ppxscal/embedding_network huggingface dataset:
A parallel programming interface for out-of-core cluster applications
Authors: Jianqi Tang, Binxing Fang, Mingzeng Hu, Hongli Zhang
Venue: Cluster Computing (2006)

Clusters of workstations are a practical approach to parallel computing that provide high performance at a low cost for many scientific and engineering applications. In order to handle problems with increasing data sets, methods supporting parallel out-of-core computations must be investigated. Since writing an out-of-core version of a program is a difficult task and virtual memory systems do not perform well in some cases, we have developed a parallel programming interface and the support library to provide efficient and convenient access to the out-of-core data. This paper focuses on how these components extend the range of problem sizes that can be solved on the cluster of workstations. Execution time of Jacobi iteration when using our interface, virtual memory and PVFS are compared to characterize the performance for various problem sizes, and it is concluded that our new interface significantly increases the sizes of problems that can be efficiently solved.
Complex systems in education: conceptual principles, methodologies, and implications for research in the learning sciences
Authors: Michael J. Jacobson, Uri Wilensky, Robert Goldstone, David Landy, Ji Son, Richard Lesh, Cindy E. Hmelo-Silver, Roger Azevedo
Venue: Proceedings of the 7th international conference on Learning sciences (2006)

The symposium has two main goals: First, it would allow the contributors to the recent JLS special issue on complex systems in education to provide an overview of the issues raised in their respective papers as well as to discuss updated research of relevance. Second, it is hoped that this symposium will provide a forum for discussing the potential implications of complex systems perspectives for research in the learning sciences, and more generally for educational research, curriculum development, and educational policy and reform initiatives.
Two unusual projection spaces
Authors: Michael Naimark
Venue: Presence: Teleoperators and Virtual Environments (2005)

Two immersive projection environments, both unconventional, both exploring different methods of 3D and panoramic imaging, and both produced as art installations, are described. Displacements (1980-1984) recreated an interior living space using a panoramic motion picture method and relief projection. Be Now Here (1995-1997) recreated outdoor public plazas using a panoramic motion picture method, stereopsis, and four channel sound. Both installations were unusual in that no intentions existed for anything more general or useful than the installations themselves as individual artworks.
Amperometric DNA sensor using gold electrode modified with polymerized mediator by layer-by-layer adsorption
Authors: S. Suye, T. Matsuura, T. Kimura, H. Zheng, T. Hori, Y. Amano, H. Katayama
Venue: Microelectronic Engineering (2005)

An amperometric DNA sensing system is proposed based on the combination of sandwich hybridization of reporter probe, capture probe, and target DNA. InvA gene of Salmonella typhimurium was used for target DNA and glucose-6-phosphate dehydrogenase (G6PDH) was used for subsequent enzymatic electrochemical detection as reporter probe. DNA sensor was constructed as follows. At first, a gold electrode was modified with mercaptopropionic acid, then PEI-Fc (ferrocene immobilized polyethylenimine)/alginic acid, diaphorase/PEI, and PEI/streptavidin layers were formed on the surface of electrode by layer-by-layer adsorption. Finally, capture probe was immobilized on the electrode via streptavidin. Hybridization of target DNA and the both probe was carried at 56^oC. Hybridization product was immobilized on the DNA sensor surface by biotin-avidin bond. Electrochemical measurement was performed in the solution containing G6P as substrate and NAD^+ as cofactor for enzyme reaction. The anodic current against glucose-6-phosphate was obtained. It indicates that reporter probe was immobilized on the electrode by hybridization with target DNA and G6PDH on the probe produced NADH. The detection limit of present DNA sensor was femto mol order of target DNA.
Development of a Low-cost PC-based Endoscope System
Authors: Jong An Park, Minhhyuk Chang
Venue: Proceedings of the 2006 International Conference on Hybrid Information Technology - Volume 01 (2006)

These days, damage in joints has increased because of traffic accidents, industrial disasters, and frequent sports injuries. For treatment of the diseases or damage in the joints, endoscope with a small camera is inserted into the joints through a less than 1cm-hole, thereby not cutting the diseased part and having expanded view of inside joints on TV. It performs both diagnosis and treatment at the same time. This study is focused on the design of a GUI based Endoscope system on a PC, which follows suggestions of clinical doctors and puts a priority on convenience of users. The study carried out a demonstrative test and a simulation analysis by designing modules for improvement in performance of the Endoscope system. Because of the participation of clinical doctors in development of a joint endocrine system, preparation of a user-oriented system, accumulation of hardware and software technologies and development of a PC based software with GUI, it is expected that our competitive power to challenge overseas markets will be reinforced.
Software Requirements Retrieval Using Use Case Terms and Structure Similarity Computation
Authors: Akadej Udomchaiporn, Nakornthip Prompoon, Pizzanu Kanongchaiyos
Venue: Proceedings of the XIII Asia Pacific Software Engineering Conference (2006)

