Event trigger identification for biomedical events extraction using domain knowledge

Motivation: In molecular biology, molecular events describe observable alterations of biomolecules, such as binding of proteins or RNA production. These events might be responsible for drug reactions or development of certain diseases. As such, biomedical event extraction, the process of automatically detecting description of molecular interactions in research articles, attracted substantial research interest recently. Event trigger identification, detecting the words describing the event types, is a crucial and prerequisite step in the pipeline process of biomedical event extraction. Taking the event types as classes, event trigger identification can be viewed as a classification task. For each word in a sentence, a trained classifier predicts whether the word corresponds to an event type and which event type based on the context features. Therefore, a well-designed feature set with a good level of discrimination and generalization is crucial for the performance of event trigger identification. Results: In this article, we propose a novel framework for event trigger identification. In particular, we learn biomedical domain knowledge from a large text corpus built from Medline and embed it into word features using neural language modeling. The embedded features are then combined with the syntactic and semantic context features using the multiple kernel learning method. The combined feature set is used for training the event trigger classifier. Experimental results on the golden standard corpus show that >2.5% improvement on F-score is achieved by the proposed framework when compared with the state-of-the-art approach, demonstrating the effectiveness of the proposed framework. © 2014 The Author 2014. The source code for the proposed framework is freely available and can be downloaded at http://cse.seu.edu.cn/people/zhoudeyu/ETI_Sourcecode.zip.

Model of Active Structural Monitoring and Decision-making for Dynamic Identification of Buildings, Monuments and Engineering Facilities

Structural monitoring and dynamic identification of the manmade and natural hazard objects is under consideration. Math model of testing object by set of weak stationary dynamic actions is offered. The response of structures to the set of signals is under processing for getting important information about object condition in high frequency band. Making decision procedure into active monitoring system is discussed as well. As an example the monitoring outcome of pillar-type monument is given.

Oculo-visual changes and clinical considerations affecting older patients with dementia

Purpose: Dementia is associated with various alterations of the eye and visual function. Over 60% of cases are attributable to Alzheimer's disease, a significant proportion of the remainder to vascular dementia or dementia with Lewy bodies, while frontotemporal dementia, and Parkinson's disease dementia are less common. This review describes the oculo-visual problems of these five dementias and the pathological changes which may explain these symptoms. It further discusses clinical considerations to help the clinician care for older patients affected by dementia. Recent findings: Visual problems in dementia include loss of visual acuity, defects in colour vision and visual masking tests, changes in pupillary response to mydriatics, defects in fixation and smooth and saccadic eye movements, changes in contrast sensitivity function and visual evoked potentials, and disturbance of complex visual functions such as in reading ability, visuospatial function, and the naming and identification of objects. Pathological changes have also been reported affecting the crystalline lens, retina, optic nerve, and visual cortex. Clinically, issues such as cataract surgery, correcting the refractive error, quality of life, falls, visual impairment and eye care for dementia have been addressed. Summary: Many visual changes occur across dementias, are controversial, often based on limited patient numbers, and no single feature can be regarded as diagnostic of any specific dementia. Nevertheless, visual hallucinations may be more characteristic of dementia with Lewy bodies and Parkinson's disease dementia than Alzheimer's disease or frontotemporal dementia. Differences in saccadic eye movement dysfunction may also help to distinguish Alzheimer's disease from frontotemporal dementia and Parkinson's disease dementia from dementia with Lewy bodies. Eye care professionals need to keep informed of the growing literature in vision/dementia, be attentive to signs and symptoms suggestive of cognitive impairment, and be able to adapt their practice and clinical interventions to best serve patients with dementia.

Multiple Dipole Source Models for Scalp-Recorded Event-Related Potentials: Example from Complex Visual Processing in the Human Brain

2000 Mathematics Subject Classification: 62P10, 92C20

The visual cortex in alzheimer's disease:laminar distribution of the pathological changes in visual areas V1 and V2

