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"abstract": "For automotive applications, 3D perception of the car's surroundings is crucial, both for driver assistance and for safety systems. In addition, a large field of view is required for future applications such as intersection assistance. A popular option to obtain 3D measurements and detect objects is to use two cameras (stereo vision). Applications based on object detection range from??Adaptive Cruise Control, Collision Mitigation Systems to Intersection Assistance Systems. Stereo vision with conventional cameras only delivers a limited field of view. We extend the field of view using fisheye lenses. In this contribution a detailed description of a fisheye stereo system for object detection is given, including the steps calibration, rectification, and stereo computation. Differences to traditional stereo systems are pointed out and the accuracy for an experimental setup is evaluated. In addition, the fisheye stereo approach is combined with optical flow measurements to obtain position and velocity data simultaneously. This so-called 6D Vision approach is extended to stereodata obtained with fisheye lenses. Results for intersection scenes are presented.",
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"abstract": "A new digital halftoning algorithm in which the halftoning algorithm is achieved by a pixelwise comparison of the gray scale image against a non-image array, the blue noise mask, is proposed. The blue noise mask is constructed such that when thresholded at any level, the resulting binary pattern has the correct first order statistics, and also its power spectrum has blue noise (high frequency) characteristics which are visually pleasing. The construction of the blue noise mask is described and experimental results are shown. Results from a psychovisual study are provided where subjects rated halftoned images that have the same first order but different second order statistics.<>",
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"abstract": "The high frequency of the image pre-filtering and sampling can not be eliminated, whereby the power spectrum of the oscillation may cause aliasing, the sampling scheme proposed two standard blue noise pattern: step blue noise and single-peak blue noise, two blue noise sampling task performance in the image plane of the well, as can the other at least in the low frequency band sampling mode, and in the high frequency band may not cause aliasing because they are mapped to white noise more effectively. experimental results show that at low sampling rates model can effectively prevent aliasing structure, at a high sampling rate to perform equally well.",
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"content": "Eye gaze estimation is an important problem in automatic human behavior understanding. This paper proposes a deep learning based method for inferring the eye gaze direction. The method is based on the use of ensemble of networks, which capture both the geometric and texture information. Firstly, a Deep Neural Network (DNN) is trained using the geometric features that are extracted from the facial landmark locations. Secondly, for the texture based features, three Convolutional Neural Networks (CNN) are trained i.e. for the patch around the left eye, right eye, and the combined eyes, respectively. Finally, the information from the four channels is fused with concatenation and dense layers are trained to predict the final eye gaze. The experiments are performed on the two publicly available datasets: Columbia eye gaze and TabletGaze. The extensive evaluation shows the superior performance of the proposed framework. We also evaluate the performance of the recently proposed swish activation function as compared to Rectified Linear Unit (ReLU) for eye gaze estimation.",
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"normalizedAbstract": "Eye gaze estimation is an important problem in automatic human behavior understanding. This paper proposes a deep learning based method for inferring the eye gaze direction. The method is based on the use of ensemble of networks, which capture both the geometric and texture information. Firstly, a Deep Neural Network (DNN) is trained using the geometric features that are extracted from the facial landmark locations. Secondly, for the texture based features, three Convolutional Neural Networks (CNN) are trained i.e. for the patch around the left eye, right eye, and the combined eyes, respectively. Finally, the information from the four channels is fused with concatenation and dense layers are trained to predict the final eye gaze. The experiments are performed on the two publicly available datasets: Columbia eye gaze and TabletGaze. The extensive evaluation shows the superior performance of the proposed framework. We also evaluate the performance of the recently proposed swish activation function as compared to Rectified Linear Unit (ReLU) for eye gaze estimation.",
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"content": "Drivers obtain information on surrounding environment using their eyesights. Experienced eye-gaze behavior is needed when driving at places where multiple risks exist to prepare for and avoid them. In this work, we analyze the change in eye-gaze behavior in such situations while a driver gains experience on the operation of a robotic wheelchair. Accurate distance information in the traffic environment is important to analyze the eye-gaze behavior. However, almost all previous works analyze eye-gaze behavior in a 2D environment, so they could not obtain accurate distance information. For this reason, we analyze eye-gaze behavior in 3D space. Concretely, we developed a novel eye-gaze behavior analysis platform based on a robotic wheelchair and estimated the driver's attention in 3D space. We try to analyze the eye-gaze behavior considering a useful field-of-view in 3D space based on the distance information instead of only the fixation point to investigate the objects that a driver implicitly pays attention to and from where s/he focuses on them. Results show that novice drivers pay attention to a single risk at a time. In contrast, they pay more attention to multiple risks simultaneously as they gain experience. Additionally, we discuss what features are effective to model the eye-gaze behavior based on the results.",
