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  • 1.
    Abdulla, Parosh
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Aronis, Stavros
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Optimal dynamic partial order reduction2014In: Proc. 41st ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, New York: ACM Press, 2014, 373-384 p.Conference paper (Refereed)
    Abstract [en]

    Stateless model checking is a powerful technique for program verification, which however suffers from an exponential growth in the number of explored executions. A successful technique for reducing this number, while still maintaining complete coverage, is Dynamic Partial Order Reduction (DPOR). We present a new DPOR algorithm, which is the first to be provably optimal in that it always explores the minimal number of executions. It is based on a novel class of sets, called source sets, which replace the role of persistent sets in previous algorithms. First, we show how to modify an existing DPOR algorithm to work with source sets, resulting in an efficient and simple to implement algorithm. Second, we extend this algorithm with a novel mechanism, called wakeup trees, that allows to achieve optimality. We have implemented both algorithms in a stateless model checking tool for Erlang programs. Experiments show that source sets significantly increase the performance and that wakeup trees incur only a small overhead in both time and space.

  • 2.
    Abdulla, Parosh Aziz
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Aronis, Stavros
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Atig, Mohamed Faouzi
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Leonardsson, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Stateless model checking for TSO and PSO2015In: Tools and Algorithms for the Construction and Analysis of Systems: TACAS 2015, Springer Berlin/Heidelberg, 2015, 353-367 p.Conference paper (Refereed)
  • 3. Aceto, Luca
    et al.
    Longo, GiuseppeVictor, BjörnUppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    The difference between concurrent and sequential computation2003Collection (editor) (Other (popular science, discussion, etc.))
  • 4. Aceto, Luca
    et al.
    Victor, BjörnUppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    EXPRESS'00: 7th International Workshop on Expressiveness in Concurrency2000Conference proceedings (editor) (Other academic)
  • 5.
    Aldmour, Ismat
    et al.
    Al Baha University, Saudi Arabia.
    Nylén, Aletta
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Impact of cultural and language background on learning Computer Science concepts2014In: Proc. 2nd International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2014, 37-40 p.Conference paper (Refereed)
    Abstract [en]

    Computer science terminology is generally based on words that have a related original meaning in English and rooted in western tradition. Hence, students from other cultures and students that are not native English speakers, will not be helped by language and culture in understanding computer science concepts. In this work, the authors review the interrelationship between language, cultural background, and the learning of computer science. A comparative study is under preparation in which this relationship is to be examined. The study will compare the intuitive understanding of computer science concepts between Saudi student groups of different English language proficiency levels and of different maturity levels. A test has been designed in order to reveal differences in the perception of computer science concepts that can be attributed to such background differences. The study will serve as a starting point for further work on how computer science education can be enhanced for students that are non-native English speakers.

  • 6. Alexander, Perry
    et al.
    Flener, PierreUppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. CSD.
    Special Issue on ASE'002003Collection (editor) (Other scientific)
  • 7.
    Alghamdi, Fayiq
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Women in computing in Saudi Arabia2016In: Proc. 3rd ACM-W Europe Celebration of Women in Computing, 2016, , 4 p.1-3 p.Conference paper (Other academic)
  • 8.
    Alghamdi, Fayiq
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science. Al-Baha University, Department of Education.
    Why do female students choose to study CS in the Kingdom of Saudi Arabia?2017In: Proc. 5th International Conference on Learning and Teaching in Computing and Engineering, IEEE Computer Society, 2017Conference paper (Other academic)
  • 9.
    Alhalaweh, Amjad
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Alzghoul, Ahmad
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Kaialy, Waseem
    Mahlin, Denny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Bergström, Christel A. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Computational predictions of glass-forming ability and crystallization tendency of drug molecules2014In: Molecular Pharmaceutics, ISSN 1543-8384, Vol. 11, no 9, 3123-3132 p.Article in journal (Refereed)
    Abstract [en]

