ppxscal/embedding_network huggingface dataset:
Gene name identification and normalization using a model organism database
Authors: Alexander A. Morgan, Lynette Hirschman, Marc Colosimo, Alexander S. Yeh, Jeff B. Colombe
Venue: Journal of Biomedical Informatics (2004)

Biology has now become an information science, and researchers are increasingly dependent on expert-curated biological databases to organize the findings from the published literature. We report here on a series of experiments related to the application of natural language processing to aid in the curation process for FlyBase. We focused on listing the normalized form of genes and gene products discussed in an article. We broke this into two steps: gene mention tagging in text, followed by normalization of gene names. For gene mention tagging, we adopted a statistical approach. To provide training data, we were able to reverse engineer the gene lists from the associated articles and abstracts, to generate text labeled (imperfectly) with gene mentions. We then evaluated the quality of the noisy training data (precision of 78%, recall 88%) and the quality of the HMM tagger output trained on this noisy data (precision 78%, recall 71%). In order to generate normalized gene lists, we explored two approaches. First, we explored simple pattern matching based on synonym lists to obtain a high recall/low precision system (recall 95%, precision 2%). Using a series of filters, we were able to improve precision to 50% with a recall of 72% (balanced F-measure of 0.59). Our second approach combined the HMM gene mention tagger with various filters to remove ambiguous mentions; this approach achieved an F-measure of 0.72 (precision 88%, recall 61%). These experiments indicate that the lexical resources provided by FlyBase are complete enough to achieve high recall on the gene list task, and that normalization requires accurate disambiguation; different strategies for tagging and normalization trade off recall for precision.
Virtual Machines, Managed Code and Component Technology
Authors: John Gough
Venue: Proceedings of the 2005 Australian conference on Software Engineering (2005)

Abstract machines have been used as an implementation mechanism for programming languages for more than thirty years. In their latest incarnation execution engines based on virtual machines offer "Managed Execution". The implications of this change go far beyond the superficial advantages of platform portability and go to the heart of software reliability. In this paper it is argued that managed execution platforms such as the .NET Common Language Runtime and the Java Virtual Machine form the only reasonable basis for trustworthy component software. There is also an overview of current research in this field, including the vexed question of version evolution.
An efficient tile-based ECO router with routing graph reduction and enhanced global routing flow
Authors: Jin-Yih Li, Yih-Lang Li
Venue: Proceedings of the 2005 international symposium on Physical design (2005)

Engineering Change Order (ECO) routing is frequently requested in the later design stage for the purpose of delay and noise optimization. ECO routing is complicated by huge existing obstacles and the requests for various design rules. Tile-based routers have work with fewer nodes of the routing graph than grid and connection-based routers; however, the number of nodes of the tile-based routing graph has grown to over a thousand millions for SOC designs. This work depicts a new ECO routing design flow with routing graph reduction and enhanced global routing flow. Routing graph reduction reduces the complexity of nodes by removing redundant tiles and aligning neighboring tiles to merge adjacent block tiles. Routing graph reduction reduces tile fragmentation such that the ECO router can run twice as fast without sacrificing routing quality. Enhanced global routing flow incorporates ECO global routing with extended routing and GCell restructuring to prevent routing failure in a routable routing. The ECO router with new design flow can perform up to 20 times faster than the original tile-based router, at the cost of only a very small decline in routing quality.
Run-Time Reconfigurable Systems for Digital Signal Processing Applications: A Survey
Authors: Alireza Shoa, Shahram Shirani
Venue: Journal of VLSI Signal Processing Systems (2005)

