nils-herrmann/clean_scirepeval huggingface dataset:
The practical impact of ontologies on biomedical informatics.

To examine recent research work in the development and evaluation of controlled biomedical terminologies - especially, the representation of structured, controlled definitional knowledge about the terms themselves; such terminologies are often referred to as 'ontologies'.



A review of the published literature using PubMed, as well as full-text searches of recent Medinfo and American Medical Informatics Association (AMIA) Symposia proceedings, searching for the terms 'ontology' and 'ontologies' and for articles discussing specific, prominent ontological work.



We summaries the ontologic aspects of twelve current terminology projects: Galen, the Unified Medical Language System (UMLS), the Medical Entities Dictionary (MED), SNOMED-CT, LOINC, the Foundational Model of Anatomy (FMA), the Gene Ontology (GO), ISO Reference Terminology Model for Nursing Diagnosis, NDF-RT, RxNorm, the NCI Thesaurus, and DOLCE+. We discuss the origins, domain, and ontologic representation of each of these and attempt to summarize the impact that each has had on terminologic work and biomedical applications. We also note the contributions of the Protégé tool to many of these efforts.



Terminologic research and development have advanced significantly in the past 20 years, especially since the recent orientation toward controlled biomedical ontologies. This work has had significant impact on the development of terminologies themselves, their acceptance and dissemination as standards, and their use in supporting biomedical information systems.
Autonomous UAV Navigation Using Reinforcement Learning

Unmanned aerial vehicles (UAV) are commonly used for missions in unknown environments, where an exact mathematical model of the environment may not be available. This paper provides a framework for using reinforcement learning to allow the UAV to navigate successfully in such environments. We conducted our simulation and real implementation to show how the UAVs can successfully learn to navigate through an unknown environment. Technical aspects regarding to applying reinforcement learning algorithm to a UAV system and UAV flight control were also addressed. This will enable continuing research using a UAV with learning capabilities in more important applications, such as wildfire monitoring, or search and rescue missions.
Plant Species Identification Using Computer Vision Techniques: A Systematic Literature Review

Species knowledge is essential for protecting biodiversity. The identification of plants by conventional keys is complex, time consuming, and due to the use of specific botanical terms frustrating for non-experts. This creates a hard to overcome hurdle for novices interested in acquiring species knowledge. Today, there is an increasing interest in automating the process of species identification. The availability and ubiquity of relevant technologies, such as, digital cameras and mobile devices, the remote access to databases, new techniques in image processing and pattern recognition let the idea of automated species identification become reality. This paper is the first systematic literature review with the aim of a thorough analysis and comparison of primary studies on computer vision approaches for plant species identification. We identified 120 peer-reviewed studies, selected through a multi-stage process, published in the last 10 years (2005-2015). After a careful analysis of these studies, we describe the applied methods categorized according to the studied plant organ, and the studied features, i.e., shape, texture, color, margin, and vein structure. Furthermore, we compare methods based on classification accuracy achieved on publicly available datasets. Our results are relevant to researches in ecology as well as computer vision for their ongoing research. The systematic and concise overview will also be helpful for beginners in those research fields, as they can use the comparable analyses of applied methods as a guide in this complex activity.
Development of An Android Application for Object Detection Based on Color, Shape, or Local Features

Object detection and recognition is an important task in many computer vision applications. In this paper an Android application was developed using Eclipse IDE and OpenCV3 Library. This application is able to detect objects in an image that is loaded from the mobile gallery, based on its color, shape, or local features. The image is processed in the HSV color domain for better color detection. Circular shapes are detected using Circular Hough Transform and other shapes are detected using Douglas-Peucker algorithm. BRISK (binary robust invariant scalable keypoints) local features were applied in the developed Android application for matching an object image in another scene image. The steps of the proposed detection algorithms are described, and the interfaces of the application are illustrated. The application is ported and tested on Galaxy S3, S6, and Note1 Smartphones. Based on the experimental results, the application is capable of detecting eleven different colors, detecting two dimensional geometrical shapes including circles, rectangles, triangles, and squares, and correctly match local features of object and scene images for different conditions. The application could be used as a standalone application, or as a part of another application such as Robot systems, traffic systems, e-learning applications, information retrieval and many others.
A Gentle Introduction to Bayesian Analysis: Applications to Developmental Research

Bayesian statistical methods are becoming ever more popular in applied and fundamental research. In this study a gentle introduction to Bayesian analysis is provided. It is shown under what circumstances it is attractive to use Bayesian estimation, and how to interpret properly the results. First, the ingredients underlying Bayesian methods are introduced using a simplified example. Thereafter, the advantages and pitfalls of the specification of prior knowledge are discussed. To illustrate Bayesian methods explained in this study, in a second example a series of studies that examine the theoretical framework of dynamic interactionism are considered. In the Discussion the advantages and disadvantages of using Bayesian statistics are reviewed, and guidelines on how to report on Bayesian statistics are provided.
Theoretical perspectives in medical education: past experience and future possibilities.