    Amorphization is an attractive formulation technique for drugs suffering from poor aqueous solubility as a result of their high lattice energy. Computational models that can predict the material properties associated with amorphization, such as glass-forming ability (GFA) and crystallization behavior in the dry state, would be a time-saving, cost-effective, and material-sparing approach compared to traditional experimental procedures. This article presents predictive models of these properties developed using support vector machine (SVM) algorithm. The GFA and crystallization tendency were investigated by melt-quenching 131 drug molecules in situ using differential scanning calorimetry. The SVM algorithm was used to develop computational models based on calculated molecular descriptors. The analyses confirmed the previously suggested cutoff molecular weight (MW) of 300 for glass-formers, and also clarified the extent to which MW can be used to predict the GFA of compounds with MW < 300. The topological equivalent of Grav3_3D, which is related to molecular size and shape, was a better descriptor than MW for GFA; it was able to accurately predict 86% of the data set regardless of MW. The potential for crystallization was predicted using molecular descriptors reflecting Hückel pi atomic charges and the number of hydrogen bond acceptors. The models developed could be used in the early drug development stage to indicate whether amorphization would be a suitable formulation strategy for improving the dissolution and/or apparent solubility of poorly soluble compounds.

  • 10.
    Alhalaweh, Amjad
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Alzghoul, Ahmad
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Mahlin, Denny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Bergström, Christel A. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Physical stability of drugs after storage above and below the glass transition temperature: Relationship to glass-forming ability2015In: International Journal of Pharmaceutics, ISSN 0378-5173, E-ISSN 1873-3476, Vol. 495, no 1, 312-317 p.Article in journal (Refereed)
    Abstract [en]

    Amorphous materials are inherently unstable and tend to crystallize upon storage. In this study, we investigated the extent to which the physical stability and inherent crystallization tendency of drugs are related to their glass-forming ability (GFA), the glass transition temperature (T-g) and thermodynamic factors. Differential scanning calorimetry was used to produce the amorphous state of 52 drugs [ 18 compounds crystallized upon heating (Class II) and 34 remained in the amorphous state (Class III)] and to perform in situ storage for the amorphous material for 12 h at temperatures 20 degrees C above or below the T-g. A computational model based on the support vector machine (SVM) algorithm was developed to predict the structure-property relationships. All drugs maintained their Class when stored at 20 degrees C below the T-g. Fourteen of the Class II compounds crystallized when stored above the T-g whereas all except one of the Class III compounds remained amorphous. These results were only related to the glass-forming ability and no relationship to e. g. thermodynamic factors was found. The experimental data were used for computational modeling and a classification model was developed that correctly predicted the physical stability above the T-g. The use of a large dataset revealed that molecular features related to aromaticity and pi-pi interactions reduce the inherent physical stability of amorphous drugs.

  • 11. Allignol, Cyril
    et al.
    Barnier, Nicolas
    Flener, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Pearson, Justin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Constraint programming for air traffic management: a survey2012In: Knowledge engineering review (Print), ISSN 0269-8889, E-ISSN 1469-8005, Vol. 27, no 3, 361-392 p.Article, review/survey (Refereed)
  • 12.
    Alzghoul, Ahmad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Alhalaweh, Amjad
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Mahlin, Denny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Bergström, Christel A. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Experimental and Computational Prediction of Glass Transition Temperature of Drugs2014In: JOURNAL OF CHEMICAL INFORMATION AND MODELING, ISSN 1549-9596, Vol. 54, no 12, 3396-3403 p.Article in journal (Refereed)
    Abstract [en]

    Glass transition temperature (T-g) is an important inherent property of an amorphous solid material which is usually determined experimentally. In this study, the relation between T-g and melting temperature (T-m) was evaluated using a data set of 71 structurally diverse druglike compounds. Further, in silico models for prediction of T-g were developed based on calculated molecular descriptors and linear (multilinear regression, partial least-squares, principal component regression) and nonlinear (neural network, support vector regression) modeling techniques. The models based on T-m predicted T-g with an RMSE of 19.5 K for the test set. Among the five computational models developed herein the support vector regression gave the best result with RMSE of 18.7 K for the test set using only four chemical descriptors. Hence, two different models that predict T-g of drug-like molecules with high accuracy were developed. If T-m is available, a simple linear regression can be used to predict T-g. However, the results also suggest that support vector regression and calculated molecular descriptors can predict T-g with equal accuracy, already before compound synthesis.

