36553676
Time and Space Efficient Algorithms for Constrained Sequence Alignment
In this paper, we study the constrained sequence alignment problem, which is a generalization of the classical sequence alignment problem with the additional constraint that some characters in the alignment must be positioned at the same columns. The problem finds important applications in Bioinformatics. Our major result is an O(ln2)-time and O(ln)-space algorithm for constructing an optimal constrained alignment of two sequences where n is the length of the longer sequence and l is the length of the constraint. Our algorithm matches the best known time complexity and reduces the best known space complexity by a factor of n for solving the problem. We also apply our technique to design time and space efficient heuristic and approximation algorithm for aligning multiple sequences.
43554221
Online and Dynamic Recognition of Squarefree Strings
The online squarefree recognition problem is to detect the first occurrence of a square in a string whose characters are provided as input one at a time. We present an efficient algorithm to solve this problem for strings over arbitrarily ordered alphabets. Its running time is O(n log n), where n is the ending position of the first square, which matches the running times of the fastest known algorithms for the analogous offline problem. We also present a very simple algorithm for a dynamic version of the problem over general alphabets in which we are initially given a squarefree string, followed by a series of updates, and the objective is to determine after each update if the resulting string contains a square and if so, report it and stop.
43458709
Algorithms for Local Forest Similarity
An ordered labeled tree is a rooted tree, where the left-to-right order among siblings is significant and each node associates a label. A forest is a sequence of ordered labeled trees. Suppose F is a forest. A substructure is a connected subgraph of F. Define a subforest as a sequence of substructures of F such that their roots are siblings. The local forest similarity problem for forests F and G is to find two most similar subforests of F and G. We answer an open problem in Paper [3], and provide efficient algorithms on it. Comparing with previous results, our algorithms achieve better performance.
29387998
An efficient and economic partitioning approach for testability
This paper presents an RT level partitioning approach for sequential circuits described as data path and control part. The data path of a circuit is partitioned at some hard-to-test points detected by an RT level testability analysis algorithm. These points are then made directly accessible by DFT techniques. The control part is also modified to control the circuit in normal mode and test mode. In the normal mode, the circuit is controlled to perform its function, while in the test mode, all partitions are controlled independently. As a result, test quality is improved by independent test generation and test application for every partition. The partitioning complexity is reduced by the use of testability analysis results and the area overhead is lower than that of full scan designs for most benchmarks we used. Experiments show results of the approach as compared with no scan, partial scan and full scan schemes.
40452783
A Buffering/Caching Mechanism for Continous Media Players
In order to reduce the playback discontinuity of a stream of data (audio for example) sent through a packet-switched network, we proposed a buffering/caching mechanism for continuous media players. The stream playback is usually implemented by two parallel processes: receiving and playing. The former receives stream chips from the network while the latter plays the received stream chips and then empties their occupied buffers for the former. Our buffering/caching mechanism makes the receiving process completely independent of the playing process. Thus, the receiving process does not need to wait for the playing process to empty buffers so that the network bandwidth can be used as much as possible. Because the cached stream chips can be played from the local disk, the response latency of the playback control operations such as REPLAY and REWIND can be reduced as well. The mechanism was developed for our hyper audio web system.
7206861
Defect-aware SOC test scheduling
In this paper we address the test scheduling problem for system-on-chip designs. Different from previous approaches where it is assumed that all tests are performed until completion, we consider the cases where the test process are terminated as soon as a defect is detected. This is common practice in production test of chips. The proposed technique takes into account the probability of defect-detection by a test in order to schedule the tests so that the expected total test time is minimized. We investigate different test bus structures, test scheduling strategies (sequential scheduling vs. concurrent scheduling), and test set assumptions (fixed test time vs. flexible test time). We have also made experiments to illustrate the efficiency of taking defect probability into account during test scheduling.
10406156
Schedulability Analysis and Optimization for the Synthesis of Multi-Cluster Distributed Embedded Systems
We present an approach to schedulability analysis for the synthesis of multi-cluster distributed embedded systems consisting of time-triggered and event-triggered clusters, interconnected via gateways. We have also proposed a buffer size and worst case queuing delay analysis for the gateways, responsible for routing inter-cluster traffic. Optimization heuristics for the priority assignment and synthesis of bus access parameters aimed at producing a schedulable system with minimal buffer needs have been proposed. Extensive experiments and a real-life example show the efficiency of our approaches.
9900155
An approach to incremental design of distributed embedded systems
In this paper we present an approach to incremental design of distributed embedded systems for hard real-time applications. We start from an already existing system running a set of applications and the design problem is to implement new functionality so that the already running applications are not disturbed and there is a good chance that, later, new functionality can easily be added to the resulted system. The mapping and scheduling problem are considered in the context of a realistic communication model based on a TDMA protocol.