Today's digital signal processing (DSP) applications use computationally complex and/or adaptive algorithms and have stringent requirements in terms of speed, size, cost, power consumption, and throughput. Efficient hardware implementation techniques should be employed to meet the requirements of these applications. Run-Time Reconfiguration (RTR) is a promising technique for reducing the hardware required for implementing DSP systems as well as improving the performance, speed and power consumption of these systems. In this survey, we explain different issues in run-time reconfigurable systems and list the implemented systems which support run-time reconfiguration. We also describe different applications of run-time reconfiguration and discuss the improvements achieved by applying run-time reconfiguration.
A Policy-Driven Autonomous System for Evolutive and Adaptive Management of Complex Services and Networks
Authors: Nigel Sheridan-Smith, John Leaney, Tim O'Neill, Mark Hunter
Venue: Proceedings of the 12th IEEE International Conference and Workshops on Engineering of Computer-Based Systems (2005)

Many existing management systems are not evolutive or adaptive, leading to multiplicity over time and increasing the management burden. Policy-based management approaches may assist in making networks less complex and more automated, but to date they have not yet been able to evolve to support new service sets or provide the capacity for differentiation. We present the architecture for a policy-based system named Pronto that helps to deal with these issues. Layered network and service models are built above an extensible virtual device model that supports heterogenous management interfaces. Interchangeable management components provide the basic building blocks to construct logical services. The integrated policy-driven service definition language automates the management of the services in a manner that is adaptive, dynamic and reactive to improve the userýs overall service experience.
Selection of Crosstalk-Induced Faults in Enhanced Delay Test
Authors: Huawei Li, Xiaowei Li
Venue: Journal of Electronic Testing: Theory and Applications (2005)

Current design trends have shown that crosstalk issues in deep sub-micron can cause severe design validation and test problems. In this paper, we address the problem of enhanced delay test considering crosstalk-induced effects. Two types of crosstalk-induced delay fault model in related works are analyzed according to their relationship to common delay fault models. The difficulties in test generation using these fault models are shown. Based on the discussion, a single precise crosstalk-induced path delay fault model, S-PCPDF model, is proposed for circuits given delay assignment. A target S-PCPDF fault gives information on a sub-path to be sensitized to generate necessary transitions coupled to a critical path. It is then convenient to enhance conventional path delay fault ATPG algorithms to implement ATPG systems for crosstalk-induced path delay faults by adding the constraints on the sub-path. We then propose two approaches to reducing the number of target S-PCPDF faults. One is based on constraints for side-inputs of paths under test. The other is based on pre-specified states during test generation for the critical path. Experimental results on ISCAS'89 benchmark circuits showed that the proposed approaches can reduce the number of target faults significantly and efficiently. The CPU time for fault list reduction and test pattern generation is acceptable for circuits of reasonable sizes.
Individual differences in multimodal integration patterns: what are they and why do they exist?
Authors: Sharon Oviatt, Rebecca Lunsford, Rachel Coulston
Venue: Proceedings of the SIGCHI conference on Human factors in computing systems (2005)

Techniques for information fusion are at the heart of multimodal system design. To develop new user-adaptive approaches for multimodal fusion, the present research investigated the stability and underlying cause of major individual differences that have been documented between users in their multimodal integration pattern. Longitudinal data were collected from 25 adults as they interacted with a map system over six weeks. Analyses of 1,100 multimodal constructions revealed that everyone had a dominant integration pattern, either simultaneous or sequential, which was 95-96% consistent and remained stable over time. In addition, coherent behavioral and linguistic differences were identified between these two groups. Whereas performance speed was comparable, sequential integrators made only half as many errors and excelled during new or complex tasks. Sequential integrators also had more precise articulation (e.g., fewer disfluencies), although their speech rate was no slower. Finally, sequential integrators more often adopted terse and direct command-style language, with a smaller and less varied vocabulary, which appeared focused on achieving error-free communication. These distinct interaction patterns are interpreted as deriving from fundamental differences in reflective-impulsive cognitive style. Implications of these findings are discussed for the design of adaptive multimodal systems with substantially improved performance characteristics.
Research note: Parallel algorithms for tree accumulations
Authors: Fatih E. Sevilgen, Srinivas Aluru, Natsuhiko Futamura
Venue: Journal of Parallel and Distributed Computing (2005)