  • 13.
    Alzghoul, Ahmad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Backe, Björn
    Löfstrand, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Byström, Arne
    Liljedahl, Bengt
    Comparing a knowledge-based and a data-driven method in querying data streams for system fault detection: A hydraulic drive system application2014In: Computers in industry (Print), ISSN 0166-3615, Vol. 65, no 8, 1126-1135 p.Article in journal (Refereed)
    Abstract [en]

    The field of fault detection and diagnosis has been the subject of considerable interest in industry. Fault detection may increase the availability of products, thereby improving their quality. Fault detection and diagnosis methods can be classified in three categories: data-driven, analytically based, and knowledge-based methods.

    In this work, we investigated the ability and the performance of applying two fault detection methods to query data streams produced from hydraulic drive systems. A knowledge-based method was compared to a data-driven method. A fault detection system based on a data stream management system (DSMS) was developed in order to test and compare the two methods using data from real hydraulic drive systems.

    The knowledge-based method was based on causal models (fault trees), and principal component analysis (PCA) was used to build the data-driven model. The performance of the methods in terms of accuracy and speed, was examined using normal and physically simulated fault data. The results show that both methods generate queries fast enough to query the data streams online, with a similar level of fault detection accuracy. The industrial applications of both methods include monitoring of individual industrial mechanical systems as well as fleets of such systems. One can conclude that both methods may be used to increase industrial system availability.

  • 14.
    Alzghoul, Ahmad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Löfstrand, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Addressing concept drift to improve system availability by updating one-class data-driven models2015In: Evolving Systems, ISSN 1868-6478, E-ISSN 1868-6486, Vol. 6, no 3, 187-198 p.Article in journal (Refereed)
    Abstract [en]

    Data-driven models have been used to detect system faults, thereby increasing industrial system availability. The ability to search data streams while dealing with concept drift are challenges for data-driven models. The objective of this work is to demonstrate a general method to manage concept drift when using one-class data-driven models. The method has been used to develop an automatically retrained and updated polygon-based model. In this paper, the available industrial data allowed for use of one-class data-driven models, and the polygon-based model was selected because it has previously been successful. Possible scenarios that allow one-class data-driven models to be retrained or updated were identified. Based on the identified scenarios, a method to automatically update a polygon-based model online is proposed. The method has been tested and verified using data collected from a Bosch Rexroth Mellansel AB hydraulic drive system. Data representing relevant faults was inserted into the data set in close collaboration with engineers from the company. The results show that the developed polygon-based model method was able to address the concept drift issue and was able to significantly improve the classification accuracy compared to the static polygon-based model. Thereby, the model could significantly improve industrial system availability when applied in the relevant production process. This paper shows that the developed polygon-based model requires small memory space while its updating procedure is simple and fast. Finally, the identified scenarios may be helpful as input for supporting other one-class data-driven models to cope with concept drift, thus increasing the generalizability of the results.

  • 15. Amadini, Roberto
    et al.
    Flener, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Pearson, Justin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Scott, Joseph D.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Stuckey, Peter J.
    Tack, Guido
    MiniZinc with strings2017In: Logic-Based Program Synthesis and Transformation, Springer, 2017, 59-75 p.Conference paper (Refereed)
  • 16.
    Andersson, Arne
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    General balanced trees1999In: Journal of Algorithms, Vol. 30, 1-28 p.Article in journal (Refereed)
    Abstract [en]

    We show that, in order to achieve efficient maintenance of a balanced binary search tree, no shape restriction other than a logarithmic height is required. The obtained class of trees, general balanced trees, may be maintained at a logarithmic amortized cost with no balance information stored in the nodes. Thus, in the case when amortized bounds are sufficient, there is no need for sophisticated balance criteria.

    The maintenance algorithms use partial rebuilding. This is important for certain applications, and has previously been used with weight-balanced trees. We show that the amortized cost incurred by general balanced trees is lower than what has been shown for weight-balanced trees.

