Using Relationships for Matching Textual Domain Models with Existing Code

We address the task of mapping a given textual domain model (e.g., an industry-standard reference model) for a given domain (e.g., ERP), with the source code of an independently developed application in the same domain. This has applications in improving the understandability of an existing application, migrating it to a more flexible architecture, or integrating it with other related applications. We use the vector-space model to abstractly represent domain model elements as well as source-code artifacts. The key novelty in our approach is to leverage the relationships between source-code artifacts in a principled way to improve the mapping process. We describe experiments wherein we apply our approach to the task of matching two real, open-source applications to corresponding industry-standard domain models. We demonstrate the overall usefulness of our approach, as well as the role of our propagation techniques in improving the precision and recall of the mapping task.

Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions

Background: The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating these findings into biomedically useful information is to find out the mechanism of the action of these genes. However, GWAS studies often implicate genes whose functions are currently unknown; for example, MYEOV, ANKLE1, TMEM45B and ORAOV1 are found to be associated with breast cancer, but their molecular function is unknown. Results: We carried out Bayesian inference of Gene Ontology (GO) term annotations of genes by employing the directed acyclic graph structure of GO and the network of protein-protein interactions (PPIs). The approach is designed based on the fact that two proteins that interact biophysically would be in physical proximity of each other, would possess complementary molecular function, and play role in related biological processes. Predicted GO terms were ranked according to their relative association scores and the approach was evaluated quantitatively by plotting the precision versus recall values and F-scores (the harmonic mean of precision and recall) versus varying thresholds. Precisions of similar to 58% and similar to 40% for localization and functions respectively of proteins were determined at a threshold of similar to 30 (top 30 GO terms in the ranked list). Comparison with function prediction based on semantic similarity among nodes in an ontology and incorporation of those similarities in a k nearest neighbor classifier confirmed that our results compared favorably. Conclusions: This approach was applied to predict the cellular component and molecular function GO terms of all human proteins that have interacting partners possessing at least one known GO annotation. The list of predictions is available at http://severus.dbmi.pitt.edu/engo/GOPRED.html. We present the algorithm, evaluations and the results of the computational predictions, especially for genes identified in GWAS studies to be associated with diseases, which are of translational interest.

KINEMATIC SYNTHESIS AND ANALYSIS OF THE RACK AND PINION MULTIPURPOSE MECHANISM

The general procedure for synthesizing the rack and pinion mechanism up to seven precision conditions is developed. To illustrate the method, the mechanism has been synthesized in closed form for three precision conditions of path generation, two positions of function generation, and a velocity condition at one of the precision points. This mechanism has a number of advantages over conventional four bar mechanisms. First, since the rack is always tangent to the pinion, the transmission angle is always 90 deg minus the pressure angle of the rack. Second, with both translation and rotation of the rock occurring, multiple outputs are available. Other advantages include the generation of monotonic functions for a wide variety of motion and nonmonotonic functions for a full range of motion as well as nonlinear amplified motions. In this work the mechanism is made to satisfy a number of amplified motions. In this work the mechanism is made to satisfy a number of practical design requirements such as completely rotatable input crank and others. By including the velocity specification, the designer has considerably more control of the output motion. The method of solution developed in this work uses the complex number method of mechanism synthesis. A numerical example is included

Kinematic Synthesis and Analysis of the Rack and Pinion Multi-Purpose Mechanism

The general procedure for synthesizing the rack and pinion mechanism up to seven precision conditions is developed. To illustrate the method, the mechanism has been synthesized in closed form for three precision conditions of path generation, two positions of function generation, and a velocity condition at one of the precision points. This mechanism has a number of advantages over conventional four bar mechanisms. First, since the rack is always tangent to the pinion, the transmission angle is always 90 deg minus the pressure angle of the rack. Second, with both translation and rotation of the rack occurring, multiple outputs are available. Other advantages include the generation of monotonic functions for a wide variety of motion and nonmonotonic functions for a full range of motion as well as nonlinear amplified motions. In this work the mechanism is made to satisfy a number of practical design requirements such as completely rotatable input crank and others. By including the velocity specification, the designer has considerably more control of the output motion. The method of solution developed in this work uses the complex number method of mechanism synthesis. A numerical example is included.

