bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proof of concept
Authors: Trieschnigg Dolf 
Published: January 2011

In this thesis we investigate the possibility to integrate domain-specific knowledge into biomedical information retrieval (IR). Recent decades have shown a fast growing interest in biomedical research, reflected by an exponential growth in scientific literature. An important problem for biomedical IR is dealing with the complex and inconsistent terminology encountered in biomedical publications. Dealing with the terminology problem requires domain knowledge stored in terminological resources: controlled indexing vocabularies and thesauri. The integration of this knowledge is, however, far from trivial.
The first research theme investigates heuristics for obtaining word-based representations from biomedical text for robust retrieval. We investigated the effect of choices in document preprocessing heuristics on retrieval effectiveness. Document preprocessing heuristics such as stop word removal, stemming, and breakpoint identification and normalization were shown to strongly affect retrieval performance. An effective combination of heuristics was identified to obtain a word-based representation from text for the remainder of this thesis.
The second research theme deals with concept-based retrieval. We compared a word-based to a concept-based representation and determined to what extent a manual concept-based representation can be automatically obtained from text. Retrieval based on only concepts was demonstrated to be significantly less effective than word-based retrieval. This deteriorated performance could be explained by errors in the classification process, limitations of the concept vocabularies and limited exhaustiveness of the concept-based document representations. Retrieval based on a combination of word-based and automatically obtained concept-based query representations did significantly improve word-only retrieval.
In the third and last research theme we propose a cross-lingual framework for monolingual biomedical IR. In this framework, the integration of a concept-based representation is viewed as a cross-lingual matching problem involving a word-based and concept-based representation language. This framework gives us the opportunity to adopt a large set of established crosslingual information retrieval methods and techniques for this domain. Experiments with basic term-to-term translation models demonstrate that this approach can significantly improve word-based retrieval.
Directions for future work are using these concepts for communication between user and retrieval system, extending upon the translation models and extending CLIR-enhanced concept-based retrieval outside the biomedical domain.
Available online from http://purl.utwente.nl/publications/72481.
In search of the Why
Authors: Verberne Suzan 
Published: January 2011

The problem of automatically answering natural language questions by pinpointing exact answers in a large text (web) corpus has been studied since the mid 1990s. Most research has been directed at answering factoid questions: questions that expect a short, clearly identifiable answer; usually a named entity such as a person name, location or year. In this dissertation, we have focused on the problem of answering why-questions (why-QA). Whyquestions require a different approach than factoid questions because their answers tend to be longer and more complex. Our main research question was: "What are the possibilities and limitations of an approach to why-QA that uses linguistic information in addition to text retrieval techniques?
We first experimented with a simple bag-of-words approach on a set of open-domain whyquestions and Wikipedia as answer corpus. With Lemur as retrieval engine and TF-IDF as ranking model, we were able to retrieve a correct answer passage in the top-10 for 45% of the questions. The most important limitation of the bag-of-words approach for why-QA is that the structure of the questions and the candidate answers is not taken into account. We studied a number of levels of linguistic information on both the side of the question and the side of the answer passage in order to find out which type of information is the most important for answering why-questions.
We implemented a re-ranking module that incorporates knowledge about the syntactic structure of why-questions and the document context of the answers. With this module, we were able to improve significantly over the already quite reasonable bag-of-words baseline. After we optimized the feature combination in a learning-to-rank set-up, our system reached an MRR of 0.35 with a success@10 score of 57%. These scores were reached with only eight overlap features, one of which was the baseline ranker TF-IDF and the others were based on linguistic information (e.g. question focus, cue words and WordNet Similarity) and document structure (e.g. document title and the position of the answer passage in the document).
For solving the remaining 43% of the questions, we found that more is needed than classic NLP. Our conclusion is that why-QA deserves renewed attention from the field of artificial intelligence.
The dissertation is available online at http://lands.let.ru.nl/~sverbern/.
Mathematizing C++ concurrency
Authors: Batty Mark , Owens Scott , Sarkar Susmit , Sewell Peter , Weber Tjark 
Published: January 2011

Shared-memory concurrency in C and C++ is pervasive in systems programming, but has long been poorly defined. This motivated an ongoing shared effort by the standards committees to specify concurrent behaviour in the next versions of both languages. They aim to provide strong guarantees for race-free programs, together with new (but subtle) relaxed-memory atomic primitives for high-performance concurrent code. However, the current draft standards, while the result of careful deliberation, are not yet clear and rigorous definitions, and harbour substantial problems in their details.
In this paper we establish a mathematical (yet readable) semantics for C++ concurrency. We aim to capture the intent of the current (`Final Committee') Draft as closely as possible, but discuss changes that fix many of its problems. We prove that a proposed x86 implementation of the concurrency primitives is correct with respect to the x86-TSO model, and describe our Cppmem tool for exploring the semantics of examples, using code generated from our Isabelle/HOL definitions.
Having already motivated changes to the draft standard, this work will aid discussion of any further changes, provide a correctness condition for compilers, and give a much-needed basis for analysis and verification of concurrent C and C++ programs.
Correct blame for contracts
Authors: Dimoulas Christos , Findler Robert Bruce , Flanagan Cormac , Felleisen Matthias 
Published: January 2011

