waashk/dblp huggingface dataset:
hsp-hmmer: a tool for protein domain identification on a large scale. hmmer is arguably the best tool for protein domain identification, which is essential for biological function prediction. there are many software and hardware enhancements of hmmer; however, most of them are not scalable to a large number of processors. the exponential growth of the number of protein sequences in public databases, which is currently set at more than 13 million, demands the use of hmmer on a very large scale. we have developed a highly scalable parallel (hsp) hmmer approach that enables identification of conserved functional domains in millions of proteins in less than a day using thousands of processing nodes on a supercomputer.
real-time multi-view vision systems using wsns. multi-view vision systems are collaborative distributed applications devoted to image processing. applications based on multi-view vision systems can recognize shapes, track moving targets, etc. to activate alarms, or to propogate information through the network. these systems require quality of service from the network and real-time support at the operating system level. wireless sensor networks (wsns) were born for monitoring applications providing best effort services in non-critical environments. nonetheless the recent evolution of hardware platforms, and the existence of real-time kernels as well as network stacks supporting real-time traffic let us envisage the deployment of wsns to new domains like that of multi-view vision. hereby we discuss the feasibility of an object detection system based on vision and deployed through a wsn. for such a purpose, we implemented in the real-time network simulator (rtns) a working model for image detection and in-network processing. referring to a simple star-shaped network scenario, we analyze the system performances from a real-time perspective.
the people, the process or the technology?: using the ace framework to make tradeoffs in service delivery improvement. in today's service-oriented economy there is a critical need for prescriptive and evolutionary methods to improve the performance of services in complex enterprises. the contribution here is the adaptive complex enterprise (ace) method for overall system improvement that integrates techniques from computer science and systems engineering. a case study of an it department within the healthcare industry is used to (a) characterize the service challenges, (b) analyze the tradeoffs and (c) make the systematic, continuous selection of improvements to achieve global lean through local behavior.
construct anticancer drug-drug correlation network. network biology methods have been promising in linking diseases, genes, and drugs. in this study, we propose a novel computational method to construct drug-drug correlation networks, which consist of drug compounds as network graph nodes and correlated protein-drug profiles above a pre-determined threshold as network graph edges. this computational method is based on extensions of related work on identifying disease-specific proteins within protein-protein sub-networks, and mining protein-drug association profiles from biomedical literature. our method provides a quantitative framework to compare how each drug compound from one therapeutic area is correlated with other drug compounds in other therapeutic areas, using a drug's protein-drug association profile mined from biomedical literature. we applied this method to the study of drug re-purposing and found that two breast cancer drugs "mitomycin" and "bleomycin" may be top drug candidates for treating pancreatic cancers.
a general service oriented approach for managing virtual machines allocation. virtualization is an essential enabling technology for building and controlling computing frameworks that can dynamically adapt available physical resources to transient tasks such as the temporary creation of a virtual computing center tailored to the needs of a virtual organization. in this paper we will report on our strategy for the creation of virtual computer clusters based on standard service-oriented architecture (soa) and hosts virtualization technologies. we will describe our infrastructure designed for dynamical allocation of resources to applications via a general control plane based on workflows of coordinated web services. the control plane is based on logically independent services that are responsible for physical resource management and virtual nodes deployment. the control plane is also responsible for operations on virtual clusters such as their creation, startup and control.
storage architecture and software support for slc/mlc combined flash memory. we propose a novel flash memory management software for slc/mlc combined flash memories which are recently introduced to provide flexible and cost-efficient embedded storage systems. to provide a fast and large capacity of flash memory, the proposed scheme utilizes the slc area as log buffer and the mlc area as data block. considering the high write cost of mlc flash, the garbage collection for the slc log buffer moves a page into the mlc data block only when the page is cold or the page invokes a small migration cost. we also propose the bypassing technique which sends a large sequential data into the mlc flash directly not through the slc log buffer. from the experiments, we can know that the proposed scheme utilizes the slc log buffer effectively providing better performance compared with the previous flash management schemes for the slc/mlc combined flash.1
runtime monitoring of web service choreographies using streaming xml. a wide range of web service choreography constraints on the content and sequentiality of messages can be translated into linear temporal logic (ltl). although they can be checked statically on abstractions of actual services, it is desirable that violations of these specifications be also detected at runtime. in this paper, we show that, given a suitable translation of ltl formul&aelig; into xquery expressions, such runtime monitoring of choreography constraints is possible by feeding the trace of messages to a streaming xquery processor. the forward-only fragment of ltl is introduced; it represents the fragment of ltl supported by available streaming engines.
