5642826
A garbage-collecting typed assembly language
Typed assembly languages usually support heap allocation safely, but often rely on an external garbage collector to deallocate objects from the heap and prevent unsafe dangling pointers. Even if the external garbage collector is provably correct, verifying the safety of the interaction between TAL programs and garbage collection is nontrivial. This paper introduces a typed assembly language whose type system is expressive enough to type-check a Cheney-queue copying garbage collector, so that ordinary programs and garbage collection can co-exist and interact inside a single typed language. The only built-in types for memory are linear types describing individual memory words, so that TAL programmers can define their own object layouts, method table layouts, heap layouts, and memory management techniques.
7951451
A New Test System for Stability Measurement of Marker Gene Selection in DNA Microarray Data Analysis
Microarray gene expression data contains informative features that reflect the critical processes controlling prominent biological functions. Feature selection algorithms have been used in previous biomedical research to find the “marker” genes whose expression value change corresponds to the most eminent difference between specimen classes. One problem encountered in such analysis is the imbalance between very large numbers of genes versus relatively fewer specimen samples. A common concern, therefore, is “overfitting” the data and deriving a set of marker genes with low stability over the entire set of possible specimens. To address this problem, we propose a new test environment in which synthetic data is perturbed to simulate possible variations in gene expression values. The goal is for the generated data to have appropriate properties that match natural data, and that are appropriate for use in testing the sensitivity of feature selection algorithms and validating the robustness of selected marker genes. In this paper, we evaluate a statistically-based resampling approach and a Principal Components Analysis (PCA)-based linear noise distribution approach. Our results show that both methods generate reasonable synthetic data and that the signal/noise rate (with variation weights at 5%, 10%, 20% and 30%) measurably impacts the classification accuracy and the marker genes selected. Based on these results, we identify the most appropriate marker gene selection and classification techniques for each type and level of noise we modeled.
7818605
A Prediction Framework for Cardiac Resynchronization Therapy Via 4D Cardiac Motion Analysis
We propose a novel framework to predict pacing sites in the left ventricle (LV) of a heart and its result can be used to assist pacemaker implantation and programming in cardiac resynchronization therapy (CRT), a widely adopted therapy for heart failure patients. In a traditional CRT device deployment, pacing sites are selected without quantitative prediction. That runs the risk of suboptimal benefits. In this work, the spherical harmonic (SPHARM) description is employed to model the ventricular surfaces and a novel SPHARM-based surface correspondence approach is proposed to capture the ventricular wall motion. A hierarchical agglomerative clustering technique is applied to the time series of regional wall thickness to identify candidate pacing sites. Using clinical MRI data in our experiments, we demonstrate that the proposed framework can not only effectively identify suitable pacing sites, but also distinguish patients from normal subjects perfectly to help medical diagnosis and prognosis.
13985475
A clustering-based approach for prediction of cardiac resynchronization therapy
This paper presents a method for predicting pacing sites in the left ventricle of a heart and its result can be used to assist device programming in cardiac resynchronization therapy (CRT), which is a widely adopted therapy for heart failure patients. In a traditional CRT device deployment, pacing sites are selected without quantitative prediction. That runs the risk of suboptimal benefits. In this work, a surface tracking method is proposed to describe the ventricular wall motion and a hierarchical agglomerative clustering technique is applied to radial motion series to find candidate pacing sites. Using clinical MRI data in our experiments, we show that the proposed method performs as well as we expect. Our approach can not only effectively identify suitable pacing sites, but also distinguish patients from normals perfectly to help medical diagnosis.
10374803
Hemispherical Harmonic Surface Description and Applications to Medical Image Analysis
The use of surface harmonics for rigid and nonrigid shape description is well known. In this paper we define a set of complete hemispherical harmonic basis functions on a hemisphere domain and propose a novel parametric shape description method to efficiently and flexibly represent the surfaces of anatomical structures in medical images. As the first application of hemispherical harmonic theory in shape description, our technique differs from the previous surface harmonics shape descriptors, all of which don't work efficiently on the hemisphere-like objects that often exist in medical anatomical structures (e.g., ventricles, atriums, etc.). We demonstrate the effectiveness of our approach through theoretic and experimental exploration of a set of medical image applications. Furthermore, an evaluation criterion for surface modeling efficiency is described and the comparison results demonstrated that our method outperformed the previous approaches using spherical harmonic models.
