ppxscal/embedding_network huggingface dataset:
A Hidden Markov Model for Gene Function Prediction from Sequential Expression Data
Authors: Xutao Deng, Hesham Ali
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Hidden Markov Models (HMMs) have demonatrated great successes in modeling noisy sequential data sets in the area of speech recognition and protein sequence profiling. Results from association test showed significant Markov dependency in time-series gene expression data, and therefore HMMs would be especially appropriate for modeling gene expressions. In this project, we developed a gene function prediction tool based on profile HMMs. Each function class is associated with a distinct HMM whose parameters are trained using yeast time-series gene expression data. The function annotations of the HMM training set were obtained from Munich Information Centre for Protein Sequences (MIPS) data base. We designed several structural variants of HMMs (single, double-split) and tested each of them on forty function classes each of which includes more than one hundred instances. The highest prediction sensitivity we achieved is 51% by using double-split HMM with 3-fold cross-validation.
Promoting multicultural education in the primary classroom: broadband videoconferencing facilities and digital video
Authors: Allen Thurston
Venue: Computers Education (2004)

The aim of this study was to explore the impact of interaction (through gathering local field data and engaging in remote reciprocal presentations) on aspects of multicultural awareness. Sixty-six 11-12-year-old Scottish primary school pupils collected data in the field from their local community through questionnaires, interviews, direct observation, digital images and video. From this they distilled a multimedia presentation, delivered by videoconference to a partner school in the USA, who reciprocated. There was some evidence of pre-post project gains in the complexity of the children's perceptions of their community environment, the ethnicity of their community, their own ethnicity, and news images. The children's use of language to define ethnicity also became more complex and their attitudes toward ethnic minorities became more inclusive. The implications for practice, policy and future research were explored.
Sorting and searching in the presence of memory faults (without redundancy)
Authors: Irene Finocchi, Giuseppe F. Italiano
Venue: Proceedings of the thirty-sixth annual ACM symposium on Theory of computing (2004)

We investigate the design of algorithms resilient to memory faults, i. e., algorithms that, despite the corruption of some memory values during their execution, are able to produce a correct output on the set of uncorrupted values. In this framework, we consider two fundamental problems: sorting and searching. In particular, we prove that any O(nlog n) comparison-based sorting algorithm can tolerate at most O((nlog n)1/2) memory faults. Furthermore, we present one comparison-based sorting algorithm with optimal space and running time that is resilient to O((nlog n)1/3) faults. We also prove polylogarithmic lower and upper bounds on fault-tolerant searching.
An NC algorithm for finding a maximal acyclic set in a graph
Authors: Aaron Windsor
Venue: Proceedings of the sixteenth annual ACM symposium on Parallelism in algorithms and architectures (2004)

An acyclic set in an undirected graph G = (V,E) is a set A ⊆ V(G) such that the induced graph on A is acyclic. A maximal acyclic set (MAS) has the further property that no vertex can be added to it without creating a cycle in the induced graph. We present the first NC algorithm that finds an MAS in any graph, running in time O(log4 n) using O((m2 + n)/log n) processors on a EREW PRAM, answering questions raised by Chen and He. Our NC algorithm for finding an MAS in a graph relies on a novel NC algorithm for finding a maximal forest in a hypergraph which may be of independent interest.
3D VR Engine
Authors: Horng-Shyang Liao, Bo-Yin Li, Charlie H. Chang, San-Liang Chu
Venue: Proceedings of the High Performance Computing and Grid in Asia Pacific Region, Seventh International Conference (2004)