For a large scale of software development, there is a tremendous number of software requirements documents in a collection which may be produced for different domains by different developer teams. They may be later reused to reduce cost and time for the next development. Thus, there is a need to retrieve ones that meet user's need efficiently. This paper presents an approach for software requirements specification retrieval in a form of use case description using use case structure and similarity computation between terms of use case query and use cases in the collection. The contribution of the paper has five main points; 1) the approach for retrieving use case description is proposed, 2) the developed tool supporting the approach is presented, 3) the experiment is designed to measure effectiveness of the approach, 4) the results of the experiment are shown to compare effectiveness of the approach to that of a general approach, and finally 5) the recommended use case description query template is proposed.
Concurrency Tradeoffs in Dynamic Adaptation
Authors: Karun N. Biyani, Sandeep S. Ku
Venue: Proceedings of the 26th IEEE International ConferenceWorkshops on Distributed Computing Systems (2006)

Software systems need to adapt as requirements change, environment conditions vary, and bugs are discovered and fixed. In context of verification of these adaptive systems, the verification needs to be done for the system before adaptation, for the system during adaptation, and for the system after adaptation. In our previous work, we presented an approach based on transitional-invariant lattice for verifying the correctness of dynamic adaptation. The size (number of nodes and edges) of the lattice affects the complexity of verifying and testing the adaptation. The size of the lattice itself is dependent on the number of steps in the adaptation, and the concurrency (dependency) among those steps. In this paper, we discuss various tradeoffs that arise because of concurrency during adaptation.
Islands of Tractability for Parsimony Haplotyping
Authors: Roded Sharan, Bjarni V. Halldorsson, Sorin Istrail
Venue: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (2006)

We study the parsimony approach to haplotype inference, which calls for finding a set of haplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genotypes. We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable.
Secure multiparty computation of approximations
Authors: Joan Feigenbaum, Yuval Ishai, Tal Malkin, Kobbi Nissim, Martin J. Strauss, Rebecca N. Wright
Venue: ACM Transactions on Algorithms (TALG) (2006)

Approximation algorithms can sometimes provide efficient solutions when no efficient exact computation is known. In particular, approximations are often useful in a distributed setting where the inputs are held by different parties and may be extremely large. Furthermore, for some applications, the parties want to compute a function of their inputs securely without revealing more information than necessary. In this work, we study the question of simultaneously addressing the above efficiency and security concerns via what we call secure approximations.We start by extending standard definitions of secure (exact) computation to the setting of secure approximations. Our definitions guarantee that no additional information is revealed by the approximation beyond what follows from the output of the function being approximated. We then study the complexity of specific secure approximation problems. In particular, we obtain a sublinear-communication protocol for securely approximating the Hamming distance and a polynomial-time protocol for securely approximating the permanent and related &num;P-hard problems.
Cork: dynamic memory leak detection for garbage-collected languages
Authors: Maria Jump, Kathryn S. McKinley
Venue: ACM SIGPLAN Notices (2007)

A memory leak in a garbage-collected program occurs when the program inadvertently maintains references to objects that it no longer needs. Memory leaks cause systematic heap growth, degrading performance and resulting in program crashes after perhaps days or weeks of execution. Prior approaches for detecting memory leaks rely on heap differencing or detailed object statistics which store state proportional to the number of objects in the heap. These overheads preclude their use on the same processor for deployed long-running applications.This paper introduces a dynamic heap-summarization technique based on type that accurately identifies leaks, is space efficient (adding less than 1% to the heap), and is time efficient (adding 2.3% on average to total execution time). We implement this approach in Cork which utilizes dynamic type information and garbage collection to summarize the live objects in a type points-from graph (TPFG) whose nodes (types) and edges (references between types) are annotated with volume. Cork compares TPFGs across multiple collections, identifies growing data structures, and computes a type slice for the user. Cork is accurate: it identifies systematic heap growth with no false positives in 4 of 15 benchmarks we tested. Cork's slice report enabled us (non-experts) to quickly eliminate growing data structures in SPECjbb2000 and Elipse, something their developers had not previously done. Cork is accurate, scalable, and efficient enough to consider using online.
Latency reduction techniques in chip multiprocessor cache systems
Authors: Krste Asanovic
Venue:  (2006)