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"abstract": "Study between visual gaze behavior and implied intent, it provides a new idea for exploring the human-computer interaction mode of non-verbal communication. Applying hidden Markov model to implicit intention inference of visual gaze, find predictive models for both efficiency and accuracy, reduction of lag in training models using historical data. The subjects' gaze data were collected, based on the hidden Markov model, two different gaze patterns are constructed, the model parameters are trained by Baum- Welch algorithm, next, the viterbi algorithm is used to solve the maximum probability hidden state sequence, then, the implicit intent prediction of the gaze behavior. On this basis, the architecture of the model and its effectiveness are verified, the relationship between human intention and gaze behavior is further discussed.",
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"affiliation": "College of Science, Wuhan University of Science and Technology,Wuhan,China",
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"affiliation": "Robotics and Intelligent Systems Research Institute, Wuhan University of Science and Technology,Wuhan,China",
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"abstract": "An important component of the modeling of sound propagation for virtual reality (VR) is the spatialization of the room impulse response (RIR) for directional listeners. This involves convolution of the listener's head-related transfer function (HRTF) with the RIR to generate a spatial room impulse response (SRIR) which can be used to auralize the sound entering the listener's ear canals. Previous approaches tend to evaluate the HRTF for each sound propagation path, though this is too slow for interactive VR latency requirements. We present a new technique for computation of the SRIR that performs the convolution with the HRTF in the spherical harmonic (SH) domain for RIR partitions of a fixed length. The main contribution is a novel perceptually-driven metric that adaptively determines the lowest SH order required for each partition to result in no perceptible error in the SRIR. By using lower SH order for some partitions, our technique saves a significant amount of computation and is almost an order of magnitude faster than the previous approach. We compared the subjective impact of this new method to the previous one and observe a strong scene-dependent preference for our technique. As a result, our method is the first that can compute high-quality spatial sound for the entire impulse response fast enough to meet the audio latency requirements of interactive virtual reality applications.",
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"content": "An important component of the modeling of sound propagation for virtual reality (VR) is the spatialization of the room impulse response (RIR) for directional listeners. This involves convolution of the listener's head-related transfer function (HRTF) with the RIR to generate a spatial room impulse response (SRIR) which can be used to auralize the sound entering the listener's ear canals. Previous approaches tend to evaluate the HRTF for each sound propagation path, though this is too slow for interactive VR latency requirements. We present a new technique for computation of the SRIR that performs the convolution with the HRTF in the spherical harmonic (SH) domain for RIR partitions of a fixed length. The main contribution is a novel perceptually-driven metric that adaptively determines the lowest SH order required for each partition to result in no perceptible error in the SRIR. By using lower SH order for some partitions, our technique saves a significant amount of computation and is almost an order of magnitude faster than the previous approach. We compared the subjective impact of this new method to the previous one and observe a strong scene-dependent preference for our technique. As a result, our method is the first that can compute high-quality spatial sound for the entire impulse response fast enough to meet the audio latency requirements of interactive virtual reality applications.",
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"abstract": "We present initial results from a new image generation approach for low-latency displays such as those needed in head-worn AR devices. Avoiding the usual video interfaces, such as HDMI, we favor direct control of the internal display technology. We illustrate our new approach with a bench-top optical see-through AR proof-of-concept prototype that uses a Digital Light Processing (DLPTM) projector whose Digital Micromirror Device (DMD) imaging chip is directly controlled by a computer, similar to the way random access memory is controlled. We show that a perceptually-continuous-tone dynamic gray-scale image can be efficiently composed from a very rapid succession of binary (partial) images, each calculated from the continuous-tone image generated with the most recent tracking data. As the DMD projects only a binary image at any moment, it cannot instantly display this latest continuous-tone image, and conventional decomposition of a continuous-tone image into binary time-division-multiplexed values would induce just the latency we seek to avoid. Instead, our approach maintains an estimate of the image the user currently perceives, and at every opportunity allowed by the control circuitry, sets each binary DMD pixel to the value that will reduce the difference between that user-perceived image and the newly generated image from the latest tracking data. The resulting displayed binary image is “neither here nor there,” but always approaches the moving target that is the constantly changing desired image, even when that image changes every 50μs. We compare our experimental results with imagery from a conventional DLP projector with similar internal speed, and demonstrate that AR overlays on a moving object are more effective with this kind of low-latency display device than with displays of similar speed that use a conventional video interface.",
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"fullName": "Feng Zheng",
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"title": "2018 IEEE International Symposium on Mixed and Augmented Reality Adjunct (ISMAR-Adjunct)",
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"title": "A Low-Latency, High-Precision Handheld Perspective Corrected Display",