  • 17.
    Andersson, Arne
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science.
    Searching and Priority Queues in o(log n) Time2005In: Handbook of Data Structures and Applications, CRC Press , 2005, 1392- p.Chapter in book (Other (popular scientific, debate etc.))
  • 18.
    Andersson, Arne
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    Balanced Binary Search Trees2005In: Handbook of Data Structures and Applications, CRC Press , 2005, 1392- p.Chapter in book (Other scientific)
  • 19.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Computing science.
    Carlsson, Per
    Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science.
    Ygge, Fredrik
    Resource Allocation with Wobbly Functions2002In: Computational Optimization and Applications, ISSN 0926-6003, Vol. 23, no 2, 171-200 p.Article in journal (Other scientific)
  • 20.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    Davidsson, Paul
    Linden, Johan
    Measure-based performance evaluation1999In: Pattern Recognition Letters, Vol. 28Article in journal (Refereed)
    Abstract [en]

    The concept of measure functions for generalization performance is suggested. This concept provides an alternative way of selecting and evaluating learned classifiers, and it allows us to define the learning problem as a computational problem.

  • 21.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science.
    Hagerup, Torben
    Nilsson, Stefan
    Raman, Rajeev
    Sorting in linear time?1998In: Journal of Computer and System Sciences, Vol. 57, 74-93 p.Article in journal (Refereed)
    Abstract [en]

    We show that a unit-cost RAM with a word length of w bits can sort n integers in the range 0 .. 2^(w-1) in O(n loglog n) time, for arbitrary w >= log n, a significant improvement over the bound of O(n sqrt(log n)) achieved by the fusion trees of Fredman and Willard. Provided that w >= (log n)^(2+epsilon) for some fixed epsilon>0, the sorting can even be accomplished in linear expected time with a randomized algorithm.

    Both of our algorithms parallelize without loss on a unit-cost PRAM with a word length of w bits. The first one yields an algorithm that uses O(log n) time and O(n loglog n) operations on a deterministic CRCW PRAM. The second one yields an algorithm that uses O(log n) expected time and O(n) expected operations on a randomized EREW PRAM, provided that w >= (log n)^(2+epsilon) for some fixed epsilon>0.

    Our deterministic and randomized sequential and parallel algorithms generalize to the lexicographic sorting problem of sorting multiple-precision integers represented in several words.

  • 22.
    Andersson, Arne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Holmström, Jim
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Willman, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    An Auction Mechanism for Polynomial-time Execution with Combinatorial Constraints2005In: Proc. 7th International Conference on E-Commerce Technology, Piscataway, NJ: IEEE , 2005, 17-24 p.Conference paper (Refereed)
  • 23.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science.
    Larsson, N. Jesper
    Swanson, Kurt
    Suffix trees on words1999In: Algorithmica, Vol. 23Article in journal (Refereed)
    Abstract [en]

    We discuss an intrinsic generalization of the suffix tree, designed to index a string of length n which has a natural partitioning into m multi-character substrings or words. This word suffix tree represents only the m suffixes that start at word boundaries. These boundaries are determined by delimiters, whose definition depends on the application.

    Since traditional suffix tree construction algorithms rely heavily on the fact that all suffixes are inserted, construction of a word suffix tree is nontrivial, in particular when only O(m) construction space is allowed. We solve this problem, presenting an algorithm with O(n) expected running time. In general, construction cost is Omega(n) due to the need of scanning the entire input. In applications that require strict node ordering, an additional cost of sorting O(m') characters arises, where m' is the number of distinct words. In either case, this is a significant improvement over previously known solutions.

    Furthermore, when the alphabet is small, we may assume that the $n$ characters in the input string occupy o(n) machine words. We illustrate that this can allow a word suffix tree to be built in sublinear time.

  • 24.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science.
    Miltersen, Peter Bro
    Thorup, Mikkel
    Fusion trees can be implemented with AC0 instructions.1999In: Theoretical Computer Science, Vol. 205, 337-344 p.Article in journal (Refereed)
    Abstract [en]

    Addressing a problem of Fredman and Willard, we implement fusion trees in deterministic linear space using AC^o instructions only. More precisely, we show that a subset of {0,...,2^(w-1)} of size n can be maintained using linear space under insertion, deletion, predecessor, and successor queries, with O(log n/loglog n) amortized time per operation on a RAM with word size w, where the only computational instructions allowed on the RAM are fuinctions in AC^0. The AC^0 instructions used are not all available on today's computers.

