5050501
Eliminating dead code on recursive data
This paper describes a powerful method for dead-code analysis and elimination in the presence of recursive data constructions. We describe partially dead recursive data using liveness patterns based on general regular tree grammars extended with the notion of live and dead, and we formulate the analysis as computing liveness patterns at all program points based on constraints constructed from the program and programming language semantics. The analysis yields the most precise program-based grammars that satisfy the constraints. The analysis algorithm takes cubic time in terms of the size of the program in the worst case but is very efficient in practice, as shown by our prototype implementation. The analysis results are used to identify and eliminate dead code. The framework for representing and analyzing properties of recursive data structures using general regular tree grammars applies to other analyses as well.
8840929
Optimized Live Heap Bound Analysis
This paper describes a general approach for optimized live heap space and live heap space-bound analyses for garbage-collected languages. The approach is based on program analysis and transformations and is fully automatic. In our experience, the space-bound analysis generally produces accurate (tight) upper bounds in the presence of partially known input structures. The optimization drastically improves the analysis efficiency. The analyses have been implemented and experimental results confirm their accuracy and efficiency.
15838270
Eliminating Dead Code on Recursive Data
This paper describes a general and powerful method for dead code analysis and elimination in the presence of recursive data constructions. We represent partially dead recursive data using liveness patterns based on general regular tree grammars extended with the notion of live and dead, and we formulate the analysis as computing liveness patterns at all program points based on program semantics. This analysis yields a most precise liveness pattern for the data at each program point, which is significantly more precise than results from previous methods. The analysis algorithm takes cubic time in terms of the size of the program in the worst case but is very efficient in practice, as shown by our prototype implementation. The analysis results are used to identify and eliminate dead code. The general framework for representing and analyzing properties of recursive data structures using general regular tree grammars applies to other analyses as well.
37778003
Automatic Accurate Cost-Bound Analysis for High-Level Languages
This paper describes a language-based approach for automatic and accurate cost-bound analysis. The approach consists of transformations for building cost-bound functions in the presence of partially known input structures, symbolic evaluation of the cost-bound function based on input size parameters, and optimizations to make the overall analysis efficient as well as accurate, all at the source-language level. The calculated cost bounds are expressed in terms of primitive cost parameters. These parameters can be obtained based on the language implementation or can be measured conservatively or approximately, yielding accurate, conservative, or approximate time or space bounds. We have implemented this approach and performed a number of experiments for analyzing Scheme programs. The results helped confirm the accuracy of the analysis.
9019278
Querying Complex Graphs
This paper presents a powerful language for querying complex graphs and a method for generating efficient implementations that can answer queries with complexity guarantees. The graphs may have edge labels that may have parameters, and easily and naturally capture complex interrelated objects in object-oriented systems and XML data. The language is built on extended regular path expressions with variables and scoping, and can express queries more easily and clearly than previous query languages.The method for implementation first transforms queries into Datalog with limited extensions. It then extends a previous method to generate specialized algorithms and complexity formulas from Datalog with these extensions.
5528420
Automatic time-bound analysis for a higher-order language
Analysis of program running time is important for several applications, including reactive systems, interactive environments, compiler optimizations and performance evaluation. Automatic and efficient prediction of accurate time bounds is particularly important, and being able to do so for high-level languages is particularly desirable. This paper presents a general approach for automatic and accurate time-bound analysis for a functional high-level language, that combines methods and techniques studied in theory, languages, and systems. The approach consists of transformations for building time-bound functions in the presence of partially known input structures, symbolic evaluation of the time-bound function based on input parameters, optimizations to make the analysis efficient as well as accurate, and measurements of primitive parameters, all at the source-language level. To handle higher-order functions, special transformations are needed to build lambda expressions for computing running times, to optimize the construction of the time lambda expressions, and to optimize the symbolic evaluation. It took us several tries to obtain the simple and concise transformations for handling lambda expressions. We describe analysis and transformation algorithms and explain how they work. We have implemented this approach and performed a large number of experiments analyzing Scheme programs. The measured worst-case times are closely bounded by the calculated bounds. We describe our prototype system, ALPA, as well as the analysis and measurement results.
