nils-herrmann/clean_scirepeval huggingface dataset:
Study design, precision, and validity in observational studies.

THE USE OF OBSERVATIONAL RESEARCH METHODS in the field of palliative care is vital to building the evidence base, identifying best practices, and understanding disparities in access to and delivery of palliative care services. As discussed in the introduction to this series, research in palliative care encompasses numerous areas in which the gold standard research design, the randomized controlled trial (RCT), is not appropriate, adequate, or even possible.1,2 The difficulties in conducting RCTs in palliative care include patient and family recruitment, gate-keeping by physicians, crossover contamination, high attrition rates, small sample sizes, and limited survival times. Furthermore, a number of important issues including variation in access to palliative care and disparities in the use and provision of palliative care simply cannot be answered without observational research methods. As research in palliative care broadens to encompass study designs other than the RCT, the collective understanding of the use, strengths, and limitations of observational research methods is critical. The goals of this first paper are to introduce the major types of observational study designs, discuss the issues of precision and validity, and provide practical insights into how to critically evaluate this literature in our field.
Practical Deep Reinforcement Learning Approach for Stock Trading

Stock trading strategy plays a crucial role in investment companies. However, it is challenging to obtain optimal strategy in the complex and dynamic stock market. We explore the potential of deep reinforcement learning to optimize stock trading strategy and thus maximize investment return. 30 stocks are selected as our trading stocks and their daily prices are used as the training and trading market environment. We train a deep reinforcement learning agent and obtain an adaptive trading strategy. The agent’s performance is evaluated and compared with Dow Jones Industrial Average and the traditional min-variance portfolio allocation strategy. The proposed deep reinforcement learning approach is shown to outperform the two baselines in terms of both the Sharpe ratio and cumulative returns.
Grounded Compositional Semantics for Finding and Describing Images with Sentences

Previous work on Recursive Neural Networks (RNNs) shows that these models can produce compositional feature vectors for accurately representing and classifying sentences or images. However, the sentence vectors of previous models cannot accurately represent visually grounded meaning. We introduce the DT-RNN model which uses dependency trees to embed sentences into a vector space in order to retrieve images that are described by those sentences. Unlike previous RNN-based models which use constituency trees, DT-RNNs naturally focus on the action and agents in a sentence. They are better able to abstract from the details of word order and syntactic expression. DT-RNNs outperform other recursive and recurrent neural networks, kernelized CCA and a bag-of-words baseline on the tasks of finding an image that fits a sentence description and vice versa. They also give more similar representations to sentences that describe the same image.
Modeling somatic and dendritic spike mediated plasticity at the single neuron and network level

Synaptic plasticity is thought to be the principal neuronal mechanism underlying learning. Models of plastic networks typically combine point neurons with spike-timing-dependent plasticity (STDP) as the learning rule. However, a point neuron does not capture the local non-linear processing of synaptic inputs allowed for by dendrites. Furthermore, experimental evidence suggests that STDP is not the only learning rule available to neurons. By implementing biophysically realistic neuron models, we study how dendrites enable multiple synaptic plasticity mechanisms to coexist in a single cell. In these models, we compare the conditions for STDP and for synaptic strengthening by local dendritic spikes. We also explore how the connectivity between two cells is affected by these plasticity rules and by different synaptic distributions. Finally, we show that how memory retention during associative learning can be prolonged in networks of neurons by including dendrites. Synaptic plasticity is the neuronal mechanism underlying learning. Here the authors construct biophysical models of pyramidal neurons that reproduce observed plasticity gradients along the dendrite and show that dendritic spike dependent LTP which is predominant in distal sections can prolong memory retention.
Burst deblurring: Removing camera shake through fourier burst accumulation

Numerous recent approaches attempt to remove image blur due to camera shake, either with one or multiple input images, by explicitly solving an inverse and inherently ill-posed deconvolution problem. If the photographer takes a burst of images, a modality available in virtually all modern digital cameras, we show that it is possible to combine them to get a clean sharp version. This is done without explicitly solving any blur estimation and subsequent inverse problem. The proposed algorithm is strikingly simple: it performs a weighted average in the Fourier domain, with weights depending on the Fourier spectrum magnitude. The method's rationale is that camera shake has a random nature and therefore each image in the burst is generally blurred differently. Experiments with real camera data show that the proposed Fourier Burst Accumulation algorithm achieves state-of-the-art results an order of magnitude faster, with simplicity for on-board implementation on camera phones.
Enteric nervous system development: migration, differentiation, and disease

