Revisiting the tree Constraint

International audienceThis paper revisits the tree constraint introduced in [2] which partitions the nodes of a n-nodes, m-arcs directed graph into a set of node-disjoint anti-arborescences for which only certain nodes can be tree roots. We introduce a new filtering algorithm that enforces generalized arc-consistency in O(n + m) time while the original filtering algorithm reaches O(nm) time. This result allows to tackle larger scale problems involving graph partitioning

Advances in Functional Decomposition: Theory and Applications

Functional decomposition aims at finding efficient representations for Boolean functions. It is used in many applications, including multi-level logic synthesis, formal verification, and testing. This dissertation presents novel heuristic algorithms for functional decomposition. These algorithms take advantage of suitable representations of the Boolean functions in order to be efficient. The first two algorithms compute simple-disjoint and disjoint-support decompositions. They are based on representing the target function by a Reduced Ordered Binary Decision Diagram (BDD). Unlike other BDD-based algorithms, the presented ones can deal with larger target functions and produce more decompositions without requiring expensive manipulations of the representation, particularly BDD reordering. The third algorithm also finds disjoint-support decompositions, but it is based on a technique which integrates circuit graph analysis and BDD-based decomposition. The combination of the two approaches results in an algorithm which is more robust than a purely BDD-based one, and that improves both the quality of the results and the running time. The fourth algorithm uses circuit graph analysis to obtain non-disjoint decompositions. We show that the problem of computing non-disjoint decompositions can be reduced to the problem of computing multiple-vertex dominators. We also prove that multiple-vertex dominators can be found in polynomial time. This result is important because there is no known polynomial time algorithm for computing all non-disjoint decompositions of a Boolean function. The fifth algorithm provides an efficient means to decompose a function at the circuit graph level, by using information derived from a BDD representation. This is done without the expensive circuit re-synthesis normally associated with BDD-based decomposition approaches. Finally we present two publications that resulted from the many detours we have taken along the winding path of our research

Changing the ideological roots of prejudice: Longitudinal effects of ethnic intergroup contact on social dominance orientation

Social Dominance Orientation (SDO) has been reported to be strongly related to a multitude of intergroup phenomena, but little is known about situational experiences that may influence SDO. Drawing from research on intergroup contact theory, we argue that positive intergroup contact is able to reduce SDO-levels. The results of an intergroup contact intervention study among high school students (Study 1, N=71) demonstrated that SDO-levels were indeed attenuated after the intervention. Furthermore, this intervention effect on SDO was especially pronounced among students reporting a higher quality of contact. A cross-lagged longitudinal survey among adults (Study 2, N=363) extended these findings by demonstrating that positive intergroup contact is able to decrease SDO over time. Moreover, we did not obtain evidence for the idea that people high in SDO would engage less in intergroup contact. These findings indicate that intergroup contact erodes one of the important socio-ideological bases of generalized prejudice and discrimination

DiffSplice: The Genome-Wide Detection of Differential Splicing Events with RNA-Seq

The RNA transcriptome varies in response to cellular differentiation as well as environmental factors, and can be characterized by the diversity and abundance of transcript isoforms. Differential transcription analysis, the detection of differences between the transcriptomes of different cells, may improve understanding of cell differentiation and development and enable the identification of biomarkers that classify disease types. The availability of high-throughput short-read RNA sequencing technologies provides in-depth sampling of the transcriptome, making it possible to accurately detect the differences between transcriptomes. In this article, we present a new method for the detection and visualization of differential transcription. Our approach does not depend on transcript or gene annotations. It also circumvents the need for full transcript inference and quantification, which is a challenging problem because of short read lengths, as well as various sampling biases. Instead, our method takes a divide-and-conquer approach to localize the difference between transcriptomes in the form of alternative splicing modules (ASMs), where transcript isoforms diverge. Our approach starts with the identification of ASMs from the splice graph, constructed directly from the exons and introns predicted from RNA-seq read alignments. The abundance of alternative splicing isoforms residing in each ASM is estimated for each sample and is compared across sample groups. A non-parametric statistical test is applied to each ASM to detect significant differential transcription with a controlled false discovery rate. The sensitivity and specificity of the method have been assessed using simulated data sets and compared with other state-of-the-art approaches. Experimental validation using qRT-PCR confirmed a selected set of genes that are differentially expressed in a lung differentiation study and a breast cancer data set, demonstrating the utility of the approach applied on experimental biological data sets. The software of DiffSplice is available at http://www.netlab.uky.edu/p/bioinfo/DiffSplice

