Miracle-dz/UniFAR-FTUs huggingface dataset:
Spectral Hashing

Semantic hashing[1] seeks compact binary codes of data-points so that the Hamming distance between codewords correlates with semantic similarity. In this paper, we show that the problem of finding a best code for a given dataset is closely related to the problem of graph partitioning and can be shown to be NP hard. By relaxing the original problem, we obtain a spectral method whose solutions are simply a subset of thresholded eigenvectors of the graph Laplacian. By utilizing recent results on convergence of graph Laplacian eigenvectors to the Laplace-Beltrami eigenfunctions of manifolds, we show how to efficiently calculate the code of a novel data-point. Taken together, both learning the code and applying it to a novel point are extremely simple. Our experiments show that our codes outperform the state-of-the art.
On the Data-Driven Combinatorial Optimization with Incomplete Information: a Distributionally Robust Optimization Approach

In this study we analyze linear combinatorial optimization problems where the cost vector is not known a priori, but is only observable through a ﬁnite data set. In contrast to the related studies, we presume that the number of observations with respect to particular components of the cost vector may vary. The goal is to ﬁnd a procedure that transforms the data set into an estimate of the expected value of the objective function (which is referred to as a prediction rule ) and a procedure that retrieves a candidate decision (which is referred to as a prescription rule ). We aim at ﬁnding the least conservative prediction and prescription rules, which satisfy some speciﬁed asymptotic guarantees. We demonstrate that the resulting vector optimization problems admit a weakly optimal solution, which can be obtained by solving a particular distributionally robust optimization problem. Speciﬁcally, the decision-maker may optimize the worst-case expected loss across all probability distributions with given component-wise relative entropy distances from the empirical marginal distributions. Finally, we perform numerical experiments to analyze the out-of-sample performance of the proposed solution approach.
FXPAL Interactive Search Experiments for TRECVID 2007

We submitted six interactive search runs for TRECVID2007, including 2 single user and 4 collaborative runs. In one single-user run (FXPAL MMA) the searchers had access to all resources including text search, text similarity, image similarity, and concept similarity search. In the other single-user submission (FXPAL MMV) the transcripts were not available and only features derived directly from the audio-visual content were available. This is a typical baseline for the manual and automatic search systems, but has been a less popular variation among the interactive search submissions. The other submitted runs (FXPAL CO*) employed a novel real-time, multi-user, collaborative search system. The complete set of submitted runs in priority order with system names and brief descriptions:
Visual Simulation of Smoke RonaldFedkiw

In this paper, we propose a new approach to numerical smoke simulation for computer graphics applications. The method proposed here exploits physics unique to smoke in order to design a numerical method that is both fast and efﬁcient on the relatively coarse grids traditionally used in computer graphics applications (as compared to the much ﬁner grids used in the computational ﬂuid dynamics literature). We use the inviscid Euler equations in our model, since they are usually more appropriate for gas modeling and less computationally intensive than the viscous Navier-Stokes equations used by others. In addition, we introduce a physically consistent vorticity conﬁnement term to model the small scale rolling features characteristic of smoke that are absent on most coarse grid simulations. Our model also correctly handles the interaction of smoke with moving objects.
Improving Mobile Networking with Concurrent Wi-Fi Connections

Achieving ubiquitous connectivity or high aggregate throughput using a series of Wi-Fi access points can cause serious performance problems for highly mobile clients. While data transfer using a single access point at a time is insufficient for supporting delayand throughputsensitive applications, leveraging concurrent data transfers through multiple access points offers a plausible alternative. To this end, we design, implement, and evaluate a system that establishes and maintains concurrent connections to 802.11 APs in a mobile environment. We demonstrate that existing multi-AP solutions do not perform well in mobile settings due to limitations imposed by the association and dhcp processes and propose an alternative design. We have implemented and evaluated our system on a vehicular testbed. Our results show that our system provides manifold improvements in throughput and connectivity over stock WiFi implementations. We compare our results against measurements of real user needs in mobile settings in terms of application use and desired session length.
Nonlinear Dynamics of Interest Rate and Inflation

According to several empirical studies US inflation and nominal interest rates as well as the real interest rate can be described as unit root processes. These results imply that nominal interest rates and expected inflation do not move one-for-one in the long run, which is incongruent with theoretical models. In this paper we introduce a new nonlinear bivariate mixture autoregressive model that seems to fit quarterly US data (1953 : II-2004 : IV) reasonably well. It is found that the three-month Treasury bill rate and inflation share a common nonlinear component that explains a large part of their persistence. The real interest rate is devoid of this component, indicating one-for-one movement of the nominal interest rate and inflation in the long run and, hence, stationarity of the real interest rate. Copyright © 2006 John Wiley & Sons, Ltd.
Dont call me a street child. Estimation and characteristics of urban street children in Georgia.

