Miracle-dz/UniFAR-FTUs huggingface dataset:
Enabling hierarchy-aware MPI collectives in dynamically changing topologies

Hierarchy-awareness for message-passing has been around since the early 2000s with the emergence of SMP systems. Since then, many works dealt with the optimization of collective communication operations (so-called collectives) for such hierarchical topologies. However, until now, all these optimizations basically assume that the hierarchical topology remains static in a parallel program. In contrast, this paper strives for a discussion of how dynamically changing topologies can be considered during runtime, especially with focus on collective communication patterns. In doing so, the discussion starter for this is the possibility of process migration, e. g. , in virtualized environments where the MPI processes are encapsulated within virtual machines. Consequently, processes originally located on distinct nodes can then (dynamically) become neighbors on the same SMP node. The central subject for the discussion on how such changes can be taken into account for optimized collectives is a new experimental MPI function that we propose and detail within this paper.
Can matrix coherence be efficiently and accurately estimated?

Matrix coherence has recently been used to characterize the ability to extract global information from a subset of matrix entries in the context of low-rank approximations and other sampling-based algorithms. The significance of these results crucially hinges upon the possibility of efficiently and accurately testing this coherence assumption. This paper precisely addresses this issue. We introduce a novel sampling-based algorithm for estimating coherence, present associated estimation guarantees and report the results of extensive experiments for coherence estimation. The quality of the estimation guarantees we present depends on the coherence value to estimate itself, but this turns out to be an inherent property of samplingbased coherence estimation, as shown by our lower bound. In practice, however, we find that these theoretically unfavorable scenarios rarely appear, as our algorithm efficiently and accurately estimates coherence across a wide range of datasets, and these estimates are excellent predictors of the effectiveness of sampling-based matrix approximation on a case-by-case basis. These results are significant as they reveal the extent to which coherence assumptions made in a number of recent machine learning publications are testable.
SEMERGY: Semantic web technology support for comprehensive building design assessment

This paper explores developmental opportunities toward effective evaluation environments for comparative assessment of alternative building design and retrofit options. Such options are to be benchmarked in view of their functional, ecological, and economical performance. Thereby, multiple use cases are to be accommodated, involving a) novice designers, b) experienced professionals, and c) area municipalities. Toward this end, the rather ill-structured nature of available design-relevant information needs to be taken into account. In this context, the web offers extensive amount of potentially useful information. This web-based potential remains, however, mostly unexploited, as its extraction is hampered by lack of sufficient structure in the encapsulation and presentation of the information. The SEMERGY project adapts the semantic web technology as a promising opportunity to improve and expedite the process of information acquisition and collation toward populating design analysis models. of the proposed environment is the incorporation of semantic web technology toward efficient search for and compilation of input information required for comprehensive analysis and evaluation of candidate design options supported by multi-objective decision support methods. 3 BACKGROUND & RELATED WORK Currently there are a number of existing online platforms that support the energy-efficient building planning and refurbishment. Examples of such online services are the Energy Globe platform (Energyglobe 2012) and the energy-saving calculator of "Raiffeisen Bank" (Raiffeisen 2012) which are meant to support the optimization These tools facilitate the input of a simplified building model, which includes building geometry and building components (walls, windows, heating, ventilation, etc.). These tools can accommodate simple use-cases, but limit the end-user to a predefined set of options, i.e., a list of generic templates. The main problem of such systems is the missing link between users' simplified component representations (e.g., "external wall", "window") versus the complexity of specifications of real world products. In other words, it remains the task of end-users, to map such simple notions of building components to appropriate real-world products that meet calculation procedures' informational requirements. Accomplishing this task for the public user is a major barrier to the widespread and effective use of such tools. The SEMERGY system is planning to bridge this gap by providing semantic links between real world products and building model’s abstract concepts and elements. Section 5 of the present paper addresses this approach in more detail (Semantic Web concepts, Linked Open Data). Another challenge pertains to capturing buildings' geometry as models' input information. The aforementioned web-based tools offer only a very limited set of possibilities for the definition of building geometry. To address this problem, SEMERGY provides two different input modalities for novice and expert users (see section 4).
Meshless animation of fracturing solids