Pedagogical practices reflect theoretical perspectives and beliefs that people hold about learning. Perspectives on learning are important because they influence almost all decisions about curriculum, teaching and assessment. Since Flexner's 1910 report on medical education, significant changes in perspective have been evident. Yet calls for major reform of medical education may require a broader conceptualisation of the educational process.


PAST AND CURRENT PERSPECTIVES
Medical education has emerged as a complex transformative process of socialisation into the culture and profession of medicine. Theory and research, in medical education and other fields, have contributed important understanding. Learning theories arising from behaviourist, cognitivist, humanist and social learning traditions have guided improvements in curriculum design and instruction, understanding of memory, expertise and clinical decision making, and self-directed learning approaches. Although these remain useful, additional perspectives which recognise the complexity of education that effectively fosters the development of knowledge, skills and professional identity are needed.


FUTURE PERSPECTIVES
Socio-cultural learning theories, particularly situated learning, and communities of practice offer a useful theoretical perspective. They view learning as intimately tied to context and occurring through participation and active engagement in the activities of the community. Legitimate peripheral participation describes learners' entry into the community. As learners gain skill, they assume more responsibility and move more centrally. The community, and the people and artefacts within it, are all resources for learning. Learning is both collective and individual. Social cognitive theory offers a complementary perspective on individual learning. Situated learning allows the incorporation of other learning perspectives and includes workplace learning and experiential learning. Viewing medical education through the lens of situated learning suggests teaching and learning approaches that maximise participation and build on community processes to enhance both collective and individual learning.
An Integrated MEMS Gyroscope Array with Higher Accuracy Output

In this paper, an integrated MEMS gyroscope array method composed of two levels of optimal filtering was designed to improve the accuracy of gyroscopes. In the firstlevel filtering, several identical gyroscopes were combined through Kalman filtering into a single effective device, whose performance could surpass that of any individual sensor. The key of the performance improving lies in the optimal estimation of the random noise sources such as rate random walk and angular random walk for compensating the measurement values. Especially, the cross correlation between the noises from different gyroscopes of the same type was used to establish the system noise covariance matrix and the measurement noise covariance matrix for Kalman filtering to improve the performance further. Secondly, an integrated Kalman filter with six states was designed to further improve the accuracy with the aid of external sensors such as magnetometers and accelerometers in attitude determination. Experiments showed that three gyroscopes with a bias drift of 35 degree per hour could be combined into a virtual gyroscope with a drift of 1.07 degree per hour through the first-level filter, and the bias drift was reduced to 0.53 degree per hour after the second-level filtering. It proved that the proposed integrated MEMS gyroscope array is capable of improving the accuracy of the MEMS gyroscopes, which provides the possibility of using these low cost MEMS sensors in high-accuracy application areas.
A methodology for estimating the value of privacy in information disclosure systems

In many types of information systems, users face an implicit tradeoff between disclosing personal information and receiving benefits, such as discounts by an electronic commerce service that requires users to divulge some personal information. While these benefits are relatively measurable, the value of privacy involved in disclosing the information is much less tangible, making it hard to design and evaluate information systems that manage personal information. Meanwhile, existing methods to assess and measure the value of privacy, such as self-reported questionnaires, are notoriously unrelated of real eworld behavior. To overcome this obstacle, we propose a methodology called VOPE (Value of Privacy Estimator), which relies on behavioral economics' Prospect Theory (Kahneman & Tversky, 1979) and valuates people's privacy preferences in information disclosure scenarios. VOPE is based on an iterative and responsive methodology in which users take or leave a transaction that includes a component of information disclosure. To evaluate the method, we conduct an empirical experiment (n 1⁄4 195), estimating people's privacy valuations in electronic commerce transactions. We report on the convergence of estimations and validate our results by comparing the values to theoretical projections of existing results (Tsai, Egelman, Cranor, & Acquisti, 2011), and to another independent experiment that required participants to rank the sensitivity of information disclosure transactions. Finally, we discuss how information systems designers and regulators can use VOPE to create and to oversee systems that balance privacy and utility.
Analyzing topic evolution in bioinformatics: investigation of dynamics of the field with conference data in DBLP

