Turku Centre for Computer Science

About: Turku Centre for Computer Science is a facility organization based out in Turku, Finland. It is known for research contribution in the topics: Decidability & Word (group theory). The organization has 382 authors who have published 1027 publications receiving 19560 citations.

SFI: A Refinement Based Layered Software Architecture

Abstract: Refinement calculus [1,5] is a formal framework for reasoning about program correctness and correctness preserving program refinements. It serves as the foundation for an object-oriented software architecture and construction method that we refer to as stepwise feature introduction (SFI) [3]. Characteristic for this approach is that each software module is described in terms of thin layers. Each layer extends the software with some new feature, in a way that preserves the features that have been introduced by earlier layers. This amounts to requiring that the new layer is a superposition refinement [4] of the layers below. The modules are interconnected using interface specifications, usually providing a more abstract view of the module state than what will actually be implemented. The implementation is required to be a data refinement [9,6] of the interface specification. SFI is based on structuring software with these two basic mechanisms, modularization and extension, while the refinement calculus provides the formal framework for reasoning about the correctness of software constructed in this way.We use UML [8] to describe the software architecture, with refinement calculus providing a rigorous mathematical semantics for the UML constructs employed. This will also give us a formal framework for reasoning about UML class diagrams, in essence using these as proof schemes when arguing about software properties.

Heap access optimizations for a hardware-accelerated Java virtual machine

Abstract: The REALJava virtual machine consists of a software partition running on a general-purpose CPU and a hardware partition containing one or more Java co-processor units. The co-processor units execute most of the bytecode, while the software partition handles complex instructions and tasks such as class loading, input and output and memory management. The software partition and the co-processors communicate using a general communication channel such as a bus. By far the most common instructions executed in the software partition are heap accesses. Because executing instructions on software is relatively slow, code-improving transformations which reduce the number of interrupts generated and the amount of communication can have a large impact on performance. An improvement on an existing technique called supersequence transformation is presented which makes the technique more general and reduces the amount of communication required between the partitions and the number of interrupts generated. The improved technique is shown to improve performance over the original in many programs.

On the expressiveness of subset-sum representations

Abstract: We develop a general theory for representing information as sums of elements in a subset of the basic set A of numbers of cardinality n, often refered to as a “knapsack vector”. How many numbers can be represented in this way depends heavily on n. The lower, resp. upper, bound for the cardinality of the set of representable numbers is quadratic, resp. exponential, in terms of n. We give an algorithm for the construction of a knapsack vector of any prescribed expressiveness (that is, the cardinality of the set of representable numbers), provided it falls within the range possible for expressiveness.

Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments

Abstract: Modern multicapillary devices allow researchers to address increasingly complex biological questions involving comparisons of gene expression patterns across electrophoretic samples under various experimental conditions. As labor-intensive visual evaluation of the electrophoretic results is often the bottleneck of large-scale differential display (DD) studies, one way to further streamline this process is to focus only on a highly compressed list of the most potential patterns that are likely to provide reliable findings. To enable the identification of such candidate patterns, we present a computer-assisted method for objective ranking of multitrace peak patterns in DD experiments. The fundamental component of the multitrace pattern ranking method (MRANK) is the multiple alignment algorithm that allows for discovery of patterns involving sets of peak complexes from various electrophoretic samples. A score value is attached to each detected pattern which characterizes how accurately the pattern resembles the desired pattern query, freely defined by the researcher. The ranked pattern list produced by MRANK is validated against visual evaluation in terms of detecting and ranking a group of relevant patterns in a DD analysis of T-helper cell differentiation. We demonstrate high enrichment of the desired patterns on top of the score-ranked list (e.g., 90% of the visually selected patterns are discovered by looking through the first 3% of patterns in the ranked list of all patterns). The results suggest that a substantial amount of manual labor can be saved without compromising the accuracy of the findings by prioritizing the patterns according to MRANK output in the visual confirmation phase.

Using DMA Aligned Buffer to Improve Software RAID Performance

Abstract: While the storage market grows rapidly, software RAID, as a low-cost solution, becomes more and more important nowadays. However the performance of software RAID is greatly constrained by its implementation. Varies methods have been taken to improve its performance. By integrating a novel buffer mechanism – DMA aligned buffer (DAB) into software RAID kernel driver, we achieved a significant performance improvement, especially on small I/O requests.