organising mas: a formal model based on organisational mechanisms. in this paper, we propose a general formal framework for organising multiagent systems whose participants are rational agents. this model is based on the idea of organisational mechanisms. these are mechanisms introduced in a multiagent system with the aim of influencing the behaviour of the agents towards more effectiveness with regard to some objectives. we define two kinds of organisational mechanisms: i) informative mechanisms which provide additional information to agents, that may persuade agents to behave in a certain way, and ii) regulative mechanisms which produce changes in the environment of the agents, that may impose certain behaviours. we also define some properties of these mechanisms which will make it possible to prove certain characteristics of organised multiagent systems. finally, we present a discussion about how the social concepts proposed by different organisational paradigms can be considered as either informative or regulative organisational mechanisms.
analysis of the secure rtp protocol on voice over wireless networks using extended medqos. this paper presents an empirical investigation of the impact of secure rtp (srtp) on voip calls over wireless networks: 802.11 and bluetooth. for the purpose of evaluating this impact we developed an analysis tool based on e-model and security aspects of srtp which attempts to determine the balance of quality of service versus security. the results demonstrate that the impact of srtp to voip should not be disregarded. mos scores of secure calls computed from e-model pointed out an undesirable level of quality of service on single calls using wireless channels. this quality degradation also leads to the reduction of channel capacity to offer simultaneous calls. the developed analysis tool indicated three important factors to this degradation: time to encrypt, time to authenticate and time to form a cryptographic context for each srtp packet sent and received.
market-based coordination for intersection control. the control of large-scale open distributed systems, where many autonomous, intelligent entities interact with the environment and with each other, is not a trivial task. market-based methods have been applied to the design and the control of such systems, by defining the "rules of the game" in such a way that a desired global outcome is obtained without any centralized decision making. the future traffic control systems, where intelligent infrastructures with sensors and computing power will interact with millions of drivers commuting from their homes to their respective workplaces, are an example of such systems. in this paper we model the traffic as a computational economy, where drivers trade with the intelligent infrastructure in a virtual marketplace. we design market rules to align the "global profit" (revenues from the infrastructure use) with the "social welfare" (average travel time), in a way that, in situations of similar traffic load, an increase of the infrastructure's monetary benefit usually implies a decrease of the drivers' average travel time.
secure routing in peer-to-peer distributed hash tables. distributed hash tables (dhts) provide efficient and scalable lookup mechanisms for locating data in peer-to-peer (p2p) networks. several issues, however, prevent dht-based p2p networks from being widely deployed -- one of which is security. malicious peers may modify, drop, misroute lookup requests, or even collude to deny the availability of target data. to address these security concerns, we propose an extension to chord named sechord. the main idea is that the source can determine whether the next hop is valid or invalid by estimating how far the next hop is from its finger pointer. if the next hop is too far away from the finger pointer, especially compared to the average distance between two consecutive peers, the source can infer some ongoing malicious activities. our modifications require no trust between two nodes except node join. moreover, each node utilizes locally available information to evaluate hops encountered during the lookup routing process for validity. these modifications have been implemented and evaluated in the presence of malicious nodes. our results show that sechord significantly enhances the security of structured p2p systems at the expense of slightly increased hop count.
early phase requirements assessment of a teletreatment trial. this paper presents the early phase requirements elicitation of a teletreatment trial and the assessment of the requirements in respect of their importance to the trial and the feasibility of the corresponding adaptations of the telemedicine system within the trial project constraints. the elicitation approach and techniques adopt the particulars of the telemedicine working practices. the proposed approach not only uses the treatment description and scenario, it also utilizes the trial design. a trial design defines the settings of a trial and develops the treatment protocols such that treatment efficacy can be evaluated based on evidence. such a design has to be a priori approved by a medical ethical committee, which may impose additional constraints that influence the elicited requirements. the approach therefore involves stakeholders who are not necessarily the users of the system to be. in line with the telemedicine working practices, the approach is moreover based on the identification and analysis of the tasks and task objectives associated to the responsibilities of the involved stakeholders. furthermore, the elicitation is cyclic and applies a collection of known techniques and informal specification styles (e.g. tables and mock-ups). results of the cycles converge to a set of requirements understood and agreed upon by the trial designers, who are medical professionals, typically unaware of the methods and techniques applied by engineers, but who co-shape the telemedicine system to be. this way of working manages expectations better, necessary in a telemedicine collaboration.
