snu-aidas/HVMap-dataset huggingface dataset:
Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort

MOTIVATION
Recent advances in high-throughput genotyping and brain imaging techniques enable new approaches to study the influence of genetic variation on brain structures and functions. Traditional association studies typically employ independent and pairwise univariate analysis, which treats single nucleotide polymorphisms (SNPs) and quantitative traits (QTs) as isolated units and ignores important underlying interacting relationships between the units. New methods are proposed here to overcome this limitation.


RESULTS
Taking into account the interlinked structure within and between SNPs and imaging QTs, we propose a novel Group-Sparse Multi-task Regression and Feature Selection (G-SMuRFS) method to identify quantitative trait loci for multiple disease-relevant QTs and apply it to a study in mild cognitive impairment and Alzheimer's disease. Built upon regression analysis, our model uses a new form of regularization, group ℓ(2,1)-norm (G(2,1)-norm), to incorporate the biological group structures among SNPs induced from their genetic arrangement. The new G(2,1)-norm considers the regression coefficients of all the SNPs in each group with respect to all the QTs together and enforces sparsity at the group level. In addition, an ℓ(2,1)-norm regularization is utilized to couple feature selection across multiple tasks to make use of the shared underlying mechanism among different brain regions. The effectiveness of the proposed method is demonstrated by both clearly improved prediction performance in empirical evaluations and a compact set of selected SNP predictors relevant to the imaging QTs.


AVAILABILITY
Software is publicly available at: http://ranger.uta.edu/%7eheng/imaging-genetics/.
A second generation computer forensic analysis system

The architecture of existing – first generation – computer forensic tools, including the widely used EnCase and FTK products, is rapidly becoming outdated. Tools are not keeping pace with increased complexity and data volumes of modern investigations. This paper discuses the limitations of first generation computer forensic tools. Several metrics for measuring the efficacy and performance of computer forensic tools are introduced. A set of requirements for second generation tools are proposed. A high-level design for a (work in progress) second generation computer forensic analysis system is presented. a 2009 Digital Forensic Research workshop. Published by Elsevier Ltd. All rights reserved.
Linear-Time Algorithms for Testing the Satisfiability of Propositional Horn Formulae

D New algorithms for deciding whether a (propositional) Horn formula is satisfiable are presented. If the Horn formula A contains K distinct propositional letters and if it is assumed that they are exactly Pi,. . . , PK, the two algorithms presented in this paper run in time O(N), where N is the total number of occurrences of literals in A. By representing a Horn proposition as a graph, the satisfiability problem can be formulated as a data flow problem, a certain type of pebbling. The difference between the two algorithms presented here is the strategy used for pebbling the graph. The first algorithm is based on the principle used for finding the set of nonterminals of a context-free grammar from which the empty string can be derived. The second algorithm is a graph traversal and uses a “call-by-need” strategy. This algorithm uses an attribute grammar to translate a propositional Horn formula to its corresponding graph in linear time. Our formulation of the satisfiability problem as a data flow problem appears to be new and suggests the possibility of improving efficiency using parallel processors. a
Protocol for developing ANN models and its application to the assessment of the quality of the ANN model development process in drinking water quality modelling

The application of Artificial Neural Networks (ANNs) in the field of environmental and water resources modelling has become increasingly popular since early 1990s. Despite the recognition of the need for a consistent approach to the development of ANN models and the importance of providing adequate details of the model development process, there is no systematic protocol for the development and documentation of ANN models. In order to address this shortcoming, such a protocol is introduced in this paper. In addition, the protocol is used to critically review the quality of the ANN model development and reporting processes employed in 81 journal papers since 2000 in which ANNs have been used for drinking water quality modelling. The results show that model architecture selection is the best implemented step, while greater focus should be given to input selection considering input independence and model validation considering replicative and structural validity. 2014 Elsevier Ltd. All rights reserved.
A Study on Knowledge , Perceptions and Attitudes about Screening and Diagnosis of Diabetes in Saudi Population