Accumulations are abstract operations on trees useful in many applications involving trees. The upward accumulation problem is to aggregate data in the subtree under each node of the tree. The downward accumulation problem is to aggregate data at all the ancestors of each node. In this paper, we present parallel algorithms for these problems on coarse-grained distributed memory parallel computers. We first show that when the accumulation function and the set of possible values at nodes of the tree form an Abelian (commutative) group, this problem can be solved by a remarkably simple algorithm-Upward accumulation takes Onp+@tp+@mnp time, where n is the number of nodes in the tree, p is the number of processors, @t is the communication latency and @m is the transfer time per unit message size. Downward accumulation takes Onp+(@t+@m)logp time, making it very communication efficient. For the general case, we present upward and downward accumulation algorithms that run in Onplogn+@tplogn+@mnplogn time.
A new environment for improving legacy software on embedded systems
Authors: Makoto Sakai, Masunori Kubota, Masaya Okita, Ken-Ichi Matsumoto, Koji Torii
Venue: Systems and Computers in Japan (2004)

In this paper, the authors propose a method of evaluating the module structure of programs for embedded software in which maintainability has deteriorated due to repeated revisions and also describe a software improvement support tool that was developed based on the proposed method. The proposed evaluation method supports the improvement of a module structure that includes the exchange of data according to external variables, which is often used in embedded software, by applying the concepts of intermodule coupling and module cohesion from structured analysis. The support tool also has the following special features: (1) by displaying the exchange of data according to external variables as an interface with a higher-level function, it can display the &ldquo;data flow between hierarchically related modules,&rdquo; which could not be displayed by conventional tools, (2) by using open source tools, it can be implemented with relatively few man-hours, and (3) it provides design guides and checklists that enable the software improvement method to be learned in a short period without regard to user expertise. From the results obtained when this tool was introduced in actual projects, it was apparent that the tool was effective in discovering and improving program structures that caused a deterioration of maintainability. &copy; 2004 Wiley Periodicals, Inc. Syst Comp Jpn, 35(9): 81&ndash;91, 2004; Published online in Wiley InterScience (). DOI 10.1002&sol;scj.10023
A generalized duality method for solving variational inequalities Applications to some nonlinear Dirichlet problems
Authors: Jos&#x00e9; M. Gallardo, Carlos Par&#x00e9;s, Manuel Castro
Venue: Numerische Mathematik (2005)

In [2] Berm&#x00fa;dez and Moreno introduced a duality algorithm for the numerical solution of variational inequalities; this algorithm is based on some properties of the Yosida regularization of maximal monotone operators. The performances of this algorithm strongly depend on the choice of two constant parameters. A generalization of the algorithm with automatic choice of parameters was discussed in [13], where the constant parameters were replaced by scalar functions, thus improving the convergence of the algorithm. In this article we present a generalization of the Berm&#x00fa;dez-Moreno algorithm that allows the use of very general operators as parameters, extending some of the results in [2], [13] and [14]. As a particular case, we analyze the use of scalar and matrix-valued parameters in a Lp(&#x03a9;)M context. We apply the results developed to some boundary value problems involving the p-Laplacian operator, where it is shown that the use of matrix-valued parameters improves the convergence of the algorithm.
Euclidean distortion and the sparsest cut
Authors: Sanjeev Arora, James R. Lee, Assaf Naor
Venue: Proceedings of the thirty-seventh annual ACM symposium on Theory of computing (2005)

We prove that every n-point metric space of negative type (in particular, every n-point subset of L1) embeds into a Euclidean space with distortion O(√log n log log n), a result which is tight up to the O(log log n) factor. As a consequence, we obtain the best known polynomial-time approximation algorithm for the Sparsest Cut problem with general demands. If the demand is supported on a subset of size k, we achieve an approximation ratio of O(√log k log log k).
Greedy EM Algorithm for Robust T-Mixture Modeling
Authors: Sibao Chen, Haixian Wang, Bin Luo
Venue: Proceedings of the Third International Conference on Image and Graphics (2004)