High-Performance Computing (HPC) has caused the data size for the simulation models increasingly larger everyday. Consequently the resulting data grow as well. This makes the visualization tasks demand HPC power too. At NCHC, this issue of visualizing large data set has incurred since the end of 90's. So we started to design the tool sets for large data visualization in 2002. 3D VR Engine is an object-oriented toolkit for developing interactive virtual reality applications. It includes eight features, tereo display, discrete Level-of-Detail(LOD), large data set, tile texture[Visual Simulation: Tiling Large Textures], 3D TrueType fonts, XML scene description language, user specified key binding, voxel projection volume rendering. It also includes some basic graphics algorithms, such as vector, matrix, bounding box, and several geometric object loaders and many image readers. Based on this toolkit, we can develop visualization and virtual reality applications relatively easily in a short period of time. This paper will discuss the architecture and some modules.
A Model for Virtual Suturing in Vascular Surgery
Venue: Proceedings of the Theory and Practice of Computer Graphics 2004 (TPCG'04) (2004)

Vascular surgery is a technically demanding surgical speciality, one component of which is the accurate placement of structures through a diseased vessel wall. Minor errors can result in thrombosis and failure of the proceedure. To develop the necessary skills takes many hours of practice which, in the past, have been acquired at the operating table.Recreating a surgical environment using virtual tools presents a number of research challenges. Conventional collision detection methods fail for deformable bodies and do not provide a mechanism to scale the response over different regions at the same time. We have developed a threaded collision test allowing the mesh to be updated whilst guaranteeing a smooth force response for haptic devises. The Finite Element Method (FEM) was adapted to allow multiple points of contact and the validity of this model is discussed with respect to known tissue behaviour. Following a preliminary examination by clinicians, a novel scheme was introduced for simulating more realistic for e responses.
Uniform Global Asymptotic Stability of Differential Inclusions
Authors: D. Angeli, B. Ingalls, E. D. Sontag, Y. Wang
Venue: Journal of Dynamical and Control Systems (2004)

Stability of differential inclusions defined by locally Lipschitz compact valued mappings is considered. It is shown that if such a differential inclusion is globally asymptotically stable, then, in fact, it is uniformly globally asymptotically stable (with respect to initial states in compacts). This statement is trivial for differential equations, but here we provide the extension to compact- (not necessarily convex-) valued differential inclusions. The main result is presented in a context which is useful for control-theoretic applications: a differential inclusion with two outputs is considered, and the result applies to the property of global error detectability.
Models and Tools for an Integrated European Environmental Management and Decision Support System, (IEEMDSS)
Authors: Keith Rennolls, Tim Richards, Alex Fedorec, Moh Ibrahim, Kevin McManus, Alun Butler
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

This paper proceeds from the assumption that a European Environmental Information and Communication System (EEICS) is already established. In the context of primary users (land-use planners, conservationists, and environmental researchers) we ask what use may be made of the EEICS for building models and tools which will be of use in building Decision Support Systems for the land-use planner. The complex task facing the next generation of environmental and forest modellers is described, and a range of relevant modelling approaches are reviewed. These include Visualization and GIS; Statistical Tabulation and Database SQL, MDA and OLAP methods. The major problem of non-comparability of the definitions and measures of forest area and timber volume is introduced and the possibility of a model-based solution is considered. The possibility of using an ambitious and challenging biogeochemical modelling approach to understanding and managing European Forests sustainably is discussed. It is emphasised that all modern methodological disciplines must be brought to bear, and a heuristic hybrid modelling approach should be used so as to ensure that the benefits of practical empirical modelling approaches are utilised in addition to the scientifically well-founded and holistic ecosystem and environmental modelling. The data and information system required is likely to end up as a grid-based-framework because of the heavy use of computationally intensive model-based facilities.
Ultra-Fine-Grain Field-Programmable VLSI Using Multiple-Valued Source-Coupled Logic
Venue: Proceedings of the 34th International Symposium on Multiple-Valued Logic (2004)

An ultra - fine - grain field - programmable VLSIprocessor using multiple-valued source-coupled logiccalled MV-FPVLSI is proposed for implementing special-purpose processors. To reduce the complexity of the interconnection blocks, a bit-serial pipeline architecture isemployed. It also involves program-counter-less processorarchitecture based on direct allocation. The MV-FPVLSIconsists of cells which are arranged in 2-D mesh array.Unlike a Field Programmable Gate Array (FPGA), datatransmission occurs only between two adjacent cells andthe overall data transmission delay is very small. Each cellconsists of programmable multiple-valued-source coupledlogic (MVSCL) circuits. Instead of using lookup tables,ultra-fine-grain logic operations can be done usingMVSCL circuits. Moreover using the same hardwareresources, each cell can be reconfigured to operate as oneof a logic function, a memory function and a counterfunction. Additional versatility can be achieved throughcurrent- mode operation.
The dog who was a cat inside
Venue: ACM SIGGRAPH 2003 video review on Electronic theater program on Electronic theater program - Volume 144 (2003)

