This paper is concerned with the mathematical structure of the immersed boundary (IB) method, which is intended for the computer simulation of fluid–structure interaction, especially in biological fluid dynamics. The IB formulation of such problems, derived here from the principle of least action, involves both Eulerian and Lagrangian variables, linked by the Dirac delta function. Spatial discretization of the IB equations is based on a fixed Cartesian mesh for the Eulerian variables, and a moving curvilinear mesh for the Lagrangian variables. The two types of variables are linked by interaction equations that involve a smoothed approximation to the Dirac delta function. Eulerian/Lagrangian identities govern the transfer of data from one mesh to the other. Temporal discretization is by a second-order Runge–Kutta method. Current and future research directions are pointed out, and applications of the IB method are briefly discussed. Introduction The immersed boundary (IB) method was introduced to study flow patterns around heart valves and has evolved into a generally useful method for problems of fluid–structure interaction. The IB method is both a mathematical formulation and a numerical scheme. The mathematical formulation employs a mixture of Eulerian and Lagrangian variables. These are related by interaction equations in which the Dirac delta function plays a prominent role. In the numerical scheme motivated by the IB formulation, the Eulerian variables are defined on a fixed Cartesian mesh, and the Lagrangian variables are defined on a curvilinear mesh that moves freely through the fixed Cartesian mesh without being constrained to adapt to it in any way at all.

/pdf/the-immersed-boundary-method-xfkx3wd291.pdf

The immersed boundary method

Aspect] is a simple and practical aspect-oriented extension to Java With just a few new constructs, AspectJ provides support for modular implementation of a range of crosscutting concerns. In AspectJ's dynamic join point model, join points are well-defined points in the execution of the program; pointcuts are collections of join points; advice are special method-like constructs that can be attached to pointcuts; and aspects are modular units of crosscutting implementation, comprising pointcuts, advice, and ordinary Java member declarations. AspectJ code is compiled into standard Java bytecode. Simple extensions to existing Java development environments make it possible to browse the crosscutting structure of aspects in the same kind of way as one browses the inheritance structure of classes. Several examples show that AspectJ is powerful, and that programs written using it are easy to understand.

An overview of AspectJ

A type system is a syntactic method for automatically checking the absence of certain erroneous behaviors by classifying program phrases according to the kinds of values they compute. The study of type systems -- and of programming languages from a type-theoretic perspective -- has important applications in software engineering, language design, high-performance compilers, and security.This text provides a comprehensive introduction both to type systems in computer science and to the basic theory of programming languages. The approach is pragmatic and operational; each new concept is motivated by programming examples and the more theoretical sections are driven by the needs of implementations. Each chapter is accompanied by numerous exercises and solutions, as well as a running implementation, available via the Web. Dependencies between chapters are explicitly identified, allowing readers to choose a variety of paths through the material.The core topics include the untyped lambda-calculus, simple type systems, type reconstruction, universal and existential polymorphism, subtyping, bounded quantification, recursive types, kinds, and type operators. Extended case studies develop a variety of approaches to modeling the features of object-oriented languages.

https://www.seas.upenn.edu/~bcpierce/tapl/contents.pdf

Types and Programming Languages

Program analysis utilizes static techniques for computing reliable information about the dynamic behavior of programs. Applications include compilers (for code improvement), software validation (for detecting errors) and transformations between data representation (for solving problems such as Y2K). This book is unique in providing an overview of the four major approaches to program analysis: data flow analysis, constraint-based analysis, abstract interpretation, and type and effect systems. The presentation illustrates the extensive similarities between the approaches, helping readers to choose the best one to utilize.