computing data cubes using exact sub-graph matching: the sequential mcg approach. in this paper, we present a novel full cube computation and representation approach, named mcg. in a data cube, each cuboid can be viewed as a set of sub-graphs. in general, redundant sub-graphs are quite common in a data cube, but their elimination is a hard problem as some previous cube approaches demonstrate. the mcg approach differentiates significantly from previous approaches since it efficiently eliminates all common sub-graphs from the entire cube, based on an exact sub-graph matching solution. we propose a matching function to guarantee one-to-one mapping between sub-graphs. the function is computed incrementally, in a top-down fashion, and its computation uses a minimal amount of information to generate unique results, regardless of whether we are using distributive, algebraic or holistic measures. mcg performance analysis demonstrates a similar runtime when compared to star approach and very low memory consumption (94--98% reduction) when compared to a full cube representation.
characterizing 1-dof henneberg-i graphs with efficient configuration spaces. we define and study exact, efficient representations of realization spaces of a natural class of underconstrained 2d euclidean distance constraint systems (linkages or frameworks) based on 1-dof henneberg-i graphs. each representation corresponds to a choice of parameters and yields a different parametrized configuration space. our notion of efficiency is based on the algebraic complexities of sampling the configuration space and of obtaining a realization from the sample (parametrized) configuration. significantly, we give purely combinatorial characterizations that capture (i) the class of graphs that have efficient configuration spaces and (ii) the possible choices of representation parameters that yield efficient configuration spaces for a given graph. our results automatically yield an efficient algorithm for sampling realizations, without missing extreme or boundary realizations. in addition, our results formally show that our definition of efficient configuration space is robust and that our characterizations are tight. we choose the class of 1-dof henneberg-i graphs in order to take the next step in a systematic and graded program of combinatorial characterizations of efficient configuration spaces. in particular, the results presented here are the first characterizations that go beyond graphs that have connected and convex configuration spaces.
retrieving valid matches for xml keyword search. adapting keyword search to xml data has been attractive recently, generalized as xml keyword search (xks). its fundamental task is to retrieve meaningful and concise result for the given keyword query, and [1] is the latest work which returns the fragments rooted at the slca (smallest lca - lowest common ancestor) nodes. to guarantee the fragments only containing meaningful nodes, [1] proposed a contributor-based filtering mechanism in its maxmatch algorithm. however, the filtering mechanism is not sufficient. it will commit the false positive problem (discarding interesting nodes) and the redundancy problem (keeping uninteresting nodes). in this paper, we propose a new filtering mechanism to overcome those two problems. the fundamental concept is valid contributor. a child v is a valid contributor to its parent u, if (1) v's label is unique among all u's children; or (2) for the siblings with same label as v, v's content is not covered by any of them. our new filtering mechanism is: all the nodes in each retrieved fragment should be valid contributors to their parents. by doing so, it not only satisfies the axiomatic properties proposed by [1], but also ensures the filtered fragment more meaningful and concise. we implement our proposal in validmatch, and compare validmatch with maxmatch on real and synthetic xml data. the result verifies our claims, and shows the effectiveness of our valid-contributor-based filtering mechanism.
securing key issuing in peer-to-peer networks. compared with the public key infrastructure (pki) technique, identity based cryptography (ibc) can simplify the key management process in peer-to-peer (p2p) networks significantly. the identity of a peer (e.g., peer identifier or peer geometric coordinate) in p2p overlay networks is used to create its public key, thus avoiding the use of any certificates. these ibc-based systems are scalable, simple to administer, and each user can carry out anytime/anywhere encryption, establish secure communication channels, prove its identity to other nodes, verify protected messages and produce a form of signature with non-repudiation properties.
clustering malware-generated spam emails with a novel fuzzy string matching algorithm. in this paper, a fuzzy-matching clustering algorithm is introduced to group subjects found in spam emails which are generated by malware. a modified scoring strategy is applied in dynamic programming to find subjects that are similar to each other. a recursive seed selection strategy allows the algorithm to detect similar patterns even when the spammer creates a variation of the original pattern. a sliding threshold based on string length helps to minimize false-positives. the algorithm proves to be effective in detecting and grouping spam emails using templates. it also helps spam investigators to collect and sort large amount of malware-generated spam more efficiently without looking at the email content.