The difference between these two animals comes to represent inner conflict and learning to live with it. The visual style is inspired by Cubism and how that style can illustrate many facets of the same thing. A mixture of traditional, hand-painted and 3D computer animation. Copyright held by creator.
'Why didn't somebody tell me?': climate, information asymmetry, and bad news about troubled projects
Authors: Mark Keil, H. Jeff Smith, Suzanne Pawlowski, Leigh Jin
Venue: ACM SIGMIS Database (2004)

The reluctance to transmit bad news is a problem that is endemic to many organizations. When large projects go awry, it often takes weeks, months, and sometimes even years, before senior management becomes fully aware of what has happened. Accurate communication concerning a project and its status is therefore critical if organizations are to avoid costly and embarrassing debacles. This paper describes the results of an experiment designed to explore some key variables that may influence an individual's willingness to report bad news in an information systems project context. We extend a basic theoretical model derived from the whistle-blowing literature by considering relevant constructs from agency theory. We then test the entire model using a controlled experiment that employs a role-playing scenario. The results explain a significant portion of the variance in the reluctance to report negative status information. Implications for research and practice are discussed, along with directions for future research.
RTVR: a flexible java library for interactive volume rendering
Authors: Lukas Mroz, Helwig Hauser
Venue: Proceedings of the conference on Visualization '01 (2001)

This paper presents several distinguishing design features of RTVR - a Java-based library for real-time volume rendering. We describe, how the careful design of data structures, which in our case are based on voxel enumeration, and an intelligent use of look-up tables enable interactive volume rendering even on low-end PC hardware. By assigning voxels to distinct objects within the volume and by using an individual setup and combination of look-up tables for each object, object-aware rendering is performed: different transfer functions, shading models, and also compositing modes can be mixed within a single scene to depict each object in the most appropriate way, while still providing rendering results in real-time. While providing frame rates similar to volume visualization using 3D consumer hardware, the approach utilized by RTVR offers much more flexibility and extensibility due to its pure software nature. Furthermore, due to the memory-efficiency of the data representation and the implementation in Java, RTVR can be used to provide volume viewing facilities over low-bandwidth networks, with almost full control over rendering and visualization mapping parameters (clipping, shading, compositing, transfer function) for the user. This paper also addresses specific problems which arise by the use of Java for interactive Visualization.
Test-Pattern Generation Based on Reed-Muller Coefficients
Authors: J. Ortega, A. L. Ruiz, A. Prieto, F. J. Pelayo
Venue: IEEE Transactions on Computers (1993)

Reed-Muller coefficients are used to generate a test-pattern selection procedure for detecting single stuck-at faults. This procedure is based on the heuristics deduced from the way in which the spectral coefficients are affected by such faults. The changes that the spectral coefficients undergo are also compared with the fault models used most frequently to model defects in combinational circuits. The proposed pattern-generating procedure does not need a simulation of the circuit for each of the possible stuck-at faults, and its complexity is proportional to the number of gates in the circuit. The proportionality constant increases exponentially as the number of inputs in the circuit increases. To evaluate the performance of the proposed method, its application to some benchmark circuits, including the ALU 74181, is presented.
Information processing in dendrites-I.: input pattern generalisation
Authors: Kevin N. Gurney
Venue: Neural Networks (2001)