The enteric nervous system (ENS) provides the intrinsic innervation of the bowel and is the most neurochemically diverse branch of the peripheral nervous system, consisting of two layers of ganglia and fibers encircling the gastrointestinal tract. The ENS is vital for life and is capable of autonomous regulation of motility and secretion. Developmental studies in model organisms and genetic studies of the most common congenital disease of the ENS, Hirschsprung disease, have provided a detailed understanding of ENS development. The ENS originates in the neural crest, mostly from the vagal levels of the neuraxis, which invades, proliferates, and migrates within the intestinal wall until the entire bowel is colonized with enteric neural crest-derived cells (ENCDCs). After initial migration, the ENS develops further by responding to guidance factors and morphogens that pattern the bowel concentrically, differentiating into glia and neuronal subtypes and wiring together to form a functional nervous system. Molecules controlling this process, including glial cell line-derived neurotrophic factor and its receptor RET, endothelin (ET)-3 and its receptor endothelin receptor type B, and transcription factors such as SOX10 and PHOX2B, are required for ENS development in humans. Important areas of active investigation include mechanisms that guide ENCDC migration, the role and signals downstream of endothelin receptor type B, and control of differentiation, neurochemical coding, and axonal targeting. Recent work also focuses on disease treatment by exploring the natural role of ENS stem cells and investigating potential therapeutic uses. Disease prevention may also be possible by modifying the fetal microenvironment to reduce the penetrance of Hirschsprung disease-causing mutations.
Rheumatic heart disease

Rheumatic heart disease, often neglected by media and policy makers, is a major burden in developing countries where it causes most of the cardiovascular morbidity and mortality in young people, leading to about 250,000 deaths per year worldwide. The disease results from an abnormal autoimmune response to a group A streptococcal infection in a genetically susceptible host. Acute rheumatic fever--the precursor to rheumatic heart disease--can affect different organs and lead to irreversible valve damage and heart failure. Although penicillin is effective in the prevention of the disease, treatment of advanced stages uses up a vast amount of resources, which makes disease management especially challenging in emerging nations. Guidelines have therefore emphasised antibiotic prophylaxis against recurrent episodes of acute rheumatic fever, which seems feasible and cost effective. Early detection and targeted treatment might be possible if populations at risk for rheumatic heart disease in endemic areas are screened. In this setting, active surveillance with echocardiography-based screening might become very important.
LOGAIDER: A Tool for Mining Potential Correlations of HPC Log Events

Today's large-scale supercomputers are producing a huge amount of log data. Exploring various potential correlations of fatal events is crucial for understanding their causality and improving the working efficiency for system administrators. To this end, we developed a toolkit, named LogAider, that can reveal three types of potential correlations: across-field, spatial, and temporal. Across-field correlation refers to the statistical correlation across fields within a log or across multiple logs based on probabilistic analysis. For analyzing the spatial correlation of events, we developed a generic, easy-to-use visualizer that can view any events queried by userson a system machine graph. LogAider can also mine spatial correlations by an optimized K-meaning clustering algorithm over a Torus network topology. It is also able to disclose the temporal correlations (or error propagations) over a certain period inside a log or across multiple logs, based on an effective similarity analysis strategy. We assessed LogAider using theone-year reliability-availability-serviceability (RAS) log of Mira system (one of the world's most powerful supercomputers), as well as its job log. We find that LogAider very helpful for revealing the potential correlations of fatal system events and job events, with an accurate mining of across-field correlation with both precision and recall of 99.9-100%, as well as precisedetection of temporal-correlation with a high similarity (up to 95%) to the ground-truth.
AutoEncoder by Forest

Auto-encoding is an important task which is typically realized by deep neural networks (DNNs) such as convolutional neural networks (CNN). In this paper, we propose EncoderForest (abbrv. eForest), the first tree ensemble based auto-encoder. We present a procedure for enabling forests to do backward reconstruction by utilizing the MaximalCompatible Rule (MCR) defined by the decision paths of the trees, and demonstrate its usage in both supervised and unsupervised setting. Experiments show that, compared with DNN based auto-encoders, eForest is able to obtain lower reconstruction error with fast training speed, while the model itself is reusable and damage-tolerable.
Empirical Scenarios of Fake Data Analysis: The Sample Generation by Replacement (SGR) Approach

