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BioN∅T: A searchable database of biomedical negated sentences

BMC Bioinformatics 2011年第1期12卷 1-7页

作者： Agarwal, Shashank Yu, Hong Kohane, Issac Medical Informatics College of Engineering and Applied Sciences University of Wisconsin-Milwaukee 3200 N. Cramer St. Milwaukee WI 53201-0784 United States Department of Computer Science and Electrical Engineering College of Engineering and Applied Sciences University of Wisconsin-Milwaukee 3200 N. Cramer St. Milwaukee WI 53201-0784 United States Department of Health Sciences College of Health Science University of Wisconsin-Milwaukee 2400 E. Hartford Ave. Milwaukee WI 53211 United States Children's Hospital Informatics Program Children's Hospital 300 Longwood Ave. Enders-6 Boston MA 02115 United States

Background: Negated biomedical events are often ignored by text-mining applications;however, such events carry scientific significance. We report on the development of BioN∅T, a database of negated sentences that can be used to extract such negated ***: Currently BioN∅T incorporates ≈32 million negated sentences, extracted from over 336 million biomedical sentences from three resources: ≈2 million full-text biomedical articles in Elsevier and the PubMed Central, as well as ≈20 million abstracts in PubMed. We evaluated BioN∅T on three important genetic disorders: autism, Alzheimer's disease and Parkinson's disease, and found that BioN∅T is able to capture negated events that may be ignored by ***: The BioN∅T database can be a useful resource for biomedical researchers. BioN∅T is freely available at http://***/. In future work, we will develop semantic web related technologies to enrich BioN∅T. © 2011 Agarwal et al;licensee BioMed Central Ltd.

关键词： Database systems

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Porantim-Opt: Optimizing the Combined Selection of Model-Based Testing Techniques

Porantim-Opt: Optimizing the Combined Selection of Model-Bas...

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IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW

作者： Arilo Claudio Dias Neto Rosiane de Freitas Rodrigues Guilherme Horta Travassos Computer Science Department Federal University of Amazonas Manaus Brazil Systems Engineering and Computer Science Program-COPPE Federal University of Rio de Janeiro Rio de Janeiro Rio de Janeiro Brazil

The combination of testing techniques is considered an effective strategy to evaluate a software product. However, the selection of which techniques to combine in a software project has been an interesting challenge in the Software engineering field. This paper presents a proposal extending an approach developed to support the combined selection of model-based testing (MBT) techniques, named Porantim, applying Multiobjective Combinatorial Optimization strategy by determining the smallest dominating set in a bipartite and weighted graph. Thus, a local search strategy algorithm is proposed generating solutions aiming at maximizing the coverage of software project characteristics and skills required by the testing team to use the techniques and minimizing the eventual effort to construct models used for test cases generation. A preliminary evaluation analyzes this new approach when compared to the Porantim's original version, and the results indicate improvements in the MBT techniques selection.

关键词： Software Testing Analytical models Software engineering Optimization programming Search problems

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A Streaming high-throughput linear sorter system with contention buffering

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International Journal of Reconfigurable Computing 2011年第1期2011卷

作者： Ortiz, Jorge Andrews, David Information and Telecommunication Technology Center University of Kansas 2335 Irving Hill Road Lawrence KS 66045 United States Department of Computer Science and Computer Engineering University of Arkansas 504 J. B. Hunt Building Fayetteville AR 72701 United States

Popular sorting algorithms do not translate well into hardware implementations. Instead, hardware-based solutions like sorting networks, systolic sorters, and linear sorters exploit parallelism to increase sorting efficiency. Linear sorters, built from identical nodes with simple control, have less area and latency than sorting networks, but they are limited in their throughput. We present a system composed of multiple linear sorters acting in parallel to increase overall throughput. Interleaving is used to increase bandwidth and allow sorting of multiple values per clock cycle, and the amount of interleaving and depth of the linear sorters can be adapted to suit specific applications. Contention for available linear sorters in the system is solved through the use of buffers that accumulate conflicting requests, dispatching them in bulk to reduce latency penalties. Implementation of this system into a field programmable gate array (FPGA) results in a speedup of 68 compared to a MicroBlaze processor running quicksort. © 2011 Jorge Ortiz and David Andrews.

关键词： Field programmable gate arrays (FPGA)

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Fusion of multispectral palmprint images for automatic person identification

Fusion of multispectral palmprint images for automatic perso...

