Imagery in multi-modal object learning

Spatial objects may not only be perceived visually but also by touch. We report recent experiments investigating to what extent prior object knowledge acquired in either the haptic or visual sensory modality transfers to a subsequent visual learning task. Results indicate that even mental object representations learnt in one sensory modality may attain a multi-modal quality. These findings seem incompatible with picture-based reasoning schemas but leave open the possibility of modality-specific reasoning mechanisms.

An efficient knowledge transfer solution to a novel SMDP formalization of a broker's decision problem

This paper introduces a new technique for optimizing the trading strategy of brokers that autonomously trade in re- tail and wholesale markets. Simultaneous optimization of re- tail and wholesale strategies has been considered by existing studies as intractable. Therefore, each of these strategies is optimized separately and their interdependence is generally ignored, with resulting broker agents not aiming for a glob- ally optimal retail and wholesale strategy. In this paper, we propose a novel formalization, based on a semi-Markov deci- sion process (SMDP), which globally and simultaneously op- timizes retail and wholesale strategies. The SMDP is solved using hierarchical reinforcement learning (HRL) in multi- agent environments. To address the curse of dimensionality, which arises when applying SMDP and HRL to complex de- cision problems, we propose an ecient knowledge transfer approach. This enables the reuse of learned trading skills in order to speed up the learning in new markets, at the same time as making the broker transportable across market envi- ronments. The proposed SMDP-broker has been thoroughly evaluated in two well-established multi-agent simulation en- vironments within the Trading Agent Competition (TAC) community. Analysis of controlled experiments shows that this broker can outperform the top TAC-brokers. More- over, our broker is able to perform well in a wide range of environments by re-using knowledge acquired in previously experienced settings.

Achievable performance gain of IEEE 802.11 multi-rate link adaptation algorithm with cross-layer design

Link quality-based rate adaptation has been widely used for IEEE 802.11 networks. However, network performance is affected by both link quality and random channel access. Selection of transmit modes for optimal link throughput can cause medium access control (MAC) throughput loss. In this paper, we investigate this issue and propose a generalised cross-layer rate adaptation algorithm. It considers jointly link quality and channel access to optimise network throughput. The objective is to examine the potential benefits by cross-layer design. An efficient analytic model is proposed to evaluate rate adaptation algorithms under dynamic channel and multi-user access environments. The proposed algorithm is compared to link throughput optimisation-based algorithm. It is found rate adaptation by optimising link layer throughput can result in large performance loss, which cannot be compensated by the means of optimising MAC access mechanism alone. Results show cross-layer design can achieve consistent and considerable performance gains of up to 20%. It deserves to be exploited in practical design for IEEE 802.11 networks.

Adaptive agents in changing environments, the role of modularity

We explored the role of modularity as a means to improve evolvability in populations of adaptive agents. We performed two sets of artificial life experiments. In the first, the adaptive agents were neural networks controlling the behavior of simulated garbage collecting robots, where modularity referred to the networks architectural organization and evolvability to the capacity of the population to adapt to environmental changes measured by the agents performance. In the second, the agents were programs that control the changes in network's synaptic weights (learning algorithms), the modules were emerged clusters of symbols with a well defined function and evolvability was measured through the level of symbol diversity across programs. We found that the presence of modularity (either imposed by construction or as an emergent property in a favorable environment) is strongly correlated to the presence of very fit agents adapting effectively to environmental changes. In the case of learning algorithms we also observed that character diversity and modularity are also strongly correlated quantities. © 2014 Springer Science+Business Media New York.

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.

A Proposed Structure of Knowledge-Based Hybrid Intelligent Systems for Sophisticated Environments

The paper deals with a problem of intelligent system’s design for complex environments. There is discussed a possibility to integrate several technologies into one basic structure. One possible structure is proposed in order to form a basis for intelligent system that would be able to operate in complex environments. The basic elements of the proposed structure have found their implemented in software system. This software system is shortly presented in the paper. The most important results of experiments are outlined and discussed at the end of the paper. Some possible directions of further research are sketched.

Multi-Agent Security System based on Neural Network Model of User's Behavior

It is proposed an agent approach for creation of intelligent intrusion detection system. The system allows detecting known type of attacks and anomalies in user activity and computer system behavior. The system includes different types of intelligent agents. The most important one is user agent based on neural network model of user behavior. Proposed approach is verified by experiments in real Intranet of Institute of Physics and Technologies of National Technical University of Ukraine "Kiev Polytechnic Institute”.

A Super-Dimension Approach in ROLAP Environments

Often the designer of ROLAP applications follows up with the question “can I create a little joiner table with just the two dimension keys and then connect that table to the fact table?” In a classic dimensional model there are two options - (a) both dimensions are modeled independently or (b) two dimensions are combined into a super-dimension with a single key. The second approach is not widely used in ROLAP environments but it is an important sparsity handling method in MOLAP systems. In ROLAP this design technique can also bring storage and performance benefits, although the model becomes more complicated. The dependency between dimensions is a key factor that the designers have to consider when choosing between the two options. In this paper we present the results of our storage and performance experiments over a real life data cubes in reference to these design approaches. Some conclusions are drawn.