15818599
Efficient Registration of 3D SPHARM Surfaces
We present SHREC, an efficient algorithm for registration of 3D SPHARM (spherical harmonic) surfaces. SHREC follows the iterative closest point (ICP) registration strategy, and alternately improves the surface correspondence and adjusts the object pose. It establishes the surface correspondence by aligning the underlying SPHARM parameterization. It employs a rotational property of the harmonic expansion to accelerate its step for parameterization rotation. It uses a hierarchical icosahedron approach to sample the rotation space and searches for the best parameterization that matches the template. Our experimental results show that SHREC can not only create more accurate registration than previous methods but also do it efficiently. SHREC is a simple, efficient and general registration method, and has a great potential to be used in many shape modeling and analysis applications.
10859494
Adaptive watermarking using relationships between wavelet coefficients
We propose an approach that hides watermarks in relationships between wavelet coefficients. This approach minimizes the perceptual distortion of watermarked images, measured by PSNR or just noticeable distortion (JND). Therefore, the strength of watermarks can be enlarged to increase the robustness of the watermarks, while keeping the quality of watermarked images visually acceptable. Experimental results show that the watermark is still detectable after common image processing operations such as JPEG compression, Gaussian filtering and sharpening.
6603995
Protein family classification and functional annotation
With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR produces the Protein Sequence Database of functionally annotated protein sequences. The annotation problems are addressed by a classification-driven and rule-based method with evidence attribution, coupled with an integrated knowledge base system being developed. The approach allows sensitive identification, consistent and rich annotation, and systematic detection of annotation errors, as well as distinction of experimentally verified and computationally predicted features. The knowledge base consists of two new databases, sequence analysis tools, and graphical interfaces. PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases. This paper describes our approach to protein functional annotation with case studies and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology.
18362184
Toward a Universal Platform for Integrating Embodied Conversational Agent Components
Embodied Conversational Agents (ECAs) are computer generated life-like characters that interact with human users in face-to-face conversations. To achieve natural multi-modal conversations, ECA systems are very sophisticated and require many building assemblies and thus are difficult for individual research groups to develop. This paper proposes a generic architecture, the Universal ECA Framework, which is currently under development and includes a blackboard-based platform, a high-level protocol to integrate general purpose ECA components and ease ECA system prototyping.
12033624
Computing motif correlations in proteins
Protein motifs, which are specific regions and conserved regions, are found by comparing multiple protein sequences. These conserved regions in general play an important role in protein functions and protein folds, for example, for their binding properties or enzymatic activities. The aim here is to find the existence correlations of protein motifs. The knowledge of protein motif/domain sharing should be important in shedding new light on the biologic functions of proteins and offering a basis in analyzing the evolution in the human genome or other genomes. The protein sequences used here are obtained from the PIR-NREF database and the protein motifs are retrieved from the PROSITE database. We apply data mining approach to discover the occurrence correlations of motif in protein sequences. The correlation of motifs mined can be used in evolution analyses and protein structure prediction. We discuss the latter, i.e., protein structure prediction in this study. The correlations mined are stored and maintained in a database system. The database is now available at http://bioinfo.csie.ncu.edu.tw/ProMotif/.
7975589
Layered access control schemes on watermarked scalable media
Intellectual property (IP) protection is a critical element in multimedia transmission and delivery systems. Conventional IP protection can be categorized into encryption and watermarking. In this paper, a structure to perform layered access control of scalable media by combining encryption and robust watermarking is proposed and implemented. By taking advantage of the nature of both encryption and watermarking, copyrights of multimedia content can be well protected. In the summated example, we assume a scalable transmission scheme over the broadcasting environment and test the effectiveness of the proposed method. The embedded watermark can be extracted with high confidence. Then, the next temporal-layer keys can be perfectly decrypted and reconstructed. Finally, the media contents are recovered and the copyrights are assured.