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Electronics, Communications and Photonics Conference (SIECPC), Saudi International

作者： Abdallah Meraoumia Salim Chitroub Ahmed Bouridane Signal and Image Processing Laboratory Electronics and Computer Science Faculty Telecommunication Department University of Science and Technology of Houari Boumedienne Algiers Algeria School of Computing Engineering and Information Sciences Northumbria University Newcastle-upon-Tyne UK

Reliability and accuracy in personal identification system is a dominant concern to the security world. Biometric has gained much attention in this subject recently. Many types of personal identification systems have been developed, and palmprint identification is one of the emerging technologies. This paper presents a novel biometric technique to automatic personal identification system using multispectral palmprint technology. In this method, each of spectrum images are aligned and then used to extract palmprint features using 1D log-Gabor filter. These features are then examined for their individual and combined performances. Finally, the hamming distance is used for matching of palmprint features. The experimental results showed that the proposed method achieve an excellent identification rate and provide more security.

关键词： Feature extraction Databases Image fusion Discrete wavelet transforms Security Accuracy Hamming distance

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Digital Sex: Causes and Consequences 11

Digital Sex: Causes and Consequences

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11th European Conference on Artificial Life, ECAL 2011

作者： Misevic, Dusan Ofria, Charles Lenski, Richard E. Université Paris Descartes Paris France Program in Ecology Evolutionary Biology and Behavior Michigan State University East LansingMI United States Department of Computer Science and Engineering Michigan State University East LansingMI United States Department of Microbiology and Molecular Genetics Michigan State University East LansingMI United States

ISBN: (纸本)9780262297141

Many theories have sought to explain the evolution of sex, but the question remains unanswered owing to the scarcity of compelling empirical tests. Here we summarize the results of two of our published studies investigating the evolution of sex using digital organisms. We used these evolving programs to test the hypothesis that sexual reproduction is advantageous in changing environments. We found that sex evolved to be the dominant mode of reproduction only when the environment was changing rapidly and substantially. Additionally, we measured the effects of sexual reproduction on genetic architecture, specifically modularity and epistasis. We found that sex profoundly influences genome organization, increasing modularity and decreasing the effects of interactions between mutations. Our studies have contributed to understanding both the causes and consequences of sexual reproduction, while also demonstrating the efficacy and power of in silico approaches to these issues. © 2011 ECAL 2011: The 11th European Conference on Artificial Life. All rights reserved.

关键词： Cell proliferation

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Exploring Time-Scales of Closed-Loop Decoder Adaptation in Brain-Machine Interfaces

Exploring Time-Scales of Closed-Loop Decoder Adaptation in B...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society

作者： Amy L. Orsborn Siddharth Dangi Helene G. Moorman Jose M. Carmena Berkeley - Unviversity of California Department of Electrical Engineering and Computer Sciences University of California Helen Wills Neuroscience Institute University of California Department of Electrical Engineering and Computer Sciences Helen Wills Neuroscience Institute and Program in Cognitive Science University of California

ISBN: (纸本)9781424441211

Performing closed-loop modifications of a brain-machine interface (BMI) decoder is a technique that shows great promise for improving performance. We compare two algorithms for implementing adaptations that update decoder parameters on different time-scales (discrete batches vs. online), and present experimental results of a non-human primate performing a standard center-out BMI task. To ensure that our experimental training models are representative of a broad range of paralyzed patients, our decoders were initially trained using neural activity recorded during subject observation of cursor movement. We find that both closed-loop adaptation algorithms can be used to boost BMI performance from 20-30% to 80%, yielding movement kinematics similar to natural arm movements. Based on insights derived from the performance of each algorithm, we propose that a hybrid of batch and online decoder adaptation may be the best approach.

关键词： Decoding Kinematics Training Educational institutions Adaptation models Kalman filters USA Councils

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Online correction of orientation estimates using spatial memory in a neuromorphic head direction system

Online correction of orientation estimates using spatial mem...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： Tarek M. Massoud Timothy K. Horiuchi Electrical and Computer Engineering Department Institute of Systems Research University of Maryland College Park MD USA Electrical and Computer Engineering Department Institute of Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

Many animals are known to maintain an internal estimate of their orientation in the environment. In the absence of external sensory cues, this estimate inevitably exhibits drift. When sensory information is available, associations between sensory landmarks and the internal estimate can be used to correct for drift. In this paper we present a neuromorphic system to model such associations between sensory landmarks in the environment (as provided by sonar) and the activity of a hardware-based head direction cell system (HDS) that continuously integrates angular velocity signals to maintain an estimate of the orientation. These associations are shown to correct for drift errors that are encountered in the HDS.