This paper concerns a greedy EM algorithm for t-mixture modeling, which is more robust than Gaussian mixture modeling when atypical points exist or the set of data has heavy tail. Local Kullback divergence is used to determine how to insert new component. The greedy algorithm obviates the complicated initialization. The results are comparable to that of Split-and-Merge EM algorithm while the proposed algorithm is faster. Also the byproduct of a sequence of mixture models is useful for model selection. Experiments of synthetic data clustering and unsupervised color image segmentation are given.
Vehicle Segmentation and Tracking from a Low-Angle Off-Axis Camera
Authors: Neeraj K. Kanhere, Shrinivas J. Pundlik, Stanley T. Birchfield
Venue: Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Volume 2 - Volume 02 (2005)

We present a novel method for visually monitoring a highway when the camera is relatively low to the ground and on the side of the road. In such a case, occlusion and the perspective effects due to the heights of the vehicles cannot be ignored. Features are detected and tracked throughout the image sequence, and then grouped together using a multi-level homography, which is an extension of the standard homography to the low-angle situation. We derive a concept called the relative height constraint that makes it possible to estimate the 3D height of feature points on the vehicles from a single camera, a key part of the technique. Experimental results on several different highways demonstrate the systemýs ability to successfully segment and track vehicles at low angles, even in the presence of severe occlusion and significant perspective changes.
Application Aware Management of Internet Data Center Software
Venue: Proceedings of the 16th USENIX conference on System administration (2002)

We have built a comprehensive solution to address the management aspects of deployment and analysis of applications in Internet Data Centers. Our work was motivated by the high total cost of ownership of operating such centers, largely due to the variety of applications and their distinctive management requirements. We have chosen an approach that encapsulates application specific knowledge (is application aware) and deployed it in a number of corporate Internet Data Centers. Operations staff found substantial cost reduction in managing applications using our approach.
Real-Time Computational Algorithm for Optimal Control of an MHD Flow System
Authors: S. S. Ravindran
Venue: SIAM Journal on Scientific Computing (2005)

The flow of weakly electrically conducting fluids can be controlled by electromagnetic forces originating from electrodes and permanent magnets. We consider the possibility of separation control for an electrically conducting bluff body flow with reduced-order modeling. The reduced-order model is derived using the proper orthogonal decomposition (POD) and Galerkin projection. The POD allows one to extract the dominant modes in the observed physical phenomena and to define the smallest possible solution space. This can be exploited in a Galerkin framework to reduce\break the nonlinear infinite dimensional model to a small finite dimensional model. We investigate the design of a reduced-order nonlinear optimal controller for flow separation in a channel. We present numerical experiments with an applied spanwise magnetic field distribution and a boundary electric potential actuation on a part of the boundary. Our methods are found to be efficient and fast, and our methods demonstrate a significant reduction in computational time.
Performance of the bi-orthogonal modulation for ultra-wideband communication systems with multiple access interference: Research Articles
Authors: Simone Morosi, Romano Fantacci, Enrico Del Re, Leonardo Goratti
Venue: Wireless Communications Mobile Computing (2005)

This paper investigates the use of bi-orthogonal modulations in multiuser communication systems based on ultra wide band impulse radio (UWB-IR) technology: the communication systems considered herein use Gaussian waveforms in AWGN channel and rely on the utilization of a time-hopping spreading technique. A hybrid pulse modulation is defined, which is obtained by combining pulse amplitude modulation (PAM) and pulse position modulation (PPM) techniques. Particularly, we have compared the bi-orthogonal system performance to the classical orthogonal one, also in the condition of lack of a general synchronism, possibly caused by the presence of interfering users that belong to a separate network. Moreover, we have taken into account the use of an M-ary alphabet, in the case of orthogonal and bi-orthogonal modulation schemes. Copyright &copy; 2005 John Wiley & Sons, Ltd.
Efficient recursive adaptive pole placement algorithm
Authors: J. Li, D. W. C. Ho
Venue: International Journal of Systems Science (2004)

