nils-herrmann/clean_scirepeval huggingface dataset:
A Generative Model for Image Segmentation Based on Label Fusion

We propose a nonparametric, probabilistic model for the automatic segmentation of medical images, given a training set of images and corresponding label maps. The resulting inference algorithms rely on pairwise registrations between the test image and individual training images. The training labels are then transferred to the test image and fused to compute the final segmentation of the test subject. Such label fusion methods have been shown to yield accurate segmentation, since the use of multiple registrations captures greater inter-subject anatomical variability and improves robustness against occasional registration failures. To the best of our knowledge, this manuscript presents the first comprehensive probabilistic framework that rigorously motivates label fusion as a segmentation approach. The proposed framework allows us to compare different label fusion algorithms theoretically and practically. In particular, recent label fusion or multiatlas segmentation algorithms are interpreted as special cases of our framework. We conduct two sets of experiments to validate the proposed methods. In the first set of experiments, we use 39 brain MRI scans - with manually segmented white matter, cerebral cortex, ventricles and subcortical structures - to compare different label fusion algorithms and the widely-used FreeSurfer whole-brain segmentation tool. Our results indicate that the proposed framework yields more accurate segmentation than FreeSurfer and previous label fusion algorithms. In a second experiment, we use brain MRI scans of 282 subjects to demonstrate that the proposed segmentation tool is sufficiently sensitive to robustly detect hippocampal volume changes in a study of aging and Alzheimer's Disease.
CAM: a topology aware minimum cost flow based resource manager for MapReduce applications in the cloud

MapReduce has emerged as a prevailing distributed computation paradigm for enterprise and large-scale data-intensive computing. The model is also increasingly used in the massively-parallel cloud environment, where MapReduce jobs are run on a set of virtual machines (VMs) on pay-as-needed basis. However, MapReduce jobs suffer from performance degradation when running in the cloud due to inefficient resource allocation. In particular, the MapReduce model is designed for and leverages information from the native clusters to operate efficiently, whereas the cloud presents a virtual cluster topology overlying or hiding actual network information. This results in two placement anomalies: loss of data locality and loss of job locality, where jobs are placed physically away from their data or other associated jobs, adversely affecting their performance.
 In this paper we propose, CAM, a cloud platform that provides an innovative resource scheduler particularly designed for hosting MapReduce applications in the cloud. CAM reconciles both data and VM resource allocation with a variety of competing constraints, such as storage utilization, changing CPU load and network link capacities. CAM uses a flow-network-based algorithm that is able to optimize MapReduce performance under the specified constraints -- not only by initial placement, but by readjusting through VM and data migration as well. Additionally, our platform exposes, otherwise hidden, lower-level topology information to the MapReduce job scheduler so that it makes optimal task assignments. Evaluation of CAM using both micro-benchmarks and simulations on a 23 VM cluster shows that compared to a state-of-the-art resource allocator, our system reduces network traffic and average MapReduce job execution time by a factor of 3 and 8.6, respectively.
Recursive unsupervised learning of finite mixture models

There are two open problems when finite mixture densities are used to model multivariate data: the selection of the number of components and the initialization. In this paper, we propose an online (recursive) algorithm that estimates the parameters of the mixture and that simultaneously selects the number of components. The new algorithm starts with a large number of randomly initialized components. A prior is used as a bias for maximally structured models. A stochastic approximation recursive learning algorithm is proposed to search for the maximum a posteriori (MAP) solution and to discard the irrelevant components.
Axel: a heterogeneous cluster with FPGAs and GPUs

This paper describes a heterogeneous computer cluster called Axel. Axel contains a collection of nodes; each node can include multiple types of accelerators such as FPGAs (Field Programmable Gate Arrays) and GPUs (Graphics Processing Units). A Map-Reduce framework for the Axel cluster is presented which exploits spatial and temporal locality through different types of processing elements and communication channels. The Axel system enables the first demonstration of FPGAs, GPUs and CPUs running collaboratively for N-body simulation. Performance improvement from 4.4 times to 22.7 times has been achieved using our approach, which shows that the Axel system can combine the benefits of the specialization of FPGA, the parallelism of GPU, and the scalability of computer clusters.
LTE System Level Simulation with Matlab

With the rapid development of 3GPP and its related techniques, evaluation of system level performance is in great need. However, LTE system level simulator is secured as commercial secrets in most 3GPP members. In this paper, we introduce our Matlab-based LTE system level simulator according to 3GPP specifications and related proposals. We mainly focus on channel model and physical abstract of transmission. Brief introduction of every part is given and physical concept and analysis are given.
Lifted graphical models: a survey