We present a new meshless animation framework for elastic and plastic materials that fracture. Central to our method is a highly dynamic surface and volume sampling method that supports arbitrary crack initiation, propagation, and termination, while avoiding many of the stability problems of traditional mesh-based techniques. We explicitly model advancing crack fronts and associated fracture surfaces embedded in the simulation volume. When cutting through the material, crack fronts directly affect the coupling between simulation nodes, requiring a dynamic adaptation of the nodal shape functions. We show how local visibility tests and dynamic caching lead to an efficient implementation of these effects based on point collocation. Complex fracture patterns of interacting and branching cracks are handled using a small set of topological operations for splitting, merging, and terminating crack fronts. This allows continuous propagation of cracks with highly detailed fracture surfaces, independent of the spatial resolution of the simulation nodes, and provides effective mechanisms for controlling fracture paths. We demonstrate our method for a wide range of materials, from stiff elastic to highly plastic objects that exhibit brittle and/or ductile fracture.
Effects of annealing and isothermal crystallization upon crystalline forms of poly(vinylidene fluoride)

Poly(vinylidene fluoride) exists in three crystalline forms. Optimum conditions for preparing form III were established by infrared spectroscopy, differential scanning calorimetry, and x-ray diffraction measurements. Form III is easily obtained by annealing mats of solution-grown crystals of form II at 175–185°C and is also preferentially formed by isothermal crystallization from the melt between 165 and 175°C. Below 165° crystallization of form II is favored. The melting point of form III is higher than that of form II.
Use of a Temporary Shunt as a Salvage Technique for Distal Extremity Amputations Requiring Repair by Vessel Grafting during Critical Ischemia

Background Although the use of temporary shunts in proximal extremity amputations has been reported, no study has described the use of temporary shunts in distal extremity amputations that require vein grafting. Moreover, the total volume of blood loss when temporary shunts are used has not been reported. The aim of this study was to investigate the applicability of a temporary shunt for distal extremity amputations requiring repair by vessel grafting with an ischemia time of >6 hours. This study also aimed to determine the total volume of blood loss when temporary shunts were used. Methods Patients who underwent distal major extremity replantation and/or revascularization with a vessel graft and who experienced ischemia for 6–8 hours between 2013 and 2014 were included in the study. A 6-Fr suction catheter was cut to 5 cm in length after the infusion of heparin, and secured with a 5-0 silk suture between the distal and the proximal ends of the artery. While bleeding continued, the bones were shortened and fixed. After the complete restoration of circulation, the arterial shunt created using the catheter was also repaired with a vein graft. Results Six patients were included in this study. The mean duration of ischemia was 7.25 hours. The mean duration of suction catheter use during limb revascularization was 7 minutes. The mean transfusion volume was 7.5 units. No losses of the extremity were observed. Conclusions This procedure should be considered in distal extremity amputations requiring repair by vessel grafting during critical ischemia.
From Network Interface to Multithreaded Web Applications

Many verifications of realistic software systems are monolithic, in the sense that they define single global invariants over complete system state. More modular proof techniques promise to support reuse of component proofs and even reduce the effort required to verify one concrete system, just as modularity simplifies standard software development. This paper reports on one case study applying modular proof techniques in the Coq proof assistant. To our knowledge, it is the first modular verification certifying a system that combines infrastructure with an application of interest to end users. We assume a nonblocking API for managing TCP networking streams, and on top of that we work our way up to certifying multithreaded, database-backed Web applications. Key verified components include a cooperative threading library and an implementation of a domain-specific language for XML processing. We have deployed our case-study system on mobile robots, where it interfaces with off-the-shelf components for sensing, actuation, and control.
A new public key cryptosystem based on higher residues

This paper describes a new public-key cryptosystem based on the hardness of computing higher residues modulo a composite RSA integer. We introduce two versions of our scheme, one deterministic and the other probabilistic. The deterministic version is practically oriented: encryption amounts to a single exponentiation w.r. t. a modulus with at least 768 bits and a 160-bit exponent. Decryption can be suitably opti- mized so as to become less demanding than a couple RSA decryptions. Although slower than RSA, the new scheme is still reasonably compet- itive and has several specific applications. The probabilistic version ex- hibits an homomorphic encryption scheme whose expansion rate is much better than previously proposed such systems. Furthermore, it has se- mantic security, relative to the hardness of computing higher residues for suitable moduli.
ReFLEX: Block Atomic Execution on Conventional ISA Cores

Modern multicore chips target thread-level parallelism at the expense of increasing instruction-level parallelism from single threaded programs. While recent work has attempted to construct a wide-ILP machine from multiple simple cores, these approaches suffer from ISA overheads or scalability challenges. In this paper, we describe an architecture that is inspired by the scalability and flexibility of the TFLEX architecture, yet elides the unorthodox ISA and the overheads that stem from its dataflow execution model. Our results focus on the tradeoff between near out-of-order execution (small out-of-order window within a block of instructions) and far out-of-order execution across blocks. Experiments indicate that a small out-of-order window combined with block-level speculation enables our proposed ReFLEX architecture to achieve comparable performance and flexibility as TFLEX yet with simpler cores and a more conventional ISA.
Looking through the eyes of the painter: from visual perception to non-photorealistic rendering