In this paper we analyze topic evolution over time within bioinformatics to uncover the underlying dynamics of that field, focusing on the recent developments in the 2000s. We select 33 bioinformatics related conferences indexed in DBLP from 2000 to 2011. The major reason for choosing DBLP as the data source instead of PubMed is that DBLP retains most bioinformatics related conferences, and to study dynamics of the field, conference papers are more suitable than journal papers. We divide a period of a dozen years into four periods: period 1 (2000–2002), period 2 (2003–2005), period 3 (2006–2008) and period 4 (2009–2011). To conduct topic evolution analysis, we employ three major procedures, and for each procedure, we develop the following novel technique: the Markov Random Field-based topic clustering, automatic cluster labeling, and topic similarity based on Within-Period Cluster Similarity and Between-Period Cluster Similarity. The experimental results show that there are distinct topic transition patterns between different time periods. From period 1 to period 3, new topics seem to have emerged and expanded, whereas from period 3 to period 4, topics are merged and display more rigorous interaction with each other. This trend is confirmed by the collaboration pattern over time.
Face Expression Recognition and Analysis: The State of the Art

The automatic recognition of facial expressions has been an active research topic since the early nineties. There have been several advances in the past few years in terms of face detection and tracking, feature extraction mechanisms and the techniques used for expression classification. This paper surveys some of the published work since 2001 till date. The paper presents a time-line view of the advances made in this field, the applications of automatic face expression recognizers, the characteristics of an ideal system, the databases that have been used and the advances made in terms of their standardization and a detailed summary of the state of the art. The paper also discusses facial parameterization using FACS Action Units (AUs) and MPEG-4 Facial Animation Parameters (FAPs) and the recent advances in face detection, tracking and feature extraction methods. Notes have also been presented on emotions, expressions and facial features, discussion on the six prototypic expressions and the recent studies on expression classifiers. The paper ends with a note on the challenges and the future work. This paper has been written in a tutorial style with the intention of helping students and researchers who are new to this field. Index Terms — Expression recognition, emotion classification, face detection, face tracking, facial action encoding, survey, tutorial, human-centered computing. ——————————  ——————————
Hidden Markov map matching through noise and sparseness

The problem of matching measured latitude/longitude points to roads is becoming increasingly important. This paper describes a novel, principled map matching algorithm that uses a Hidden Markov Model (HMM) to find the most likely road route represented by a time-stamped sequence of latitude/longitude pairs. The HMM elegantly accounts for measurement noise and the layout of the road network. We test our algorithm on ground truth data collected from a GPS receiver in a vehicle. Our test shows how the algorithm breaks down as the sampling rate of the GPS is reduced. We also test the effect of increasing amounts of additional measurement noise in order to assess how well our algorithm could deal with the inaccuracies of other location measurement systems, such as those based on WiFi and cell tower multilateration. We provide our GPS data and road network representation as a standard test set for other researchers to use in their map matching work.
Blockchains for decentralized optimization of energy resources in microgrid networks

We present an architecture for peer-to-peer energy markets which can guarantee that operational constraints are respected and payments are fairly rendered, without relying on a centralized utility or microgrid aggregator. We demonstrate how to address trust, security, and transparency issues by using blockchains and smart contracts, two emerging technologies which can facilitate decentralized coordination between non-trusting agents. While blockchains are receiving considerable interest as a platform for distributed computation and data management, this is the first work to examine their use to facilitate distributed optimization and control. Using the Alternating Direction Method of Multipliers (ADMM), we pose a decentralized optimal power flow (OPF) model for scheduling a mix of batteries, shapable loads, and deferrable loads on an electricity distribution network. The DERs perform local optimization steps, and a smart contract on the blockchain serves as the ADMM coordinator, allowing the validity and optimality of the solution to be verified. The optimal schedule is securely stored on the blockchain, and payments can be automatically, securely, and trustlessly rendered without requiring a microgrid operator.
Bioinspired Early Detection through Gas Flow Modulation in ChemoSensory Systems