Introduction: Timely screening and treatment of diabetes can considerably reduce associated health adverse effects. The purpose of the study was to evaluate the knowledge about diabetes and perceptions and attitude about screening and early diagnosis of diabetes among the population. Methods: A cross-sectional questionnaire-based study conducted among non-diabetes adult people attending primary health care centers in Jeddah, Saudi Arabia. Participants’ knowledge about diabetes risk factors and complications and perceptions and attitude regarding screening and early diagnosis of diabetes was assessed and different scores were calculated. Results: Total 202 patients were included: mean (SD) age was 38.19 (13.25) years and 55.0% were females. Knowledge about diabetes risk factors and complications was 60.41%84.77% and 44.67%-67.51%, respectively, depending on the item. Perceptions about screening and early diagnosis showed that 81.19% believed that screening tests exist and 75.14% believed that it is possible to diagnose diabetes before complication stage; while 84.16% believed that early diagnosis increases treatment efficacy, decreases incidence of complications (83.66%), and allows early treatment (83.66%). Regarding attitude, 86.14% agreed to undergo diabetes screening if advised by the physician and 60.40% would do on their own initiative. Linear regression showed a positive correlation of attitude score with knowledge about diabetes risk factors (OR=1.87; p<0.0001) and complications (OR=1.46; p<0.0001); perception about feasibility of screening (OR=1.93; p<0.0001) and benefits of early diagnosis (OR=1.69; p<0.0001). Conclusions: The improvement of knowledge about diabetes risk factors and complications as well as the perception about feasibility and benefits of screening are prerequisites for the promotion of diabetes screening among the population.
Computational intelligence in sports: Challenges and opportunities within a new research domain

Computational intelligence is a branch of artificial intelligence that comprises algorithms inspired by nature. The common characteristics of all these algorithms is their collective intelligence and adaptability to a changing environment. Due to their efficiency and simplicity, these algorithms have been employed for problem solving across social and natural sciences. The aim of this paper is to demonstrate that nature-inspired algorithms are also useful within the domain of sport, in particular for obtaining safe and effective training plans targeting various aspects of performance. We outline the benefits and opportunities of applying computational intelligence in sports, and we also comment on the pitfalls and challenges for the future development of this emerging research domain. © 2015 Elsevier Inc. All rights reserved.
A novel end-to-end classifier using domain transferred deep convolutional neural networks for biomedical images

BACKGROUND AND OBJECTIVES
Highly accurate classification of biomedical images is an essential task in the clinical diagnosis of numerous medical diseases identified from those images. Traditional image classification methods combined with hand-crafted image feature descriptors and various classifiers are not able to effectively improve the accuracy rate and meet the high requirements of classification of biomedical images. The same also holds true for artificial neural network models directly trained with limited biomedical images used as training data or directly used as a black box to extract the deep features based on another distant dataset. In this study, we propose a highly reliable and accurate end-to-end classifier for all kinds of biomedical images via deep learning and transfer learning.


METHODS
We first apply domain transferred deep convolutional neural network for building a deep model; and then develop an overall deep learning architecture based on the raw pixels of original biomedical images using supervised training. In our model, we do not need the manual design of the feature space, seek an effective feature vector classifier or segment specific detection object and image patches, which are the main technological difficulties in the adoption of traditional image classification methods. Moreover, we do not need to be concerned with whether there are large training sets of annotated biomedical images, affordable parallel computing resources featuring GPUs or long times to wait for training a perfect deep model, which are the main problems to train deep neural networks for biomedical image classification as observed in recent works.


RESULTS
With the utilization of a simple data augmentation method and fast convergence speed, our algorithm can achieve the best accuracy rate and outstanding classification ability for biomedical images. We have evaluated our classifier on several well-known public biomedical datasets and compared it with several state-of-the-art approaches.


CONCLUSIONS
We propose a robust automated end-to-end classifier for biomedical images based on a domain transferred deep convolutional neural network model that shows a highly reliable and accurate performance which has been confirmed on several public biomedical image datasets.
Logarithmic regret algorithms for online convex optimization

In an online convex optimization problem a decision-maker makes a sequence of decisions, i.e., chooses a sequence of points in Euclidean space, from a fixed feasible set. After each point is chosen, it encounters a sequence of (possibly unrelated) convex cost functions. Zinkevich (ICML 2003) introduced this framework, which models many natural repeated decision-making problems and generalizes many existing problems such as Prediction from Expert Advice and Cover’s Universal Portfolios. Zinkevich showed that a simple online gradient descent algorithm achieves additive regret $O(\sqrt{T})$ , for an arbitrary sequence of T convex cost functions (of bounded gradients), with respect to the best single decision in hindsight. In this paper, we give algorithms that achieve regret O(log (T)) for an arbitrary sequence of strictly convex functions (with bounded first and second derivatives). This mirrors what has been done for the special cases of prediction from expert advice by Kivinen and Warmuth (EuroCOLT 1999), and Universal Portfolios by Cover (Math. Finance 1:1–19, 1991). We propose several algorithms achieving logarithmic regret, which besides being more general are also much more efficient to implement. The main new ideas give rise to an efficient algorithm based on the Newton method for optimization, a new tool in the field. Our analysis shows a surprising connection between the natural follow-the-leader approach and the Newton method. We also analyze other algorithms, which tie together several different previous approaches including follow-the-leader, exponential weighting, Cover’s algorithm and gradient descent.
Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