  • 25.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    Petersson, Ola
    Approximate Indexed Lists.1998In: Journal of Algorithms, Vol. 29, no 2Article in journal (Refereed)
    Abstract [en]

    Let the position of a list element in a list be the number of elements preceding it plus one. An indexed list supports the following operations on a list: Insert; delete; return the position of an element; and return the element at a certain position. The order in which the elements appear in the list is completely determined by where the insertions take place; we do not require the presence of any keys that induce the ordering.

    We consider approximate indexed lists, and show that a tiny relaxation in precision of the query operations allows a considerable improvement in time complexity. The new data structure has applications in two other problems; namely, list labeling and subset rank.

  • 26.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    Tenhunen, Mattias
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    Ygge, Fredrik
    Integer Programming for Combinatorial Auction Winner Determination.2000In: Proc. of the Fourth International Conference on Multiagent Systems (ICMAS-00), 2000Conference paper (Refereed)
    Abstract [en]

    Combinatorial auctions are important as they enable bidders to place bids on combinations of items; compared to other auction mechanisms, they often increase the efficiency of the auction, while keeping risks for bidders low. However, the determination of an optimal winner combination in combinatorial auctions is a complex computational problem.

    In this paper we (i) compare recent algorithms for winner determination to traditional algorithms, (ii) present and benchmark a mixed integer progra mming approach to the problem, which enables very general auctions to be treated efficiently by standard integer programming algorithms (and hereby also by commercially available software), and (iii) discuss the impact of the probability distributions chosen for benchmarking.

  • 27.
    Andersson, Arne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Thorup, Mikkel
    Dynamic Ordered Sets with Exponential Search Trees2007In: Journal of the ACM, ISSN 0004-5411, E-ISSN 1557-735X, Vol. 54, no 3, 1236460- p.Article in journal (Refereed)
    Abstract [en]

    We introduce exponential search trees as a novel technique for converting static polynomial space search structures for ordered sets into fully-dynamic linear space data structures. This leads to an optimal bound of O(log n/log log n) for searching and updating a dynamic set X of n integer keys in linear space. Searching X for an integer y means finding the maximum key in X which is smaller than or equal to y. This problem is equivalent to the standard text book problem of maintaining an ordered set. The best previous deterministic linear space bound was O(log n/log log n) due to Fredman and Willard from STOC 1990. No better deterministic search bound was known using polynomial space. We also get the following worst-case linear space trade-offs between the number n, the word length W, and the maximal key U < 2W: O(min log log n + log n/logW, log log n log log U/log log log U). These trade-offs are, however, not likely to be optimal. Our results are generalized to finger searching and string searching, providing optimal results for both in terms of n.

  • 28.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science.
    Thorup, Mikkel
    Tight(er) Worst-case Bounds on Dynamic Searching and Priority Queues.2000In: IEEE Symposium on Theory of Computing (STOC), 2000Conference paper (Refereed)
    Abstract [en]

    We introduce a novel technique for converting static polynomial space search structures for ordered sets into fully-dynamic linear space data structures. Based on this we present optimal bounds for dynamic integer searching, including finger search, and exponentially improved bounds for priority queues.

  • 29.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science.
    Thorup, Mikkel
    Dynamic String Searching2001In: ACM-SIAM symposium on Discrete algorithms, SODA, 2001Conference paper (Refereed)
  • 30.
    Andersson, Arne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Wilenius, Jim
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    A New Analysis of Revenue in the Combinatorial and Simultaneous Auction2009Report (Other academic)
    Abstract [en]

    We prove that in many cases, a first-price sealed-bid combinatorial auction gives higher expected revenue than a sealed-bid simultaneous auction. This is the first theoretical evidence that combinatorial auctions indeed generate higher revenue, which has been a common belief for decades.

    We use a model with many bidders and items, where bidders are of two types: (i) single-bidders interested in only one item and (ii) synergy-bidders, each interested in one random combination of items. We provide an upper bound on the expected revenue for simultaneous auctions and a lower bound on combinatorial auctions. Our bounds are parameterized on the number of bidders and items, combination size, and synergy.

    We derive an asymptotic result, proving that as the number of bidders approach infinity, expected revenue of the combinatorial auction will be higher than that of the simultaneous auction. We also provide concrete examples where the combinatorial auction is revenue-superior.