17413518
Enhancing the Effectiveness of Clustering with Spectra Analysis
For many clustering algorithms, such as K-Means, EM, and CLOPE, there is usually a requirement to set some parameters. Often, these parameters directly or indirectly control the number of clusters, that is, k, to return. In the presence of different data characteristics and analysis contexts, it is often difficult for the user to estimate the number of clusters in the data set. This is especially true in text collections such as Web documents, images, or biological data. In an effort to improve the effectiveness of clustering, we seek the answer to a fundamental question: How can we effectively estimate the number of clusters in a given data set? We propose an efficient method based on spectra analysis of eigenvalues (not eigenvectors) of the data set as the solution to the above. We first present the relationship between a data set and its underlying spectra with theoretical and experimental results. We then show how our method is capable of suggesting a range of k that is well suited to different analysis contexts. Finally, we conclude with further empirical results to show how the answer to this fundamental question enhances the clustering process for large text collections.
14257785
Comparison of probabilistic combination methods for protein secondary structure prediction
MOTIVATION
Protein secondary structure prediction is an important step towards understanding how proteins fold in three dimensions. Recent analysis by information theory indicates that the correlation between neighboring secondary structures are much stronger than that of neighboring amino acids. In this article, we focus on the combination problem for sequences, i.e. combining the scores or assignments from single or multiple prediction systems under the constraint of a whole sequence, as a target for improvement in protein secondary structure prediction.


RESULTS
We apply several graphical chain models to solve the combination problem and show that they are consistently more effective than the traditional window-based methods. In particular, conditional random fields (CRFs) moderately improve the predictions for helices and, more importantly, for beta sheets, which are the major bottleneck for protein secondary structure prediction.
23025365
A structural approach to recognizing incomplete graphic objects
We propose a structural approach to recognizing incomplete graphic objects, which aims to recognize a graphic object before the user finishes drawing all its strokes. In our approach, we first create a spatial division tree (SDT) for the input object and then search for similar objects in the database of graphic object models based on this representation. Along with the SDT, an intersection-based relationship model is also proposed in our approach to describe the relationships among strokes. The experiment result has shown that our approach can significantly save user's input time for complex graphic objects. Moreover, it also proves that our approach can response to user's input in real-time and is independent of the user's drawing style.
17761777
Risk-Sensitive Planning with One-Switch Utility Functions: Value Iteration
Decision-theoretic planning with nonlinear utility functions is important since decision makers are often risk-sensitive in high-stake planning situations. One-switch utility functions are an important class of nonlinear utility functions that can model decision makers whose decisions change with their wealth level. We study how to maximize the expected utility of a Markov decision problem for a given one-switch utility function, which is difficult since the resulting planning problem is not decomposable. We first study an approach that augments the states of the Markov decision problem with the wealth level. The properties of the resulting infinite Markov decision problem then allow us to generalize the standard risk-neutral version of value iteration from manipulating values to manipulating functions that map wealth levels to values. We use a probabilistic blocks-world example to demonstrate that the resulting risk-sensitive version of value iteration is practical.
36759557
Geometrical analysis of two sets of 3D correspondence data patterns
Given two sets of image correspondence data, the analysis of the corresponding rigid body transformation that accurately describes the object's motion in 3D space is a fundamental problem in image understanding. While many methods have been put forward to analyse 3D transformations, such methods do not make use of the vector distance between feature points and angular information as constraints to analyse transformation parameters. Current methods and algorithms have also suffered from the problems of lack of efficiency, sensitivity to noise, and multiplicity of solutions. In this paper we present a novel geometrical analysis of rigid body transformations and a novel algorithm to calibrate transformation parameters based on image correspondence. The algorithm is validated through experimental calibration and a comparison is made with calibration implemented by the least squares method. We demonstrate that the proposed algorithm works well in the presence of noise and that its performance is in general superior to algorithms based on the least squares method.