pinecone/core-2020-05-10-deduplication huggingface dataset:
A computational pipeline to identify new potential regulatory motifs in melanoma progression

Molecular biology experiments allow to obtain reliable data about the expression of different classes of molecules involved in several cellular processes. This information is mostly static and does not give much clue about the causal relationships (i.e., regulation) among the different molecules. A typical scenario is the presence of a set of modulated mRNAs (up or down regulated) along with an over expression of one or more small non-coding RNAs molecules like miRNAs. To computationally identify the presence of transcriptional or post-transcriptional regulatory modules between one or more miRNAs and a set of target modulated genes, we propose a computational pipeline designed to integrate data from multiple online data repositories. The pipeline produces a set of three types of putative regulatory motifs involving coding genes, intronic miRNAs, and transcription factors. We used this pipeline to analyze the results of a set of expression experiments on a melanoma cell line that showed an over expression of miR-214 along with the modulation of a set of 73 other genes. The results suggest the presence of 27 putative regulatory modules involving miR-214, NFKB1, SREBPF2, miR-33a and 9 out of the 73 miR-214 modulated genes (ALCAM, POSTN, TFAP2A, ADAM9, NCAM1, SEMA3A, PVRL2, JAG1, EGFR1). As a preliminary experimental validation we focused on 9 out of the 27 identified regulatory modules that involve miR-33a and SREBF2. The results confirm the importance of the predictions obtained with the presented computational approac
On the Move to Meaningful Internet Systems: OTM 2015 Workshops
 : 
Confederated International Workshops: OTM Academy, OTM Industry Case Studies Program, EI2N, FBM, INBAST, ISDE, META4eS, and MSC 2015, Rhodes, Greece, October 26-30, 2015. Proceedings

International audienceThis volume constitutes the refereed proceedings of the following 8 International Workshops: OTM Academy; OTM Industry Case Studies Program; Enterprise Integration, Interoperability, and Networking, EI2N; International Workshop on Fact Based Modeling 2015, FBM; Industrial and Business Applications of Semantic Web Technologies, INBAST; Information Systems, om Distributed Environment, ISDE; Methods, Evaluation, Tools and Applications for the Creation and Consumption of Structured Data for the e-Society, META4eS; and Mobile and Social Computing for collaborative interactions, MSC 2015. These workshops were held as associated events at OTM 2015, the federated conferences "On The Move Towards Meaningful Internet Systems and Ubiquitous Computing", in Rhodes, Greece, in October 2015.The 55 full papers presented together with 3 short papers and 2 popsters were carefully reviewed and selected from a total of 100 submissions. The workshops share the distributed aspects of modern computing systems, they experience the application pull created by the Internet and by the so-called Semantic Web, in particular developments of Big Data, increased importance of security issues, and the globalization of mobile-based technologies
Thoughts on 3D Digital Subplane Recognition and Minimum-Maximum of a Bilinear Congruence Sequence

International audienceIn this paper we take first steps in addressing the 3D Digital Subplane Recognition Problem. Let us consider a digital plane P : 0 ≤ ax + by − cz + d < c (w.l.o.g. 0 ≤ a ≤ b ≤ c) and a finite subplane S of P dened as the points (x, y, z) of P such that (x, y) ∈ [x0, x1] × [y0, y1]. The Digital Subplane Recognition Problem consists in determining the characteristics of the subplane S in less than linear (in the number of voxels) complexity. We discuss approaches based on remainder values ax+by+d c , (x, y) ∈ [x0, x1] × [y0, y1] of the subplane. This corresponds to a bilinear congruence sequence. We show that one can determine if the sequence contains a value in logarithmic time. An algorithm to determine the minimum and maximum of such a bilinear congruence sequence is also proposed. This is linked to leaning points of the subplane with remainder order conservation properties. The proposed algorithm has a complexity in, if m = x1 −x0 < n = y1 −y0, O(m log (min(a, c − a)) or O(n log (min(b, c − b)) otherwise
Incremental Updating of 3D Topological Maps to Describe Videos

International audienceA topological map is an efficient mathematical model for representing an image subdivision where all cells and adjacency relations between elements are represented. It has been proved to be a very good tool for video processing when video is seen as a 3D image. However the construction of a topological map for representing a video needs the availability of the complete image sequence. In this paper we propose a procedure for online updating a topological map in order to build it as the video is produced, allowing to use it in real time
Optimization of Low-Dose Tomography via Binary Sensing Matrices