Large scale multi-view stereopsis evaluation

The seminal multiple view stereo benchmark evaluations from Middlebury and by Strecha et al. have played a major role in propelling the development of multi-view stereopsis methodology. Although seminal, these benchmark datasets are limited in scope with few reference scenes. Here, we try to take these works a step further by proposing a new multi-view stereo dataset, which is an order of magnitude larger in number of scenes and with a significant increase in diversity. Specifically, we propose a dataset containing 80 scenes of large variability. Each scene consists of 49 or 64 accurate camera positions and reference structured light scans, all acquired by a 6-axis industrial robot. To apply this dataset we propose an extension of the evaluation protocol from the Middlebury evaluation, reflecting the more complex geometry of some of our scenes. The proposed dataset is used to evaluate the state of the art multiview stereo algorithms of Tola et al., Campbell et al. and Furukawa et al. Hereby we demonstrate the usability of the dataset as well as gain insight into the workings and challenges of multi-view stereopsis. Through these experiments we empirically validate some of the central hypotheses of multi-view stereopsis, as well as determining and reaffirming some of the central challenges.

Multi-model fitting based on minimum spanning tree

This paper presents a novel approach to the computation of primitive geometrical structures, where no prior knowledge about the visual scene is available and a high level of noise is expected. We based our work on the grouping principles of proximity and similarity, of points and preliminary models. The former was realized using Minimum Spanning Trees (MST), on which we apply a stable alignment and goodness of fit criteria. As for the latter, we used spectral clustering of preliminary models. The algorithm can be generalized to various model fitting settings, without tuning of run parameters. Experiments demonstrate the significant improvement in the localization accuracy of models in plane, homography and motion segmentation examples. The efficiency of the algorithm is not dependent on fine tuning of run parameters like most others in the field.

On the k-anonymization of time-varying and multi-layer social graphs

The popularity of online social media platforms provides an unprecedented opportunity to study real-world complex networks of interactions. However, releasing this data to researchers and the public comes at the cost of potentially exposing private and sensitive user information. It has been shown that a naive anonymization of a network by removing the identity of the nodes is not sufficient to preserve users’ privacy. In order to deal with malicious attacks, k -anonymity solutions have been proposed to partially obfuscate topological information that can be used to infer nodes’ identity. In this paper, we study the problem of ensuring k anonymity in time-varying graphs, i.e., graphs with a structure that changes over time, and multi-layer graphs, i.e., graphs with multiple types of links. More specifically, we examine the case in which the attacker has access to the degree of the nodes. The goal is to generate a new graph where, given the degree of a node in each (temporal) layer of the graph, such a node remains indistinguishable from other k-1 nodes in the graph. In order to achieve this, we find the optimal partitioning of the graph nodes such that the cost of anonymizing the degree information within each group is minimum. We show that this reduces to a special case of a Generalized Assignment Problem, and we propose a simple yet effective algorithm to solve it. Finally, we introduce an iterated linear programming approach to enforce the realizability of the anonymized degree sequences. The efficacy of the method is assessed through an extensive set of experiments on synthetic and real-world graphs.

A coordinated control scheme for power demand changes in a PMSG based multi-terminal DC wind farm

Although maximum power point tracking (MPPT) is crucial in the design of a wind power generation system, the necessary control strategies should also be considered for conditions that require a power reduction, called de-loading in this paper. A coordinated control scheme for a proposed current source converter (CSC) based DC wind energy conversion system is presented in this paper. This scheme combines coordinated control of the pitch angle, a DC load dumping chopper and the DC/DC converter, to quickly achieve wind farm de-loading. MATLAB/Simulink simulations and experiments are used to validate the purpose and effectiveness of the control scheme, both at the same power level. © 2013 IEEE.