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"abstract": "Perspective Corrected Displays (PCDs) show the perspective projection of a 3D scene computed from the viewer's position that is updated in real-time. By moving their head in front of the display, users perceive the motion parallax effect, a strong depth perception cue [6]. “fish-tank virtual reality” systems are well-known instantiation of PCDs involving a fixed planar display and stereo rendering is added to the motion parallax depth cue [5]. More recently, PCDs have been arranged to form small volumes such as a cube (i.e. gCu-bik [2] and pCubee [4]). This gives the illusion that the scene is contained inside the display. Because of the small size of the displays, users can rotate them in their hands, hence the Handheld in HPCD. This creates the strong illusion of holding the virtual scene in one's hands. In addition, rotating the display in hands requires much less effort than moving the whole body in front of the display. Hence, HPCDs allow users to experience more motion parallax than PCDs. However, the two previous implementations of cubic HPCDs required the presence of complex electronic on the display. As a result, they are connected with a thick wire to a rendering computer. This prevents to display on all faces as one of them is used for the connection. In addition, a significant part of the cube's sides is occluded by the displays' bezels.",
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"abstract": "Visual stimuli can modulate the temperature at which people perceive heat pain. However, very little research exists on the potential use of Augmented Reality (AR) to modulate the heat pain threshold (HPT). In this paper, we investigate whether participants’ HPTs can be modulated observing virtual flames on their hands through a video see-through head-mounted display (VST-HMD). In a pilot study (n = 7), we found that rendering virtual flames had a significant effect (p < 0.05) on the HPT. The virtual flames on the participant’s hand led to a decrease in the temperature at which they would perceive pain related to heat. These results indicate that AR-induced stimuli may be an effective way to achieve top-down modulation of the experience of pain.",
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"content": "Visual stimuli can modulate the temperature at which people perceive heat pain. However, very little research exists on the potential use of Augmented Reality (AR) to modulate the heat pain threshold (HPT). In this paper, we investigate whether participants’ HPTs can be modulated observing virtual flames on their hands through a video see-through head-mounted display (VST-HMD). In a pilot study (n = 7), we found that rendering virtual flames had a significant effect (p < 0.05) on the HPT. The virtual flames on the participant’s hand led to a decrease in the temperature at which they would perceive pain related to heat. These results indicate that AR-induced stimuli may be an effective way to achieve top-down modulation of the experience of pain.",
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"abstract": "The emergent importance of the sleep medicine together with the rapid adoption of mobile devices and wearables along with a growing habit for using these devices on the daily-living activities offer an opportunity to use them as a sleep monitor. Traditional sleep monitoring systems, such as polysomnography, involves a myriad of sensors attached around the patients' body, and therefore is limited to clinical usage. In line with this, alternative solutions have been widely investigated focused both to infer sleep information based on a reduced number of sensors, and to use non-invasive and feasible technologies. This study presents an ubiquitous architecture based on portability and interoperability concepts in which a smartwatch is combined with a smartphone to implement a sleep monitoring system. This system joints heart rate, accelerometer, and sound signals collected into the smartwatch. Thus, the preliminary results revealed that the proposed system is feasible and suitable for sleep monitoring. In spite of the early stage of this system, the developed framework already includes an API for data exchange between the smartwatch and the smartphone. However, additional studies should be addressed in order to complement and enhanced the proposed system with novel algorithms for signal treatment, including the development of several classifiers specific oriented to snore, motion and sleep detection.",
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"abstract": "Sleep-wake cycle is a complex process relates to a variety of neurotransmitters and receptors in the central nervous system (CNS), also involves a large number of gene transcription and translation. MicroRNAs (miRNAs) have emerged as important regulators of gene expression, which mediate translational repression and/or mRNA decay of a target gene. Dopamine D2 receptor (DRD2) gene is predicted as a target gene of a brain-enriched miRNA, miR-9, but their functions in sleep-wake cycle remain unknown. In this study, we reported that REM sleep deprivation decreases the level of miR-9 and this induction is associated with the expression of DRD2 proteins. Thus, miR-9 may control DRD2 gene translation in the prefrontal cortex for processing sleep deprivation. Our findings may have implications in understanding the biological relevance of the genetic associations of sleep disorders. Furthermore, miR-9 may be considered as potential drug targets for the treatment of disorders involving abnormal DRD2 function, such as insomnia.",
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"abstract": "Online Laboratories and Virtual Experiments start to play an increasingly important role in the education of Engineering and Science Education. While several repositories for online and virtual experiments are available, a common method for annotating experiments to simplify their discovery is not yet available and accepted. In 2010, an international group of online lab providers formed the Global Online Lab Consortium (GOLC) to address the issues of interoperability between online laboratories and laboratory compilations, one of its activities is the establishment of an ontology and a common metadata set that addresses not only the needs of typical lab providers and lab users, but also of storage and archival institutions such as libraries. This article describes the current status of the GOLC activities in the metadata subcommittee, lists the requirements of various user groups of the metadata set and provides insight into both the underlying ontology and the metadata specifications themselves.",
