological systems from limited data. To overcome this limitation, we propose an approach to evaluate network inference algorithms according to their ability to recover a complex functional network from biologically reasonable simulated data. RESULTS: We designed a simulator to generate data representing a complex biological system at multiple levels of organization: behaviour, neural anatomy, brain electrophysiology, and gene expression of songbirds. About 90% of the simulated variables are unregulated by other variables in the system and are included simply as distracters. We sampled the simulated data at intervals as one would sample from a biological system in practice, and then used the sampled data to evaluate the effectiveness of an algorithm we developed for functional network inference. We found that our algorithm is highly effective at recovering the functional network structure of the simulated system-including the irrelevance of unregulated variables-from sampled data alone. To assess the reproducibility of these results, we tested our inference algorithm on 50 separately simulated sets of data and it consistently recovered almost perfectly the complex functional network structure underlying the simulated data. To our knowledge, this is the first approach for evaluating the effectiveness of functional network inference algorithms at recovering models from limited data. Our simulation approach also enables researchers a priori to design experiments and data-collection protocols that are amenable to functional network inference.