Micro-mechanical stages with enhanced range

We present concepts and an optimization-based methodology for the design of micro-mechanical stages that have not only high precision but also an enhanced range. Joint-free distributed compliant designs provide high precision and easy manufacturability at macro and micro scales. The range of motion is enhanced by using displacement-amplifying compliant mechanisms (DaCMs). The main issue addressed in this paper is how to retain the decoupling between the X and Y motions in the stage when it is equipped with DaCMs. The natural frequency of the stage is also not compromised in enhancing the range. The optimized design has 2.5 times more range than the designs reported in the literature. Furthermore, the sensitivity improved by a factor of two when the stage is optimized for an accelerometer.

Polarization-rotation resonances with subnatural widths using a control laser

We demonstrate extremely narrow resonances for polarization rotation in an atomic vapor. The resonances are created using a strong control laser on the same transition, which polarizes the atoms due to optical pumping among the magnetic sublevels. As the power in the control laser is increased, successively higher-order nested polarization-rotation resonances are created, with progressively narrower linewidths. We study these resonances in the D-2 line of Rb in a room temperature vapor cell, and demonstrate a width of 0.14 G for the third-order rotation. The physical basis for the observed resonances is that optical pumping results in a simplified. AV-type level structure with differential dressing of the levels by the control laser, which is why the control power has to be sufficiently high for each resonance to appear. This explanation is borne out by a density-matrix analysis of the system. The dispersive lineshape and subnatural width of the resonance lends itself naturally to applications such as laser locking to atomic transitions and precision measurements. Copyright (c) EPLA, 2014

Parallel Flow-Sensitive Pointer Analysis by Graph-Rewriting

Precise pointer analysis is a problem of interest to both the compiler and the program verification community. Flow-sensitivity is an important dimension of pointer analysis that affects the precision of the final result computed. Scaling flow-sensitive pointer analysis to millions of lines of code is a major challenge. Recently, staged flow-sensitive pointer analysis has been proposed, which exploits a sparse representation of program code created by staged analysis. In this paper we formulate the staged flow-sensitive pointer analysis as a graph-rewriting problem. Graph-rewriting has already been used for flow-insensitive analysis. However, formulating flow-sensitive pointer analysis as a graph-rewriting problem adds additional challenges due to the nature of flow-sensitivity. We implement our parallel algorithm using Intel Threading Building Blocks and demonstrate considerable scaling (upto 2.6x) for 8 threads on a set of 10 benchmarks. Compared to the sequential implementation of staged flow-sensitive analysis, a single threaded execution of our implementation performs better in 8 of the benchmarks.

TSpred: a web server for the rational design of temperature-sensitive mutants

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

Survey of vector-like fermion extensions of the Standard Model and their phenomenological implications

With the renewed interest in vector-like fermion extensions of the Standard Model, we present here a study of multiple vector-like theories and their phenomenological implications. Our focus is mostly on minimal flavor conserving theories that couple the vector-like fermions to the SM gauge fields and mix only weakly with SM fermions so as to avoid flavor problems. We present calculations for precision electroweak and vector-like state decays, which are needed to investigate compatibility with currently known data. We investigate the impact of vector-like fermions on Higgs boson production and decay, including loop contributions, in a wide variety of vector-like extensions and their parameter spaces.

Precise Slicing in Imperative Programs via Term-Rewriting and Abstract Interpretation

We propose a new approach for producing precise constrained slices of programs in a language such as C. We build upon a previous approach for this problem, which is based on term-rewriting, which primarily targets loop-free fragments and is fully precise in this setting. We incorporate abstract interpretation into term-rewriting, using a given arbitrary abstract lattice, resulting in a novel technique for slicing loops whose precision is linked to the power of the given abstract lattice. We address pointers in a first-class manner, including when they are used within loops to traverse and update recursive data structures. Finally, we illustrate the comparative precision of our slices over those of previous approaches using representative examples.