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"abstract": "A rotorcraft UAV provides an ideal experimental platform for vision-based navigation. This paper describes the flight tests of the US Army PALACE project, which implements Moravec's pseudo-normalized correlation tracking algorithm. The tracker uses the movement of the landing site in the camera, a laser range, and the aircraft attitude from an IMU to estimate the relative motion of the UAV. The position estimate functions as a GPS equivalent to enable the rotorcraft to maneuver without the aid of GPS. With GPS data as a baseline, tests were performed in simulation and inflight that measure the accuracy of the position estimation",
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"abstract": "This paper proposes a new design scheme of carrier runway simulation system. The system can be used for simulating training for the aircraft of carrier landing, and it can provide pilots with an environment being closer to the actual landing. The carrier runway simulation system mainly includes runway motion simulation system and the ideal landing point simulation system. The simulation system of ideal landing point simulates the height variation of the ideal landing point by using the horizontal variation of optical virtual arresting cable, it can offer crucial movement information to the carrier aircraft pilot. The runway motion simulation system employs a programmable multi-axis controller to control the linear motion guides moving with the infrared cooperative targets, which can simulate the carrier runway movement. And the high-precision magnetic grid measurement sensor collects motion information and transfers the information into the computer. In this paper, an 8:1 scale experiment has been designed and the runway motion simulation system is implemented. The experiment results show that the maximum height error of the targets between actual and setting motion is 0.02m, which meets the requirement of the simulation system and verifies the feasibility of the runway motion simulation system. What's more, the simulation system is beneficial to the later research work of carrier-based aircraft landing ground simulation.",
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"content": "This paper proposes a new design scheme of carrier runway simulation system. The system can be used for simulating training for the aircraft of carrier landing, and it can provide pilots with an environment being closer to the actual landing. The carrier runway simulation system mainly includes runway motion simulation system and the ideal landing point simulation system. The simulation system of ideal landing point simulates the height variation of the ideal landing point by using the horizontal variation of optical virtual arresting cable, it can offer crucial movement information to the carrier aircraft pilot. The runway motion simulation system employs a programmable multi-axis controller to control the linear motion guides moving with the infrared cooperative targets, which can simulate the carrier runway movement. And the high-precision magnetic grid measurement sensor collects motion information and transfers the information into the computer. In this paper, an 8:1 scale experiment has been designed and the runway motion simulation system is implemented. The experiment results show that the maximum height error of the targets between actual and setting motion is 0.02m, which meets the requirement of the simulation system and verifies the feasibility of the runway motion simulation system. What's more, the simulation system is beneficial to the later research work of carrier-based aircraft landing ground simulation.",
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"Aircraft Landing Guidance",
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"affiliation": null,
"fullName": "Mingyan Zhang",
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"fullName": "Wei Wang",
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"fullName": "Yue Meng",
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"fullName": "Hao Han",
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"title": "Visual-inertial State Estimation for the Civil Aircraft Landing in Low Visibility Conditions",
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"abstract": "This paper proposes a visual-inertial navigation algorithm for the civil aircraft landing in low visibility conditions. The algorithm includes the following key steps: 1) Detect and extract real runway features from forward-looking infrared (FLIR) image; 2) Generate synthetic runway features based on airport geo-referenced data; 3) Set up vision measurement and fuse inertial data with visual cues in SR-UKF; 4) Correct the INS measurements by the estimated errors. The experimental results demonstrate that our proposed algorithm can be used for civil aircraft precise landing in GPS-denied and low visibility environments.",
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"content": "This paper proposes a visual-inertial navigation algorithm for the civil aircraft landing in low visibility conditions. The algorithm includes the following key steps: 1) Detect and extract real runway features from forward-looking infrared (FLIR) image; 2) Generate synthetic runway features based on airport geo-referenced data; 3) Set up vision measurement and fuse inertial data with visual cues in SR-UKF; 4) Correct the INS measurements by the estimated errors. The experimental results demonstrate that our proposed algorithm can be used for civil aircraft precise landing in GPS-denied and low visibility environments.",
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"affiliation": "Northwestern Polytechnical University, School of Computer Science and Engineering, Xi'an, PR. China",
"fullName": "Lei Zhang",
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"title": "Control validation with software-in-the-loop for a fixed-wing vertical takeoff and landing unmanned aerial vehicle with multiple flight stages",