A quantitative charcterization of control flow context: software measures for programming environments

A review of published measures of control flow complexity in programs reveals three major deficiencies: loss of information, lack of specificity, and lack of analytical support. A new approach is used to characterize the control structure of a program, with the aim of defining properties and measures of control flow that can be of immediate use to programmers, regardless of their utility as complexity measures. Mathematical rigor and analytical evaluation techniques are used to define a set of properties of control structure and a corresponding vector of measures. Instead of defining the properties and measures for an entire flowgraph, they are defined at the node level, reflecting the control flow surrounding each node in a flowgraph. The properties and their measures reflect the following characteristics of control flow: nesting, iteration, structuredness, and predecessors. Algorithms for computing the properties and their measures are presented. An assessment of the computational complexity of the algorithms shows that they are feasible programming environment tools;A finite path set, representing all possible execution sequences, is evaluated as a characterizing property. Desired characteristics of the path set are defined and used to evaluate four published path subset criteria. Those criteria are shown to be deficient, so a fifth criterion is defined. However, the path set satisfying this fifth criterion is shown to be too large to be of practical use to a programmer

Optimizing Service Orchestration in OutSystems

The growing demand for continuous development and deployment is causing many to steer away from the traditional monolithic architectural style and opt instead for Service- Oriented Architectures (SOAs). Adopting an architecture that is based on loosely-coupled services leads to enhanced modularity and flexibility, further translated into a philosophy of iterative, evolutionary development. The benefits of this development pattern were also made available in the OutSystems low-code platform, with the introduction of services as a new development building-block. Moreover, the independence innate to the multiple services that comprise a SOA hints at possible opportunities for task parallelism: as long as different remote calls to services don’t interfere with each other, they could be performed in parallel. As an immediate result, there could be speedups in multiple parts of an application’s layers. Idle time waiting for data could be reduced, along with internal business logic that could be carried out faster, factors that would positively impact the overall flow of any application. In this thesis we propose the design and implementation of an optimization process that targets the heart of the SOA: the orchestrator itself, the conductor of service interaction that enables the different business processes involved in a software system. The work produced comprises a set of data analysis and representation techniques that work together with the goal of detecting and informing opportunities for safe parallelism in the interaction and composition of the services that make up software factories. The formal definition of the algorithm is accompanied with a prototype that targets the OutSystems platform, with the achievement of considerable speedups in common scenarios. The results obtained suggest the viability of such a mechanism in the world of SOAs

Waddle - Always-canonical Intermediate Representation

Program transformations that are able to rely on the presence of canonical properties of the program undergoing optimization can be written to be more robust and efficient than an equivalent but generalized transformation that also handles non-canonical programs. If a canonical property is required but broken earlier in an earlier transformation, it must be rebuilt (often from scratch). This additional work can be a dominating factor in compilation time when many transformations are applied over large programs. This dissertation introduces a methodology for constructing program transformations so that the program remains in an always-canonical form as the program is mutated, making only local changes to restore broken properties

To-many or to-one? All-in-one! Efficient purely functional multi-maps with type-heterogeneous hash-tries

An immutable multi-map is a many-to-many map data structure with expected fast insert and lookup operations. This data structure is used for applications processing graphs or many-to-many relations as applied in compilers, runtimes of programming languages, or in static analysis of object-oriented systems. Collection data structures are assumed to carefully balance execution time of operations with memory consumption characteristics and need to scale gracefully from a few elements to multiple gigabytes at least. When processing larger in-memory data sets the overhead of the data structure encoding itself becomes a memory usage bottleneck, dominating the overall performance. In this paper we propose AXIOM, a novel hash-trie data structure that allows for a highly efficient and type-safe multi-map encoding by distinguishing inlined values of singleton sets from nested sets of multi-mappings