The design of bioinspired systems for chemical sensing is an engaging line of research in machine olfaction. Developments in this line could increase the lifetime and sensitivity of artificial chemo-sensory systems. Such approach is based on the sensory systems known in live organisms, and the resulting developed artificial systems are targeted to reproduce the biological mechanisms to some extent. Sniffing behaviour, sampling odours actively, has been studied recently in neuroscience, and it has been suggested that the respiration frequency is an important parameter of the olfactory system, since the odour perception, especially in complex scenarios such as novel odourants exploration, depends on both the stimulus identity and the sampling method. In this work we propose a chemical sensing system based on an array of 16 metal-oxide gas sensors that we combined with an external mechanical ventilator to simulate the biological respiration cycle. The tested gas classes formed a relatively broad combination of two analytes, acetone and ethanol, in binary mixtures. Two sets of lowfrequency and high-frequency features were extracted from the acquired signals to show that the high-frequency features contain information related to the gas class. In addition, such information is available at early stages of the measurement, which could make the technique ∗Corresponding author.  Chemical August 15, 2014 suitable in early detection scenarios. The full data set is made publicly available to the community.
Inference, Learning and Attention Mechanisms that Exploit and Preserve Sparsity in Convolutional Networks

While CNNs naturally lend themselves to densely sampled data, and sophisticated implementations are available, they lack the ability to efficiently process sparse data. In this work we introduce a suite of tools that exploit sparsity in both the feature maps and the filter weights, and thereby allow for significantly lower memory footprints and computation times than the conventional dense framework when processing data with a high degree of sparsity. Our scheme provides (i) an efficient GPU implementation of a convolution layer based on direct, sparse convolution; (ii) a filter step within the convolution layer, which we call attention, that prevents fill-in, i.e., the tendency of convolution to rapidly decrease sparsity, and guarantees an upper bound on the computational resources; and (iii) an adaptation of the backpropagation algorithm, which makes it possible to combine our approach with standard learning frameworks, while still exploiting sparsity in the data and the model.
Unsupervised Document Embedding With CNNs.

We propose a new model for unsupervised document embedding. Leading existing approaches either require complex inference or use recurrent neural networks (RNN) that are difficult to parallelize. We take a different route and develop a convolutional neural network (CNN) embedding model. Our CNN architecture is fully parallelizable resulting in over 10x speedup in inference time over RNN models. Parallelizable architecture enables to train deeper models where each successive layer has increasingly larger receptive field and models longer range semantic structure within the document. We additionally propose a fully unsupervised learning algorithm to train this model based on stochastic forward prediction. Empirical results on two public benchmarks show that our approach produces comparable to state-of-the-art accuracy at a fraction of computational cost.
Understanding Android App Piggybacking: A Systematic Study of Malicious Code Grafting

The Android packaging model offers ample opportunities for malware writers to piggyback malicious code in popular apps, which can then be easily spread to a large user base. Although recent research has produced approaches and tools to identify piggybacked apps, the literature lacks a comprehensive investigation into such phenomenon. We fill this gap by: 1) systematically building a large set of piggybacked and benign apps pairs, which we release to the community; 2) empirically studying the characteristics of malicious piggybacked apps in comparison with their benign counterparts; and 3) providing insights on piggybacking processes. Among several findings providing insights analysis techniques should build upon to improve the overall detection and classification accuracy of piggybacked apps, we show that piggybacking operations not only concern app code, but also extensively manipulates app resource files, largely contradicting common beliefs. We also find that piggybacking is done with little sophistication, in many cases automatically, and often via library code.
Improving Collaborative Recommendation via User-Item Subgroups

Collaborative filtering (CF) is out of question the most widely adopted and successful recommendation approach. A typical CF-based recommender system associates a user with a group of like-minded users based on their individual preferences over all the items, either explicit or implicit, and then recommends to the user some unobserved items enjoyed by the group. However, we find that two users with similar tastes on one item subset may have totally different tastes on another set. In other words, there exist many user-item subgroups each consisting of a subset of items and a group of like-minded users on these items. It is more reasonable to predict preferences through one user's correlated subgroups, but not the entire user-item matrix. In this paper, to find meaningful subgroups, we formulate a new Multiclass Co-Clustering (MCoC) model, which captures relations of user-to-item, user-to-user, and item-to-item simultaneously. Then, we combine traditional CF algorithms with subgroups for improving their top- <inline-formula><tex-math notation="LaTeX">$N$</tex-math><alternatives> <inline-graphic xlink:type="simple" xlink:href="cai-ieq1-2566622.gif"/></alternatives></inline-formula> recommendation performance. Our approach can be seen as a new extension of traditional clustering CF models. Systematic experiments on several real data sets have demonstrated the effectiveness of our proposed approach.