关键词： High definition video Robot sensing systems Neurons Navigation Sonar detection Neuromorphics

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Adaptive Kalman filtering for closed-loop Brain-Machine Interface systems

Adaptive Kalman filtering for closed-loop Brain-Machine Inte...

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International IEEE/EMBS Conference on Neural engineering, CNE

作者： Siddharth Dangi Suraj Gowda Rodolphe Héliot Jose M. Carmena Department of Electrical Engineering and Computer Sciences University of California Berkeley CA USA CEA-LETI France Department of Electrical Engineering and Computer Sciences Helen Wills Neuroscience Institute and Program in Cognitive Science University of California Berkeley CA USA

Brain-Machine Interface (BMI) decoding algorithms are often trained offline, but this paradigm ignores both the non-stationarity of neural signals and the feedback that exists in online, closed-loop control. To address these problems, we have developed an Adaptive Kalman Filter (AKF), a Kalman filter variant that adaptively updates its model parameters during training. For a Kalman filter decoder, batch retraining methods require completely re-estimating the parameter matrices from sufficient data to perform regression accurately, even if only small changes are necessary. Conversely, the AKF is designed to update the decoder parameters continuously and more intelligently. We simulated a population of 41 neurons learning to control a 2D computer cursor. The AKF yielded significantly faster skill acquisition and better robustness to perturbation and neuron loss than a standard Kalman filter with periodic batch retraining.

关键词： Decoding Kalman filters Mathematical model Equations Kinematics Neurons Training

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Characteristics of low latitude nocturnal ionospheric irregularities over India-Arab longitudes during solar maximum

Characteristics of low latitude nocturnal ionospheric irregu...

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2011 30th URSI General Assembly and Scientific Symposium, URSIGASS 2011

作者： Chu, Fang-Dar Chen, Wei-Sheng Lee, Chien-Chih Hsu, Wei-Chih Lin, Huang-Tien Liao, Chia-Shu National Standard Time and Frequency Lab. of Telecommunication Laboratories Chunghwa Telecom. Co. Ltd. Yangmei City Taoyuan County 32601 Taiwan General Education Center Ching Yun University Zhongli City Taoyuan County 32097 Taiwan Department of Computer and Communication Engineering National Kaohsiung First University of Science and Technology Kaohsiung City 81164 Taiwan

ISBN: (纸本)9781424451173

This study investigated the low latitude nocturnal ionospheric irregularities at India-Arab longitudes using phase fluctuations of the global positioning system during solar maximum. The results showed that the low latitude irregularities in this region develop easier in equinoctial months and December-solstice months than in June-solstice months. In addition, the low latitude irregularities mainly come from the magnetic equator. Moreover, at the crest of equatorial anomaly the irregularities in June-solstice months maybe come from middle latitudes. Many details are discussed. © 2011 IEEE.

关键词： Cities and towns Fluctuations Global Positioning System Ionosphere Satellite broadcasting Satellites Time frequency analysis

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Interactive content-based texture image retrieval

Interactive content-based texture image retrieval

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International Conference on computer and Communication Technology (ICCCT)

作者： Pushpa B. Patil Manesh B. Kokare Department of Computer Science and Engineering BLDEAs V.P.Dr. P. G. Halakatti CET. Bijapur India Department of Electronic and Telecommunication S.G.G.S. Institute of Engineering and Technology Nanded India

Due to the semantic gap between low-level image features and high level concepts, content-Based image retrieval (CBIR) systems are incapable to provide the effective results to the user. To address this problem, we have presented a framework for effective image retrieval by proposing a novel idea of cumulative learning using Support Vector Machines (SVM). It creates a knowledge base model to increase the training samples by simply accumulating the samples based on user interactions. As we know relevance feedback (RF) is online process, so we have optimized the learning process by considering the most positive image selection on each feedback iteration. To learn the system we have used SVM. The main significances of our system are to address the small training sample and to reduce retrieval time. Experiments are conducted on 1856 texture images to demonstrate the effectiveness of the proposed framework.

关键词： Radio frequency Accuracy Image retrieval Wavelet transforms Training data Training

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