Rough set models of Physarum machines

In this paper, we consider transition system models of behaviour of Physarum machines in terms of rough set theory. A Physarum machine, a biological computing device implemented in the plasmodium of Physarum polycephalum (true slime mould), is a natural transition system. In the behaviour of Physarum machines, one can notice some ambiguity in Physarum motions that influences exact anticipation of states of machines in time. To model this ambiguity, we propose to use rough set models created over transition systems. Rough sets are an appropriate tool to deal with rough (ambiguous, imprecise) concepts in the universe of discourse.     

Computational Ability of Cells based on Cell Dynamics and Adaptability

Learning how biological systems solve problems could help to design new methods of computation. Information processing in simple cellular organisms is interesting, as they have survived for almost 1 billion years using a simple system of information processing. Here we discuss a well-studied model system: the large amoeboid Physarum plasmodium. This amoeba can find approximate solutions for combinatorial optimization problems, such as solving a maze or a shortest network problem. In this report, we describe problem solving by the amoeba, and the computational methods that can be extracted from biological behaviors. The algorithm designed based on Physarum is both simple and useful. Tutorial series of three invited papers

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Approximating Mexican highways with slime mould

Plasmodium of Physarum polycephalum is a single cell visible by unaided eye. During its foraging behavior the cell spans spatially distributed sources of nutrients with a protoplasmic network. The geometrical structure of the protoplasmic networks allows the plasmodium to optimize transport of nutrients between remote parts of its body. Assuming major Mexican cities are sources of nutrients that need to be distributed across Mexico, how much does the structure of the Physarum protoplasmic network correspond to the structure of Mexican Federal highway network? To address the issue we undertook a series of laboratory experiments with living P. polycephalum. We represent geographical locations of major cities (19 locations) by oat flakes, place a piece of plasmodium in the area corresponding to Mexico city, record the plasmodium’s foraging behavior and extract topology of the resulting nutrient transport networks. Results of our experiments show that the protoplasmic network formed by Physarum is isomorphic, subject to limitations imposed, to a network of principal highways. Ideas and results in the paper may contribute towards future developments in bio-inspired road planning.     

Construction of living cellular automata using the Physarum plasmodium

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba that has an amorphous cell body. To clearly observe how the plasmodium makes decisions in its motile and exploratory behaviours, we developed a new experimental system to pseudo-discretize the motility of the organism. In our experimental space that has agar surfaces arranged in a two-dimensional lattice, the continuous and omnidirectional movement of the plasmodium was limited to the stepwise one, and the direction of the locomotion was also limited to four neighbours. In such an experimental system, a cellular automata-like system was constructed using the living cell. We further analysed the exploratory behaviours of the plasmodium by duplicating the experimental results in the simulation models of cellular automata. As a result, it was revealed that the behaviours of the plasmodium are not reproduced by only local state transition rules; and for the reproduction, a kind of historical rule setting is needed.     

A simulated annealing‐based maximum‐margin clustering algorithm

Maximum‐margin clustering is an extension of the support vector machine (SVM) to clustering. It partitions a set of unlabeled data into multiple groups by finding hyperplanes with the largest margins. Although existing algorithms have shown promising results, there is no guarantee of convergence of these algorithms to global solutions due to the nonconvexity of the optimization problem. In this paper, we propose a simulated annealing‐based algorithm that is able to mitigate the issue of local minima in the maximum‐margin clustering problem. The novelty of our algorithm is twofold, ie, (i) it comprises a comprehensive cluster modification scheme based on simulated annealing, and (ii) it introduces a new approach based on the combination of k‐means++ and SVM at each step of the annealing process. More precisely, k‐means++ is initially applied to extract subsets of the data points. Then, an unsupervised SVM is applied to improve the clustering results. Experimental results on various benchmark data sets (of up to over a million points) give evidence that the proposed algorithm is more effective at solving the clustering problem than a number of popular clustering algorithms.     

