nils-herrmann/clean_scirepeval huggingface dataset:
The Cellular and Molecular Basis of Translational Immunometabolism.

The immune response requires major changes to metabolic processes, and indeed, energy metabolism and functional activation are fully integrated in immune cells to determine their ability to divide, differentiate, and carry out effector functions. Immune cell metabolism has therefore become an attractive target area for therapeutic purposes. A neglected aspect in the translation of immunometabolism is the critical connection between systemic and cellular metabolism. Here, we discuss the importance of understanding and manipulating the integration of systemic and immune cell metabolism through in-depth analysis of immune cell phenotype and function in human metabolic diseases and, in parallel, of the effects of conventional metabolic drugs on immune cell differentiation and function. We examine how the recent identification of selective metabolic programs operating in distinct immune cell subsets and functions has the potential to deliver tools for cell- and function-specific immunometabolic targeting.
mwetoolkit: a Framework for Multiword Expression Identification

This paper presents the Multiword Expression Toolkit (mwetoolkit), an environment for type and language-independent MWE identification from corpora. The mwetoolkit provides a targeted list of MWE candidates, extracted and filtered according to a number of user-defined criteria and a set of standard statistical association measures. For generating corpus counts, the toolkit provides both a corpus indexation facility and a tool for integration with web search engines, while for evaluation, it provides validation and annotation facilities. The mwetoolkit also allows easy integration with a machine learning tool for the creation and application of supervised MWE extraction models if annotated data is available. In our experiments, the mwetoolkit was tested and evaluated in the context of MWE extraction in the biomedical domain. Our preliminary results show that the toolkit performs better than other approaches, especially concerning recall. Moreover, this first version can be extended in several ways in order to improve the quality of the results.
Residual Algorithms: Reinforcement Learning with Function Approximation

A number of reinforcement learning algorithms have been developed that are guaranteed to converge to the optimal solution when used with lookup tables. It is shown, however, that these algorithms can easily become unstable when implemented directly with a general function-approximation system, such as a sigmoidal multilayer perceptron, a radial-basisfunction system, a memory-based learning system, or even a linear function-approximation system. A new class of algorithms, residual gradient algorithms, is proposed, which perform gradient descent on the mean squared Bellman residual, guaranteeing convergence. It is shown, however, that they may learn very slowly in some cases. A larger class of algorithms, residual algorithms, is proposed that has the guaranteed convergence of the residual gradient algorithms, yet can retain the fast learning speed of direct algorithms. In fact, both direct and residual gradient algorithms are shown to be special cases of residual algorithms, and it is shown that residual algorithms can combine the advantages of each approach. The direct, residual gradient, and residual forms of value iteration, Qlearning, and advantage learning are all presented. Theoretical analysis is given explaining the properties these algorithms have, and simulation results are given that demonstrate these properties.
Genome-Wide Regression and Prediction with the BGLR Statistical Package

Many modern genomic data analyses require implementing regressions where the number of parameters (p, e.g., the number of marker effects) exceeds sample size (n). Implementing these large-p-with-small-n regressions poses several statistical and computational challenges, some of which can be confronted using Bayesian methods. This approach allows integrating various parametric and nonparametric shrinkage and variable selection procedures in a unified and consistent manner. The BGLR R-package implements a large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures (Bayesian reproducing kernel Hilbert spaces regressions, RKHS). The software was originally developed for genomic applications; however, the methods implemented are useful for many nongenomic applications as well. The response can be continuous (censored or not) or categorical (either binary or ordinal). The algorithm is based on a Gibbs sampler with scalar updates and the implementation takes advantage of efficient compiled C and Fortran routines. In this article we describe the methods implemented in BGLR, present examples of the use of the package, and discuss practical issues emerging in real-data analysis.
Introduction to 3D Non-Photorealistic Rendering: Silhouettes and Outlines

In these notes, we survey some of the basic tools used for non-photorealistic rendering of 3D scenes. We will primarily focus on detecting outlines of object shape: silhouettes, boundaries, and creases. (Hatching and shading, which are also very important for communicating shape, are discussed elsewhere in the course notes.) The algorithms in this section can be divided into algorithms that operate in the image space (2D), and algorithms that operate in world space (3D).
Small cell backhaul: challenges and prospective solutions