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"abstract": "Unmanned Aerial Vehicles (UAVs) are aircraft without a human aboard that can fly autonomously or be remotely piloted. Several configurations of UAVs have been developed to fulfill the requirements of different applications. Between them, it is possible to highlight the tailsitter, a hybrid design with the advantages of fixed-wing and Vertical TakeOff and Landing (VTOL) aircraft. A tailsitter UAV with simplicity as its main characteristic is AVALON (Autonomous VerticAL takeOff and laNding), which also has the disadvantage of a complex operation due to its multiple flight stages. To enable its autonomous procedure, AVALON requires a control system capable of stabilising the flight during its entire operation. Therefore, this paper reports the validation of control structures based on proportional-derivative controllers for AVALON's flight stages with software-in-the-loop experiments in the flight simulator X-Plane. The results show small errors for most of the flight stages, with the exception of landing. Despite of being able to land vertically, it still presented large errors and a yaw variation during this last stage.",
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"content": "Unmanned Aerial Vehicles (UAVs) are aircraft without a human aboard that can fly autonomously or be remotely piloted. Several configurations of UAVs have been developed to fulfill the requirements of different applications. Between them, it is possible to highlight the tailsitter, a hybrid design with the advantages of fixed-wing and Vertical TakeOff and Landing (VTOL) aircraft. A tailsitter UAV with simplicity as its main characteristic is AVALON (Autonomous VerticAL takeOff and laNding), which also has the disadvantage of a complex operation due to its multiple flight stages. To enable its autonomous procedure, AVALON requires a control system capable of stabilising the flight during its entire operation. Therefore, this paper reports the validation of control structures based on proportional-derivative controllers for AVALON's flight stages with software-in-the-loop experiments in the flight simulator X-Plane. The results show small errors for most of the flight stages, with the exception of landing. Despite of being able to land vertically, it still presented large errors and a yaw variation during this last stage.",
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"affiliation": "Universidade Tecnológica Federal do Paraná,Cornélio Procópio,Brazil",
"fullName": "Natassya B. F. Silva",
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"affiliation": "Universidade de São Paulo,São Carlos,Brazil",
"fullName": "João V. C. Fontes",
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"affiliation": "Universidade de São Paulo,São Carlos,Brazil",
"fullName": "Kalinka R. L. J. C. Branco",
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"abstract": "The full loss of thrust of an aircraft requires fast and reliable decisions of the pilot. If no published landing field is within reach, an emergency landing field must be selected. The choice of a suitable emergency landing field denotes a crucial task to avoid unnecessary damage of the aircraft, risk for the civil population as well as the crew and all passengers on board. Especially in case of instrument meteorological conditions it is indispensable to use a database of suitable emergency landing fields. Thus, based on public available digital orthographic photos and digital surface models, we created various datasets with different sample sizes to facilitate training and testing of neural networks. Each dataset consists of a set of data layers. The best compositions of these data layers as well as the best performing transfer learning models are selected. The hyperparameters of the chosen models for each sample size are optimized with Bayesian and Bandit optimization. The models outputs were investigated with respect to the input data by the utilization of layer-wise relevance propagation. With optimized models we created an ensemble model to improve the segmentation performance. Finally, an area around the airport of Arnsberg in North Rhine-Westphalia was segmented into 26.252 km<sup>2</sup> as landable and 221.329 km<sup>2</sup> as not suitable for an emergency landing. In sum 54,997 emergency landing fields are identified and stored in a database. The verification of the final approach's obstacle clearance is left unconsidered.",
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"content": "The full loss of thrust of an aircraft requires fast and reliable decisions of the pilot. If no published landing field is within reach, an emergency landing field must be selected. The choice of a suitable emergency landing field denotes a crucial task to avoid unnecessary damage of the aircraft, risk for the civil population as well as the crew and all passengers on board. Especially in case of instrument meteorological conditions it is indispensable to use a database of suitable emergency landing fields. Thus, based on public available digital orthographic photos and digital surface models, we created various datasets with different sample sizes to facilitate training and testing of neural networks. Each dataset consists of a set of data layers. The best compositions of these data layers as well as the best performing transfer learning models are selected. The hyperparameters of the chosen models for each sample size are optimized with Bayesian and Bandit optimization. The models outputs were investigated with respect to the input data by the utilization of layer-wise relevance propagation. With optimized models we created an ensemble model to improve the segmentation performance. Finally, an area around the airport of Arnsberg in North Rhine-Westphalia was segmented into 26.252 km<sup>2</sup> as landable and 221.329 km<sup>2</sup> as not suitable for an emergency landing. In sum 54,997 emergency landing fields are identified and stored in a database. The verification of the final approach's obstacle clearance is left unconsidered.",
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"title": "2020 International Conference on Robots & Intelligent System (ICRIS)",