This study is the first comprehensive assessment of street children ever done in Georgia and sets a unique precedent as few such studies have been carried out anywhere in the world. The research aimed to provide estimated numbers of street children in the four target urban locations and describe their characteristics so that evidence-based policy and programmatic recommendations could be drawn. The study used a three stage approach: a) pre-surveillance Time-Location Mapping; b) quantitative Point-Count Estimate and; c) face-to-face interviewing. All three stages were implemented during the three months of June September and November of 2007. Data entry and cleaning and data analysis took place in February / March of 2008. (Excerpt)
BIOINFORMATICS ORIGINAL

Motivation: Controlled vocabularies such as the Medical Subject Headings (MeSH) thesaurus and the Gene Ontology (GO) provide an efﬁcient way of accessing and organizing biomedical information by reducing the ambiguity inherent to free-text data. Different methods of automating the assignment of MeSH concepts have been proposed to replace manual annotation, but they are either limited to a small subset of MeSH or have only been compared with a limited number of other systems. Results: We compare the performance of six MeSH classiﬁcation systems [MetaMap, EAGL, a language and a vector space model-based approach, a K-Nearest Neighbor (KNN) approach and MTI] in terms of reproducing and complementing manual MeSH annotations. A KNN system clearly outperforms the other published approaches and scales well with large amounts of text using the full MeSH thesaurus. Our measurements demonstrate to what extent manual MeSH annotations can be reproduced and how they can be complemented by automatic annotations. We also show that a statistically signiﬁcant improvement can be obtained in information retrieval (IR) when the text of a user’s query is automatically annotated with MeSH concepts, compared to using the original textual query alone. Conclusions: The annotation of biomedical texts using controlled vocabularies such as MeSH can be automated to improve text-only IR. Furthermore, the automatic MeSH annotation system we propose is highly scalable and it generates improvements in IR comparable with those observed for manual annotations.
Formalism of the access control model based on the marked Petri Nets

Access control system is a mandatory step in the security policy implementation. Accesses carried out according to certain modes (read, write .) by subjects (users, process, programs) on objects (data, files, programs). To specify, implement and reason within a formal framework allow ensuring the correction of the programs that in turn guarantee the proper functioning of this policy. This article deals, on the one hand, with designing a model within a formal framework in which both the comparison and the composition of access control policies can be expressed, and on the other hand, with elaborating new techniques ensuring the re-use of this model. Such formal models have already been developed but suffer from too many constraints, are not expressive enough and are specific to professional activities. They all deserve to be reconsidered and extended within a uniform framework in order to study their links and to come up with re-use techniques. The main object of this work is the use of Petri Nets for system modeling. Our results enable us to combine formalism and new access control policies. Moreover, the access control policies are considered as the instances within a more general scheme.
Isoprene and monoterpenes over Russia and their impacts in tropospheric ozone formation

Ground-based levels of important biogenic volatile organic compounds (BVOCs), isoprene and monoterpenes, as well as NO x and O 3 measured simultaneously along the Trans-Siberian railway on a mobile railway laboratory in TROICA-12 campaign in summer 2008 are analyzed. It was shown that the highest isoprene (≥ 2.5 ppb) concentration was observed in the daytime in the Far East region where several favorable factors for its emissions occurred: a large amount of deciduous forests, high temperatures (>28°C) and light conditions. Maximum levels of monoterpenes (up to 3-9 ppb) along the Trans-Siberian railway were observed during the nighttime in the Ural region and in Central Siberia where coniferous vegetation is located. To evaluate the relative importance of isoprene and monoterpenes in ground-level ozone formation in Russian cities along the Trans-Siberian railway, where high NO x concentration leads to tropospheric ozone generation, daytime ozone-forming potential (OFP) was calculated. The chemical losses of the studied BVOCs during their transport from sources to the measurement point were taken into account. Calculated OFPs due to isoprene (OFP iso ) and monoterpenes (OFP mono ) along the Trans-Siberian railway are in average 15±13 and 18±25 ppbv of ozone, respectively. The highest OFP iso (up to 40 ppbv) were estimated in Central Siberia and in the Far East. OFP mono was the highest in the regions of coniferous vegetation, Ural and Central Siberia, and reached 80 ppbv. In the most cities along the Trans-Siberian railway, where high NO x concentration (10-20 ppbv) along with high daytime temperatures (>25°C) were observed, monoterpenes made a main contribution to tropospheric ozone formation. Only in the Far East cities, where the largest deciduous vegetation area of the Trans-Siberian railway is located, isoprene played the main role in tropospheric ozone generation. It was also noted that OFP iso increases with the population-size of the cities. It can be either due to the greater proportion of deciduous vegetation in the large cities along the Trans-Siberian railway or due to the impact of anthropogenic isoprene source. OFP mono the lowest in the medium cities and the highest in the small ones.
Contextualizing the information space in Federated Digital Libraries

