ppxscal/embedding_network huggingface dataset:
Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies
Authors: George Lee, Carlos Rodriguez, Anant Madabhushi
Venue: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (2008)

The recent explosion in procurement and availability of high-dimensional gene- and protein-expression profile datasets for cancer diagnostics has necessitated the development of sophisticated machine learning tools with which to analyze them. A major limitation in the ability to accurate classify these high-dimensional datasets stems from the 'curse of dimensionality', occurring in situations where the number of genes or peptides significantly exceeds the total number of patient samples. Previous attempts at dealing with this issue have mostly centered on the use of a dimensionality reduction (DR) scheme, Principal Component Analysis (PCA), to obtain a low-dimensional projection of the high-dimensional data. However, linear PCA and other linear DR methods, which rely on Euclidean distances to estimate object similarity, do not account for the inherent underlying nonlinear structure associated with most biomedical data. The motivation behind this work is to identify the appropriate DR methods for analysis of high-dimensional gene- and protein-expression studies. Towards this end, we empirically and rigorously compare three nonlinear (Isomap, Locally Linear Embedding, Laplacian Eigenmaps) and three linear DR schemes (PCA, Linear Discriminant Analysis, Multidimensional Scaling) with the intent of determining a reduced subspace representation in which the individual object classes are more easily discriminable.
Comparison of van der Waals coefficient $C_{6}$ of sodium clusters obtained via spherical jellium background model and all-electron ab initio method
Authors: Arup Banerjee, Manoj K. Harbola
Venue: Journal of Computational Methods in Sciences and Engineering (2007)

In this paper we employ two distinct approaches - all-electron ab initio method and the spherical jellium background model- within time dependent density functional theory to calculate the long range dipole-dipole dispersion coefficient (van der Waals coefficient) $C_{6}$ of sodium atom clusters containing even number of atoms ranging from 2 to 20 atoms. The dispersion coefficients are obtained via Casimir-Polder relation. All the calculations are carried out with local density approximation for exchange-correlation energy functional. These two sets of results are compared to assess the accuracy of jellium based results and to ascertain the effect of detail ionic structure of the clusters on the van der Waals coefficient.
On Browsing Domain Ontologies for Information Base Content
Authors: Troels Andreasen, Henrik Bulskov
Venue: Proceedings of the 12th international Fuzzy Systems Association world congress on Foundations of Fuzzy Logic and Soft Computing (2007)

This paper presents a conceptual querying approach with reference to a document collection where the target is the concepts appearing in documents, rather than the documents in the collection. An ontology formalism and a special notion of "instantiated ontology" are introduced. The latter is a structure reflecting the content in the document collection in that; it is a restriction of a general world knowledge ontology to the concepts instantiated in the collection. The notion of ontology-based similarity is briefly described and a language for navigation and retrieval of concepts in the ontology is presented.
Detecting cow's lameness using force sensors
Authors: M. Pastell, M. Kujala, A. -M. Aisla, M. Hautala, V. Poikalainen, J. Praks, I. Veermäe, J. Ahokas
Venue: Computers and Electronics in Agriculture (2008)

Our aim is to automatically detect cow's leg problems. The first system is a four-balance system, where each of the legs is weighed when a cow is in a milking robot. Its functionality is limited to milking robot and complications in interpreting results occur, since often not all of the legs are properly in each balance or the cow is leaning the robot. Therefore, we introduce a new system. It is a mat made of electromechanical film, Emfit, which can detect only dynamic forces. Its benefit is that its use is not limited to milking robot, but it can be set up in any corridor along which the cows walk. Preliminary tests with walking cows indicate that it has potentiality to separate lame cows from healthy cows by different force-time behaviour.
Prototype System for Semantic Retrieval of Neurological PET Images
Authors: Stephen Batty, John Clark, Tim Fryer, Xiaohong Gao
Venue: Medical Imaging and Informatics: 2nd International Conference, MIMI 2007, Beijing, China, August 14-16, 2007 Revised Selected Papers (2008)