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"abstract": "In order to overcome the problems of low guidance accuracy, poor autonomy and high experimental cost during the landing of UA V, a method of scene simulation and cooperative target detection in uav autonomous landing is proposed. In this method, QR code image with strong error correction ability is adopted as the cooperation target, Unreal Engine 4 (UE4) is used to build UA V landing simulation scene, and the UnrealCV plug-in is installed to enable UE4 to communicate with external programs. Finally, in the scene, the accuracy of yolov3 (You Only Look Once v3), a object detection algorithm based on deep learning adopted in this paper, to detect the cooperative target position on the runway is verified. The simulation results show that the algorithm can detect the landing target position with 100% accuracy and recall rate, ensuring the smooth completion of the whole landing process.",
"abstracts": [
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"content": "In order to overcome the problems of low guidance accuracy, poor autonomy and high experimental cost during the landing of UA V, a method of scene simulation and cooperative target detection in uav autonomous landing is proposed. In this method, QR code image with strong error correction ability is adopted as the cooperation target, Unreal Engine 4 (UE4) is used to build UA V landing simulation scene, and the UnrealCV plug-in is installed to enable UE4 to communicate with external programs. Finally, in the scene, the accuracy of yolov3 (You Only Look Once v3), a object detection algorithm based on deep learning adopted in this paper, to detect the cooperative target position on the runway is verified. The simulation results show that the algorithm can detect the landing target position with 100% accuracy and recall rate, ensuring the smooth completion of the whole landing process.",
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"abstract": "Based on the depth, efficiency of financial development and the scale of securities market, through the Unit Root Test, Co-integration Test and Granger Causality Test methods, we analyzed the causality between financial development and economic growth of Fujian Province during the period from 1978 to 2008. We find out that there is a bidirectional causality between the depth of financial development and economic growth. The efficiency of financial development is the cause of economic growth, but economic growth has no effect on the efficiency of financial development. There is no Granger causality between securities market and economic growth. In the end, we give some policy advices so as to improve financial development and accelerate economic growth.",
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"abstract": "Two pattern recognition algorithms are proposed to detect two types of knots in lumber, lumped and surface knots, using an optical scanner. It is shown that lumped knots can be recognized by a log profile approach and surface knots can be detected by an image processing approach. A mathematical model for describing the geometry of the knots inside the log based on the surface parameters of the knots is presented. By a log breakdown strategy, the log can be cut into a maximum number of boards with prescribed dimensionalities. The mathematical knot model can be used to predict the locations, sizes, orientations, and shapes of the knots on these boards, whereby their lumber grades can be determined. Summing up the value yields of all the boards gives the value yield of the log. By computing all the possible value yields of the log from different log orientations, one can determine a maximum value yield of a log.<>",
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"abstract": "Recent advances in liquid chromatography-mass spectrometry (LC-MS) technology have led to newer approaches for measuring changes in peptide/protein abundances. Label-free LC-MS methods have been used for extraction of quantitative information and for detection of differentially abundant peptides/proteins. However, difference detection by analysis of data derived from label-free LC-MS methods requires various preprocessing steps including filtering, baseline correction, peak detection, alignment, and normalization, and transformation. Although several specialized tools have been developed to analyze LC-MS data, determining the most appropriate computational pipeline remains challenging partly due to lack of established gold standards. In this paper, we use a spike-in experiment to evaluate the performance of three software tools in accurately detecting changes in peptide abundances from LC-MS data obtained by a label-free LC-MS method. We observe that tools that incorporate peptide isotope cluster and multiple charge information lead to more accurate difference detection with fewer false positives.",
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"content": "Recent advances in liquid chromatography-mass spectrometry (LC-MS) technology have led to newer approaches for measuring changes in peptide/protein abundances. Label-free LC-MS methods have been used for extraction of quantitative information and for detection of differentially abundant peptides/proteins. However, difference detection by analysis of data derived from label-free LC-MS methods requires various preprocessing steps including filtering, baseline correction, peak detection, alignment, and normalization, and transformation. Although several specialized tools have been developed to analyze LC-MS data, determining the most appropriate computational pipeline remains challenging partly due to lack of established gold standards. In this paper, we use a spike-in experiment to evaluate the performance of three software tools in accurately detecting changes in peptide abundances from LC-MS data obtained by a label-free LC-MS method. We observe that tools that incorporate peptide isotope cluster and multiple charge information lead to more accurate difference detection with fewer false positives.",
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{
"proceeding": {
"id": "12OmNyRg4m8",
"title": "2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)",
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"groupId": "1001585",
"volume": "0",
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"year": "2010",
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"article": {
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"doi": "10.1109/BIBMW.2010.5703856",
"title": "A novel peak alignment method for LC-MS data analysis using cluster-based techniques",
"normalizedTitle": "A novel peak alignment method for LC-MS data analysis using cluster-based techniques",