In this paper and its companion, we address the question as to whether there are any general principles underlying information processing in the dendritic trees of biological neurons. In order to address this question, we make two assumptions. First, the key architectural feature of dendrites responsible for many of their information processing abilities is the existence of independent sub-units performing local non-linear processing. Second, any general functional principles operate at a level of abstraction in which neurons are modelled by Boolean functions. To accommodate these assumptions, we therefore define a Boolean model neuron--the multi-cube unit (MCU)--which instantiates the notion of the discrete functional sub-unit. We then use this model unit to explore two aspects of neural functionality: generalisation (in this paper) and processing complexity (in its companion). Generalisation is dealt with from a geometric viewpoint and is quantified using a new metric--the set of order parameters. These parameters are computed for threshold logic units (TLUs), a class of random Boolean functions, and MCUs. Our interpretation of the order parameters is consistent with our knowledge of generalisation in TLUs and with the lack of generalisation in randomly chosen functions. Crucially, the order parameters for MCUs imply that these functions possess a range of generalisation behaviour. We argue that this supports the general thesis that dendrites facilitate input pattern generalisation despite any local non-linear processing within functionally isolated sub-units.
Imperative objects as mobile processes
Authors: Josva Kleist, Davide Sangiorgi
Venue: Science of Computer Programming (2002)

An interpretation of Abadi and Cardelli's first-order Imperative ç-calculus into a typed π-calculus is presented. The interpretation validates the subtyping relation and the typing judgments of the ç-calculus, and is computationally adequate. The proof of computational adequacy makes use of (a π-calculus version) of ready simulation, and of a factorization of the interpretation into a functional part and a very simple imperative part. The interpretation can be extended to accommodate various type features. The interpretation can be used to compare and contrast the Imperative and the Functional ç-calculus, and to prove properties about them, within a unified framework.
Analog VLSI System for Active Drag Reduction
Authors: Bhusan Gupta, Rodney Goodman, Fukang Jiang, Yu-Chong Tai, Steve Tung, Chih-Ming Ho
Venue: IEEE Micro (1996)

We describe an analog CMOS VLSI system that can process real-time signals from surface-mounted shear stress sensors to detect regions of high shear stress along a surface in an airflow. The outputs of the CMOS circuit control the actuation of micromachined flaps with the goal of reducing this high shear stress on the surface and thereby lowering the total drag. We have designed, fabricated, and tested parts of this system in a wind tunnel in both laminar and turbulent flow regimes.
Energy-Monitoring Tool for Low-Power Embedded Programs
Authors: Dongkun Shin, Hojun Shim, Yongsoo Joo, Han-Saem Yun, Jihong Kim, Naehyuck Chang
Venue: IEEE Design Test (2002)

Designing cost sensitive embedded products such as cellular phones and portable media players requires maximizing a platform's performance while minimizing energy use. For example, iftwo software implementations of an MPEG-4 decoder perform quite differently on the same target platform, clearly the more efficient version will result in a more cost-effective product.Developing efficient embedded software requires a wide range of knowledge and skills. Programmersmust have a good understanding not only of the target algorithms and target processor's intricacies, but also of a program's overall performance behavior. For example, if a program execution incurs extra performance overheads from resource conflicts, such as conflict cachemisses, programmers should identify and eliminate the problems for maximum performance. In addition, programmers should be able to remove hot spots that could degrade a program's overall perfomance.
RMP: Fault-Tolerant Group Communication
Authors: Weijia Jia, Jörg Kaiser, Edgar Nett
Venue: IEEE Micro (1996)

Fault-tolerant group communication is highly desirable for maintaining a consistent state in distributed systems. Many existing protocols are quite expensive and of limited benefit for distributed systems in terms of efficiency. This article presents a novel group communication protocol including dynamic assessment of membership. It achieves fault tolerant group communication based on a logical token ring approach. The protocol ensures total ordering of messages and atomicity of delivery in the presence of communication faults and site faults, guaranteeing that all operational members belonging to the same group observe a consistent view of ordered events. The dynamic membership and failure recovery algorithms can handle site faults and restart, group partitions and merges, dynamic members join and leave. The efficiency of the protocol is shown with some performance figures.
TCOT-A Timeout-Based Mobile Transaction Commitment Protocol
Authors: Vijay Kumar, Nitin Prabhu, Magaret H. Dunham, Ayse Yasemin Seydim
Venue: IEEE Transactions on Computers (2002)