Principles of program analysis

We consider supervised learning in the presence of very many irrelevant features, and study two different regularization methods for preventing overfitting. Focusing on logistic regression, we show that using L1 regularization of the parameters, the sample complexity (i.e., the number of training examples required to learn "well,") grows only logarithmically in the number of irrelevant features. This logarithmic rate matches the best known bounds for feature selection, and indicates that L1 regularized logistic regression can be effective even if there are exponentially many irrelevant features as there are training examples. We also give a lower-bound showing that any rotationally invariant algorithm---including logistic regression with L2 regularization, SVMs, and neural networks trained by backpropagation---has a worst case sample complexity that grows at least linearly in the number of irrelevant features.

/pdf/feature-selection-l1-vs-l2-regularization-and-rotational-1ag6v8llm6.pdf

Feature selection, L1 vs. L2 regularization, and rotational invariance

Digital content is for copying: quotation, revision, plagiarism, and file sharing all create copies. Document fingerprinting is concerned with accurately identifying copying, including small partial copies, within large sets of documents.We introduce the class of local document fingerprinting algorithms, which seems to capture an essential property of any finger-printing technique guaranteed to detect copies. We prove a novel lower bound on the performance of any local algorithm. We also develop winnowing, an efficient local fingerprinting algorithm, and show that winnowing's performance is within 33% of the lower bound. Finally, we also give experimental results on Web data, and report experience with MOSS, a widely-used plagiarism detection service.

/pdf/winnowing-local-algorithms-for-document-fingerprinting-1cm7aw0099.pdf

Winnowing: local algorithms for document fingerprinting

We present a statistical debugging algorithm that isolates bugs in programs containing multiple undiagnosed bugs. Earlier statistical algorithms that focus solely on identifying predictors that correlate with program failure perform poorly when there are multiple bugs. Our new technique separates the effects of different bugs and identifies predictors that are associated with individual bugs. These predictors reveal both the circumstances under which bugs occur as well as the frequencies of failure modes, making it easier to prioritize debugging efforts. Our algorithm is validated using several case studies, including examples in which the algorithm identified previously unknown, significant crashing bugs in widely used systems.

/pdf/scalable-statistical-bug-isolation-cze7jeumv9.pdf

Scalable statistical bug isolation

We describe a new technique for finding potential buffer overrun vulnerabilities in security-critical C code. The key to success is to use static analysis: we formulate detection of buffer overruns as an integer range analysis problem. One major advantage of static analysis is that security bugs can be eliminated before code is deployed. We have implemented our design and used our prototype to find new remotely-exploitable vulnerabilities in a large, widely deployed software package. An earlier hand audit missed

/pdf/a-first-step-towards-automated-detection-of-buffer-overrun-4foxumxqba.pdf

A First Step Towards Automated Detection of Buffer Overrun Vulnerabilities.

We propose a low-overhead sampling infrastructure for gathering information from the executions experienced by a program's user community. Several example applications illustrate ways to use sampled instrumentation to isolate bugs. Assertion-dense code can be transformed to share the cost of assertions among many users. Lacking assertions, broad guesses can be made about predicates that predict program errors and a process of elimination used to whittle these down to the true bug. Finally, even for non-deterministic bugs such as memory corruption, statistical modeling based on logistic regression allows us to identify program behaviors that are strongly correlated with failure and are therefore likely places to look for the error.

/pdf/bug-isolation-via-remote-program-sampling-4w8u70mrjv.pdf

Bug isolation via remote program sampling

We present a novel technique for static race detection in Java programs, comprised of a series of stages that employ a combination of static analyses to successively reduce the pairs of memory accesses potentially involved in a race. We have implemented our technique and applied it to a suite of multi-threaded Java programs. Our experiments show that it is precise, scalable, and useful, reporting tens to hundreds of serious and previously unknown concurrency bugs in large, widely-used programs with few false alarms.

/pdf/effective-static-race-detection-for-java-dwzdfz4vmx.pdf

Alex Aiken

Papers

Winnowing: local algorithms for document fingerprinting

Scalable statistical bug isolation

A First Step Towards Automated Detection of Buffer Overrun Vulnerabilities.

Bug isolation via remote program sampling

Effective static race detection for Java