Operators are currently considering the deployment of small cells to complement their macrocellular networks and in crease their coverage and capacity. However, in order to roll-out a large number of small cells and allow anytime, anywhere wireless broadband connectivity through wireless technologies, operators must still face the challenge of backhauling the traffic from the small cells to the core network in a cost-effective manner. In this paper, backhaul challenges for small cell base stations (BSs) are discussed, and potential wired and wireless solutions together with their benefits and drawbacks are presented. The use of large scale antennas systems and free-space optics is also discussed. Moreover, a wireless backhaul planning tool targeted at finding the most cost-effective backhaul solution using a mixture of wireless technologies is presented. Simulation results confirm that the optimum backhaul solution is a combination of various options, which can overcome inherent scenario constraints while providing a cost-effective performance.
Fully Automated Neuropsychological Assessment for Detecting Mild Cognitive Impairment

We present an end-to-end system for automatically scoring spoken responses to a narrative recall test administered to seniors when screening for cognitive impairment. In Wechsler Logical Memory (WLM) test, a patient listens to a brief narrative, then retells the story once immediately and again after a brief delay. We transcribe the retellings automatically using an ASR system, align the transcripts to the source narrative, extract features that replicate the standard clinical scoring method, and then use the features for automatic assessment using a classifier. On a test corpus of 72 subjects, we empirically evaluate different ASR adaptation strategies and analyze the errors with respect to clinical assessment. Despite imperfect recognition, the system presented here yields classification accuracy comparable to that of manually assigned scores. Our results show that automatic assessment of neuropsychological tests such as the WLM is practical for screening large cohorts.
M-tree: An Efficient Access Method for Similarity Search in Metric Spaces

A new access method called M tree is pro posed to organize and search large data sets from a generic metric space i e where ob ject proximity is only de ned by a distance function satisfying the positivity symmetry and triangle inequality postulates We detail algorithms for insertion of objects and split management which keep the M tree always balanced several heuristic split alternatives are considered and experimentally evaluated Algorithms for similarity range and k nearest neighbors queries are also described Re sults from extensive experimentation with a prototype system are reported considering as the performance criteria the number of page I O s and the number of distance computa tions The results demonstrate that the M tree indeed extends the domain of applica bility beyond the traditional vector spaces performs reasonably well in high dimensional data spaces and scales well in case of growing les
The String B-tree: A New Data Structure for String Search in External Memory and Its Applications

We introduce a new text-indexing data structure, the String B-Tree, that can be seen as a link between some traditional external-memory and string-matching data structures. In a short phrase, it is a combination of B-trees and Patricia tries for internal-node indices that is made more effective by adding extra pointers to speed up search and update operations. Consequently, the String B-Tree overcomes the theoretical limitations of inverted files, B-trees, prefix B-trees, suffix arrays, compacted tries and suffix trees. String B-trees have the same worst-case performance as B-trees but they manage unbounded-length strings and perform much more powerful search operations such as the ones supported by suffix trees. String B-trees are also effective in main memory (RAM model) because they improve the online suffix tree search on a dynamic set of strings. They also can be successfully applied to database indexing and software duplication.
Detection and analysis of drive-by-download attacks and malicious JavaScript code

JavaScript is a browser scripting language that allows developers to create sophisticated client-side interfaces for web applications. However, JavaScript code is also used to carry out attacks against the user's browser and its extensions. These attacks usually result in the download of additional malware that takes complete control of the victim's platform, and are, therefore, called "drive-by downloads." Unfortunately, the dynamic nature of the JavaScript language and its tight integration with the browser make it difficult to detect and block malicious JavaScript code.
 This paper presents a novel approach to the detection and analysis of malicious JavaScript code. Our approach combines anomaly detection with emulation to automatically identify malicious JavaScript code and to support its analysis. We developed a system that uses a number of features and machine-learning techniques to establish the characteristics of normal JavaScript code. Then, during detection, the system is able to identify anomalous JavaScript code by emulating its behavior and comparing it to the established profiles. In addition to identifying malicious code, the system is able to support the analysis of obfuscated code and to generate detection signatures for signature-based systems. The system has been made publicly available and has been used by thousands of analysts.
Symbolic Model Checking without BDDs

Symbolic Model Checking [3, 14] has proven to be a powerful technique for the verification of reactive systems.  have traditionally been used as a symbolic representation of the system. In this paper we show how boolean decision procedures, like St ̊ almarck’s Method  or the Davis & Putnam Procedure [7], can replace BDDs. This new technique avoids the space blow up of BDDs, generates counterexamples much faster, and sometimes speeds up the verification. In addition, it produces counterexamples of minimal length. We introduce abounded model checking procedure for LTL which reduces model checking to propositional satisfiability. We show that bounded LTL model checking can be done without a tableau construction. We have implemented a model checkerBMC , based on bounded model checking, and preliminary results are presented.
Football analysis using spatio-temporal tools