UNLABELLED
Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir


IMPORTANCE
Wine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional microbial biodiversity.
Deeper Inside PageRank

This paper serves as a companion or extension to the “Inside PageRank” paper by Bianchini et al. [19]. It is a comprehensive survey of all issues associated with PageRank, covering the basic PageRank model, available and recommended solution methods, storage issues, existence, uniqueness, and convergence properties, possible alterations to the basic model, suggested alternatives to the traditional solution methods, sensitivity and conditioning, and finally the updating problem. We introduce a few new results, provide an extensive reference list, and speculate about exciting areas of future research.
The somatic marker hypothesis: A critical evaluation

The somatic marker hypothesis (SMH; [Damasio, A. R., Tranel, D., Damasio, H., 1991. Somatic markers and the guidance of behaviour: theory and preliminary testing. In Levin, H.S., Eisenberg, H.M., Benton, A.L. (Eds.), Frontal Lobe Function and Dysfunction. Oxford University Press, New York, pp. 217-229]) proposes that emotion-based biasing signals arising from the body are integrated in higher brain regions, in particular the ventromedial prefrontal cortex (VMPFC), to regulate decision-making in situations of complexity. Evidence for the SMH is largely based on performance on the Iowa Gambling Task (IGT; [Bechara, A., Tranel, D., Damasio, H., Damasio, A.R., 1996. Failure to respond autonomically to anticipated future outcomes following damage to prefrontal cortex. Cerebral Cortex 6 (2), 215-225]), linking anticipatory skin conductance responses (SCRs) to successful performance on a decision-making paradigm in healthy participants. These 'marker' signals were absent in patients with VMPFC lesions and were associated with poorer IGT performance. The current article reviews the IGT findings, arguing that their interpretation is undermined by the cognitive penetrability of the reward/punishment schedule, ambiguity surrounding interpretation of the psychophysiological data, and a shortage of causal evidence linking peripheral feedback to IGT performance. Further, there are other well-specified and parsimonious explanations that can equally well account for the IGT data. Next, lesion, neuroimaging, and psychopharmacology data evaluating the proposed neural substrate underpinning the SMH are reviewed. Finally, conceptual reservations about the novelty, parsimony and specification of the SMH are raised. It is concluded that while presenting an elegant theory of how emotion influences decision-making, the SMH requires additional empirical support to remain tenable.
Distributed active transformer-a new power-combining andimpedance-transformation technique

In this paper, we compare the performance of the newly introduced distributed active transformer (DAT) structure to that of conventional on-chip impedance-transformations methods. Their fundamental power-efficiency limitations in the design of high-power fully integrated amplifiers in standard silicon process technologies are analyzed. The DAT is demonstrated to be an efficient impedance-transformation and power-combining method, which combines several low-voltage push-pull amplifiers in series by magnetic coupling. To demonstrate the validity of the new concept, a 2.4-GHz 1.9-W 2-V fully integrated power-amplifier achieving a power-added efficiency of 41% with 50input and output matching has been fabricated using 0.35-μm CMOS transistors Item Type: Article Additional Information: © Copyright 2002 IEEE. Reprinted with permission. Manuscript received May 27, 2001. [Posted online: 2002-08-07] This work was supported by the Intel Corporation, the Army Research Office, the Jet Propulsion Laboratory, Infinion, and the National Science Foundation. The authors thank Conexant Systems for chip fabrication, particularly R. Magoon, F. In’tveld, J. Powell, A. Vo, and K. Moye. K. Potter, D. Ham, and H.Wu, all of the California Institute of Technology (Caltech), Pasadena, deserve special thanks for their assistance. The technical support for CAD tools from Agilent Technologies and Sonnet Software Inc., Liverpool, NY, are also appreciated. “Special Issue on Silicon-Based RF and Microwave Integrated Circuits”, IEEE Transactions on Microwave Theory and Techniques, vol. 50, no. 1, part 2 Subject
Facilitating Object Detection and Recognition through Eye Gaze