X-ray computed tomography (CT) is one of the most widely used imaging modalities for diagnostic tasks in the clinical application. As X-ray dosage given to the patient has potential to induce undesirable clinical consequences, there is a need for reduction in dosage while maintaining good quality in reconstruction. The present work attempts to address low-dose tomography via an optimization method. In particular, we formulate the reconstruction problem in the form of a matrix system involving a binary matrix. We then recover the image deploying the ideas from the emerging field of compressed sensing (CS). Further, we study empirically the radial and angular sampling parameters that result in a binary matrix possessing sparse recovery parameters. The experimental results show that the performance of the proposed binary matrix with reconstruction using TV minimization by Augmented Lagrangian and ALternating direction ALgorithms (TVAL3) gives comparably better results than Wavelet based Orthogonal Matching Pursuit (WOMP) and the Least Squares solution
Relative Convex Hull Determination from Convex Hulls in the Plane

A new algorithm for the determination of the relative convex hull in the
plane of a simple polygon A with respect to another simple polygon B which
contains A, is proposed. The relative convex hull is also known as geodesic
convex hull, and the problem of its determination in the plane is equivalent to
find the shortest curve among all Jordan curves lying in the difference set of
B and A and encircling A. Algorithms solving this problem known from
Computational Geometry are based on the triangulation or similar decomposition
of that difference set. The algorithm presented here does not use such
decomposition, but it supposes that A and B are given as ordered sequences of
vertices. The algorithm is based on convex hull calculations of A and B and of
smaller polygons and polylines, it produces the output list of vertices of the
relative convex hull from the sequence of vertices of the convex hull of A.Comment: 15 pages, 4 figures, Conference paper published. We corrected two
  typing errors in Definition 2: $I_S$ has to be defined based on $O_S$, and
  $I_E$ has to be defined based on $O_E$ (not just using $O$). These errors
  appeared in the text of the original conference paper, which also contained
  the pseudocode of an algorithm where $I_S$ and $I_E$ appeared as correctly
  define
On the Globalization of Domain-Specific Languages

International audienceIn the software engineering community, research on domain-specific languages (DSLs) is focused on providing technologies for designing languages and tools that enable domain experts to develop system solutions eciently. Unfortunately, the current lack of support to explicitly relate concepts expressed in di↵erent DSLs makes it dicult for software and system engineers to reason about information distributed across models or programs describing di↵erent system aspects, at di↵er-ent levels of abstraction. Supporting the coordinated use of DSLs is what we call the globalization of DSLs. In this chapter, we introduce a grand challenge of the globalization of DSLs, and we present a few motivating scenarios for such a grand chalenge
Conceptual Model of the Globalization for Domain-Specific Languages

International audienceDomain Specific Languages (DSL) have received some prominence recently. Designing a DSL and all their tools is still cumbersome and lots of work. Engineering of DSLs is still at infancy, not even the terms have been coined and agreed on. In particular globalization and all its consequences need to be precisely defined and discussed. This chapter provides a definition of the relevant terms and relates them, such that a conceptual model emerges. The authors think that this clarification of terms and the meaning will foster the field of ecient DSL definition and evolution in the future. 1 Towards a Conceptual Model Of Globalization Software Engineering, unlike other engineering disciplines, such as Civil, Chemical or Material, deals with constructing precise descriptions of highly complex systems, where each new application contains structure and behaviour that is essentially unique. In essence, each new application is a novel theory of structure and execution, and requires a way of expressing this meta-information [2]. Traditionally General Purpose Languages (GPLs) have been used to encode the theories in executable, but implicit forms (e.g., libraries). However recent advances in language engineering technologies have made it possible to develop Domain Specific Languages (DSLs) each of which is more suited to encoding theories relating to specific application domains [4]. Modern applications tend to be large, heterogeneous and distributed, involving the use of many di↵erent languages including mixtures of GPLs and DSLs. Given that an application consists of many di↵erent subsystems written in di↵erent languages, there is a requirement to ensure that the languages and therefore the subsystems work together e↵ectively and must share the same concepts (theories). Subsystems written in DSLs are attractive because the languages can provide better support for the specific application domains, however they tend to be less mature than their GPL counterparts and therefore there is an interesting research challenge: how to achieve language globalization [1
Motivating Use Cases for the Globalization of DSLs