  • 31.
    Andersson, Arne
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Computing science.
    Ygge, Fredrik
    Efficient resource allocation with non-concave objective functions2001In: Computational Optimization and Applications, ISSN 0926-6003, Vol. 20, no 3, 281-298 p.Article in journal (Refereed)
    Abstract [en]

    We consider resource allocation with separable objective functions defined over subranges of the integers. While it is well known that (the maximization version of) this problem can be solved efficiently if the objective functions are concave, the general

  • 32.
    Andersson, Daniel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    Vorobyov, Sergei
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Computing Science. Datalogi.
    Fast Algorithms for Monotonic Discounted Linear Programs with Two Variables per Inequality2006Report (Other scientific)
    Abstract [en]

    We suggest new strongly polynomial algorithms for solving linear programs

    min( \Sigma x_i |S ) with constraints S of the monotonic discounted form x_i ≥ λx_j + β with 0 < λ < 1. The algorithm for the case when the discounting factor λ is equal for all constraints is O(mn2 ), whereas the algorithm for the case when λ may vary between the constraints is O(mn2 log m), where n is the number of variables and m is the number of constraints. As applications, we obtain the best currently available algorithm for two-player discounted payoff games and a new faster strongly subexponential algorithm for

    the ergodic partition problem for mean payoff games.

  • 33.
    Andrejev, Andrej
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computing Science.
    Semantic Web Queries over Scientific Data2016Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Semantic Web and Linked Open Data provide a potential platform for interoperability of scientific data, offering a flexible model for providing machine-readable and queryable metadata. However, RDF and SPARQL gained limited adoption within the scientific community, mainly due to the lack of support for managing massive numeric data, along with certain other important features – such as extensibility with user-defined functions, query modularity, and integration with existing environments and workflows.

    We present the design, implementation and evaluation of Scientific SPARQL – a language for querying data and metadata combined, represented using the RDF graph model extended with numeric multidimensional arrays as node values – RDF with Arrays. The techniques used to store RDF with Arrays in a scalable way and process Scientific SPARQL queries and updates are implemented in our prototype software – Scientific SPARQL Database Manager, SSDM, and its integrations with data storage systems and computational frameworks. This includes scalable storage solutions for numeric multidimensional arrays and an efficient implementation of array operations. The arrays can be physically stored in a variety of external storage systems, including files, relational databases, and specialized array data stores, using our Array Storage Extensibility Interface. Whenever possible SSDM accumulates array operations and accesses array contents in a lazy fashion.

    In scientific applications numeric computations are often used for filtering or post-processing the retrieved data, which can be expressed in a functional way. Scientific SPARQL allows expressing common query sub-tasks with functions defined as parameterized queries. This becomes especially useful along with functional language abstractions such as lexical closures and second-order functions, e.g. array mappers.

    Existing computational libraries can be interfaced and invoked from Scientific SPARQL queries as foreign functions. Cost estimates and alternative evaluation directions may be specified, aiding the construction of better execution plans. Costly array processing, e.g. filtering and aggregation, is thus preformed on the server, saving the amount of communication. Furthermore, common supported operations are delegated to the array storage back-ends, according to their capabilities. Both expressivity and performance of Scientific SPARQL are evaluated on a real-world example, and further performance tests are run using our mini-benchmark for array queries.

  • 34.
    Andrejev, Andrej
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    He, Xueming
    Risch, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Scientific data as RDF with arrays: Tight integration of SciSPARQL queries into MATLAB2014In: Proc. ISWC 2014 Posters & Demonstrations Track, RWTH Aachen University , 2014, 221-224 p.Conference paper (Refereed)
    Abstract [en]

    We present an integrated solution for storing and querying scientific data and metadata, using MATLAB envi ronment as client front-end and our prototype DBMS on the server. We use RDF for experiment metadata, and numeric arrays for the rest. Our extension of SPARQL supports array operations and extensibility with foreign functions.