A power law in the exploratory behavior of the <Emphasis Type="Italic">Physarum</Emphasis> plasmodium

The plasmodium of Physarum polycephalum is a unicellular giant amoeba that grows up to macroscopic scale under appropriate condition, and is known to its computational abilities. In this study, we tried to observe the long-term exploratory behavior of the plasmodium in an open environment and to evaluate its efficiency. For this purpose, we developed an experimental system with an extendable substrate. As a result of the experiment, we found that the frequency distribution of the speed of plasmodial locomotion is fitted by power function. By simulation, we further tried to estimate the efficiency of the exploration implemented with the patterns from the plasmodium, and confirmed that it is actually effective.     

基于DSP的鱼雷主动电磁引信信号处理平台设计

主动电磁引信是在世界各国海军鱼雷兵器中得到广泛应用的一种非触发引信,主动电磁引信要发挥其最大作用,信号处理是关键,针对目前我国鱼雷引信信号处理尚处于模拟滤波阶段,提出了采用数字技术的鱼雷引信信号处理机设计方案;采用高性能DSP和FPGA构成核心处理模块,使系统在具有强大运算能力的同时又具有强大的外设管理能力;同时,对数据采集、数据通信和数据存储进行了优化设计,使该信号处理机的功能得到了进一步的扩展,不仅可用于主动电磁引信,也可以作为通用的数字信号处理机使用。     

GS<Superscript>3</Superscript>: a Grid Storage System with Security Features

Technological trend and the advent of worldwide networks, such as the Internet, made computing systems more and more powerful, increasing both processing and storage capabilities. In Grid computing infrastructures, the data storage subsystem is physically distributed among several nodes and logically shared among several users. This highlights the necessity of a) availability for authorized users only, b) confidentiality, and c) integrity of information and data: in one term security. In this work we face the problem of data security in Grid, by proposing a lightweight cryptography algorithm combining the strong and highly secure asymmetric cryptography technique (RSA) with the symmetric cryptography (AES). The proposed algorithm, we named Grid secure storage system (GS³), has been implemented on top of the Grid file access library (GFAL) of the gLite middleware, in order to provide a file system service with cryptography capability and POSIX interface. The choice of implementing GS³ as a file system, the GS3FS, allows to protect the file system structure also, and to overcome the well-known problem of file rewriting in gLite/GFAL environments. In the specification of the GS3FS, particular care is addressed on providing a usable user interface and on implementing a file system that has low impact on the middleware. The final result is the introduction of a new storage Grid service into the gLite middleware, whose overall characteristics are never offered before, at the best of authors’ knowledge. The paper describes and details both the GS³ algorithm and its implementation; the performance of such implementation are evaluated discussing the obtained results and possible application scenarios in order to demonstrate its effectiveness and usefulness.     

XOR Storage Schemes for Frequently Used Data Patterns

In parallel image processing and numerical analysis, various matrix manipulation operations are used intensively. In the past decades, many parallel storage schemes, called skewing schemes, have been proposed to provide simultaneous access to various data patterns (slices of a matrix). The existing storage schemes have the following limitations: (1) The address generation mechanism is dependent on the size of the matrix to be processed, thus the system hardware must be changed to efficiently process different sized matrices. (2) Many schemes have limitations on the machine size and image size (N × N), such as N must be an even power of 2. (3) As more and more frequently used data patterns have been recognized, most schemes can only provide parallel access to a limited range of data patterns. (4) With existing routing techniques, the data alignment (connecting each memory module to a proper processor) may require special hardware. This paper proposes several storage schemes (EE, MG, EE-MG, and EE*MG). They employ only exclusive-or operations for address generation which can be completed in constant time. The address generation mechanism is independent of the matrix size so that different sized matrices can be processed efficiently on a fixed-size machine. The system uses N memory modules where N is any (even or odd) power of 2. These schemes cover more data patterns than any other scheme yet proposed. Patterns of N elements that can be accessed in one memory cycle include diagonals, blocks with various shapes, points scattered over various blocks, and chessboards with various shapes. Data alignment requirements can be easily realized on a general-purpose interconnection network, such as a hypercube or MINs.     