Alzheimer's disease (AD) is an important neurodegenerative disorder causing visual problems in the elderly population. The pathology of AD includes the deposition in the brain of abnormal aggregates of β-amyloid (Aβ) in the form of senile plaques (SP) and abnormally phosphorylated tau in the form of neurofibrillary tangles (NFT). A variety of visual problems have been reported in patients with AD including loss of visual acuity (VA), colour vision and visual fields; changes in pupillary responses to mydriatics, defects in fixation and in smooth and saccadic eye movements; changes in contrast sensitivity and in visual evoked potentials (VEP); and disturbances in complex visual tasks such as reading, visuospatial function, and in the naming and identification of objects. In addition, pathological changes have been observed to affect the eye, visual pathway, and visual cortex in AD. To better understand degeneration of the visual cortex in AD, the laminar distribution of the SP and NFT was studied in visual areas V1 and V2 in 18 cases of AD which varied in disease onset and duration. In area V1, the mean density of SP and NFT reached a maximum in lamina III and in laminae II and III respectively. In V2, mean SP density was maximal in laminae III and IV and NFT density in laminae II and III. The densities of SP in laminae I of V1 and NFT in lamina IV of V2 were negatively correlated with patient age. No significant correlations were observed in any cortical lamina between the density of NFT and disease onset or duration. However, in area V2, the densities of SP in lamina II and lamina V were negatively correlated with disease duration and disease onset respectively. In addition, there were several positive correlations between the densities of SP and NFT in V1 with those in area V2. The data suggest: (1) NFT pathology is greater in area V2 than V1, (2) laminae II/III of V1 and V2 are most affected by the pathology, (3) the formation of SP and NFT in V1 and V2 are interconnected, and (4) the pathology may spread between visual areas via the feed-forward short cortico-cortical connections. © 2012 by Nova Science Publishers, Inc. All rights reserved.

Developmental dissociation of analytical and holistic object recognition in adolescence

Previous research (e.g., Jüttner et al, 2013, Developmental Psychology, 49, 161-176) has shown that object recognition may develop well into late childhood and adolescence. The present study extends that research and reveals novel di erences in holistic and analytic recognition performance in 7-11 year olds compared to that seen in adults. We interpret our data within Hummel’s hybrid model of object recognition (Hummel, 2001, Visual Cognition, 8, 489-517) that proposes two parallel routes for recognition (analytic vs. holistic) modulated by attention. Using a repetition-priming paradigm, we found in Experiment 1 that children showed no holistic priming, but only analytic priming. Given that holistic priming might be thought to be more ‘primitive’, we confirmed in Experiment 2 that our surprising finding was not because children’s analytic recognition was merely a result of name repetition. Our results suggest a developmental primacy of analytic object recognition. By contrast, holistic object recognition skills appear to emerge with a much more protracted trajectory extending into late adolescence

The value of tablets as reading aids for individuals with central visual field loss:an evaluation of eccentric reading with static and scrolling text

Purpose: Technological devices such as smartphones and tablets are widely available and increasingly used as visual aids. This study evaluated the use of a novel app for tablets (MD_evReader) developed as a reading aid for individuals with a central field loss resulting from macular degeneration. The MD_evReader app scrolls text as single lines (similar to a news ticker) and is intended to enhance reading performance using the eccentric viewing technique by both reducing the demands on the eye movement system and minimising the deleterious effects of perceptual crowding. Reading performance with scrolling text was compared with reading static sentences, also presented on a tablet computer. Methods: Twenty-six people with low vision (diagnosis of macular degeneration) read static or dynamic text (scrolled from right to left), presented as a single line at high contrast on a tablet device. Reading error rates and comprehension were recorded for both text formats, and the participant’s subjective experience of reading with the app was assessed using a simple questionnaire. Results: The average reading speed for static and dynamic text was not significantly different and equal to or greater than 85 words per minute. The comprehension scores for both text formats were also similar, equal to approximately 95% correct. However, reading error rates were significantly (p=0.02) less for dynamic text than for static text. The participants’ questionnaire ratings of their reading experience with the MD_evReader were highly positive and indicated a preference for reading with this app compared with their usual method. Conclusions: Our data show that reading performance with scrolling text is at least equal to that achieved with static text and in some respects (reading error rate) is better than static text. Bespoke apps informed by an understanding of the underlying sensorimotor processes involved in a cognitive task such as reading have excellent potential as aids for people with visual impairments.

How do practitioners understand? Practitioner perceptions of an object-oriented programming.

In the computer science community, there is considerable debate about the appropriate sequence for introducing object-oriented concepts to novice programmers. Research into novice programming has struggled to identify the critical aspects that would provide a consistently successful approach to teaching introductory object-oriented programming. Starting from the premise that the conceptions of a task determine the type of output from the task, assisting novice programmers to become aware of what the required output should be, may lay a foundation for improving learning. This study adopted a phenomenographic approach. Thirty one practitioners were interviewed about the ways in which they experience object-oriented programming and categories of description and critical aspects were identified. These critical aspects were then used to examine the spaces of learning provided in twenty introductory textbooks. The study uncovered critical aspects that related to the way that practitioners expressed their understanding of an object-oriented program and the influences on their approach to designing programs. The study of the textbooks revealed a large variability in the cover of these critical aspects.