Behavioral software contracts supplement interface information with logical assertions. A rigorous enforcement of contracts provides useful feedback to developers if it signals contract violations as soon as they occur and if it assigns blame to violators with preciseexplanations. Correct blame assignment gets programmers started with the debugging process and can significantly decrease the time needed to discover and fix bugs.
Sadly the literature on contracts lacks a framework for making statements about the correctness of blame assignment and for validating such statements. This paper fills the gap and uses the framework to demonstrate how one of the proposed semantics for higher-order contracts satisfies this criteria and another semantics occasionally assigns blame to the wrong module.

Concretely, the paper applies the framework to the
lax
enforcement of dependent higher-order contracts and the
picky
one. A higher-order dependent contract specifies constraints for the domain and range of higher-order functions and also relates arguments and results in auxiliary assertions. The picky semantics ensures that the use of arguments in the auxiliary assertion satisfies the domain contracts and the lax one does not. While the picky semantics discovers more contract violations than the lax one, it occasionally blames the wrong module. Hence the paper also introduces a third semantics, dubbed
indy
, which fixes the problems of the picky semantics without giving up its advantages.
Expressive modular fine-grained concurrency specification
Authors: Jacobs Bart , Piessens Frank 
Published: January 2011

Compared to coarse-grained external synchronization of operations on data structures shared between concurrent threads, fine-grained, internal synchronization can offer stronger progress guarantees and better performance. However, fully specifying operations that perform internal synchronization modularly is a hard, open problem. The state of the art approaches, based on linearizability or on concurrent abstract predicates, have important limitations on the expressiveness of specifications. Linearizability does not support ownership transfer, and the concurrent abstract predicates-based specification approach requires hardcoding a particular usage protocol. In this paper, we propose a novel approach that lifts these limitations and enables fully general specification of fine-grained concurrent data structures. The basic idea is that clients pass the ghost code required to instantiate an operation's specification for a specific client scenario into the operation in a simple form of higher-order programming.
We machine-checked the theory of the paper using the Coq proof assistant. Furthermore, we implemented the approach in our program verifier VeriFast and used it to verify two challenging fine-grained concurrent data structures from the literature: a multiple-compare-and-swap algorithm and a lock-coupling list.
Automating string processing in spreadsheets using input-output examples
Authors: Gulwani Sumit 
Published: January 2011

We describe the design of a string programming/expression language that supports restricted forms of regular expressions, conditionals and loops. The language is expressive enough to represent a wide variety of string manipulation tasks that end-users struggle with. We describe an algorithm based on several novel concepts for synthesizing a desired program in this language from input-output examples. The synthesis algorithm is very efficient taking a fraction of a second for various benchmark examples. The synthesis algorithm is interactive and has several desirable features: it can rank multiple solutions and has fast convergence, it can detect noise in the user input, and it supports an active interaction model wherein the user is prompted to provide outputs on inputs that may have multiple computational interpretations.
The algorithm has been implemented as an interactive add-in for Microsoft Excel spreadsheet system. The prototype tool has met the golden test - it has synthesized part of itself, and has been used to solve problems beyond author's imagination.
Bisimulation for quantum processes
Authors: Feng Yuan , Duan Runyao , Ying Mingsheng 
Published: January 2011

Quantum cryptographic systems have been commercially available, with a striking advantage over classical systems that their security and ability to detect the presence of eavesdropping are provable based on the principles of quantum mechanics. On the other hand, quantum protocol designers may commit much more faults than classical protocol designers since human intuition is much better adapted to the classical world than the quantum world. To offer formal techniques for modeling and verification of quantum protocols, several quantum extensions of process algebra have been proposed. One of the most serious issues in quantum process algebra is to discover a quantum generalization of the notion of bisimulation, which lies in a central position in process algebra, preserved by parallel composition in the presence of quantum entanglement, which has no counterpart in classical computation. Quite a few versions of bisimulation have been defined for quantum processes in the literature, but in the best case they are only proved to be preserved by parallel composition of purely quantum processes where no classical communications are involved.
Many quantum cryptographic protocols, however, employ the LOCC (Local Operations and Classical Communications) scheme, where classical communications must be explicitly specified. So, a notion of bisimulation preserved by parallel composition in the circumstance of both classical and quantum communications is crucial for process algebra approach to verification of quantum cryptographic protocols. In this paper we introduce a novel notion of bisimulation for quantum processes and prove that it is congruent with respect to various process algebra combinators including parallel composition even when both classical and quantum communications are present. We also establish some basic algebraic laws for this bisimulation. In particular, we prove uniqueness of the solutions to recursive equations of quantum processes, which provides a powerful proof technique for verifying complex quantum protocols.
Multipliers for floating-point double precision and beyond on FPGAs
Authors: Banescu Sebastian , de Dinechin Florent , Pasca Bogdan , Tudoran Radu 
Published: January 2011