Rapid growth in the volume of documents, their diversity, and terminologicalvariationsrender federated digitallibrariesincreas-ingly di(cid:14)cult to manage. Suitable abstraction mechanisms are required to construct meaningful and scalable document clusters, forming a cross-digital library information space for browsing and semantic searching. This paper addresses the above issues, proposes a distributed semantic framework that achieves a logical partitioning of the information space according to topic areas, and provides facilities to contextualize and landscape the available document sets in subject-speci(cid:12)c categories.
ENSO Weather and Coral Bleaching on the Great Barrier Reef, Australia

The most devastating mass coral bleaching has occurred during El Niño events, with bleaching reported to be a direct result of increased sea surface temperatures (SSTs). However, El Niño itself does not cause SSTs to rise in all regions that experience bleaching. Nor is the upper ocean warming trend of 0.11°C per decade since 1971, attributed to global warming, sufficient alone to exceed the thermal tolerance of corals. Here we show that weather patterns during El Niño that result in reduced cloud cover, higher than average air temperatures and higher than average atmospheric pressures, play a crucial role in determining the extent and location of coral bleaching on the world's largest coral reef system, the World Heritage Great Barrier Reef (GBR), Australia. Accordingly, synoptic‐scale weather patterns and local atmosphere‐ocean feedbacks related to El Niño–Southern Oscillation (ENSO) and not large‐scale SST warming due to El Niño alone and/or global warming are often the cause of coral bleaching on the GBR.
The cognitive modeling of human behavior : Why a model is ( sometimes ) better than 10 , 000 words Action

In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: Editorial The cognitive modeling of human behavior: Why a model is (sometimes) better than 10,000 words
a l

In this paper, we propose a two-pass error-resilience transcoding scheme based on adaptive intra-refresh for inserting error-resilience features to a compressed video at the intermediate transcoder of a three-tier streaming system. The proposed transcoder adaptively adjusts the intra-refresh rate according to the video content and the channel’s packet-loss rate to protect the most important macroblocks against packet loss. In this work, we consider the problem of multicast of video to multiple clients having disparate channel-loss proﬁles. We propose a MINMAX loss rate estimation scheme to determine a single intra-refresh rate for all the clients in a multicast group. For the scenario that a quality variation constraint is imposed on the users, we also propose a grouping method to partition a multicast group of heterogeneous users into a minimal number of subgroups to minimize the channel bandwidth consumption while meeting the quality variation constraint. Experimental results show that the proposed method can effectively mitigate the error propagation due to packet loss as well as achieve fairness among clients in a multicast.
Automatic annotation of organellar genomes with DOGMA

The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar (plant chloroplast and animal mitochondrial) genomes. It is a Web-based package that allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. DOGMA provides a graphical user interface for viewing and editing annotations. Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank.
A Secrecy-Preserving Language for Distributed and Object-Oriented Systems January 25, 2019