Positron Emission Tomography (PET) is used within neurology to study the underlying biochemical basis of cognitive functioning. Due to the inherent lack of anatomical information its study in conjunction with image retrieval is limited. Content based image retrieval (CBIR) relies on visual features to quantify and classify images with a degree of domain specific saliency. Numerous CBIR systems have been developed semantic retrieval, has however not been performed. This paper gives a detailed account of the framework of visual features and semantic information utilized within a prototype image retrieval system, for PET neurological data. Images from patients diagnosed with different and known forms of Dementia are studied and compared to controls. Image characteristics with medical saliency are isolated in a top down manner, from the needs of the clinician - to the explicit visual content. These features are represented via Gabor wavelets and mean activity levels of specific anatomical regions. Preliminary results demonstrate that these representations are effective in reflecting image characteristics and subject diagnosis; consequently they are efficient indices within a semantic retrieval system.
Towards a Categorical Matching Method to Process High-Dimensional Emergency Knowledge Structures
Authors: Qingquan Wang, Lili Rong, Kai Yu
Venue: Proceedings of the 5th international symposium on Neural Networks: Advances in Neural Networks, Part II (2008)

To keep the original semantic information, Textual data in emergency knowledge acquisitions can be actually represented in categorical semantic structures based on typed category theory. These netted topological structures preserve high-dimensions to achieve higher reliability of knowledge processing that relates to the various scenarios of emergency responses. This paper presents a categorical matching method for effective processing on such high-dimensional structures of textual data. The quantification of the matching is achieved through the Greatest Common Subcategory between two categorical structures. Simulated experimental results show a reasonable matching rate for the semantic oriented high-dimensional knowledge processing.
Differential Fault Analysis of Trivium
Authors: Michal Hojsík, Bohuslav Rudolf
Venue: Fast Software Encryption: 15th International Workshop, FSE 2008, Lausanne, Switzerland, February 10-13, 2008, Revised Selected Papers (2008)

Trivium is a hardware-oriented stream cipher designed in 2005 by de Cannière and Preneel for the European project eStream, and it has successfully passed the first and the second phase of this project. Its design has a simple and elegant structure. Although Trivium has attached a lot of interest, it remains unbroken.In this paper we present differential fault analysis of Trivium and propose two attacks on Trivium using fault injection. We suppose that an attacker can corrupt exactly one random bit of the inner state and that he can do this many times for the same inner state. This can be achieved e.g. in the CCA scenario. During experimental simulations, having inserted 43 faults at random positions, we were able to disclose the trivium inner state and afterwards the private key.As far as we know, this is the first time differential fault analysis is applied to a stream cipher based on shift register with non-linear feedback.
On geometric variational models for inpainting surface holes
Authors: V. Caselles, G. Haro, G. Sapiro, J. Verdera
Venue: Computer Vision and Image Understanding (2008)

Geometric approaches for filling-in surface holes are introduced and studied in this paper. The basic principle is to choose the completing surface as one which minimizes a power of the mean curvature. We interpret this principle in a level set formulation, that is, we represent the surface of interest in implicit form and we construct an energy functional for the embedding function u. We first explore two different formulations (which can be considered as alternative) inspired by the above principle: in the first one we write the mean curvature as the divergence of the normal vector field @q to the isosurfaces of u; in the second one we used the signed distance function D to the surface as embedding function and we write the mean curvature in terms of it. Then we solve the Euler-Lagrange equations of these functionals which consist of a system of second order partial differential equations (PDEs) for u and @q, in the first case, or a fourth order PDE for D in the second case. Then, simpler methods based on second order elliptic PDEs, like Laplace equation or the absolutely minimizing Lipschitz extension, are also proposed and compared with the above higher order methods. The theoretical and computational framework, as well as examples with synthetic and real data, are presented in this paper.
Screening self-assembled monolayers as Cu diffusion barriers
Authors: A. Maestre Caro, G. Maes, G. Borghs, C. M. Whelan
Venue: Microelectronic Engineering (2008)