The implementation of high-precision floating-point applications on reconfigurable hardware requires large multipliers. Full multipliers are the core of floating-point multipliers. Truncated multipliers, trading resources for a well-controlled accuracy degradation, are useful building blocks in situations where a full multiplier is not needed.
This work studies the automated generation of such multipliers using the embedded multipliers and adders present in the DSP blocks of current FPGAs. The optimization of such multipliers is expressed as a tiling problem, where a tile represents a hardware multiplier, and super-tiles represent combinations of several hardware multipliers and adders, making efficient use of the DSP internal resources. This tiling technique is shown to adapt to full or truncated multipliers. It addresses arbitrary precisions including single, double but also the quadruple precision introduced by the IEEE-754-2008 standard and currently unsupported by processor hardware. An open-source implementation is provided in the FloPoCo project.
On Mappings with Contractive Iterate at a Point in Generalized Metric Spaces
Authors: Gajić Ljiljana , Lozanov-Crvenković Zagorka 
Published: January 2011

AbstractUsing the setting of generalized metric space, the so-called G-metric space, fixed point theorems for mappings with a contractive and a generalized contractive iterate at a point are proved. These results generalize some comparable results in the literature. A common fixed point result is also proved.
Strong Convergence of Modified Halpern Iterations in CAT(0) Spaces
Authors: Cuntavepanit A , Panyanak B 
Published: January 2011

AbstractStrong convergence theorems are established for the modified Halpern iterations of nonexpansive mappings in CAT(0) spaces. Our results extend and improve the recent ones announced by Kim and Xu (2005), Hu (2008), Song and Chen (2008), Saejung (2010), and many others.
Sublexical Properties of Spoken Words Modulate Activity in Broca's Area but Not Superior Temporal Cortex: Implications for Models of Speech Recognition
Authors: Vaden Kenneth I. , Piquado Tepring , Hickok Gregory 
Published: January 2011

Abstract
Many models of spoken word recognition posit that the acoustic stream is parsed into phoneme level units, which in turn activate larger representations [McClelland, J. L., & Elman, J. L. The TRACE model of speech perception. Cognitive Psychology, 18, 1–86, 1986], whereas others suggest that larger units of analysis are activated without the need for segmental mediation [Greenberg, S. A multitier theoretical framework for understanding spoken language. In S. Greenberg & W. A. Ainsworth (Eds.), Listening to speech: An auditory perspective (pp. 411–433). Mahwah, NJ: Erlbaum, 2005; Klatt, D. H. Speech perception: A model of acoustic-phonetic analysis and lexical access. Journal of Phonetics, 7, 279–312, 1979; Massaro, D. W. Preperceptual images, processing time, and perceptual units in auditory perception. Psychological Review, 79, 124–145, 1972]. Identifying segmental effects in the brain's response to speech may speak to this question. For example, if such effects were localized to relatively early processing stages in auditory cortex, this would support a model of speech recognition in which segmental units are explicitly parsed out. In contrast, segmental processes that occur outside auditory cortex may indicate that alternative models should be considered. The current fMRI experiment manipulated the phonotactic frequency (PF) of words that were auditorily presented in short lists while participants performed a pseudoword detection task. PF is thought to modulate networks in which phoneme level units are represented. The present experiment identified activity in the left inferior frontal gyrus that was positively correlated with PF. No effects of PF were found in temporal lobe regions. We propose that the observed phonotactic effects during speech listening reflect the strength of the association between acoustic speech patterns and articulatory speech codes involving phoneme level units. On the basis of existing lesion evidence, we interpret the function of this auditory–motor association as playing a role primarily in production. These findings are consistent with the view that phoneme level units are not necessarily accessed during speech recognition.
A Neural Region of Abstract Working Memory
Authors: Cowan Nelson , Li Dawei , Moffitt Amanda , Becker Theresa M. , Martin Elizabeth A. , Saults J. Scott , Christ Shawn E. 
Published: January 2011