Virtual‐machine‐based heterogeneous checkpointing

Checkpointing an application is the act of saving the application's state during its execution on stable storage, so that if the application fails it can be restarted from the last saved state, thereby avoiding loss of the work that was already done. A heterogeneous checkpoint/restart mechanism allows one to restart an application on a possibly different hardware architecture and/or operating system than those in which the application was saved. This paper explores how to construct such a mechanism at the virtual machine level. That is, rather than dumping the entire state of the application process, the mechanism reported here dumps the state of the application as maintained by a virtual machine. During restart, the saved state is loaded into a new copy of the virtual machine, which continues running from there. The heterogeneous checkpoint/restart mechanism reported here was developed for the OCaml variant of ML. The paper reports on the main issues encountered in building such a mechanism and the design choices made, presents performance evaluations, and discusses some lessons and ideas for extending the work to native code OCaml and Java. Copyright © 2002 John Wiley & Sons, Ltd.     

Petri net models for Physarum machines built to realise Boolean functions

Abstract

In the paper, we describe the possible usage of the biological substrate in the form of Physarum polycephalum in realisation of Boolean functions in their canonical forms. To extort proper behavior from the substrate, Physarum machines (biological computing devices experimentally implemented in plasmodium of P. polycephalum) determining distribution of stimuli (attractants and/or repellents) are created. To model behavior of Physarum machines, we propose to use Petri nets with inhibitor arcs which can be treated as their high-level models.     

基于k个标记样本的弱监督学习框架

聚类是机器学习领域中的一个研究热点,弱监督学习是半监督学习中一个重要的研究方向,有广泛的应用场景.在对聚类与弱监督学习的研究中,提出了一种基于k个标记样本的弱监督学习框架.该框架首先用聚类及聚类置信度实现了标记样本的扩展.其次,对受限玻尔兹曼机的能量函数进行改进,提出了基于k个标记样本的受限玻尔兹曼机学习模型.最后,完成了对该模型的推理并设计相关算法.为了完成对该框架和模型的检验,选择公开的数据集进行对比实验,实验结果表明,基于k个标记样本的弱监督学习框架实验效果较好.     

New Media and the ‘Anchor Baby’ Boom

The term ‘anchor baby’ refers to children born in the U.S. to undocumented migrant parents who are thought to have been conceived in order to improve their parents' chances of attaining citizenship. Though the term is considered racist and dehumanizing by many, it has recently entered into common usage. This study investigates the process by which this has occurred. We test hypotheses derived from theories of mass and new media using multiple data sources and methods of analysis, and find that the main sources of the anchor baby boom are partisan news websites. The findings suggest that new media may be influencing mass media by creating unique and unprecedented opportunities for medium‐sized partisan news organizations.     

A DNA-based memory with <Emphasis Type="Italic">in vitro</Emphasis> learning and associative recall

A DNA-based memory was implemented with in vitro learning and associative recall.The learning protocol stored the sequences to which it was exposed, and memories were recalled by sequence content through DNA-to-DNA template annealing reactions. Experiments demonstrated that biological DNA could be learned, that sequences similar to the training DNA were recalled correctly, and that unlike sequences were differentiated. Theoretically, the memory has a pattern separation capability that is very large, and can learn long DNA sequences. The learning and recall protocols are massively parallel, as well as simple, inexpensive, and quick. The memory has several potential applications in detection and classification of biological sequences, as well as a massive storage capacity for non-biological data.     

计算机实验室的资源配置及维护策略

本文提出了采取NAT技术、VMware虚拟机技术及Serv-U FTP服务器对计算机实验室的资源进行合理配置．解决了IP地址不足、一机多用及用户数据存储；采取网络硬盘还原卡，实现了硬盘数据保护及网络对拷，达到了减少维护工作量的目的。     