Self-assembled monolayers (SAMs) are investigated as potential Cu diffusion barriers for application in back-end-of-line (BEOL) interconnections. A screening of SAMs derived from molecules with different head group (SiCl"3, Si(OCH"3)"3, Si(OCH"3)Cl"2) bonding to the dielectric substrate, chain lengths (n=3-21) and terminal group (CH"3, Br, CN, NH"2, C"5H"4N and SH) bonding to the Cu overlayer are compared in terms of inhibition of interfacial Cu diffusion and promotion of Cu-SiO"2 adhesion. SAM barrier properties against Cu silicide formation are examined upon annealing from 200 to 400^oC by visual inspection, sheet resistance measurements (Rs) and X-ray Diffraction Spectroscopy (XRD). Cu/SAM/SiO"2 adhesion is evaluated by tape test and four-point probe measurements. Results indicate that NH"2-SAM derived from 3-aminopropyltrimethoxysilane is the most promising for Cu diffusion barrier application. Silicide formation is inhibited to at least 400^oC, essential stability for BEOL integration. However, the 2.9Gc (J/m^2) adhesion of the layer compared with 3.1Gc (J/m^2) on SiO"2 does need improvement.
Fred Terman, the Father of Silicon Valley
Authors: Carolyn Tajnai
Venue: IEEE Design Test (1985)

Silicon Valley, located on the San Francisco, California, peninsula, radiates outward from Stanford University. It is containedby the San Francisco Bayon the east, the Santa Cruz Mountains on the west, and the Coast Range to the southeast. At the turnof the century, when fruit orchards predominated, the area was known as the Valley of Heart's Delight. Today, semiconductorchips, made of silicon, are the principal product of the local high-tech industries. It has been said that an institutionis but the lengthened shadow of one great man. Inasmuch as Silicon Valley is an institution, Fred Terman was such a man. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Optimized User Revocation for Group Signature Based Privacy-Aware PKI
Authors: Wei Ren, Kui Ren, Wenjing Lou
Venue: Proceedings of the 2008 The 28th International Conference on Distributed Computing Systems Workshops (2008)

Privacy-aware Public Key Infrastructure (PKI) can maintain user access control and yet protect user privacy, which is important for many applications. The applicability of privacy-aware PKI highly relies on the performance of user revocation. The requirements of user revocation are various in general, such as subscription expiration, violation of access policy, group changing, and key exposure. To satisfy different requirements, multiple revocation approaches may interact each other. In this paper, we study how to achieve optimized user revocation cost with respect to various revocation approaches. We also propose a practical scheme Delta-RL that can fulfill an optimal overall performance on the base of extensive analysis.
A Study on Iris Feature Watermarking on Face Data
Authors: Kang Ryoung Park, Dae Sik Jeong, Byung Jun Kang, Eui Chul Lee
Venue: Proceedings of the 8th international conference on Adaptive and Natural Computing Algorithms, Part II (2007)

In this paper, we propose a new iris feature watermarking method on face data. This research has following three objectives. First, by using watermarked iris features in addition to face data, the multimodal biometric authentication can be possible, which can increase the authentication accuracy. Second, in case that the saved face data is illegally let out and privacy infringement happens, by checking the inserted iris feature watermark, we can solve the legal responsibility problem about the outflow of face data. In detail, if the iris feature watermark cannot be extracted from the outflow face data, we can insist that the face data is let out from other organization instead of ours. Third, in case that "the iris features need to be transmitted via non-secure and noisy communication channel" [1], it can be invisibly hidden on face data by our method. For the first objective, the face recognition accuracy with iris feature watermark should not be degraded. For the second and third objectives, the inserted iris watermark should be "strong" enough to be extracted irrespective of various kinds of attacks (such as blurring, cropping and rotation attacks) and noise insertion on face data. This research has three advantages compared to previous works. First, to overcome the vulnerability of blurring attack to previous biometric watermarking based on spatial domain, we use the watermarking method in frequency domain. Second, to reduce the degradation of face recognition accuracy due to iris watermarking, we insert the watermark into mid and high frequency bands. Third, through using individual unique iris features for biometric watermarking information and secondary authentication, the security level is much enhanced and we can solve legal responsibility problem about the outflow of face data. Experimental results showed that our algorithm could be used to accomplish above objectives.
GEOTOOL: a tool to manage polygonal meshes and build
Authors: Francisco Ramos, Miguel Chover, Jesus Gumbau, Ricardo Quiros
Venue: Proceedings of the 7th WSEAS International Conference on Applied Computer and Applied Computational Science (2008)