Analysing a football match is without doubt an important task for coaches, talent scouts, players and even media; and with current technologies more and more match data is collected. Several companies offer the ability to track the position of the players and the ball with high accuracy and high resolution. They also offer software that include basic analysis tools, for example straight-forward statistics about distance run and number of passes. It is, however, a non-trivial task to perform more advanced analysis. We present a collection of tools that we developed specifically for analysing the performance of football players and teams.
Decision strategies and susceptibility to phishing

Phishing emails are semantic attacks that con people into divulging sensitive information using techniques to make the user believe that information is being requested by a legitimate source. In order to develop tools that will be effective in combating these schemes, we first must know how and why people fall for them. This study reports preliminary analysis of interviews with 20 non-expert computer users to reveal their strategies and understand their decisions when encountering possibly suspicious emails. One of the reasons that people may be vulnerable to phishing schemes is that awareness of the risks is not linked to perceived vulnerability or to useful strategies in identifying phishing emails. Rather, our data suggest that people can manage the risks that they are most familiar with, but don't appear to extrapolate to be wary of unfamiliar risks. We explore several strategies that people use, with varying degrees of success, in evaluating emails and in making sense of warnings offered by browsers attempting to help users navigate the web.
1 The Innovator ' s Dilemma

When I began my search for an answer to the puzzle of why the best firms can fail, a friend offered some sage advice. "Those who study genetics avoid studying humans," he noted. "Because new generations come along only every thirty years or so, it takes a long time to understand the cause and effect of any changes. Instead, they study fruit flies, because they are conceived, born, mature, and die all within a single day. If you want to understand why something happens in business, study the disk drive industry. Those companies are the closest things to fruit flies that the business world will ever see."
DeepMimic: example-guided deep reinforcement learning of physics-based character skills

A longstanding goal in character animation is to combine data-driven specification of behavior with a system that can execute a similar behavior in a physical simulation, thus enabling realistic responses to perturbations and environmental variation. We show that well-known reinforcement learning (RL) methods can be adapted to learn robust control policies capable of imitating a broad range of example motion clips, while also learning complex recoveries, adapting to changes in morphology, and accomplishing user-specified goals. Our method handles keyframed motions, highly-dynamic actions such as motion-captured flips and spins, and retargeted motions. By combining a motion-imitation objective with a task objective, we can train characters that react intelligently in interactive settings, e.g., by walking in a desired direction or throwing a ball at a user-specified target. This approach thus combines the convenience and motion quality of using motion clips to define the desired style and appearance, with the flexibility and generality afforded by RL methods and physics-based animation. We further explore a number of methods for integrating multiple clips into the learning process to develop multi-skilled agents capable of performing a rich repertoire of diverse skills. We demonstrate results using multiple characters (human, Atlas robot, bipedal dinosaur, dragon) and a large variety of skills, including locomotion, acrobatics, and martial arts.
Locally Adaptive Color Correction for Underwater Image Dehazing and Matching

Underwater images are known to be strongly deteriorated by a combination of wavelength-dependent light attenuation and scattering. This results in complex color casts that depend both on the scene depth map and on the light spectrum. Color transfer, which is a technique of choice to counterbalance color casts, assumes stationary casts, defined by global parameters, and is therefore not directly applicable to the locally variable color casts encountered in underwater scenarios. To fill this gap, this paper introduces an original fusion-based strategy to exploit color transfer while tuning the color correction locally, as a function of the light attenuation level estimated from the red channel. The Dark Channel Prior (DCP) is then used to restore the color compensated image, by inverting the simplified Koschmieder light transmission model, as for outdoor dehazing. Our technique enhances image contrast in a quite effective manner and also supports accurate transmission map estimation. Our extensive experiments also show that our color correction strongly improves the effectiveness of local keypoints matching.
A Diversity-Promoting Objective Function for Neural Conversation Models