In this paper we present a brief overview of the processing in the primary visual cortex, the multi-scale line/edge and keypoint representations, and a model of brightness perception. This model, which is being extended from 1D to 2D, is based on a symbolic line and edge interpretation: lines are represented by scaled Gaussians and edges by scaled, Gaussian-windowed error functions. We show that this model, in combination with standard techniques from graphics, provides a very fertile basis for non-photorealistic image rendering.
TELECOM ParisTech at ImageClef 2009: Large Scale Visual Concept Detection and Annotation Task

In this paper we describe the participation of TELECOM ParisTech in the Large Scale Visual Concept Detection and Annotation Task at the ImageClef 2009 challenge. This year, the focus was in the extension of (i) the amount of data available for tr aining and testing, and (ii) the number of concepts to be annotated. We use Canonical Correlation Analysis in order to infer a latent space where text and visual description are highly correlated. Starting from a visual description of a test image, we first map it into the latent spa ce, then we predict the underlying text features (and also annotations) which best fit the visua l ones in the latent space. Our method is very fast while achieving good results.
Fragile States of Mind: Neuroticism, Vulnerability and the Long-Term Outcome of Depression

Background This paper considers the extent to which vulnerability to the outcome of major affective disorder is conferred through personality deviance. Results are based upon a 12 year longitudinal follow-up study of 80 patients with a primary depressive disorder, originally selected from a consecutive series seeking care at a hospital in Scotland. Methods The study included detailed clinical course assessments in association with the formal application of diagnostic criteria. Assessments on recovery from the index episode included measures of self-confidence and of neuroticism. Experience of selected severe loss events over the study period was also determined. Results Limited self-confidence was strongly related, unlike neuroticism, to the subsequent first recurrence of affective disorder. Relationships between psychosocial, clinical and demographic factors and long-term outcome revealed psychosocial factors, in particular neuroticism and a lack of self-confidence, to have the greatest prognostic significance. Conclusions These results reveal the heightened risk over the long-term of a poor outcome for depressive disorder consequent upon measures of personality deviance and of exposure to adversity. While giving only limited support to narrowly defined psychosocial models of depression, they clarify the risk gradients involved and through this may provide a firmer basis than hitherto for relapse prevention.
α1 Subunit-Containing GABA Type A Receptors in Forebrain Contribute to the Effect of Inhaled Anesthetics on Conditioned Fear

Inhaled anesthetics are believed to produce anesthesia by their actions on ion channels. Because inhaled anesthetics robustly enhance GABA A receptor (GABAA-R) responses to GABA, these receptors are considered prime targets of anesthetic action. However, the importance of GABAA-Rs and individual GABAA-R subunits to specific anesthetic-induced behavioral effects in the intact animal is unknown. We hypothesized that inhaled anesthetics produce amnesia, as assessed by loss of fear conditioning, by acting on the forebrain GABAA-Rs that harbor the α1 subunit. To test this, we used global knockout mice that completely lack the α1 subunit and forebrain-specific, conditional knockout mice that lack the α1 subunit only in the hippocampus, cortex, and amygdala. Both knockout mice were 75 to 145% less sensitive to the amnestic effects of the inhaled anesthetic isoflurane. These results indicate that α1-containing GABAA-Rs in the hippocampus, amygdala, and/or cortex influence the amnestic effects of inhaled anesthetics and may be an important molecular target of the drug isoflurane.
Data Linkage from Clinical to Study Databases via an R Data Warehouse User Interface

Summary Background: Data that needs to be documented for clinical studies has often been acquired and documented in clinical routine. Usually this data is manually transferred to Case Report Forms (CRF) and/or directly into an electronic data capture (EDC) system. Objectives: To enhance the documentation process of a large clinical follow-up study targeting patients admitted for acutely decompensated heart failure by accessing the data created during routine and study visits from a hospital information system (HIS) and by transferring it via a data warehouse (DWH) into the study‘s EDC system. Methods: This project is based on the clinical DWH developed at the University of Würzburg. The DWH was extended by several new data domains including data created by the study team itself. An R user interface was developed for the DWH that allows to access its source data in all its detail, to transform data as comprehensively as possible by R into study-specific variables and to support the creation of data and catalog tables. Results: A data flow was established that starts with labeling patients as study patients within the HIS and proceeds with updating the DWH with this label and further data domains at a daily rate. Several study-specific variables were defined using the implemented R user interface of the DWH. This system was then used to export these variables as data tables ready for import into our EDC system. The data tables were then used to initialize the first 296 patients within the EDC system by pseudonym, visit and data values. Afterwards, these records were filled with clinical data on heart failure, vital parameters and time spent on selected wards. Conclusions: This solution focuses on the comprehensive access and transformation of data for a DWH-EDC system linkage. Using this system in a large clinical study has demonstrated the feasibility of this approach for a study with a complex visit schedule.
Early History of Gauge Theories and Kaluza-Klein Theories, with a Glance at Recent Developments