Querying sequence databases with transducers

This paper develops a database query language called Transducer Datalog motivated by the needs of a new and emerging class of database applications. In these applications, such as text databases and genome databases, the storage and manipulation of long character sequences is a crucial feature. The issues involved in managing this kind of data are not addressed by traditional database systems, either in theory or in practice. To address these issues, we recently introduced a new machine model called a generalized sequence transducer. These generalized transducers extend ordinary transducers by allowing them to invoke other transducers as “subroutines.” This paper establishes the computational properties of Transducer Datalog, a query language based on this new machine model. In the process, we develop a hierarchy of time-complexity classes based on the Ackermann function. The lower levels of this hierarchy correspond to well-known complexity classes, such as polynomial time and hyper-exponential time. We establish a tight relationship between levels in this hierarchy and the depth of subroutine calls within Transducer Datalog programs. Finally, we show that Transducer Datalog programs of arbitrary depth express exactly the sequence functions computable in primitive-recursive time. Received: 12 March 1998 / 30 August 1999     

Closed-form solutions of singular KYP lemma: strongly passive systems,and fast lossless trajectories

In this paper, we deal with a special class of passive systems, which possess the characteristic property of having no finite spectral zeros. We call these systems strongly passive. It is well known that, for these systems, storage functions, i.e. solutions to the linear matrix inequality (LMI) arising from the Kalman–Yakubovich–Popov (KYP) lemma, cannot be obtained by the conventional approach of algebraic Riccati equations (AREs) and Hamiltonian matrices. In this paper, we first show that a strongly passive system always admits a unique storage function. We then provide a closed-form expression for this unique storage function. Using the closed-form formula of the unique storage function we characterise the ‘lossless’ trajectories of strongly passive systems and show that such systems admit impulsive lossless trajectories on the half-line; we call them fast lossless trajectories. This adds to the existing notion that such systems do not admit any ‘slow’ lossless trajectories.     

A novel machine vision application for analysis and visualization of confocal microscopic images

In this paper, a novel machine vision application is presented for analyzing and visualizing confocal microscopy images of biological preparations. The proposed system is divided into three subsystems: a 3D curved surface extraction subsystem that generates 3D surfaces passing through selected key points in confocal image stacks; a 2D image projection subsystem that produces a flattened projection of the extracted curved surface; and an image mosaic subsystem that concatenates a series of image projections to form a view of an entire biological preparation. A combination of cubic interpolation and boundary matching is employed to reconstruct the 3D curved surface that passes through selected key points. The projection process integrates data fidelity and local smoothness constraints, producing a color or intensity projection along the desired 3D surface. Registration is achieved by aligning and minimizing the sum of the squared distances (SSD) between the intensities of the corresponding pixels. Two biological applications of the proposed system are reported to illustrate how the vision system could aid in biological research.Received: 18 August 2003, Accepted: 18 March 2004, Published online: 4 November 2004 Correspondence to: David M. Chelberg     

Experiences building a communication‐oriented JavaOS

Mobile code makes it easier to maintain, debug, update, and customize a system. Active networks are one of the more interesting applications of mobile code: code is injected into the nodes of a network to customize the network's functionality, such as routing, and to add new features, such as special‐purpose congestion control and filtering algorithms. The challenge is to develop a communication‐oriented platform for such systems. We refer to mobile code targeted at low‐level, communication‐oriented systems like active networks as liquid software, the key distinction being that liquid software is focused on the efficient transfer of data, not high‐performance computation. To this end, we have designed and implemented Joust, which consists of a complete re‐implementation of the Java virtual machine (including both the runtime system and a just‐in‐time compiler), running on the Scout operating system (a configurable, communication‐oriented OS). The result is a configurable, high‐performance platform for running liquid software. We present the results of implementing two different applications of liquid software on Joust, including a prototype architecture for active networks. Copyright © 2000 John Wiley & Sons, Ltd.     

Classification of functional data: A segmentation approach

We suggest a classification and feature extraction method on functional data where the predictor variables are curves. The method, called functional segment discriminant analysis (FSDA), combines the classical linear discriminant analysis and support vector machine. FSDA is particularly useful for irregular functional data, characterized by spatial heterogeneity and local patterns like spikes. FSDA not only reduces the computation and storage burden by using a fraction of the spectrum, but also identifies important predictors and extracts features. FSDA is highly flexible, easy to incorporate information from other data sources and/or prior knowledge from the investigators. We apply FSDA to two public domain data sets and discuss the understanding developed from the study.