Abstract
Over 350 years ago, Descartes proposed that the neural basis of consciousness must be a brain region in which sensory inputs are combined. Using fMRI, we identified at least one such area for working memory, the limited information held in mind, described by William James as the trailing edge of consciousness. Specifically, a region in the left intraparietal sulcus was found to demonstrate load-dependent activity for either visual stimuli (colored squares) or a combination of visual and auditory stimuli (spoken letters). This result was replicated across two experiments with different participants and methods. The results suggest that this brain region, previously well known for working memory of visually presented materials, actually holds or refers to information from more than one modality.
Double Dissociation of Dopamine Genes and Timing in Humans
Authors: Wiener Martin , Lohoff Falk W. , Coslett H. Branch 
Published: January 2011

Abstract
A number of lines of evidence implicate dopamine in timing [Rammsayer, T. H. Neuropharmacological approaches to human timing. In S. Grondin (Ed.), Psychology of time (pp. 295–320). Bingley, UK: Emerald, 2008; Meck, W. H. Neuropharmacology of timing and time perception. Brain Research, Cognitive Brain Research, 3, 227–242, 1996]. Two human genetic polymorphisms are known to modulate dopaminergic activity. DRD2/ANKK1-Taq1a is a D2 receptor polymorphism associated with decreased D2 density in the striatum [Jönsson, E. G., Nothen, M. M., Grunhage, F., Farde, L., Nakashima, Y., Propping, P., et al. Polymorphisms in the dopamine D2 receptor gene and their relationships to striatal dopamine receptor density of healthy volunteers. Molecular Psychiatry, 4, 290–296, 1999]; COMT Val158Met is a functional polymorphism associated with increased activity of the COMT enzyme such that catabolism of synaptic dopamine is greater in pFC [Meyer-Lindenberg, A., Kohn, P. D., Kolachana, B., Kippenhan, S., McInerney-Leo, A., Nussbaum, R., et al. Midbrain dopamine and prefrontal function in humans: Interaction and modulation by COMT genotype. Nature Neuroscience, 8, 594–596, 2005]. To investigate the role of dopamine in timing, we genotyped 65 individuals for DRD2/ANKK1-Taq1a, COMT Val158Met, and a third polymorphism, BDNF Val66Met, a functional polymorphism affecting the expression of brain-derived neurotrophic factor [Egan, M. F., Kojima, M., Callicott, J. H., Goldberg, T. E., Kolachana, B. S., Bertolino, A., et al. The BDNF val66met polymorphism affects activity-dependent secretion of BDNF and human memory and hippocampal function. Cell, 112, 257–269, 2003]. Subjects were tested on a temporal discrimination task with sub- and supra-second intervals (500- and 2000-msec standards) as well as a spontaneous motor tempo task. We found a double dissociation for temporal discrimination: the DRD2/ANKK1-Taq1a polymorphism (A1+ allele) was associated with significantly greater variability for the 500-msec duration only, whereas the COMT Val158Met polymorphism (Val/Val homozygotes) was associated with significantly greater variability for the 2000-msec duration only. No differences were detected for the BDNF Vall66Met variant. Additionally, the DRD2/ANKK1-Taq1a polymorphism was associated with a significantly slower preferred motor tempo. These data provide a potential biological basis for the distinctions between sub- and supra-second timing and suggest that BG are integral for the former whereas pFC is implicated in the latter.
Evolution of Multiscale Vortices in the Development of Hurricane Dolly (2008)
Authors: Fang Juan , Zhang Fuqing 
Published: January 2011

AbstractAs a follow-up to a previously published article on the initial development and genesis of Hurricane Dolly (2008), this study further examines the evolution of, and interactions among, multiscale vortices ranging from the system-scale main vortex (L &gt; 150 km) to the intermediate-scale cloud clusters (50 km &lt; L &lt; 150 km) and individual vorticity-rich convective cells (L &lt; 50 km). It is found that there are apparent self-similarities among these vortices at different scales, each of which may undergo several cycles of alternating accumulation and release of convective available potential energy. Enhanced surface fluxes below individual cyclonic vortices at each scale contribute to the sustainment and reinvigoration of moist convection that in turn contributes to the maintenance and upscale growth of these vortices.Spectral analysis of horizontal divergence and relative vorticity further suggests that the cloud-cluster-scale and system-scale vortices are predominantly balanced while the individual convective vortices are largely unbalanced. The vorticity and energy produced by these individual vorticity-rich convective cells first saturate at convective scales that are subsequently transferred to larger scales. The sum of the diabatic heating released from these convective cells may be regarded as a persistent forcing on the quasi-balanced system-scale vortex. The secondary circulation induced by such forcing converges the cluster- and convective-scale vorticity anomalies into the storm center region. Convergence and projections of the smaller-scale vorticity to the larger scales eventually produce the spinup of the system-scale vortex. Meanwhile, convectively induced negative vorticity anomalies also converge toward the storm center, which are weaker and shorter lived, and thus are absorbed rather than expelled.