13475813
Compositional Reasoning for Pointer Structures
This paper studies the compositional definition and behaviour of properties that arise in pointer structures. A pointer structure is represented as a (pointer) graph. A pointer property is a set of pointer structures. A parameterised binary combinator is defined that enables important properties (like acyclicity, canonicity and reachability) to be defined in a compositional manner. The technique of parameterising a combinator derives from the definition of parallel-by-merge in ‘Unifying Theories of Programming'. It is applied here to the study of disjointness combinators that extend the separating conjunction of Separation Logic. A case study is provided to demonstrate how these ideas are used, in the form of rules of Hoare logic, to verify the correctness of an Object-Oriented program.
15862425
A Fixpoint Theory for Non-monotonic Parallelism
This paper studies parallel recursions. The trace specification language used in this paper incorporates sequentiality, nondeterminism, reactiveness (including infinite traces), conjunctive parallelism and general recursion. The language is the minimum of its kind and thus provides a context in which we can study parallel recursions in general. In order to use Tarski's theorem to determine the fixpoints of recursions, we need to identify a well-founded partial order. A theorem of this paper shows that no appropriate order exists. Tarski's theorem alone is not enough to determine the fixpoints of parallel recursions. Instead of using Tarski's theorem directly, we reason about the fixpoints of terminating and nonterminating behaviours separately. Such reasoning is supported by the laws of a new composition called partition. We propose a fixpoint technique called the partitioned fixpoint, which is the least fixpoint of the nonterminating behaviours after the terminating behaviours reach their greatest fixpoint. The surprising result is that although a recursion may not be monotonic with regard to the lexical order, it must have the partitioned fixpoint, which equals the least lexical-order fixpoint. Since the partitioned fixpoint is well defined in any complete lattice, the results are applicable to various semantic models. Major existing fixpoint techniques simply become special cases of the partitioned fixpoint. For example, an Egli-Milner-monotonic recursion has its least Egli-Milner fixpoint, which can be shown to be the same as the partitioned fixpoint. The new technique is more general than the least Egli-Milner fixpoint in that the partitioned fixpoint can be determined even when a recursion is not Egli-Milner monotonic. Examples of non-monotonic recursions with fair-interleaving parallelism are studied. Their partitioned fixpoints are shown to be consistent with our intuitions.
17662809
Hierarchical Organisation of Predicate-Semantic Models
This paper introduces techniques to organise predicate- semantic models in a hierarchical structure so that a new model can inherit the laws of the existing ones. Generic composition is used to simplify the manipulation of predicates. Necessary restrictions are imposed on the definition of each model so that the inheritance relation can be established by checking a few conditions on the healthiness conditions and the commands. Much of the checking can be supported by laws of generic composition. The techniques also help simplify the proof of well-definedness of program combinators (i.e. their closure in the semantic space) so that we no longer need to prove it (in predicate calculus) for every new model.
211611
Automatic Time Expression Labeling for English and Chinese Text
In this paper, we describe systems for automatic labeling of time expressions occurring in English and Chinese text as specified in the ACE Temporal Expression Recognition and Normalization (TERN) task. We cast the chunking of text into time expressions as a tagging problem using a bracketed representation at token level, which takes into account embedded constructs. We adopted a left-to-right, token-by-token, discriminative, deterministic classification scheme to determine the tags for each token. A number of features are created from a predefined context centered at each token and augmented with decisions from a rule-based time expression tagger and/or a statistical time expression tagger trained on different type of text data, assuming they provide complementary information. We trained one-versus-all multi-class classifiers using support vector machines. We participated in the TERN 2004 recognition task and achieved competitive results.
45104603
A Similarity Search Algorithm to Predict Protein Structures
Accurate prediction of protein structures is very important for many applications such as drug discovery and biotechnology. Building side chains is an essential to get any reliable prediction of the protein structure for any given a protein main chain conformation. Most of the methods that predict side chain conformations use statistically generated data from known protein structures. It is a computationally intractable problem to search suitable side chains from all possible rotamers simultaneously using information of known protein structures. Reducing the number of possibility is a main issue to predict side chain conformation. This paper proposes an enumeration based similarity search algorithm to predict side chain conformations. By introducing “beam search” technique, a significant number of unrelated side chain rotamers can easily be eliminated. As a result, we can search for suitable residue side chains from all possible side chain conformations.
18836133
On the epigenetic regulation of the human reelin promoter
Reln mRNA and protein levels are reduced by approximately 50% in various cortical structures of post-mortem brain from patients diagnosed with schizophrenia or bipolar illness with psychosis. To study mechanisms responsible for this down-regulation, we have analyzed the promoter of the human reelin gene. We show that the reelin promoter directs expression of a reporter construct in multiple human cell types: neuroblastoma cells (SHSY5Y), neuronal precursor cells (NT2), differentiated neurons (hNT) and hepatoma cells (HepG2). Deletion constructs confirmed the presence of multiple elements regulating Reln expression, although the promoter activity is promiscuous, i.e. activity did not correlate with expression of the endogenous gene as reflected in terms of reelin mRNA levels. Co-transfection of the -514 bp human reelin promoter with either Sp1 or Tbr1 demonstrated that these transcription factors activate reporter expression by 6- and 8.5-fold, respectively. Within 400 bp of the RNA start site there are 100 potential CpG targets for DNA methylation. Retinoic acid (RA)-induced differentiation of NT2 cells to hNT neurons was accompanied by increased reelin expression and by the appearance of three DNase I hypersensitive sites 5' to the RNA start site. RA-induced differentiation was also associated with demethylation of the reelin promoter. To test if methylation silenced reelin expression, we methylated the promoter in vitro prior to transfection. In addition, we treated NT2 cells with the methylation inhibitor aza-2'-deoxycytidine and observed a 60-fold increase in reelin mRNA levels. The histone deacetylase inhibitors trichostatin A (TSA) and valproic acid also induced expression of the endogenous reelin promoter, although TSA was considerably more potent. These findings indicate that one determinant responsible for regulating reelin expression is the methylation status of the promoter. Our data also raise the interesting possibility that the down-regulation of reelin expression documented in psychiatric patients might be the consequence of inappropriate promoter hypermethylation.
18226391
Rough-Set Multiple-Criteria ABC Analysis
Multiple-criteria ABC (MCABC) analysis is conducted using a dominance-based rough set approach. ABC analysis, a well-known technique for inventory planning and control, divides stock-keeping units (SKUs) into three classes according to annual dollar usage. But MCABC analysis offers more managerial flexibility by including other criteria, such as lead time and criticality, in the classification of SKUs. The objective of this paper is to propose an MCABC method that uses the dominance-based rough set approach to generate linguistic rules that represent a decision-maker's preferences based on the classification of a test data set. These linguistic rules are then used to classify all SKUs. A case study demonstrates that the procedure is feasible.
646545
Designing and Evaluating an XPath Dialect for Linguistic Queries
Linguistic research and natural language processing employ large repositories of ordered trees. XML, a standard ordered tree model, and XPath, its associated language, are natural choices for linguistic data and queries. However, several important expressive features required for linguistic queries are missing or hard to express in XPath. In this paper, we motivate and illustrate these features with a variety of linguistic queries. Then we propose extensions to XPath to support linguistic queries, and design an efficient query engine based on a novel labeling scheme. Experiments demonstrate that our language is not only sufficiently expressive for linguistic trees but also efficient for practical usage.