In applications such as video games, real-time visualization becomes essential to maintain the quality and performance of the application by managing the geometry of the scenes. Among the different techniques to achieve that balance, we highlight simplification and level of detail techniques. In this paper, we present a standalone application useful to quickly simplify and generate multiresolution models for arbitrary geometry and for trees.
What a memory looks like in the brain? towards the modeling and simulation of a partial software neocortex for learning
Authors: Thang N. Nguyen
Venue: Proceedings of the 10th WSEAS International Conference on Automatic Control, Modelling & Simulation (2008)

This paper addresses the basic question "What a memory looks like in the brain?" It is with the hope that if a possible answer can be framed and hypothesized, a suitable description of a memory will give insights into the modeling and simulation of a partial software neocortex model for potential learning. The paper discusses prior findings and hypotheses on memory by researchers at three levels of abstraction: cellular (middle), network (higher) and molecular (lower) levels. The paper attempts to combine them, together with the author's own hypothesis on what a memory looks like, to suggest an integrated view of memory. The paper then suggests an approach towards a software memory model based on an (arguably) observable parallelism between (1) the natural hierarchy and (2) the software hierarchy, ultimately to be simulated for potential learning as does a human newborn. It is realized that there are questionable items in this initial formulation, which are subject to future investigation.
What Happened in CLEF 2006
Authors: Carol Peters
Venue: Evaluation of Multilingual and Multi-modal Information Retrieval: 7th Workshop of the Cross-Language Evaluation Forum, CLEF 2006, Alicante, Spain, September 20-22, 2006, Revised Selected Papers (2007)

The organization of the CLEF 2006 evaluation campaign is described and details are provided concerning the tracks, test collections, evaluation infrastructure, and participation.
Finding Unmanipulable Singularities in Parallel Mechanisms Using Jacobian Decomposition
Authors: Yawei Yang, John F. O'Brien
Venue: Journal of Intelligent and Robotic Systems (2008)

A geometric method is presented to determine the unmanipulable singular configurations of a general class of parallel mechanisms. In unmanipulable singular configurations, the composite Jacobian matrix that maps active joints velocities to end-effector velocity loses rank, indicating the loss of a task degree-of-freedom. Finding unmanipulable configurations is difficult due to the complexity of the Jacobian matrix. The problem is greatly simplified by a novel decomposition of the matrix presented in this paper. The method is used to find singularities in several example parallel machines.
Novel Global Asymptotic Stability Conditions for Hopfield Neural Networks with Time Delays
Authors: Ming Gao, Baotong Cui, Li Sheng
Venue: Proceedings of the 4th international symposium on Neural Networks: Advances in Neural Networks (2007)

In this paper, the global asymptotic stability of Hopfield neural networks with time delays is investigated. Some novel sufficient conditions are presented for the global stability of a given delayed Hopfield neural networks by constructing Lyapunov functional and using some well-known inequalities. A linear matrix inequality (LMI) approach is developed to establish sufficient conditions for the given neural networks. An illustrative example is provided to demonstrate the effectiveness of our theoretical results.
User Experience Using Motion Capture: Simulation of Human Motion for Multimedia Applications
Authors: Jong Sze Joon, Harold Thwaites, Khong Chee Weng
Venue: Proceedings of the 2008 Fifth International Conference on Computer Graphics, Imaging and Visualisation (2008)