One of the major developments of twentieth century physics has been the gradual recognition that a common feature of the known fundamental interactions is their gauge structure. In this article the authors review the early history of gauge theory, from Einstein's theory of gravitation to the appearance of non-abelian gauge theories in the fifties. The authors also review the early history of dimensional reduction, which played an important role in the developement of gauge-theory. A description is given how, in recent times, the ideas of gauge-theory and dimensional reduction have emerged naturally in the context of string theory and non-commutative geometry.
AN INNOVATIVE VOLUME BASED VIDEO FEATURE EXTRACTION TECHNIQUE

Based on the video frames, a spatial-temporal volume data structure represents more flexible processing methods than traditional 2D sequential images approach in computer vision. This paper describes the data structure of the spatial-temporal volume and the feature volume coming from the original video data. A compressed volume structure called a feature video is presented showing how a feature volume can be build based on the sequential frames. The existent 3D volume processing methods such as slice processing, 3D filters and CFD methods are also introduced in this paper. As a practical application, human gait analysis based on volume slice processing is described. This includes the video capture, volume organized and the slice feature extraction. The result of experimental data shows the different features between different behaviors of gait.
Familial Aggregation of Left Ventricular Geometry and Association With Parental Heart Failure: The Framingham Heart Study

Background—Data regarding the familial aggregation of left ventricular (LV) geometry and its relations to parental heart failure (HF) are limited. Methods and Results—We evaluated concordance of LV geometry within 1093 nuclear families in 5758 participants of the original (parents) (n=2351) and offspring (n=3407) cohorts of the Framingham Heart Study undergoing routine echocardiography in mid- to late adulthood. LV geometry was categorized based on cohort- and sex-specific 80th percentile cutoffs of LV mass and relative wall thickness (RWT) into normal (both <80th percentile), concentric remodeling (LV mass <80th percentile; RWT >80th percentile), concentric hypertrophy (both >80th percentile), and eccentric hypertrophy (LV mass >80th percentile; RWT <80th percentile). Within nuclear families, LV geometry was concordant among related pairs (parent-child, sibling-sibling) (P=0.0015) but not among unrelated spousal pairs (P=0.60), a finding that remained unchanged after adjusting for clinical covariates known to influence LV remodeling (age, systolic blood pressure, body mass index), excluding individuals with prevalent HF and myocardial infarction, and varying the thresholds for defining LV geometry. The prevalence of abnormal LV geometry was higher in family members of affected individuals, with recurrence risks of 1.4 for concentric remodeling (95% CI, 1.2 to 1.7) and eccentric hypertrophy (95% CI, 1.1 to 1.8) and 3.9 (95% CI, 3.2 to 4.6) for concentric hypertrophy. In a subset of 1497 offspring, we observed an association between parental HF (n=458) and eccentric hypertrophy in offspring (P<0.0001). Conclusions—Our investigation of a 2-generational community-based sample demonstrates familial aggregation of LV geometry, with the greatest recurrence risk for concentric LV geometry, and establishes an association between eccentric LV geometry and parental HF.
Memory-Based Hypothesis Formation: Heuristic Learning of Commonsense Causal Relations from Text

Abstract We present a memory-based approach to learning commonsense causal relations from episodic text. The method relies on dynamic memory that consists of events, event schemata, episodes, causal heuristics, and causal hypotheses. The learning algorithms are based on applying causal heuristics'to precedents of new information. The heuristics are derived from principles of causation, and, to a limited extent, from domain-related causal reasoning. Learning is defined as finding—and later augmenting—inter-episodal and intea-episodal causal connections. The learning algorithms enable inductive generalization of causal associations into AND/OR graphs. The methodology has been implemented and tested in the program NEXUS.
Computational Aspects in Gene Expression Analysis

Acknowledgements First and foremost, I would like to thank my supervisor prof. Nir Friedman for bringing me into the world of research and showing me the ways of science. I would also like to thank my dear friends in the lab: and Ilan Wapinski, for helping me in each and every step; without them, this work would have never been written. I am deeply thankful to Ronnen Segman, Naftali Kaminski and the rest of the PTSD team, for proving how fruitful an interdisciplinary collaboration can be. I am also grateful to Zohar Itzhaki for his part in the investigation of classification significance, and for working together. I am indebted to my family and friends for their patience and support along the way. And last but not least, I would like to thank Eli, for his wise advice, enormous support and infinite love.