Single-chip multiprocessors (CMPs) solve several bottlenecks facing chip designers today. Compared to traditional superscalars, CMPs deliver higher performance at lower power for thread-parallel workloads. In this thesis, we consider tiled CMPs, a class of CMPs where each tile contains a slice of the total on-chip L2 cache storage, and tiles are connected by an on-chip network. Two basic schemes are currently used to manage L2 slices. First, each slice can be used as a private L2 for the tile. Private L2 caches provide the lowest hit latency but reduce the total effective cache capacity because each tile creates a local copy of any block it touches. Second, all slices are aggregated to form a single large L2 shared by all tiles. A shared L2 cache increases the effective cache capacity for shared data, but incurs longer hit latencies when L2 data is on a remote tile. In practice, either private or shared works better for a given workload. We present two new policies, victim replication and victim migration, both of which combine the advantages of private and shared designs. They are variants of the shared scheme which attempt to keep copies of local L1 cache victims within the local L2 cache slice. Hits to these replicated copies reduce the effective latency of the shared L2 cache, while retaining the benefits of a higher effective capacity for shared data. We evaluate the various schemes using full-system simulation of single-threaded, multi-threaded, and multi-programmed workloads running on an eight-processor tiled CMP. We show that both techniques achieve significant performance improvement over baseline private and shared schemes for these workloads. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Fisheye Tree Views and Lenses for Graph Visualization
Authors: Christian Tominski, James Abello, Frank van Ham, Heidrun Schumann
Venue: Proceedings of the conference on Information Visualization (2006)

We present interactive visual aids to support the exploration and navigation of graph layouts. They include Fisheye Tree Views and Composite Lenses. These views provide, in an integrated manner, overview+detail and focus+context. Fisheye Tree Views are novel applications of the well known fisheye distortion technique. They facilitate the exploration of the hierarchy trees associated with clustered graphs. Composite Lenses are the result of the integration of several lens techniques. They facilitate the display of local graph information that may be otherwise difficult to grasp in large and dense graph layouts.
A situated model for sensory-motor coordination in gaze control
Authors: G. de Croon, E. O. Postma, H. J. van den Herik
Venue: Pattern Recognition Letters (2006)

This paper shows that sensory-motor coordination contributes to the performance of situated models on the high-level task of artificial gaze control for gender recognition in static natural images. To investigate the advantage of sensory-motor coordination, we compare a non-situated model of gaze control with a situated model. The non-situated model is incapable of sensory-motor coordination. It shifts the gaze according to a fixed set of locations, optimised by an evolutionary algorithm. The situated model determines gaze shifts on the basis of local inputs in a visual scene. An evolutionary algorithm optimises the model's gaze control policy. In the experiments performed, the situated model outperforms the non-situated model. By adopting a Bayesian framework, we show that the mechanism of sensory-motor coordination is the cause of this performance difference. The essence is that the mechanism maximises task-specific information in the observations over time, by establishing dependencies between multiple actions and observations.
Computer supported interaction analysis of group problem solving
Authors: Martin Mühlenbrock, Ulrich Hoppe
Venue: Proceedings of the 1999 conference on Computer support for collaborative learning (1999)

Collaboration is widely regarded as beneficial for learning. Collaboration is the mutual engagement of participants in a coordinated effort to solve a problem together. It has been conclusively argued that a focus on the process of collaboration is necessary in order to understand the value of working together with peers for learning.In accordance with the approach of open distributed learning environments (ODLEs), we have developed a framework system for computer-supported cooperative learning and working. This distributed shared workspace system is well suited for monitoring and assessing group interaction in co-located and distant scenarios. It provides adaptable mechanisms for the automated micro-analysis of processes of collaboration as well as for visualization and feedback.The system has been used in determining conflicts in focus setting as well as initiative shifts in aggregation and revision phases during a sample of collaborative sessions on puzzle problem solving.
The Effect of Divided Attention on Encoding and Retrieval in Episodic Memory Revealed by Positron Emission Tomography
Authors: Tetsuya Iidaka, Nicole D. Anderson, Shitij Kapur, Roberto Cabeza, Fergus I. M. Craik
Venue: Journal of Cognitive Neuroscience (2000)