Many self-report measures of attitudes, beliefs, personality, and pathology include items whose responses can be easily manipulated or distorted, as an example in order to give a positive impression to others, to obtain financial compensation, to avoid being charged with a crime, to get a job, or else. This fact confronts both researchers and practitioners with the crucial problem of biases yielded by the usage of standard statistical models. The current paper presents three empirical applications to the issue of faking of a recent probabilistic perturbation procedure called Sample Generation by Replacement (SGR; Lombardi and Pastore, 2012). With the intent to study the behavior of some statistics under fake perturbation and data reconstruction processes, ad-hoc faking scenarios were implemented and tested. Overall, results proved that SGR could be successfully applied both in the case of research designs traditionally proposed in order to deal with faking (e.g., use of fake-detecting scales, experimentally induced faking, or contrasting applicants vs. incumbents), and in the case of ecological research settings, where no information as regards faking could be collected by the researcher or the practitioner. Implications and limitations are presented and discussed.
Charliecloud: unprivileged containers for user-defined software stacks in HPC

Supercomputing centers are seeing increasing demand for user-defined software stacks (UDSS), instead of or in addition to the stack provided by the center. These UDSS support user needs such as complex dependencies or build requirements, externally required configurations, portability, and consistency. The challenge for centers is to provide these services in a usable manner while minimizing the risks: security, support burden, missing functionality, and performance. We present Charliecloud, which uses the Linux user and mount namespaces to run industry-standard Docker containers with no privileged operations or daemons on center resources. Our simple approach avoids most security risks while maintaining access to the performance and functionality already on offer, doing so in just 800 lines of code. Charliecloud promises to bring an industry-standard UDSS user workflow to existing, minimally altered HPC resources.
Teachers ’ ICT Literacy and Utilization in English Language Teaching

The successful integration of Information and Communications Technology (ICT) into the teaching and learning of English Language is largely dependent on the level of teacher’s ICT competence, the actual utilization of ICT in the language classroom and factors that challenge teachers to use it in language teaching. The study therefore assessed the Secondary School English language teachers’ ICT literacy, the extent of ICT utilization in English language teaching and the challenges that prevent language teachers to integrate ICT in teaching. To answer the problems, three sets of survey questionnaires were distributed to 30 English teachers in the 11 schools of Cluster 1 (CarCanMadCarLan). Data gathered were analyzed using descriptive statistics and frequency count. The results revealed that the teachers’ ICT literacy was moderate. The findings provided evidence that there was only a limited use of ICT in language teaching. Feedback gathered from questionnaires show that teachers faced many challenges that demotivate them from using ICT in language activities. Based on these findings, it is recommended the teachers must be provided with intensive ICT-based trainings to equip them with knowledge of ICT and its utilization in language teaching. School administrators as well as stakeholders may look for interventions to upgrade school’s ICTbased resources for its optimum use in teaching and learning. Most importantly, a larger school-wide ICT development plan may be implemented to ensure coherence of ICT implementation in the teaching-learning activities. ‘ICT & Innovations in Education’ International Journal International Electronic Journal | ISSN 2321 – 7189 | www.ictejournal.com Volume 2, Issue 1 | February 2014
ViType: A Cost Efficient On-Body Typing System through Vibration

Nowadays, smart wristbands have become one of the most prevailing wearable devices as they are small and portable. However, due to the limited size of the touch screens, smart wristbands typically have poor interactive experience. There are a few works appropriating the human body as a surface to extend the input. Yet by using multiple sensors at high sampling rates, they are not portable and are energy-consuming in practice. To break this stalemate, we proposed a portable, cost efficient text-entry system, termed ViType, which firstly leverages a single small form factor sensor to achieve a practical user input with much lower sampling rates. To enhance the input accuracy with less vibration information introduced by lower sampling rate, ViType designs a set of novel mechanisms, including an artificial neural network to process the vibration signals, and a runtime calibration and adaptation scheme to recover the error due to temporal instability. Extensive experiments have been conducted on 30 human subjects. The results demonstrate that ViType is robust to fight against various confounding factors. The average recognition accuracy is 94.8% with an initial training sample size of 20 for each key, which is 1.52 times higher than the state-of-the-art on-body typing system. Furthermore, when turning on the runtime calibration and adaptation system to update and enlarge the training sample size, the accuracy can reach around 98% on average during one month.
Adaptive Motion Planning

