24712591
Integrating Priority with Share in the Priority-Based Weighted Fair Queuing Scheduler for Real-Time Networks
The Weighted Fair Queuing (WFQ) scheduler has been closely studied due to its desirable properties of bandwidth guarantee and bounded delay. However, the queuing delay bound of a communication session is tightly coupled with the session's allocated service share. To receive a low queuing delay, a session must reserve a high share. In this paper, we study a new fair queuing algorithm called Priority-based Weighted Fair Queuing (PWFQ). PWFQ combines a session's allocated share to achieve the bandwidth guarantee and the session's priority to adjust the delay bound inside a sliding window. The new algorithm decouples the delay from the service share so that a session with a low share but a high priority may still receive a small delay. We analyze the worst-case delay bound of PWFQ and propose a simple algorithm to assign session priorities.
15828117
Enhancing external consistency in real-time transactions
Real-time computing brings two new requirements to database management. The first is the deadline constraint which requires better scheduling algorithms to meet transaction deadfines. The second requirement is the temporal validity, or external consistency[Lin89], requirement of data: a real-time database must prevent data from being corrupted not only by the executions of concurrent transactions but also by the delay from sharing computing resources and real-time scheduler decisions. In this paper, we study the external consistency requirement in real-time databases. We propose a semantic-based concurrency control scheme that prefers the external consistency to the traditional serializability. Two new concepts are introduced in our work. An update of a physical object value is considered to be compatible to those read operations that need to access the most recent data. Secondly, if a transaction depends strongly on the validity of the value of an object, a new update may cause the transaction to be aborted since continuing the transaction may be harmful to the appfication. A real-Life example is the stock market database. A trading program may be executed for a long time and its read operations should not block any new updates. Moreover, if there is a big sudden change in a particular stock price, it may be better to abort an on-going transaction rather than letting it make some invalid decisions.
14104203
SM: real-time multicast protocols for simultaneous message delivery
Traditionally, a multicast message is sent once by a sender. All receivers will receive the same message but may receive it at different times. This may result in unfair advantage for some receivers. Simultaneous Multicast (SM) applications require that all receivers receive the same message at the same time. SM protocols therefore need to meet a strict deadline to ensure that each receiver will receive a message at the same time, regardless of the network conditions, heterogeneity of the environment and differences between the local clocks in the receivers. Such a real time SM protocol is proposed so that the coordinated deadline can be met by controlling the reserved bandwidth and without the overhead of clock synchronization. A sensing protocol is also proposed to continuously search for better levels of quality and to avoid the overhead of an external feedback protocol. The protocols are bandwidth conscious, enforce fairness and provide scalability.
13997680
Distributed real-time system design using CBS-based end-to-end scheduling
Distributed real-time applications share a group of processors connected by some local area network. A rigorous and sound methodology to design real-time systems from independently designed distributed real-time applications is needed. In this paper, we study a distributed real-time system design scheme using CBS-based end-to-end scheduling. The scheduling scheme utilizes CBS to allocate both CPU shares and network bandwidth to a distributed real-time application when it arrives at the system. Our proposed solution uses the same scheduling paradigm for both resources. In this way, we believe the system can have a more consistent scheduling objective and may achieve a tighter schedulability condition.
22001959
A Pinwheel Scheduler for Three Distinct Numbers with a Tight Schedulability Bound
Abstract. Given a multiset of positive integers 
 $A=\{a_1,a_2,\ldots,a_n\}$ , the pinwheel problem is to find an infinite sequence over 
 $\{1,2,\ldots,n\}$ such that there is at least one symbol i within any subsequence of length ai. The density of A is defined as 
 $\rho(A)=\sum^n_{i=1} (1/a_i)$ . In this paper we limit ourselves to instances composed of three distinct integers. The best scheduler [5] published previously can schedule all instances with a density of less than 0.77. A new and fast scheduling scheme based on spectrum partitioning is presented in this paper which improves the 0.77 result to a new 
 $\frac{5}{6}\approx 0.83$ density threshold. This scheduler has achieved the tight schedulability bound of this problem.
15072976
The design and implementation of real-time schedulers in RED-linux
Researchers in the real-time system community have designed and studied many advanced scheduling algorithms. However, most of these algorithms have not been implemented since it is very difficult to support new scheduling algorithms on most operating systems. To address this problem, we enhance the scheduling mechanism in Linux to provide a flexible scheduling framework. In the real-time and embedded Linux (RED-Linux) project, we implement a general scheduling framework which divides the system scheduler into two components: dispatcher and allocator. The dispatcher provides the mechanism of system scheduling and resides in the kernel space. The allocator is used to define the scheduling policy and implemented as a user space function. This framework allows users to implement application-specific schedulers in the user space which is easy to program and to debug. The framework also relieves the deficiency from the stock Linux scheduler which is not designed for real-time applications. To further enhance its power, a hierarchical scheduling mechanism has been provided in RED-Linux to allow a system designer to integrate different real-time applications together. Using scheduling groups, real-time jobs can be managed and scheduled in a hierarchical manner. In this paper, we discuss how the group mechanism is implemented in RED-Linux.