This paper presents a motion-capture-based control framework by simulating three core motions namely walking, jumping and running to enhance user experience for Multimedia applications. Using MWalker V1 application, a user can directly control the full body motion of an avatar in virtual environments with different physical attributes for various multimedia applications. However, there are still a few fundamental problems. This research outlines how different physique produces different behavioural patterns based upon mass and proportion. This research considers 'motion' to identify the differences in each subject's physical attributes by sampling subjects of physical differences. The purpose of the research is to study the detail of motion of various subjects with differences in physical attributes, for simulation of human motion for multimedia applications.
Deriving Safety Software Requirements from an AltaRica System Model
Authors: Sophie Humbert, Christel Seguin, Charles Castel, Jean-Marc Bosc
Venue: Proceedings of the 27th international conference on Computer Safety, Reliability, and Security (2008)

This paper presents a methodology to derive software functional requirements from Preliminary System Safety Assessment analysis (PSSA) of helicopter turboshaft engines. The proposed process starts by extracting functional failure paths from system failure propagation models, using AltaRica models and AltaRica tools. Then the paper shows how to analyse these paths to generate minimal combinations of functional software requirements. This approach is applied to a part of the control system of a helicopter turboshaft engine.
Plenary lecture IV: analytical synthesis method: a new circuit design method for arbitrary requirements
Authors: Chun-Ming Chang
Venue: Proceedings of the 8th WSEAS International Conference on Multimedia systems and signal processing (2008)

Analytical Synthesis Method (ASM) has been presented in several papers published in the IEEE Transactions on Circuits and Systems since 2003. It is one of the powerful design methods in the field of analog circuit design. It is the method using a succession of innovative algebra manipulation operations to decompose a complicated transfer function representing the relationship between the output and the input signals of a design project into many simple equations feasible by using the corresponding simple sub-circuitries. The simple sub-circuitries can be constructed by the desired configuration of the element such as the single-ended-input operational transconductance amplifiers (OTAs) and the grounded capacitors, both of which are used for absorbing and reducing the shunt parasitic capacitance and lead to have more precise output responses. In addition to this, the ASM can control the number of the terms in the complicated decomposition process such that the number of both active and passive components used in the circuit is the least compared to the previously reported ones. Then, the ASM is the only one method which can simultaneously achieve the three important criteria for the design of OTA-C circuits without trade-offs. Due to the flexibility of the ASM, the simple sub-circuitries used in the circuit design can be changed and chosen according to different necessities for the target of the circuit design. For example, if the reduction of the number of the active and passive components used in the circuit is more important than the type of the element configurations like single-ended-input/differential-input OTAs and grounded/floating capacitors due to the consideration about power consumption, chip area, noise, and total parasitics......, etc., the minimum component OTA-C circuit can also be investigated and developed successfully using the ASMs. The fully flexible characteristic and the real demonstration in the literature of the ASM may make it be one of the most prospective methods in the field of analog circuit design in the near future.
Classes of Kernels for Hit Definition in Compound Screening
Authors: Karol Kozak, Katarzyna Stapor
Venue: Proceedings of the 9th international conference on Artificial Intelligence and Soft Computing (2006)

In this paper we analyze Support Vector Machine (SVM) algorithm to the problem of chemical compounds screening with a desired activity, definition of hits. The support vector machine transforms the input data in an (unknown) high dimensional feature space and the kernel technique is applied to calculate the inner-product of feature data.The problem of automatically tuning multiple parameters for pattern recognition SVMs using our new introduced kernel for chemical compounds is considered. This is done by simple eigen analysis method which is applied to the matrix of the same dimension as the kernel matrix to find the structure of feature data, and to find the kernel parameter accordingly. We characterize distribution of data by the principle component analysis method.