Neural activity during object perception in schizophrenia patients is associated with illness duration and affective symptoms

Background - Abnormalities in visual processes have been observed in schizophrenia patients and have been associated with alteration of the lateral occipital complex and visual cortex. However, the relationship of these abnormalities with clinical symptomatology is largely unknown. Methods - We investigated the brain activity associated with object perception in schizophrenia. Pictures of common objects were presented to 26 healthy participants (age = 36.9; 11 females) and 20 schizophrenia patients (age = 39.9; 8 females) in an fMRI study. Results - In the healthy sample the presentation of pictures yielded significant activation (pFWE (cluster) < 0.001) of the bilateral fusiform gyrus, bilateral lingual gyrus, and bilateral middle occipital gyrus. In patients, the bilateral fusiform gyrus and bilateral lingual gyrus were significantly activated (pFWE (cluster) < 0.001), but not so the middle occipital gyrus. However, significant bilateral activation of the middle occipital gyrus (pFWE (cluster) < 0.05) was revealed when illness duration was controlled for. Depression was significantly associated with increased activation, and anxiety with decreased activation, of the right middle occipital gyrus and several other brain areas in the patient group. No association with positive or negative symptoms was revealed. Conclusions - Illness duration accounts for the weak activation of the middle occipital gyrus in patients during picture presentation. Affective symptoms, but not positive or negative symptoms, influence the activation of the right middle occipital gyrus and other brain areas.

A multimedia indexing and retrieval framework for multimedia database systems

The main challenges of multimedia data retrieval lie in the effective mapping between low-level features and high-level concepts, and in the individual users' subjective perceptions of multimedia content. ^ The objectives of this dissertation are to develop an integrated multimedia indexing and retrieval framework with the aim to bridge the gap between semantic concepts and low-level features. To achieve this goal, a set of core techniques have been developed, including image segmentation, content-based image retrieval, object tracking, video indexing, and video event detection. These core techniques are integrated in a systematic way to enable the semantic search for images/videos, and can be tailored to solve the problems in other multimedia related domains. In image retrieval, two new methods of bridging the semantic gap are proposed: (1) for general content-based image retrieval, a stochastic mechanism is utilized to enable the long-term learning of high-level concepts from a set of training data, such as user access frequencies and access patterns of images. (2) In addition to whole-image retrieval, a novel multiple instance learning framework is proposed for object-based image retrieval, by which a user is allowed to more effectively search for images that contain multiple objects of interest. An enhanced image segmentation algorithm is developed to extract the object information from images. This segmentation algorithm is further used in video indexing and retrieval, by which a robust video shot/scene segmentation method is developed based on low-level visual feature comparison, object tracking, and audio analysis. Based on shot boundaries, a novel data mining framework is further proposed to detect events in soccer videos, while fully utilizing the multi-modality features and object information obtained through video shot/scene detection. ^ Another contribution of this dissertation is the potential of the above techniques to be tailored and applied to other multimedia applications. This is demonstrated by their utilization in traffic video surveillance applications. The enhanced image segmentation algorithm, coupled with an adaptive background learning algorithm, improves the performance of vehicle identification. A sophisticated object tracking algorithm is proposed to track individual vehicles, while the spatial and temporal relationships of vehicle objects are modeled by an abstract semantic model. ^

Adaptive software fault prediction approach using object-oriented metrics

As users continually request additional functionality, software systems will continue to grow in their complexity, as well as in their susceptibility to failures. Particularly for sensitive systems requiring higher levels of reliability, faulty system modules may increase development and maintenance cost. Hence, identifying them early would support the development of reliable systems through improved scheduling and quality control. Research effort to predict software modules likely to contain faults, as a consequence, has been substantial. Although a wide range of fault prediction models have been proposed, we remain far from having reliable tools that can be widely applied to real industrial systems. For projects with known fault histories, numerous research studies show that statistical models can provide reasonable estimates at predicting faulty modules using software metrics. However, as context-specific metrics differ from project to project, the task of predicting across projects is difficult to achieve. Prediction models obtained from one project experience are ineffective in their ability to predict fault-prone modules when applied to other projects. Hence, taking full benefit of the existing work in software development community has been substantially limited. As a step towards solving this problem, in this dissertation we propose a fault prediction approach that exploits existing prediction models, adapting them to improve their ability to predict faulty system modules across different software projects.

A theoretical analysis of eyewitness identification: Dual -process theory, signal detection theory and eyewitness confidence