A recursive adaptive pole placement algorithm is presented. The stability and convergence of the algorithm are established respectively. Since a one-step iterative formulation in computing a controller's parameters is used. the on-line computation cost is greatly reduced with respected to the traditional algorithm. The algorithm with feed-forward can follow the arbitrarily bounded output. The algorithm is also extended to a multivariable case. Simulation examples show the efficiency and robustness of the algorithms.
A new multistack radiation boundary condition for FDTD based on self-teleportation of fields
Authors: Rodolfo E. Diaz, Igor Scherbatko
Venue: Journal of Computational Physics (2005)

In [Electromagnetics 23 (2003) 187], a technique for injecting perfect plane waves into finite regions of space in FDTD was reported. The essence of the technique, called Field Teleportation, is to invoke the principle of equivalent sources using FDTDs discrete definition of the curl to copy any field propagating in one FDTD domain to a finite region of another domain. In this paper, we apply this technique of Field Teleportation to the original domain itself to create a transparent boundary across which any outward traveling FDTD field produces an exact negative copy of itself. When this copied field is teleported one cell ahead and one cell forward in time it causes significant self-cancelation of the original field. Illustrative experiments in two-dimensions show that a two-layer (10-cell thick) multi-stack Radiation Boundary Condition (RBC) with a simplest Huygens's termination readily yields reflection coefficients of the order of -80 dB up to grazing incidence for all the fields radiated by a harmonic point source (@l=30 cells) in free space located 20 cells away from the boundary. Similarly low levels of artificial reflection are demonstrated for a case in which the RBC cuts through five different magnetodielectric materials.
JavaServer Faces: An Excellent Learning Tool
Authors: Hector Zenil Chavez
Venue: IEEE Distributed Systems Online (2005)

A review of "JavaServer Faces" by Hans Bergsten.
Photometric Stereo via Locality Sensitive High-Dimension Hashing
Authors: Lin Zhong, James J. Little
Venue: Proceedings of the 2nd Canadian conference on Computer and Robot Vision (2005)

In this paper, we extend the new photometric stereo method of Hertzmenn and Seitz that uses many images of an object together with a calibration object. For each point in the registered collection of images, we have a large number of brightness values. Photometric stereo finds a similar collection of brightness values from the calibration object and overdetermines the surface normal. With a large number of images, finding similar brightnesses becomes costly search in high dimensions. To speed up the search, we apply locality sensitive high dimensional hashing(LSH) to compute the irregular target object's surface orientation. The experimental results of a simplified photometric stereo experiment show consistent results in surface orientation. LSH can be implemented very efficiently and offers the possibility of practical photometric stereo computation with a large number of images.
Effects of profiles and conditioning methods of heater surfaces on deposited TiN film thickness and uniformity
Authors: Z. W. Zhong, T. M. Lye
Venue: Microelectronic Engineering (2004)

The deposition rate and the uniformity of the TiN (titanium nitride) film thickness depend on the wafer temperature in a TiN CVD (chemical vapor deposition) process. The heater surface profiles can affect the heat transfer efficiency from the heater surface to the wafer, and therefore greatly affect the process performance. Also, after the chamber preventive maintenance, it is difficult to achieve the process specifications for thickness and uniformity due to surface conditions of the newly installed heater. In this paper, the effects of heater surface conditioning methods (surface pre-coating and plasma treatment) are evaluated. They are useful and effective to control the deposited film thickness and improve the uniformity. The recovery time needed after performing the chamber preventive maintenance can be shortened. Thus, the chamber utilization can be improved and the cost incurred during the preventive maintenance can be reduced. Furthermore, the origin of hot spots is identified by detailed study of the heater surface profiles. The manufacturing process is revised to prevent hot spots and improve heater performance. The uniformity problem caused by hot spots can be minimized.