"abstract": "Recently, liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technique for identifying differential abundance of peaks as biomarkers. Two major problems in the preprocessing of LC-MS data analysis are how to adjust and align multiple LC-MS datasets efficiently and correctly. Hence, an effective algorithm is needed to adjust the variation in retention time and align protein signals automatically. In this study, we proposed a novel algorithm, PeakAlign, based on a clustering technique for adjusting the shifted peaks and aligning the same protein signals from different samples. The PeakAlign algorithm consists of two phases, namely adjustment phase and alignment phase. In the adjustment phase, a LOESS regression method is used to adjust the shifting trend among peaks. In the alignment phase, a cluster-based technique is applied to align the adjusted peaks. For experimental evaluation, two different alignment approaches, SlidingWin algorithm and DTW algorithm, were implemented. Through analyzing the real LC-MS dataset, we demonstrate the usefulness of our proposed algorithm, PeakAlign, on the LC-MS-based samples.",
"abstracts": [
{
"abstractType": "Regular",
"content": "Recently, liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technique for identifying differential abundance of peaks as biomarkers. Two major problems in the preprocessing of LC-MS data analysis are how to adjust and align multiple LC-MS datasets efficiently and correctly. Hence, an effective algorithm is needed to adjust the variation in retention time and align protein signals automatically. In this study, we proposed a novel algorithm, PeakAlign, based on a clustering technique for adjusting the shifted peaks and aligning the same protein signals from different samples. The PeakAlign algorithm consists of two phases, namely adjustment phase and alignment phase. In the adjustment phase, a LOESS regression method is used to adjust the shifting trend among peaks. In the alignment phase, a cluster-based technique is applied to align the adjusted peaks. For experimental evaluation, two different alignment approaches, SlidingWin algorithm and DTW algorithm, were implemented. Through analyzing the real LC-MS dataset, we demonstrate the usefulness of our proposed algorithm, PeakAlign, on the LC-MS-based samples.",
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"normalizedAbstract": "Recently, liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technique for identifying differential abundance of peaks as biomarkers. Two major problems in the preprocessing of LC-MS data analysis are how to adjust and align multiple LC-MS datasets efficiently and correctly. Hence, an effective algorithm is needed to adjust the variation in retention time and align protein signals automatically. In this study, we proposed a novel algorithm, PeakAlign, based on a clustering technique for adjusting the shifted peaks and aligning the same protein signals from different samples. The PeakAlign algorithm consists of two phases, namely adjustment phase and alignment phase. In the adjustment phase, a LOESS regression method is used to adjust the shifting trend among peaks. In the alignment phase, a cluster-based technique is applied to align the adjusted peaks. For experimental evaluation, two different alignment approaches, SlidingWin algorithm and DTW algorithm, were implemented. Through analyzing the real LC-MS dataset, we demonstrate the usefulness of our proposed algorithm, PeakAlign, on the LC-MS-based samples.",
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"keywords": [
"Biological Techniques",
"Biology Computing",
"Chromatography",
"Mass Spectroscopic Chemical Analysis",
"Molecular Biophysics",
"Pattern Clustering",
"Proteins",
"Regression Analysis",
"Spectral Analysis",
"Peak Alignment Method",
"LC MS Data Analysis",
"Cluster Based Techniques",
"Liquid Chromatography Coupled Mass Spectrometry",
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"Biomarkers",
"LC MS Data Preprocessing",
"Retention Time Variation",
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"Peak Align Algorithm",
"Peak Align Adjustment Phase",
"Peak Align Alignment Phase",
"LOESS Regression Method",
"Sliding Win Algorithm",
"DTW Algorithm",
"Accuracy",
"Clustering Algorithms",
"Proteins",
"Algorithm Design And Analysis",
"Heuristic Algorithms",
"Mathematical Model",
"Equations"
],
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{
"affiliation": "Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan, R.O.C.",
"fullName": "Yu-Cheng Liu",
"givenName": "Yu-Cheng",
"surname": "Liu",
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{
"affiliation": "Institute of Information Science, Academia Sinica, Taiwan, R.O.C.",
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"surname": "Chen",
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},
{
"affiliation": "Institute of Medical Informatics, National Cheng Kung University, Taiwan, R.O.C.",
"fullName": "Hui-Yin Chang",
"givenName": "Hui-Yin",
"surname": "Chang",
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},
{
"affiliation": "Department of Environmental and Occupational Health, National Cheng Kung University, Taiwan, R.O.C.",
"fullName": "Hsin-Yi Wu",
"givenName": "Hsin-Yi",
"surname": "Wu",
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},
{
"affiliation": "Department of Environmental and Occupational Health, National Cheng Kung University, Taiwan, R.O.C.",
"fullName": "Pao-Chi Liao",
"givenName": "Pao-Chi",
"surname": "Liao",
"__typename": "ArticleAuthorType"
},
{
"affiliation": "Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan, R.O.C.",
"fullName": "Vincent S. Tseng",
"givenName": "Vincent S.",
"surname": "Tseng",
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{
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"doi": null,
"abstractUrl": "/proceedings-article/bibm/2010/05706589/12OmNwnH4U9",
"parentPublication": {
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{
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"parentPublication": {
"id": "proceedings/bibm/2011/1799/0",
"title": "2011 IEEE International Conference on Bioinformatics and Biomedicine",
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{
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"doi": null,
"abstractUrl": "/proceedings-article/bibm/2011/06120456/12OmNzaQoh9",
"parentPublication": {
"id": "proceedings/bibm/2011/1799/0",