Given the growing number of wrongful convictions involving faulty eyewitness evidence and the strong reliance by jurors on eyewitness testimony, researchers have sought to develop safeguards to decrease erroneous identifications. While decades of eyewitness research have led to numerous recommendations for the collection of eyewitness evidence, less is known regarding the psychological processes that govern identification responses. The purpose of the current research was to expand the theoretical knowledge of eyewitness identification decisions by exploring two separate memory theories: signal detection theory and dual-process theory. This was accomplished by examining both system and estimator variables in the context of a novel lineup recognition paradigm. Both theories were also examined in conjunction with confidence to determine whether it might add significantly to the understanding of eyewitness memory. ^ In two separate experiments, both an encoding and a retrieval-based manipulation were chosen to examine the application of theory to eyewitness identification decisions. Dual-process estimates were measured through the use of remember-know judgments (Gardiner & Richardson-Klavehn, 2000). In Experiment 1, the effects of divided attention and lineup presentation format (simultaneous vs. sequential) were examined. In Experiment 2, perceptual distance and lineup response deadline were examined. Overall, the results indicated that discrimination and remember judgments (recollection) were generally affected by variations in encoding quality and response criterion and know judgments (familiarity) were generally affected by variations in retrieval options. Specifically, as encoding quality improved, discrimination ability and judgments of recollection increased; and as the retrieval task became more difficult there was a shift toward lenient choosing and more reliance on familiarity. ^ The application of signal detection theory and dual-process theory in the current experiments produced predictable results on both system and estimator variables. These theories were also compared to measures of general confidence, calibration, and diagnosticity. The application of the additional confidence measures in conjunction with signal detection theory and dual-process theory gave a more in-depth explanation than either theory alone. Therefore, the general conclusion is that eyewitness identifications can be understood in a more complete manor by applying theory and examining confidence. Future directions and policy implications are discussed. ^

Using sonic enhancement to augment non-visual tabular navigation

More information is now readily available to computer users than at any time in human history; however, much of this information is often inaccessible to people with blindness or low-vision, for whom information must be presented non-visually. Currently, screen readers are able to verbalize on-screen text using text-to-speech (TTS) synthesis; however, much of this vocalization is inadequate for browsing the Internet. An auditory interface that incorporates auditory-spatial orientation was created and tested. For information that can be structured as a two-dimensional table, links can be semantically grouped as cells in a row within an auditory table, which provides a consistent structure for auditory navigation. An auditory display prototype was tested.^ Sixteen legally blind subjects participated in this research study. Results demonstrated that stereo panning was an effective technique for audio-spatially orienting non-visual navigation in a five-row, six-column HTML table as compared to a centered, stationary synthesized voice. These results were based on measuring the time- to-target (TTT), or the amount of time elapsed from the first prompting to the selection of each tabular link. Preliminary analysis of the TTT values recorded during the experiment showed that the populations did not conform to the ANOVA requirements of normality and equality of variances. Therefore, the data were transformed using the natural logarithm. The repeated-measures two-factor ANOVA results show that the logarithmically-transformed TTTs were significantly affected by the tonal variation method, F(1,15) = 6.194, p= 0.025. Similarly, the results show that the logarithmically transformed TTTs were marginally affected by the stereo spatialization method, F(1,15) = 4.240, p=0.057. The results show that the logarithmically transformed TTTs were not significantly affected by the interaction of both methods, F(1,15) = 1.381, p=0.258. These results suggest that some confusion may be caused in the subject when employing both of these methods simultaneously. The significant effect of tonal variation indicates that the effect is actually increasing the average TTT. In other words, the presence of preceding tones increases task completion time on average. The marginally-significant effect of stereo spatialization decreases the average log(TTT) from 2.405 to 2.264.^

Waveguide microgripper for identification, sensing and manipulation

A Waveguide Microgripper utilizes flexible optical waveguides as gripping arms, which provide the physical means for grasping a microobject, while simultaneously enabling light to be delivered and collected. This unique capability allows extensive optical characterization of the structure being held such as transmission, reflection or fluorescence. One of the simplest capabilities of the waveguide microgripper is to be able to detect the presence of a microobject between the microgripper facets by monitoring the transmitted intensity of light coupled through the facets. The intensity of coupled light is expected to drop when there is an object obstructing the path of light. The optical sensing and characterization function of the microgripper is a strong function of the optical power incident on the structure of interest. Hence it is important to understand the factors affecting the power distribution across the facet. The microgripper is also capable of detecting the fluorescence. This capability of microgripper is expected to have applications in medical, bio-medical and related fields.

A ROS-based Workspace Control and Trajectory Planner for a seven degrees of freedom Robotic arm

In this Bachelor Thesis I want to provide readers with tools and scripts for the control of a 7DOF manipulator, backed up by some theory of Robotics and Computer Science, in order to better contextualize the work done. In practice, we will see most common software, and developing environments, used to cope with our task: these include ROS, along with visual simulation by VREP and RVIZ, and an almost "stand-alone" ROS extension called MoveIt!, a very complete programming interface for trajectory planning and obstacle avoidance. As we will better appreciate and understand in the introduction chapter, the capability of detecting collision objects through a camera sensor, and re-plan to the desired end-effector pose, are not enough. In fact, this work is implemented in a more complex system, where recognition of particular objects is needed. Through a package of ROS and customized scripts, a detailed procedure will be provided on how to distinguish a particular object, retrieve its reference frame with respect to a known one, and then allow navigation to that target. Together with technical details, the aim is also to report working scripts and a specific appendix (A) you can refer to, if desiring to put things together.