Lifted graphical models provide a language for expressing dependencies between different types of entities, their attributes, and their diverse relations, as well as techniques for probabilistic reasoning in such multi-relational domains. In this survey, we review a general form for a lifted graphical model, a par-factor graph, and show how a number of existing statistical relational representations map to this formalism. We discuss inference algorithms, including lifted inference algorithms, that efficiently compute the answers to probabilistic queries over such models. We also review work in learning lifted graphical models from data. There is a growing need for statistical relational models (whether they go by that name or another), as we are inundated with data which is a mix of structured and unstructured, with entities and relations extracted in a noisy manner from text, and with the need to reason effectively with this data. We hope that this synthesis of ideas from many different research groups will provide an accessible starting point for new researchers in this expanding field.
Optimized cutting plane algorithm for support vector machines

We have developed a new Linear Support Vector Machine (SVM) training algorithm called OCAS. Its computational effort scales linearly with the sample size. In an extensive empirical evaluation OCAS significantly outperforms current state of the art SVM solvers, like SVMlight, SVMperf and BMRM, achieving speedups of over 1,000 on some datasets over SVMlight and 20 over SVMperf, while obtaining the same precise Support Vector solution. OCAS even in the early optimization steps shows often faster convergence than the so far in this domain prevailing approximative methods SGD and Pegasos. Effectively parallelizing OCAS we were able to train on a dataset of size 15 million examples (itself about 32GB in size) in just 671 seconds --- a competing string kernel SVM required 97,484 seconds to train on 10 million examples sub-sampled from this dataset.
An Analysis of Linux Scalability to Many Cores

This paper analyzes the scalability of seven system applications (Exim, memcached, Apache, PostgreSQL, gmake, Psearchy, and MapReduce) running on Linux on a 48core computer. Except for gmake, all applications trigger scalability bottlenecks inside a recent Linux kernel. Using mostly standard parallel programming techniques— this paper introduces one new technique, sloppy counters—these bottlenecks can be removed from the kernel or avoided by changing the applications slightly. Modifying the kernel required in total 3002 lines of code changes. A speculative conclusion from this analysis is that there is no scalability reason to give up on traditional operating system organizations just yet.
Evaluation of existing District Health Management Information Systems: A case study of the District Health Systems in Kenya

This paper discusses some of the issues and challenges of implementing appropriate and coordinated District Health Management Information System (DHMIS) in environments dependent on external support especially when insufficient attention has been given to the sustainability of systems. It also discusses fundamental issues which affect the usability of DHMIS to support District Health System (DHS), including meeting user needs and user education in the use of information for management; and the need for integration of data from all health-providing and related organizations in the district.



This descriptive cross-sectional study was carried out in three DHSs in Kenya. Data was collected through use of questionnaires, focus group discussions and review of relevant literature, reports and operational manuals of the studied DHMISs.



Key personnel at the DHS level were not involved in the development and implementation of the established systems. The DHMISs were fragmented to the extent that their information products were bypassing the very levels they were created to serve. None of the DHMISs was computerized. Key resources for DHMIS operation were inadequate. The adequacy of personnel was 47%, working space 40%, storage space 34%, stationery 20%, 73% of DHMIS staff were not trained, management support was 13%. Information produced was 30% accurate, 19% complete, 26% timely, 72% relevant; the level of confidentiality and use of information at the point of collection stood at 32% and 22% respectively and information security at 48%. Basic DHMIS equipment for information processing was not available. This inhibited effective and efficient provision of information services.



An effective DHMIS is essential for DHS planning, implementation, monitoring and evaluation activities. Without accurate, timely, relevant and complete information the existing information systems are not capable of facilitating the DHS managers in their day-today operational management. The existing DHMISs were found not supportive of the DHS managers' strategic and operational management functions. Consequently DHMISs were found to be plagued by numerous designs, operational, resources and managerial problems. There is an urgent need to explore the possibilities of computerizing the existing manual systems to take advantage of the potential uses of microcomputers for DHMIS operations within the DHS. Information system designers must also address issues of cooperative partnership in information activities, systems compatibility and sustainability.
Casper the Friendly Finality Gadget

We introduce Casper, a proof of stake-based finality system which overlays an existing proof of work blockchain. Casper is a partial consensus mechanism combining proof of stake algorithm research and Byzantine fault tolerant consensus theory. We introduce our system, prove some desirable features, and show defenses against long range revisions and catastrophic crashes. The Casper overlay provides almost any proof of work chain with additional protections against block reversions.
Multi-view Stereo Beyond Lambert