20361854
Protein Metal Binding Residue Prediction Based on Neural Networks
Over one-third of protein structures contain metal ions, which are the necessary elements in life systems. Traditionally, structural biologists were used to investigate properties of metalloproteins (proteins which bind with metal ions) by physical means and interpreting the function formation and reaction mechanism of enzyme by their structures and observations from experiments in vitro. Most of proteins have primary structures (amino acid sequence information) only; however, the 3-dimension structures are not always available. In this paper, a direct analysis method is proposed to predict the protein metal-binding amino acid residues from its sequence information only by neural networks with sliding window-based feature extraction and biological feature encoding techniques. In four major bulk elements (Calcium, Potassium, Magnesium, and Sodium), the metal-binding residues are identified by the proposed method with higher than 90% sensitivity and very good accuracy under 5-fold cross validation. With such promising results, it can be extended and used as a powerful methodology for metal-binding characterization from rapidly increasing protein sequences in the future.
1161117
Fast Similarity Search in the Presence of Noise, Scaling, and Translation in Time-Series Databases
We introduce a new model of similarity of time sequences that captures the intuitive notion that two sequences should be considered similar if they have enough non-overlapping time-ordered pairs of subsequences thar are similar. The model allows the amplitude of one of the two sequences to be scaled by any suitable amount and its offset adjusted appropriately. Two subsequences are considered similar if one can be enclosed within an envelope of a specified width drawn around the other. The model also allows non-matching gaps in the matching subsequences. The matching subsequences need not be aligned along the time axis. Given this model of similarity, we present fast search techniques for discovering all similar sequences in a set of sequences. These techniques can also be used to find all (sub)sequences similar to a given sequence. We applied this matching system to the U.S. mutual funds data and discovered interesting matches.
16978334
Evaluating a class of distance-mapping algorithms for data mining and clustering
A distance-mapping algorithm takes a set of objects and a distance metric and then maps those objects to a Euclidean or pseudoEuclidean space in such a way that the distances among objects are approximately preserved. Distance mapping algorithms are a useful tool for clustering and visualization in data intensive applications, because they replace expensive distance calculations by sum-of-square calculations. This can make clustering in large databases with expensive distance metrics practical. In this paper we present five distance-mapping algorithms and conduct experiments to compare their performance in data clustering applications. These include two algorithms called FastMap and MetricMap, and three hybrid heuristics that combine the two algorithms in different ways. Experimental results on both synthetic and RNA data show the superiority of the hybrid algorithms. The results imply that FastMap and MetricMap capture complementary information about distance metrics and therefore can be used together to great benefit. The net effect is that multi-day computations may be done in minutes.
5848136
Protein metal binding residue prediction based on neural networks
Over one-third of protein structures contain metal ions, which are the necessary elements in life systems. Traditionally, structural biologists were used to investigate properties of metalloproteins (proteins which bind with metal ions) by physical means and interpreting the function formation and reaction mechanism of enzyme by their structures and observations from experiments in vitro. Most of proteins have primary structures (amino acid sequence information) only; however, the 3-dimension structures are not always available. In this paper, a direct analysis method is proposed to predict the protein metal-binding amino acid residues from its sequence information only by neural networks with sliding window-based feature extraction and biological feature encoding techniques. In four major bulk elements (Calcium, Potassium, Magnesium, and Sodium), the metal-binding residues are identified by the proposed method with higher than 90% sensitivity and very good accuracy under 5-fold cross validation. With such promising results, it can be extended and used as a powerful methodology for metal-binding characterization from rapidly increasing protein sequences in the future.
46019766
A Study on Textual Entailment
In this paper we study a graph-based approach to the task of textual entailment between a text and hypothesis. The approach takes into account the full lexico-syntactic context of both the text and hypothesis and relies heavily on the concept of subsumption. It starts with mapping the text and hypothesis into graph structures where nodes represent concepts and edges represent lexico-syntactic relations among concepts. Based on a subsumption score between the text-graph and hypothesis-graph an entailment decision is then made. The impact of synonymy on entailment is quantified and discussed. An important advantage of our solution is the ability to customize it so that high-confidence results are obtained