When compared to image recognition, object detection is a much more challenging task because it requires the accurate real-time localization of an object in the target image. In interaction scenarios, this pipeline can be simplified by incorporating the users’ point of regard. Wearable eye trackers can estimate the gaze direction, but lack own processing capabilities. We enable mobile gaze-aware applications by developing an open-source platform which supports mobile eye tracking based on the Pupil headset and a smartphone running Android OS. Through our platform, we offer researchers and developers a rapid prototyping environment for gaze-enabled applications. We describe the concept, our current progress, and research implications. ACM Classification
A Framework for Dynamic Image Sampling Based on Supervised Learning

Sparse sampling schemes can broadly be classified into two main categories: static sampling where the sampling pattern is predetermined, and dynamic sampling where each new measurement location is selected based on information obtained from previous measurements. Dynamic sampling methods are particularly appropriate for pointwise imaging methods, in which pixels are measured sequentially in arbitrary order. Examples of pointwise imaging schemes include certain implementations of atomic force microscopy, electron back scatter diffraction, and synchrotron X-ray imaging. In these pointwise imaging applications, dynamic sparse sampling methods have the potential to dramatically reduce the number of measurements required to achieve a desired level of fidelity. However, the existing dynamic sampling methods tend to be computationally expensive and are, therefore, too slow for many practical applications. In this paper, we present a framework for dynamic sampling based on machine learning techniques, which we call a supervised learning approach for dynamic sampling (SLADS). In each step of SLADS, the objective is to find the pixel that maximizes the expected reduction in distortion (ERD) given previous measurements. SLADS is fast because we use a simple regression function to compute the ERD, and it is accurate because the regression function is trained using datasets that are representative of the specific application. In addition, we introduce an approximate method to terminate dynamic sampling at a desired level of distortion. We then extend our algorithm to incorporate multiple measurements at each step, which we call groupwise SLADS. Finally, we present results on computationally generated synthetic data and experimentally collected data to demonstrate a dramatic improvement over state-of-the-art static sampling methods
Rationalizing Neural Predictions

Prediction without justification has limited applicability. As a remedy, we learn to extract pieces of input text as justifications – rationales – that are tailored to be short and coherent, yet sufficient for making the same prediction. Our approach combines two modular components, generator and encoder, which are trained to operate well together. The generator specifies a distribution over text fragments as candidate rationales and these are passed through the encoder for prediction. Rationales are never given during training. Instead, the model is regularized by desiderata for rationales. We evaluate the approach on multi-aspect sentiment analysis against manually annotated test cases. Our approach outperforms attention-based baseline by a significant margin. We also successfully illustrate the method on the question retrieval task.1
Maintaining Integrity: How Nurses Navigate Boundaries in Pediatric Palliative Care.

PURPOSE
To explore how nurses manage personal and professional boundaries in caring for seriously ill children and their families.


DESIGN AND METHODS
Using a constructivist grounded theory approach, a convenience sample of 18 registered nurses from four practice sites was interviewed using a semi-structured interview guide.


RESULTS
Nurses across the sites engaged in a process of maintaining integrity whereby they integrated two competing, yet essential, aspects of their nursing role - behaving professionally and connecting personally. When skillful in both aspects, nurses were satisfied that they provided high-quality, family-centered care to children and families within a clearly defined therapeutic relationship. At times, tension existed between these two aspects and nurses attempted to mitigate the tension. Unsuccessful mitigation attempts led to compromised integrity characterized by specific behavioral and emotional indicators. Successfully mitigating the tension with strategies that prioritized their own needs and healing, nurses eventually restored integrity. Maintaining integrity involved a continuous effort to preserve completeness of both oneself and one's nursing practice.


CONCLUSIONS
Study findings provide a theoretical conceptualization to describe the process nurses use in navigating boundaries and contribute to an understanding for how this specialized area of care impacts health care providers.


PRACTICE IMPLICATIONS
Work environments can better address the challenges of navigating boundaries through offering resources and support for nurses' emotional responses to caring for seriously ill children. Future research can further refine and expand the theoretical conceptualization of maintaining integrity presented in this paper and its potential applicability to other nursing specialties.