In modern systems it is often necessary to distinguish between confidential (low-level) and non-confidential (high-level) information. Confidential information should be protected and not communicated or shared with low-level users. The non-interference policy is an information flow policy stipulating that low-level viewers should not be able to observe a difference between any two executions with the same low-level inputs. Only high-level viewers may observe confidential output. This is a non-trivial challenge when considering modern distributed systems involving concurrency and communication. The present paper addresses this challenge, by choosing language mechanisms that are both useful for programming of distributed systems and allow modular system analysis. We consider a general concurrency model for distributed systems, based on concurrent objects communicating by asynchronous methods. This model is suitable for modeling of modern service-oriented systems, and gives rise to efficient interaction avoiding active waiting and low-level synchronization primitives such as explicit signaling and lock operations. This concurrency model has a simple semantics and allows us to focus on information flow at a high level of abstraction, and allows realistic analysis by avoiding unnecessary restrictions on information flow between confidential and non-confidential data. Due to the non-deterministic nature of concurrent and distributed systems, we define a notion of interaction non-interference policy tailored to this setting. We provide two kinds of static analysis: a secrecy-type system and a trace analysis system, to capture inter-object and network level communication, respectively. We prove that interaction non-interference is satisfied by the combination of these analysis techniques. Thus any deviation from the policy caused by implicit information leakage visible through observation of network communication patterns, can be detected. The contribution of the paper lies in the definition of the notion of interaction non-interference, and in the formalization of a secrecy type system and a static trace analysis that together ensure interaction non-interference. We also provide several versions of a main example (a news subscription service) to demonstrate network leakage.
Information Technology and Organizational Contexts: Orienting Our Work Along Key Dimensions

The locus of the Information Systems discipline is at the intersection of organizations, people, and those technologies and systems specifically related to the acquisition, storage, analysis, interpretation, and communication of data. However, much of the published research is trifurcated, emphasizing one dimension and virtually ignoring the others. We argue that a deeper understanding of and an appropriate emphasis on the technological dimension, the information technology artifact, will significantly benefit research in the discipline. By doing this in a manner that explicitly recognizes the organizational and human contexts, we will better orient our work toward the needs of our various constituencies. We look at two specific examples of potentially rich areas of enquiry: workflow management and the semantic Web. Using a design science paradigm, we describe how these two can serve as exemplars to address the key research concerns of the discipline. We conclude by discussing the roles that authors, journals, and the discipline itself can play in addressing the challenges that are presented.
Impact of habitual intake of glucosamine, fresh fruit, and tea on the risk of urolithiasis: A two-sample Mendelian randomization study

Dietary patterns have a significant impact on the occurrence of urolithiasis. This study aimed to investigate the causal relationships between the consumption of glucosamine, fresh fruits, and tea, and the predisposition to urinary stones using a Mendelian randomization (MR) approach. Genetic proxies for these dietary factors were obtained from the UK Biobank, while the summary data for urolithiasis genome-wide association analyses were sourced from the FinnGen consortium. Five MR methodologies, namely inverse variance weighted (IVW), MR-Egger regression, weighted median, weighted mode, and simple mode, were employed in the analysis. To validate the findings, sensitivity evaluations such as the MR-PRESSO disruption test and Cochran Q test for heterogeneity were performed. The IVW method showed that glucosamine consumption had a strong inverse association with urolithiasis risk (Odds Ratio [OR] = 0.006, 95% Confidence Interval [CI] 0.0001–0.287, P = .009), surpassing the associations of fresh fruits (OR = 0.464, 95% CI 0.219–0.983, P = .045) and tea (OR = 0.550, 95% CI 0.345–0.878, P = .012). These findings were consistent when verified using alternative MR techniques, and the sensitivity analyses further supported their credibility. The results of this MR analysis demonstrate that regular consumption of glucosamine, fresh fruits, and tea is inversely correlated with the risk of developing urolithiasis.
Candida albicans translocation through the intestinal epithelial barrier is promoted by fungal zinc acquisition and limited by NFκB-mediated barrier protection

The opportunistic fungal pathogen Candida albicans thrives on human mucosal surfaces as a harmless commensal, but frequently causes infections under certain predisposing conditions. Translocation across the intestinal barrier into the bloodstream by intestine-colonizing C. albicans cells serves as the main source of disseminated candidiasis. However, the host and microbial mechanisms behind this process remain unclear. In this study we identified fungal and host factors specifically involved in infection of intestinal epithelial cells (IECs) using dual-RNA sequencing. Our data suggest that host-cell damage mediated by the peptide toxin candidalysin-encoding gene ECE1 facilitates fungal zinc acquisition. This in turn is crucial for the full virulence potential of C. albicans during infection. IECs in turn exhibit a filamentation- and damage-specific response to C. albicans infection, including NFκB, MAPK, and TNF signaling. NFκB activation by IECs limits candidalysin-mediated host-cell damage and mediates maintenance of the intestinal barrier and cell-cell junctions to further restrict fungal translocation. This is the first study to show that candidalysin-mediated damage is necessary for C. albicans nutrient acquisition during infection and to explain how IECs counteract damage and limit fungal translocation via NFκB-mediated maintenance of the intestinal barrier.