We consider the problem of estimating the shape and radiance of an object from a calibrated set of views under the assumption that the reflectance of the object is non-Lambertian. Unlike traditional stereo, we do not solve the correspondence problem by comparing image-to-image. Instead, we exploit a rank constraint on the radiance tensor field of the surface in space, and use it to define a discrepancy measure between each image and the underlying model. Our approach automatically returns an estimate of the radiance of the scene, along with its shape, represented by a dense surface. The former can be used to generate novel views that capture the non-Lambertian appearance of the scene.
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of five MGU74A mouse GeneChip arrays, part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip arrays; and part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip arrays. We display some familiar features of the perfect match and mismatch probe (PM and MM) values of these data, and examine the variance-mean relationship with probe-level data from probes believed to be defective, and so delivering noise only. We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of the PM and MM using spike-in data and assess three commonly used summary measures: Affymetrix's (i) average difference (AvDiff) and (ii) MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index (MBEI). The exploratory data analyses of the probe level data motivate a new summary measure that is a robust multi-array average (RMA) of background-adjusted, normalized, and log-transformed PM values. We evaluate the four expression summary measures using the dilution study data, assessing their behavior in terms of bias, variance and (for MBEI and RMA) model fit. Finally, we evaluate the algorithms in terms of their ability to detect known levels of differential expression using the spike-in data. We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities.
OpenCV . js : Computer Vision Processing for the Web

The Web is the most ubiquitous computing platform. There are already billions of devices connected to the web that have access to a plethora of visual information. Understanding images is a complex and demanding task which requires sophisticated algorithms and implementations. OpenCV is the defacto library for general computer vision application development, with hundreds of algorithms and efficient implementation in C++. However, there is no comparable computer vision library for the Web offering an equal level of functionality and performance. This is in large part due to the fact that most web applications used to adopt a clientserver approach in which the computational part is handled by the server. However, with HTML5 and new client-side technologies browsers are capable of handling more complex tasks. This work brings OpenCV to the Web by making it available natively in JavaScript, taking advantage of its efficiency, completeness, API maturity, and its community’s collective knowledge. We developed an automatic approach to compile OpenCV source code into JavaScript in a way that is easier for JavaScript engines to optimize significantly and provide an API that makes it easier for users to adopt the library and develop applications. We were able to translate more than 800 OpenCV functions from different vision categories while achieving near-native performance for most of them.
AN MR BRAIN IMAGES CLASSIFIER VIA PRINCIPAL COMPONENT ANALYSIS AND KERNEL SUPPORT

Automated and accurate classification of MR brain images is extremely important for medical analysis and interpretation. Over the last decade numerous methods have already been proposed. In this paper, we presented a novel method to classify a given MR brain image as normal or abnormal. The proposed method first employed wavelet transform to extract features from images, followed by applying principle component analysis (PCA) to reduce the dimensions of features. The reduced features were submitted to a kernel support vector machine (KSVM). The strategy of Kfold stratified cross validation was used to enhance generalization of KSVM. We chose seven common brain diseases (glioma, meningioma, Alzheimer’s disease, Alzheimer’s disease plus visual agnosia, Pick’s disease, sarcoma, and Huntington’s disease) as abnormal brains, and collected 160 MR brain images (20 normal and 140 abnormal) from Harvard Medical School website. We performed our proposed methods with four different kernels, and found that the GRB kernel achieves the highest classification accuracy as 99.38%. The LIN, HPOL, and IPOL kernel achieves 95%, 96.88%, and 98.12%, respectively. We also compared our method to those from literatures in the last decade, and the results showed our DWT+PCA+KSVM with GRB kernel still achieved the best accurate classification results. The averaged processing time for a 256× 256 size image on a laptop of P4 IBM with 3GHz processor and 2 GB RAM is 0.0448 s. From the experimental data, our method was effective and rapid. It could be applied to the field of MR brain image classification and can assist the doctors to diagnose where a patient is normal or abnormal to certain degrees.  2012,  July 2012, Scheduled 19 August 2012 *  Yudong Zhang (zhangyudongnuaa@gmail.com).
Bilinear classifiers for visual recognition