Sequence-to-sequence neural network models for generation of conversational responses tend to generate safe, commonplace responses (e.g.,I don’t know) regardless of the input. We suggest that the traditional objective function, i.e., the likelihood of output (responses) given input (messages) is unsuited to response generation tasks. Instead we propose using Maximum Mutual Information (MMI) as objective function in neural models. Experimental results demonstrate that the proposed objective function produces more diverse, interesting, and appropriate responses, yielding substantive gains in BLEU scores on two conversational datasets.
A Pneumatic-Driven Haptic Glove with Force and Tactile Feedback

The advent of Oculus Rift indicates the start of a booming era of virtual reality. In order to increase the immersive feeling of interaction with the virtual world, haptic devices allow us to touch and manipulate virtual objects in an intuitive way. In this paper, we introduce a portable and low-cost haptic glove that provides both force and tactile feedback using a direct-control pneumatic concept. To produce force feedback, two inlet ports of a double acting pneumatic cylinder are opened and closed via solenoid DC valves through Pulse-width modulation (PWM) technique. For tactile feedback, an air bladder is actuated using a diaphragm pump via PWM operated solenoid valve. Experiments on a single finger prototype validated that the glove can provide force and tactile feedback with sufficient moving range of the finger joints. The maximum continuous force is 9 Newton and the response time is less than 400ms. The glove is light weighted and easy to be mounted on the index finger. The proposed glove could be potentially used for virtual reality grasping scenarios and for teleoperation of a robotic hand for handling hazardous objects.
A Deep Learning Approach for Population Estimation from Satellite Imagery

Knowing where people live is a fundamental component of many decision making processes such as urban development, infectious disease containment, evacuation planning, risk management, conservation planning, and more. While bottom-up, survey driven censuses can provide a comprehensive view into the population landscape of a country, they are expensive to realize, are infrequently performed, and only provide population counts over broad areas. Population disaggregation techniques and population projection methods individually address these shortcomings, but also have shortcomings of their own. To jointly answer the questions of "where do people live" and "how many people live there," we propose a deep learning model for creating high-resolution population estimations from satellite imagery. Specifically, we train convolutional neural networks to predict population in the USA at a 0.01°x0.01° resolution grid from 1-year composite Landsat imagery. We validate these models in two ways: quantitatively, by comparing our model's grid cell estimates aggregated at a county-level to several US Census county-level population projections, and qualitatively, by directly interpreting the model's predictions in terms of the satellite image inputs. We find that aggregating our model's estimates gives comparable results to the Census county-level population projections and that the predictions made by our model can be directly interpreted, which give it advantages over traditional population disaggregation methods. In general, our model is an example of how machine learning techniques can be an effective tool for extracting information from inherently unstructured, remotely sensed data to provide effective solutions to social problems.
FAST , CHEAP AND OUT OF CONTROL : A ROBOT INVASION OF THE SOLAR SYSTEM

Complex systems and complex missions take years of planning and force launches to become incredibly expensive. The longer the planning and the more expensive the mission, the more catastrophic if it fails. The solution has always been to plan better, add redundancy, test thoroughly and use high quality components. Based on our experience in building ground based mobile robots (legged and wheeled) we argue here for cheap, fast missions using large numbers of mass produced simple autonomous robots that are small by today's standards (1 to 2 Kg). We argue that the time between mission conception and implementation can be radically reduced, that launch mass can be slashed, that totally autonomous robots can be more reliable than ground controlled robots, and that large numbers of robots can change the tradeoff between reliability of individual components and overall mission success. Lastly, we suggest that within a few years it will be possible at modest cost to invade a planet with millions of tiny robots.
A Formal Technique for Automated Dialogue Development

A number of notations exist by which a designer can specify the behavior of a human-computer interface in relatively formal terms. In this paper we show how many of the dialogue specifications described using these notations are amenable to automated analysis to detect potential problems such as user actions that are never enabled or have effects that are hard to reverse. In many situations, a dialogue specification can be thought of as a finite state machine in which the transition between states is signalled as an event from the user or system. The trouble with this state transition model is that states quickly multiply presenting two problems to the analyst: (i) how to easily describe all of the possible dialogue states and state transitions; and (ii) how to analyze a very large SIN. This paper reviews possible solutions to both of these problems. A tabular interface to Olsen’s Propositional Production System is described and goes some way towards solving the descriptive problem. This representation is also useful for simulating requirements scenarios in a validation exercise. For the analytic problem, we make use of finite state model checking technology that allows for automated analysis of very large state machines. We demonstrate how eight categories of dialogue verification properties can be analyzed with this approach. Together, dialogue simulation and automated verification leads to a more complete analytic framework for dialogue development.