The effects of divided attention (DA) on episodic memory encoding and retrieval were investigated in 12 normal young subjects by positron emission tomography (PET). Cerebral blood flow was measured while subjects were concurrently performing a memory task (encoding and retrieval of visually presented word pairs) and an auditory tone-discrimination task. The PET data were analyzed using multivariate Partial Least Squares (PLS), and the results revealed three sets of neural correlates related to specific task contrasts. Brain activity, relatively greater under conditions of full attention (FA) than DA, was identified in the occipital-temporal, medial, and ventral-frontal areas, whereas areas showing relatively more activity under DA than FA were found in the cerebellum, temporo-parietal, left anterior-cingulate gyrus, and bilateral dorsolateral-prefrontal areas. Regions more active during encoding than during retrieval were located in the hippocampus, temporal and the prefrontal cortex of the left hemisphere, and regions more active during retrieval than during encoding included areas in the medial and right-prefrontal cortex, basal ganglia, thalamus, and cuneus. DA at encoding was associated with specific decreases in rCBF in the left-prefrontal areas, whereas DA at retrieval was associated with decreased rCBF in a relatively small region in the right-prefrontal cortex. These different patterns of activity are related to the behavioral results, which showed a substantial decrease in memory performance when the DA task was performed at encoding, but no change in memory levels when the DA task was performed at retrieval.
QoS Adaptive ISHM Systems
Authors: Yansheng Zhang, Jicheng Fu, I-Ling Yen, Farokh Bastani, Ann T. Tai, Savio Chau, Farrokh Vatan, Amir Fijany
Venue: Proceedings of the 18th IEEE International Conference on Tools with Artificial Intelligence (2006)

Embedded systems are becoming highly complex and increasingly being used in critical applications. Integrated system health management (ISHM) techniques have therefore been developed to ensure the proper operation of these systems. However, some ISHM systems are relatively complex and may consume a significant amount of resources. In some situations, activating the full ISHM system may cause resource contention and prevents the target system from timely completing critical tasks. Thus, it is imperative to introduce the notion of adaptivity into ISHM systems. This paper systematically discusses the issues that need to be addressed in an adaptive ISHM system with a focus on adaptation in terms of QoS aspects. A novel model, Adaptive Diagnosis Quality-Oriented System Model (ADQSM), is proposed to model the QoS specification and fault diagnosis quality measurement issues as well as the abstraction of the adaptation problem. We then present the method to evaluate various diagnosability attributes based on a modified fault signature matrix. We further map the ADQSM model to the Particle Swarm Optimization (PSO) problem model and use PSO for rapid configuration decision making.
Neural network modelling of continuous microbial cultivation accounting for the memory effects
Authors: P. Koprinkova-Hristova, T. Patarinska
Venue: International Journal of Systems Science (2006)

Three approaches to the problem of Neural Network (NN) modelling of chemostat microbial culture accounting for the memory effects are considered and, based on the results they are compared. The first approach uses feedforward NNs with time delay feedback connections from and to the output neurons, for the entire process modelling. The second and third approach relay on Hybrid NN modelling. The second one applies feedforward NNs with time delayed inputs for the specific growth rate approximation within the framework of the classical unstructured model. In this case the specific consumption rate is assumed to be proportional to the specific growth rate. The yield factor is assumed to be constant or polynomial function of the substrate concentration. The third approach is also based on a classical unstructured model, but different feedforward NNs with delay elements for both specific growth rate and specific consumption rate approximation are adopted. On the example of the growth of a strain Saccharomyces cerevisiae on a glucose limited medium different NN topologies are studied and a suitable model is figured out.
Self-Organizing Dynamics of Lexical Access in Normals and Aphasics
Authors: Mark G. Mcnellis, Sheila E. Blumstein
Venue: Journal of Cognitive Neuroscience (2001)

The goal of this article is to illustrate the application of self-organizing dynamics in the design of a model of lexical access. We focus particularly on the mapping of sound structure on to the lexicon and the influence of that structure on lexical access. The approach is tested in a series of two sets of simulations that explicate how lexical access might occur in normal subjects and aphasic patients. Both sets of simulations address the behavioral effects of both phonological and phonetic variability of prime stimuli on the magnitude of semantic priming. Results show that the model can successfully account for the behavioral effects associated with several kinds of acoustic manipulation, competitor presence, and the unfolding of those effects over time - primarily because it balances three important control parameters: resting lexical activation, positive feedback, and negative feedback. These simulations are offered as support (in the form of an existence proof) that deficits in the degree of lexical activation can account for the lexical processing impairments shown by Broca's aphasics who have reduced lexical activation, and Wernicke's aphasics who have increased lexical activation. Overall, results suggest that the present approach promises to offer a coherent theoretical framework within which to link empirical evidence in language processing and cognitive neuroscience in terms of possible underlying mechanisms.