"title": "2011 IEEE International Conference on Bioinformatics and Biomedicine",
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{
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"doi": null,
"abstractUrl": "/journal/tb/2013/02/ttb2013020494/13rRUwIF6cx",
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{
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{
"proceeding": {
"id": "12OmNzZmZqg",
"title": "2009 Fifth International Conference on Natural Computation",
"acronym": "icnc",
"groupId": "1001312",
"volume": "2",
"displayVolume": "0",
"year": "2009",
"__typename": "ProceedingType"
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"article": {
"id": "12OmNxcMSeQ",
"doi": "10.1109/ICNC.2009.420",
"title": "A Proteome Characteristic Pattern of Unstable Angina was Found by Two-Dimensional Difference Gel Electrophoresis and Least Angle Regression",
"normalizedTitle": "A Proteome Characteristic Pattern of Unstable Angina was Found by Two-Dimensional Difference Gel Electrophoresis and Least Angle Regression",
"abstract": "Unstable angina is now a severe burden on society and family in both industrialized and developing countries, but the traditional related factors can not explain the whole situations and the traditional “golden indicator” for the diagnosis meet many new challenges. The aim of this study was to analyze the proteome characteristic pattern of unstable angina. Plasma samples were obtained from twelve unstable angina patients and twelve healthy volunteers. A polyclonal antibody affinity column was used to remove the six most abundant proteins. Then, the two classes of samples were separated by Two-dimensional difference gel electrophoresis (2D-DIGE). The differentially expressed protein spots were selected and identified with matrix-assisted laser desorption /ionization time-of-flight mass spectrometry (MALDI-TOF-MS) or MS-MS. In the end, using least angle regression algorithm, we studied the proteome characteristic pattern of unstable angina. The result is that, there are significant difference between unstable angina patients and healthy volunteers. The twenty-four proteins made pattern gain by least angle regression could distinguish unstable angina patients from the healthy people and it is probably the proteome characteristic pattern of unstable angina. To have a conclusion, the twenty-four proteins made pattern maybe the proteome characteristic pattern of unstable angina.",
"abstracts": [
{
"abstractType": "Regular",
"content": "Unstable angina is now a severe burden on society and family in both industrialized and developing countries, but the traditional related factors can not explain the whole situations and the traditional “golden indicator” for the diagnosis meet many new challenges. The aim of this study was to analyze the proteome characteristic pattern of unstable angina. Plasma samples were obtained from twelve unstable angina patients and twelve healthy volunteers. A polyclonal antibody affinity column was used to remove the six most abundant proteins. Then, the two classes of samples were separated by Two-dimensional difference gel electrophoresis (2D-DIGE). The differentially expressed protein spots were selected and identified with matrix-assisted laser desorption /ionization time-of-flight mass spectrometry (MALDI-TOF-MS) or MS-MS. In the end, using least angle regression algorithm, we studied the proteome characteristic pattern of unstable angina. The result is that, there are significant difference between unstable angina patients and healthy volunteers. The twenty-four proteins made pattern gain by least angle regression could distinguish unstable angina patients from the healthy people and it is probably the proteome characteristic pattern of unstable angina. To have a conclusion, the twenty-four proteins made pattern maybe the proteome characteristic pattern of unstable angina.",
"__typename": "ArticleAbstractType"
}
],
"normalizedAbstract": "Unstable angina is now a severe burden on society and family in both industrialized and developing countries, but the traditional related factors can not explain the whole situations and the traditional “golden indicator” for the diagnosis meet many new challenges. The aim of this study was to analyze the proteome characteristic pattern of unstable angina. Plasma samples were obtained from twelve unstable angina patients and twelve healthy volunteers. A polyclonal antibody affinity column was used to remove the six most abundant proteins. Then, the two classes of samples were separated by Two-dimensional difference gel electrophoresis (2D-DIGE). The differentially expressed protein spots were selected and identified with matrix-assisted laser desorption /ionization time-of-flight mass spectrometry (MALDI-TOF-MS) or MS-MS. In the end, using least angle regression algorithm, we studied the proteome characteristic pattern of unstable angina. The result is that, there are significant difference between unstable angina patients and healthy volunteers. The twenty-four proteins made pattern gain by least angle regression could distinguish unstable angina patients from the healthy people and it is probably the proteome characteristic pattern of unstable angina. To have a conclusion, the twenty-four proteins made pattern maybe the proteome characteristic pattern of unstable angina.",
"fno": "3736b104",
"keywords": [
"Data Mining Least Angle Regression Characteristic Pattern Unstable Angina Plasma Two Dimensional Difference Gel Electrophoresis Proteomics"
],
"authors": [
{
"affiliation": null,
"fullName": "Huihui Zhao",
"givenName": "Huihui",
"surname": "Zhao",
"__typename": "ArticleAuthorType"
},
{
"affiliation": null,
"fullName": "Jianxin Chen",
"givenName": "Jianxin",
"surname": "Chen",
"__typename": "ArticleAuthorType"
},
{
"affiliation": null,
"fullName": "Na Hou",
"givenName": "Na",
"surname": "Hou",
"__typename": "ArticleAuthorType"
},
{
"affiliation": null,
"fullName": "Weidong Lu",
"givenName": "Weidong",
"surname": "Lu",
"__typename": "ArticleAuthorType"
},
{
"affiliation": null,
"fullName": "Wei Wang",
"givenName": "Wei",
"surname": "Wang",
"__typename": "ArticleAuthorType"
}
],
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"pubDate": "2009-08-01T00:00:00",
"pubType": "proceedings",
"pages": "104-108",
"year": "2009",
"issn": null,
"isbn": "978-0-7695-3736-8",
"notes": null,
"notesType": null,
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