We describe an algorithm for learning bilinear SVMs. Bilinear classifiers are a discriminative variant of bilinear models, which capture the dependence of data on multiple factors. Such models are particularly appropriate for visual data that is better represented as a matrix or tensor, rather than a vector. Matrix encodings allow for more natural regularization through rank restriction. For example, a rank-one scanning-window classifier yields a separable filter. Low-rank models have fewer parameters and so are easier to regularize and faster to score at run-time. We learn low-rank models with bilinear classifiers. We also use bilinear classifiers for transfer learning by sharing linear factors between different classification tasks. Bilinear classifiers are trained with biconvex programs. Such programs are optimized with coordinate descent, where each coordinate step requires solving a convex program in our case, we use a standard off-the-shelf SVM solver. We demonstrate bilinear SVMs on difficult problems of people detection in video sequences and action classification of video sequences, achieving state-of-the-art results in both.
A Survey of Music Information Retrieval Systems

This survey paper provides an overview of content-based music information retrieval systems, both for audio and for symbolic music notation. Matching algorithms and indexing methods are briefly presented. The need for a TREC-like comparison of matching algorithms such as MIREX at ISMIR becomes clear from the high number of quite different methods which so far only have been used on different data collections. We placed the systems on a map showing the tasks and users for which they are suitable, and we find that existing content-based retrieval systems fail to cover a gap between the very general and the very specific retrieval tasks.
Bilingual Lexicon Induction by Learning to Combine Word-Level and Character-Level Representations

We study the problem of bilingual lexicon induction (BLI) in a setting where some translation resources are available, but unknown translations are sought for certain, possibly domain-specific terminology. We frame BLI as a classification problem for which we design a neural network based classification architecture composed of recurrent long short-term memory and deep feed forward networks. The results show that wordand character-level representations each improve state-of-the-art results for BLI, and the best results are obtained by exploiting the synergy between these wordand character-level representations in the classification model.
Obstacle avoidance and path planning for humanoid robots using stereo vision

This work presents methods for path planning and obstacle avoidance for the humanoid robot QRIO, allowing the robot to autonomously walk around in a home environment. For an autonomous robot, obstacle detection and localization as well as representing them in a map are crucial tasks for the success of the robot. Our approach is based on plane extraction from data captured by a stereo-vision system that has been developed specifically for QRIO. We briefly overview the general software architecture composed of perception, short and long term memory, behavior control, and motion control, and emphasize on our methods for obstacle detection by plane extraction, occupancy grid mapping, and path planning. Experimental results complete the description of our system.
A Study on WEKA Tool for Data Preprocessing , Classification and Clustering

250   The basic principles of data mining is to analyze the data from different angle, categorize it and finally to summarize it. In today's world data mining have increasingly become very interesting and popular in terms of all application. The need for data mining is that we have too much data, too much technology but don't have useful information. Data mining software allows user to analyze data. This paper introduces the key principle of data pre-processing, classification, clustering and introduction of WEKA tool. Weka is a data mining tool. In this paper we are describing the steps of how to use WEKA tool for these technologies. It provides the facility to classify the data through various algorithms.
Outperforming LRU with an adaptive replacement cache algorithm

The self-tuning, low-overhead, scan-resistant adaptive replacement cache algorithm outperforms the least-recently-used algorithm by dynamically responding to changing access patterns and continually balancing between workload recency and frequency features. Caching, a fundamental metaphor in modern computing, finds wide application in storage systems, databases, Web servers, middleware, processors, file systems, disk drives, redundant array of independent disks controllers, operating systems, and other applications such as data compression and list updating. In a two-level memory hierarchy, a cache performs faster than auxiliary storage, but it is more expensive. Cost concerns thus usually limit cache size to a fraction of the auxiliary memory's size.
Semantically Consistent Regularization for Zero-Shot Recognition

The role of semantics in zero-shot learning is considered. The effectiveness of previous approaches is analyzed according to the form of supervision provided. While some learn semantics independently, others only supervise the semantic subspace explained by training classes. Thus, the former is able to constrain the whole space but lacks the ability to model semantic correlations. The latter addresses this issue but leaves part of the semantic space unsupervised. This complementarity is exploited in a new convolutional neural network (CNN) framework, which proposes the use of semantics as constraints for recognition. Although a CNN trained for classification has no transfer ability, this can be encouraged by learning an hidden semantic layer together with a semantic code for classification. Two forms of semantic constraints are then introduced. The first is a loss-based regularizer that introduces a generalization constraint on each semantic predictor. The second is a codeword regularizer that favors semantic-to-class mappings consistent with prior semantic knowledge while allowing these to be learned from data. Significant improvements over the state-of-the-art are achieved on several datasets.