We present a transaction commit protocol, ¿Transaction Commit On Timeout (TCOT),¿ based on a ¿timeout¿ approach for Mobile Database Systems (MDS), which can be universally used to reach a final transaction termination decision (e.g., commit, abort, etc.) in any message-oriented system. Particularly suited for a wireless environment, a timeout mechanism is the only way to minimize the impact of the slow and unreliable wireless link. We compare TCOT to a modified version of 2PC to show its superiority based on commit time.
Simple laboratory experiments to observe the manifestations of the sinc function
Authors: Daniel D. Traficante, Michael M. Mcgregor
Venue: Concepts in Magnetic Resonance: an Educational Journal (2002)

In NMR spectroscopy, the sinc function manifests itself in a variety of ways, only two of which are discussed in this article. Specifically, the manifestation of this function is discussed in terms of the excitation pulse and in terms of the received signal in high-resolution liquid-state NMR. A mathematical theory has been published that predicts the relative intensities and phases of the RFs that excite the nuclei. However, another mathematical treatment is described here that is considerably easier to understand, but it applies only when the tip angle is small, e.g., less than approximately 10°. In addition, this theory is also used to predict the appearance of the sinc "wiggles" that appear when a Fourier transform is performed on a truncated free induction decay (FID) that has been zero-filled. For the excitation pulse, the intensities of the frequencies delivered to the nuclei follow the classic (sin x)/x, or sinc function, when the tip angle is small. This is demonstrated by a simple experiment. The transmitter offset is stepped in a series of experiments, with each FID summed with all of the previously collected ones. When the series is completed, the FID is Fourier transformed. After correcting for instrumental effects, the resulting spectrum shows that the amplitudes of the excitation frequencies contained within the pulse follow the shape of a sinc function. To demonstrate the formation of sinc "wiggles," the acquisition time for an FID is set so that it is very heavily truncated and then zero-filled to eight times the original number of points. The Fourier transform shows that the "wiggles" cross the zero-intensity line at intervals equal to half-integer multiples of the reciprocal of the acquisition time, and not at integer multiples, as is often assumed. The difference is that the Fourier transform of a rectangular function of width τ is typically performed by integrating using the limits of -τ/2 to τ/2. In the real spectrum, this would produce zero-crossing at an integer number of reciprocals of the width of the rectangle, i.e., 1/τ In the laboratory, however, the limits of the collected signal are from 0 to τ. These limits produce crossings at intervals of 1/(2τ).
Multiphase Complete Exchange: A Theoretical Analysis
Authors: Shahid H. Bokhari
Venue: IEEE Transactions on Computers (1996)

Abstract-Complete Exchange requires each of N processors to send a unique message to each of the remaining N¿ 1 processors. For a circuit switched hypercube with N = 2d processors, the Direct and Standard algorithms for Complete Exchange are time optimal for very large and very small message sizes, respectively. For intermediate sizes, a hybrid Multiphase algorithm is better. This carries out Direct exchanges on a set of subcubes whose dimensions are a partition of the integer d. The best such algorithm for a given message size m could hitherto only be found by enumerating all partitions of d.The Multiphase algorithm is analyzed assuming a high performance communication network. It is proved that only algorithms corresponding to equipartitions of d (partitions in which the maximum and minimum elements differ by at most one) can possibly be optimal. The run times of these algorithms plotted against m form a hull of optimality. It is proved that, although there is an exponential number of partitions, 1) the number of faces on this hull is $\Theta \left( {\sqrt d} \right)$, 2) the hull can be found in $\Theta \left( {\sqrt d} \right)$ time, and 3) once it has been found, the optimal algorithm for any given m can be found in ¿(log d) time.These results provide a very fast technique for minimizing communication overhead in many important applications, such as matrix transpose, fast Fourier transform, and alternating directions implicit (ADI).