  • 35.
    Andrejev, Andrej
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Misev, Dimitar
    Jacobs Univ, Dept Comp Sci & Elect Engn, Bremen, Germany..
    Baumann, Peter
    Jacobs Univ, Dept Comp Sci & Elect Engn, Bremen, Germany..
    Risch, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Spatio-Temporal Gridded Data Processing on the Semantic Web2015In: 2015 IEEE International Conference On Data Science And Data Intensive Systems, 2015, 38-45 p.Conference paper (Refereed)
    Abstract [en]

    Multidimensional array data, such as remote-sensing imagery and timeseries, climate model simulations, telescope observations, and medical images, contribute massively to virtually all science and engineering domains, and hence play a key role in 'Big Data' challenges. Pure array storage management and analytics is relatively well understood today. However, arrays in practice never come alone, but are accompanied by metadata, including domain, range, provenance information, etc. The structure of this metadata is far less regular than arrays or tables, and may be incomplete or different from one array instance to another. Particularly in the field of the Semantic Web such integrated representations must convey a sufficiently complete and reasonable semantics for machine-machine communication. We show how the Resource Description Framework (RDF), the Semantic Web graph model for metadata, can be leveraged for such data/metadata integration specifically for representing spatio-temporal grid data. Based on the notion of a coverage as established by the Open Geospatial Consortium (OGC) we present a hybrid data store where efficiently represented arrays are incorporated as nodes into RDF graphs and connected to their metadata. We have extended the Semantic Web query language SPARQL to incorporate array query semantics and other functionality making it suitable for processing of large numeric arrays, including geo coverages.

  • 36.
    Andrejev, Andrej
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Risch, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Scientific SPARQL: Semantic web queries over scientific data2012In: Proc. 28th International Conference on Data Engineering Workshops, IEEE Computer Society, 2012, 5-10 p.Conference paper (Refereed)
  • 37.
    Andrejev, Andrej
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Risch, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Scientific analysis by queries in extended SPARQL over a scalable e-Science data store2013In: Proc. 9th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2013, 98-106 p.Conference paper (Refereed)
  • 38. Arafailova, Ekaterina
    et al.
    Beldiceanu, Nicolas
    Carlsson, Mats
    Flener, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Francisco Rodríguez, María Andreína
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Pearson, Justin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Simonis, Helmut
    Systematic derivation of bounds and glue constraints for time-series constraints2016In: Principles and Practice of Constraint Programming: CP 2016, Springer, 2016, 13-29 p.Conference paper (Refereed)
  • 39. Arafailova, Ekaterina
    et al.
    Beldiceanu, Nicolas
    Douence, Rémi
    Carlsson, Mats
    Flener, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Francisco Rodríguez, María Andreína
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Pearson, Justin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Simonis, Helmut
    Global Constraint Catalog: Volume II, time-series constraints2016Report (Other academic)
  • 40. Arafailova, Ekaterina
    et al.
    Beldiceanu, Nicolas
    Douence, Rémi
    Flener, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Francisco Rodríguez, María Andreína
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Pearson, Justin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Simonis, Helmut
    Time-series constraints: Improvements and application in CP and MIP contexts2016In: Integration of AI and OR Techniques in Constraint Programming, Springer, 2016, 18-34 p.Conference paper (Refereed)
  • 41. Armstrong, Alasdair
    et al.
    Struth, Georg
    Weber, Tjark
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Kleene Algebra2013In: Archive of Formal Proofs, ISSN 2150-914xArticle in journal (Refereed)
  • 42. Armstrong, Alasdair
    et al.
    Struth, Georg
    Weber, Tjark
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Programming and automating mathematics in the Tarski-Kleene hierarchy2014In: Journal of Logical and Algebraic Methods in Programming, ISSN 2352-2208, Vol. 83, no 2, 87-102 p.Article in journal (Refereed)
    Abstract [en]

    We present examples from a reference implementation of variants of Kleene algebras and Tarski's relation algebras in the theorem proving environment Isabelle/HOL. For Kleene algebras we show how models can be programmed, including sets of traces and paths, languages, binary relations, max-plus and min-plus algebras, matrices, formal power series. For relation algebras we discuss primarily proof automation in a comprehensive library and present an advanced formalisation example. 