Mobile robots are increasingly being deployed in the real world in response to a heightened demand for applications such as transportation, delivery and inspection. The motion planning systems for these robots are expected to have consistent performance across the wide range of scenarios that they encounter. While state-of-the-art planners, with provable worst-case guarantees, can be employed to solve these planning problems, their finite time performance varies across scenarios. This thesis proposes that the planning module for a robot must adapt its search strategy to the distribution of planning problems encountered to achieve real-time performance. We address three principal challenges of this problem. Firstly, we show that even when the planning problem distribution is fixed, designing a nonadaptive planner can be challenging as the performance of planning strategies fluctuates with small changes in the environment. We characterize the existence of complementary strategies and propose to hedge our bets by executing a diverse ensemble of planners. Secondly, when the distribution is varying, we require a meta-planner that can automatically select such an ensemble from a library of black-box planners. We show that greedily training a list of predictors to focus on failure cases leads to an effective meta-planner. For situations where we have no training data, we show that we can learn an ensemble on-the-fly by adopting algorithms from online paging theory. Thirdly, in the interest of efficiency, we require a white-box planner that directly adapts its search strategy during a planning cycle. We propose an efficient procedure for training adaptive search heuristics in a data-driven imitation learning framework. We also draw a novel connection to Bayesian active learning, and propose algorithms to adaptively evaluate edges of a graph. Our approach leads to the synthesis of a robust real-time planning module that allows a UAV to navigate seamlessly across environments and speed-regimes. We evaluate our framework on a spectrum of planning problems and show closed-loop results on 3 UAV platforms a full-scale autonomous helicopter, a large scale hexarotor and a small quadrotor. While the thesis was motivated by mobile robots, we have shown that the individual algorithms are broadly applicable to other problem domains such as informative path planning and manipulation planning. We also establish novel connections between the disparate fields of motion planning and active learning, imitation learning and online paging which opens doors to several new research problems.
Parallel computer architecture - a hardware / software approach

The most exciting development in parallel computer architecture is the convergence of traditionally disparate approaches on a common machine structure. This book explains the forces behind this convergence of shared-memory, message-passing, data parallel, and data-driven computing architectures. It then examines the design issues that are critical to all parallel architecture across the full range of modern design, covering data access, communication performance, coordination of cooperative work, and correct implementation of useful semantics. It not only describes the hardware and software techniques for addressing each of these issues but also explores how these techniques interact in the same system. Examining architecture from an application-driven perspective, it provides comprehensive discussions of parallel programming for high performance and of workload-driven evaluation, based on understanding hardware-software interactions.
Shifts in selective visual attention: towards the underlying neural circuitry.

Psychophysical and physiological evidence indicates that the visual system of primates and humans has evolved a specialized processing focus moving across the visual scene. This study addresses the question of how simple networks of neuron-like elements can account for a variety of phenomena associated with this shift of selective visual attention. Specifically, we propose the following: (1) A number of elementary features, such as color, orientation, direction of movement, disparity etc. are represented in parallel in different topographical maps, called the early representation. (2) There exists a selective mapping from the early topographic representation into a more central non-topographic representation, such that at any instant the central representation contains the properties of only a single location in the visual scene, the selected location. We suggest that this mapping is the principal expression of early selective visual attention. One function of selective attention is to fuse information from different maps into one coherent whole. (3) Certain selection rules determine which locations will be mapped into the central representation. The major rule, using the conspicuity of locations in the early representation, is implemented using a so-called Winner-Take-All network. Inhibiting the selected location in this network causes an automatic shift towards the next most conspicious location. Additional rules are proximity and similarity preferences. We discuss how these rules can be implemented in neuron-like networks and suggest a possible role for the extensive back-projection from the visual cortex to the LGN.
Random Walk-based Beneficial Collaborators Recommendation Exploiting Dynamic Research Interests and Academic Influence

It is laborious for researchers to find proper collaborators who can provide researching guidance besides collaborating. Beneficial Collaborators (BCs), researchers who have a high academic level and relevant topics, can genuinely help researchers to enrich their research. Though many efforts have made to develop collaborator recommendation, most of existing works have mainly focused on recommending most possible collaborators with no intention to recommend specifically the BCs. In this paper, we propose the Beneficial Collaborator Recommendation (BCR) model that considers the dynamic research interest of researcher’s and academic level of collaborators to recommend the BCs. First, we run the LDA model on the abstract of researchers’ publications in each year for topic clustering. Second, we fix generated topic distribution matrix by a time function to fit interest dynamic transformation. Third, we compute the similarity between the collaboration candidate's feature matrix and the target researcher. Finally, we combine the similarity and influence in collaborators network to fix rank score and mine the candidates with high academic level and academic social impact. BCR generates the topN BCs recommendation. Extensive experiments on a dataset with citation network demonstrate that BCR performs better in terms of precision, recall, F1 score and the recommendation quality compared to baseline methods.