Mining Unit Tests for Discovery and Migration of Math APIs

Today's programming languages are supported by powerful third-party APIs. For a given application domain, it is common to have many competing APIs that provide similar functionality. Programmer productivity therefore depends heavily on the programmer's ability to discover suitable APIs both during an initial coding phase, as well as during software maintenance. The aim of this work is to support the discovery and migration of math APIs. Math APIs are at the heart of many application domains ranging from machine learning to scientific computations. Our approach, called MATHFINDER, combines executable specifications of mathematical computations with unit tests (operational specifications) of API methods. Given a math expression, MATHFINDER synthesizes pseudo-code comprised of API methods to compute the expression by mining unit tests of the API methods. We present a sequential version of our unit test mining algorithm and also design a more scalable data-parallel version. We perform extensive evaluation of MATHFINDER (1) for API discovery, where math algorithms are to be implemented from scratch and (2) for API migration, where client programs utilizing a math API are to be migrated to another API. We evaluated the precision and recall of MATHFINDER on a diverse collection of math expressions, culled from algorithms used in a wide range of application areas such as control systems and structural dynamics. In a user study to evaluate the productivity gains obtained by using MATHFINDER for API discovery, the programmers who used MATHFINDER finished their programming tasks twice as fast as their counterparts who used the usual techniques like web and code search, IDE code completion, and manual inspection of library documentation. For the problem of API migration, as a case study, we used MATHFINDER to migrate Weka, a popular machine learning library. Overall, our evaluation shows that MATHFINDER is easy to use, provides highly precise results across several math APIs and application domains even with a small number of unit tests per method, and scales to large collections of unit tests.

Constraints on the omega pi form factor from analyticity and unitarity

Motivated by the discrepancies noted recently between the theoretical calculations of the electromagnetic omega pi form factor and certain experimental data, we investigate this form factor using analyticity and unitarity in a framework known as the method of unitarity bounds. We use a QCD correlator computed on the spacelike axis by operator product expansion and perturbative QCD as input, and exploit unitarity and the positivity of its spectral function, including the two-pion contribution that can be reliably calculated using high-precision data on the pion form factor. From this information, we derive upper and lower bounds on the modulus of the omega pi form factor in the elastic region. The results provide a significant check on those obtained with standard dispersion relations, confirming the existence of a disagreement with experimental data in the region around 0.6 GeV.

Limiting two-Higgs-doublet models

We update the constraints on two-Higgs-doublet models (2HDMs) focusing on the parameter space relevant to explain the present muon g - 2 anomaly, Delta alpha(mu), in four different types of models, type I, II, ``lepton specific'' (or X) and ``flipped'' (or Y). We show that the strong constraints provided by the electroweak precision data on the mass of the pseudoscalar Higgs, whose contribution may account for Delta alpha(mu), are evaded in regions where the charged scalar is degenerate with the heavy neutral one and the mixing angles alpha and beta satisfy the Standard Model limit beta - alpha approximate to pi/2. We combine theoretical constraints from vacuum stability and perturbativity with direct and indirect bounds arising from collider and B physics. Possible future constraints from the electron g - 2 are also considered. If the 126 GeV resonance discovered at the LHC is interpreted as the light CP-even Higgs boson of the 2HDM, we find that only models of type X can satisfy all the considered theoretical and experimental constraints.

Silicon isotopes: from cosmos to benthos

Silicon is the second most abundant element on the Earth and one of the more abundant elements in our Solar System. Variations in the relative abundance of the stable isotopes of Si (Si isotope fractionation) in different natural reservoirs, both terrestrial (surface and deep Earth) as well as extra-terrestrial (e.g. meteorites, lunar samples), are a powerful tracer of present and past processes involving abiotic as well as biotic systems. The versatility of the Si isotope tracer is reflected in its wide-ranging applications from understanding the origin of early Solar System objects, planetary differentiation, Moon formation, mantle melting and magma differentiation on the Earth, ancient sea-water composition, to modern-day weathering, clay formation and biological fractionation on land as well as in the oceans. The application of Si isotopes as tracers of natural processes started over six decades ago and its usage has seen a sudden increase over the last decade due to improvements in mass spectrometry, particularly the advent of multi-collector inductively coupled plasma mass spectrometers, which has made Si isotope measurements safe and relatively easy while simultaneously improving the accuracy and precision of measurements.

Sparse coding based VLAD for efficient image retrieval

Representing images and videos in the form of compact codes has emerged as an important research interest in the vision community, in the context of web scale image/video search. Recently proposed Vector of Locally Aggregated Descriptors (VLAD), has been shown to outperform the existing retrieval techniques, while giving a desired compact representation. VLAD aggregates the local features of an image in the feature space. In this paper, we propose to represent the local features extracted from an image, as sparse codes over an over-complete dictionary, which is obtained by K-SVD based dictionary training algorithm. The proposed VLAD aggregates the residuals in the space of these sparse codes, to obtain a compact representation for the image. Experiments are performed over the `Holidays' database using SIFT features. The performance of the proposed method is compared with the original VLAD. The 4% increment in the mean average precision (mAP) indicates the better retrieval performance of the proposed sparse coding based VLAD.