  • 43. Armstrong, Alasdair
    et al.
    Struth, Georg
    Weber, Tjark
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Program Analysis and Verification Based on Kleene Algebra in Isabelle/HOL2013In: Interactive Theorem Proving: ITP 2013, Springer Berlin/Heidelberg, 2013, 197-212 p.Conference paper (Refereed)
    Abstract [en]

    Schematic Kleene algebra with tests (SKAT) supports the equational verification of flowchart scheme equivalence and captures simple while-programs with assignment statements. We formalise SKAT in Isabelle/HOL, using the quotient type package to reason equationally in this algebra. We apply this formalisation to a complex flowchart transformation proof from the literature. We extend SKAT with assertion statements and derive the inference rules of Hoare logic. We apply this extension in simple program verification examples and the derivation of additional Hoare-style rules. This shows that algebra can provide an abstract semantic layer from which different program analysis and verification tasks can be implemented in a simple lightweight way.

  • 44.
    Aronis, Stavros
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Papaspyrou, Nikolaos
    Roukounaki, Katerina
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Tsiouris, Yiannis
    Venetis, Ioannis E.
    A scalability benchmark suite for Erlang/OTP2012In: Proc. 11th ACM SIGPLAN Workshop on Erlang, New York: ACM Press, 2012, 33-42 p.Conference paper (Refereed)
    Abstract [en]

    Programming language implementers rely heavily on benchmarking for measuring and understanding performance of algorithms, architectural designs, and trade-offs between alternative implementations of compilers, runtime systems, and virtual machine components. Given this fact, it seems a bit ironic that it is often more difficult to come up with a good benchmark suite than a good implementation of a programming language.

    This paper presents the main aspects of the design and the current status of bencherl, a publicly available scalability benchmark suite for applications written in Erlang. In contrast to other benchmark suites, which are usually designed to report a particular performance point, our benchmark suite aims to assess scalability, i.e., help developers to study a set of performance points that show how an application's performance changes when additional resources (e.g., CPU cores, schedulers, etc.) are added. We describe the scalability dimensions that the suite aims to examine and present its infrastructure and current set of benchmarks. We also report some limited set of performance results in order to show the capabilities of our suite.

  • 45.
    Aronis, Stavros
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    On using Erlang for parallelization: Experience from parallelizing Dialyzer2013In: Trends in Functional Programming, Springer Berlin/Heidelberg, 2013, 295-310 p.Conference paper (Refereed)
  • 46.
    Asai, Kenichi
    et al.
    Ochanomizu Univ, Tokyo 112, Japan..
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science. NTUA, Athens, Greece..
    Selected and extended papers from Partial Evaluation and Program Manipulation 2015 (PEPM ' 15)2017In: Science of Computer Programming, ISSN 0167-6423, E-ISSN 1872-7964, Vol. 137, 1-1 p.Article in journal (Other academic)
  • 47.
    Ashcroft, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Using Bayesian networks in business analytics: Overview and short case study2012In: Business Informatics, ISSN 1507-3858, Vol. 3, no 25Article in journal (Refereed)
  • 48.
    Ashcroft, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Performing Decision-Theoretic Inference in Bayesian Network Ensemble Models2013In: Twelfth Scandinavian Conference on Artificial Intelligence / [ed] Jaeger, M; Nielsen, TD; Viappiani, P, 2013, Vol. 257, 25-34 p.Conference paper (Refereed)
    Abstract [en]

    The purpose of this paper is to present a simple extension to an existing inference algorithm on influence diagrams (i.e. decision theoretic extensions to Bayesian networks) that permits these algorithms to be applied to ensemble models. The extension, though simple, is important because of the power and robustness that such ensemble models provide [1]. This paper is intended principally as a 'recipe' that can be used even by those unfamiliar with the algorithms extended. Accordingly, I present the algorithms that the original contribution builds upon in full, though references are given to less concise renditions. Those familiar with these algorithms are invited to skip the elucidation. The consequence is a useful paper with more background and less original input than usual.

  • 49.
    Ashcroft, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Bayesian Networks in Business Analytics2012In: 2012 FEDERATED CONFERENCE ON COMPUTER SCIENCE AND INFORMATION SYSTEMS (FEDCSIS), 2012, 955-961 p.Conference paper (Refereed)
  • 50.
    Ashcroft, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    An Introduction To Bayesian Networks in Systems and Control2012Conference paper (Refereed)
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