Adaptive fault-tolerant teleoperation

While the robots gradually become a part of our daily lives, they already play vital roles in many critical operations. Some of these critical tasks include surgeries, battlefield operations, and tasks that take place in hazardous environments or distant locations such as space missions. ^ In most of these tasks, remotely controlled robots are used instead of autonomous robots. This special area of robotics is called teleoperation. Teleoperation systems must be reliable when used in critical tasks; hence, all of the subsystems must be dependable even under a subsystem or communication line failure. ^ These systems are categorized as unilateral or bilateral teleoperation. A special type of bilateral teleoperation is described as force-reflecting teleoperation, which is further investigated as limited- and unlimited-workspace teleoperation. ^ Teleoperation systems configured in this study are tested both in numerical simulations and experiments. A new method, Virtual Rapid Robot Prototyping, is introduced to create system models rapidly and accurately. This method is then extended to configure experimental setups with actual master systems working with system models of the slave robots accompanied with virtual reality screens as well as the actual slaves. Fault-tolerant design and modeling of the master and slave systems are also addressed at different levels to prevent subsystem failure. ^ Teleoperation controllers are designed to compensate for instabilities due to communication time delays. Modifications to the existing controllers are proposed to configure a controller that is reliable in communication line failures. Position/force controllers are also introduced for master and/or slave robots. Later, controller architecture changes are discussed in order to make these controllers dependable even in systems experiencing communication problems. ^ The customary and proposed controllers for teleoperation systems are tested in numerical simulations on single- and multi-DOF teleoperation systems. Experimental studies are then conducted on seven different systems that included limited- and unlimited-workspace teleoperation to verify and improve simulation studies. ^ Experiments of the proposed controllers were successful relative to the customary controllers. Overall, by employing the fault-tolerance features and the proposed controllers, a more reliable teleoperation system is possible to design and configure which allows these systems to be used in a wider range of critical missions. ^

Foundational forensic techniques for cellular and ad hoc multi-hop networks

The Internet has become an integral part of our nation’s critical socio-economic infrastructure. With its heightened use and growing complexity however, organizations are at greater risk of cyber crimes. To aid in the investigation of crimes committed on or via the Internet, a network forensics analysis tool pulls together needed digital evidence. It provides a platform for performing deep network analysis by capturing, recording and analyzing network events to find out the source of a security attack or other information security incidents. Existing network forensics work has been mostly focused on the Internet and fixed networks. But the exponential growth and use of wireless technologies, coupled with their unprecedented characteristics, necessitates the development of new network forensic analysis tools. This dissertation fostered the emergence of a new research field in cellular and ad-hoc network forensics. It was one of the first works to identify this problem and offer fundamental techniques and tools that laid the groundwork for future research. In particular, it introduced novel methods to record network incidents and report logged incidents. For recording incidents, location is considered essential to documenting network incidents. However, in network topology spaces, location cannot be measured due to absence of a ‘distance metric’. Therefore, a novel solution was proposed to label locations of nodes within network topology spaces, and then to authenticate the identity of nodes in ad hoc environments. For reporting logged incidents, a novel technique based on Distributed Hash Tables (DHT) was adopted. Although the direct use of DHTs for reporting logged incidents would result in an uncontrollably recursive traffic, a new mechanism was introduced that overcome this recursive process. These logging and reporting techniques aided forensics over cellular and ad-hoc networks, which in turn increased their ability to track and trace attacks to their source. These techniques were a starting point for further research and development that would result in equipping future ad hoc networks with forensic components to complement existing security mechanisms.

Local biomass control on the composition and reactivity of particulate organic matter in aquatic environments

Freshwater ecosystems have been recognized as important components of the global carbon cycle, and the flux of organic matter (OM) from freshwater to marine environments can significantly affect estuarine and coastal productivity. The focus of this study was the assessment of carbon dynamics in two aquatic environments, namely the Florida Everglades and small prairie streams in Kansas, with the aim of characterizing the biogeochemistry of OM. In the Everglades, particulate OM (POM) is mostly found as a layer of flocculent material (floc). While floc is believed to be the main energy source driving trophic dynamics in this oligotrophic wetland, not much is known about its biogeochemistry. The objective of this study was to determine the origin/sources of OM in floc using biomarkers and pigment-based chemotaxonomy to assess specific biomass contributions to this material, on a spatial (freshwater marshes vs. mangrove fringe) and seasonal (wet vs. dry) scales. It was found that floc OM is derived from the local vegetation (mainly algal components and macrophyte litter) and its composition is controlled by seasonal drivers of hydrology and local biomass productivity. Photo-reactivity experiments showed that light exposure on floc resulted in photo-dissolution of POC with the generation of significant amounts of both dissolved OM (DOM) and nutrients (N & P), potentially influencing nutrient dynamics in this ecosystem. The bio-reactivity experiments determined as the amount and rate of CO2 evolution during incubation were found to vary on seasonal and spatial scales and were highly influenced by phosphorus limitation. Not much is known on OM dynamics in small headwater streams. The objective of this study was to determine carbon dynamics in sediments from intermittent prairie streams, characterized by different vegetation cover for their watershed (C4 grasses) vs. riparian zone (C3 plants). In this study sedimentary OM was characterized using a biomarker and compound specific carbon stable isotope approach. It was found that the biomarker composition of these sediments is dominated by higher plant inputs from the riparian zone, although inputs from adjacent prairie grasses were also apparent. Conflicting to some extent with the River Continuum Concept, sediments of the upper reaches contained more degraded OM, while the lower reaches were enriched in fresh material deriving from higher plants and plankton sources as a result of hydrological regimes and particle sorting.