boosting the performance of computing systems through adaptive configuration tuning. good system performance depends on the correct setting of its configuration parameters. it is observed that such optimal configuration relies on the incoming workload of the system. in this paper, we utilize the markov decision process (mdp) theory and present a reinforcement learning strategy to discover the complex relationship between the system workload and the corresponding optimal configuration. considering the limitations of current reinforcement learning algorithms used in system management, we present a different learning architecture to facilitate the configuration tuning task which includes two units: the actor and critic. while the actor realizes a stochastic policy that maps the system state to the corresponding configuration setting, the critic uses a value function to provide the reinforcement feedback to the actor. both the actor and critic are implemented by multiple layer neural networks, and the error back-propagation algorithm is used to adjust the network weights based on the temporal difference error produced in the learning. experimental results demonstrate that the proposed learning process can identify the correct configuration tuning rule which in turn improves the system performance significantly.
hits algorithm improvement using anchor-related text extracted by dom structure analysis. kleinberg's hits algorithm is a popular algorithm to rank web pages. one of its problems is the topic drift problem. previous researchers have tried to solve this problem using anchor-related text. we proposed another type of anchor-related text in our previous study. this is found by executing a deep analysis on the dom structures of web pages. we call our anchor-related text dom-based anchor-related text (dom-text). in this paper, we investigate the effectiveness of using dom-text for improving the hits algorithm. we examine how much we can improve the hits algorithm. we also compare dom-text with anchor-related text of other kinds. the experimental results show that the use of dom-text is the best for improving the hits algorithm.
identifying discourse mistakes in web debates: moderation in the dcc. integrating consultative and deliberative environments for popular participation in democratic issues and creating virtual communities make it possible to model decision-making processes. for this reason, the democratic citizenship community (dcc) was developed, based on the government-citizen interactive model. in this model, debates are structured in a different manner and the moderator's participation in debates is based on discourse theory, in relation to discourse mistakes. this research analyzes the moderator's role by means of a case study.
evaluating algorithms that learn from data streams. learning from data streams is a research area of increasing importance. nowadays, several stream learning algorithms have been developed. most of them learn decision models that continuously evolve over time, run in resource-aware environments, and detect and react to changes in the environment generating data. one important issue, not yet conveniently addressed, is the design of experimental work to evaluate and compare decision models that evolve over time. in this paper we propose a general framework for assessing the quality of streaming learning algorithms. we defend the use of predictive sequential error estimates over a sliding window to assess performance of learning algorithms that learn from open-ended data streams in non-stationary environments. this paper studies properties of convergence and methods to comparatively assess algorithms performance.
semantic information and sensor networks. embedded networked sensing involves untethered, networked devices tightly coupled to the physical world, to monitor and interact with it. raw sensor observation can be annotated with semantic metadata to provide interpretation and context for it. in this paper, we discuss what, why and how of semantic sensor data and semantic sensor networks. specifically, we explore (i) benefits of augmenting sensor data with semantics, (ii) domain-specific and spatio-temporal problems to be addressed, (iii) role of knowledge representation and reasoning (semantic web technology), and (iv) standardization efforts underway to make sensor-related data and sensor observations widely available.
extended static checking in jml4: benefits of multiple-prover support. the implementations of many seemingly simple algorithms are beyond the ability of traditional extended static checking (esc) tools to verify. not being able to verify toy examples is often enough to turn users off of the idea of using formal methods. esc4, the esc component of the jml4 project, is able to verify many more kinds of methods in part because of its use of novel techniques which apply multiple theorem provers. in particular, we present offline user-assisted esc (oua-esc), a new form of verification that lies between esc and full static program verification (fspv), that allows users to control the level of completeness of the tool. esc4's improved performance should encourage greater use of static verification.
efficient maintenance of distributed data in highly dynamic opportunistic grids. opportunistic grids are a class of computational grids that can leverage the idle processing and storage capacity of shared workstations in laboratories, companies, and universities to perform useful computation. oppstore is a middleware that allows using the free disk space of machines from an opportunistic grid for the distributed storage of application data. but when machines depart from the grid, it is necessary to reconstruct the fragments that were stored in that machines. depending on the amount of stored data and the rate of machine departures, the generated traffic may make the distributed storage of data infeasible. in this work we present and evaluate a fragment recovery mechanism that makes viable to achieve redundancy and large data scale in a dynamic environment.