International audienceThe development of complex software-intensive systems involves many stakeholders who contribute their expertise on specific aspects of the system under construction. Domain-specific languages (DSLs) are typically used by stakeholders to express their knowledge of the system using dedicated tools and abstractions. In this chapter, we explore different scenarios that lead to the globalization of DSLs through two motivating case studies – a command and control wind tunnel and a smart emergency response system – and outline the concrete engineering challenges they raise. Finally, we list some of the general research challenges related to the globalization of DSMLs and discuss some promising approaches for addressing them
Integrating simplified inverse representation and CRC for face recognition

© Springer International Publishing Switzerland 2015. The representation based classification method (RBCM) has attracted much attention in the last decade. RBCM exploits the linear combination of training samples to represent the test sample, which is then classified according to the minimum reconstruction residual. Recently, an interesting concept, Inverse Representation (IR), is proposed. It is the inverse process of conventional RBCMs. IR applies test samples’ information to represent each training sample, and then classifies the training sample as a useful supplement for the final classification. The relative algorithm CIRLRC, integrating IR and linear regression classification (LRC) by score fusing, shows superior classification performance. However, there are two main drawbacks in CIRLRC. First, the IR in CIRLRC is not pure, because the test vector contains some training sample information. The other is the computation inefficiency because CIRLRC should solve C linear equations for classifying the test sample respectively, where C is the number of the classes. Therefore, we present a novel method integrating simplified IR (SIR) and collaborative representation classification (CRC), named SIRCRC, for face recognition. In SIRCRC, only test sample information is fully used in SIR, and CRC is more efficient than LRC in terms of speed, thus, one linear equation system is needed. Extensive experimental results on face databases show that it is very competitive with both CIRLRC and the state-of-the-art RBCM
Crisis Mapping during Natural Disasters via Text Analysis of Social Media Messages

Recent disasters demonstrated the central role of social media during emergencies thus motivating the exploitation of such data for crisis mapping. We propose a crisis mapping system that addresses limitations of current state-of-the-art approaches by analyzing the textual content of disaster reports from a twofold perspective. A damage detection component employs a SVM classifier to detect mentions of damage among emergency reports. A novel geoparsing technique is proposed and used to perform message geolocation. We report on a case study to show how the information extracted through damage detection and message geolocation can be combined to produce accurate crisis maps. Our crisis maps clearly detect both highly and lightly damaged areas, thus opening up the possibility to prioritize rescue efforts where they are most needed
Semi-supervised document clustering via loci

Document clustering is one of the prominent methods for mining important information from the vast amount of data available on the web. However, document clustering generally suffers from the curse of dimensionality. Providentially in high dimensional space, data points tend to be more concentrated in some areas of clusters. We take advantage of this phenomenon by introducing a novel concept of dynamic cluster representation named as loci. Clusters’ loci are efficiently calculated using documents’ ranking scores generated from a search engine. We propose a fast loci-based semi-supervised document clustering algorithm that uses clusters’ loci instead of conventional centroids for assigning documents to clusters. Empirical analysis on real-world datasets shows that the proposed method produces cluster solutions with promising quality and is substantially faster than several benchmarked centroid-based semi-supervised document clustering methods
FreeS: A fast algorithm to discover frequent free subtrees using a novel canonical form

Web data can often be represented in free tree form; however, free tree mining methods seldom exist. In this paper, a computationally fast algorithm FreeS is presented to discover all frequently occurring free subtrees in a database of labelled free trees. FreeS is designed using an optimal canonical form, BOCF that can uniquely represent free trees even during the presence of isomorphism. To avoid enumeration of false positive candidates, it utilises the enumeration approach based on a tree-structure guided scheme. This paper presents lemmas that introduce conditions to conform the generation of free tree candidates during enumeration. Empirical study using both real and synthetic datasets shows that FreeS is scalable and significantly outperforms (i.e. few orders of magnitude faster than) the state-of-the-art frequent free tree mining algorithms, HybridTreeMiner and FreeTreeMiner
Hierarchical Gaussian Mixture Model with Objects Attached to Terminal
  and Non-terminal Dendrogram Nodes

A hierarchical clustering algorithm based on Gaussian mixture model is
presented. The key difference to regular hierarchical mixture models is the
ability to store objects in both terminal and nonterminal nodes. Upper levels
of the hierarchy contain sparsely distributed objects, while lower levels
contain densely represented ones. As it was shown by experiments, this ability
helps in noise detection (modelling). Furthermore, compared to regular
hierarchical mixture model, the presented method generates more compact
dendrograms with higher quality measured by adopted F-measure.Comment: This article was presented on CORES2015 conference
  http://cores.pwr.wroc.pl/ . The final publication is available at Springer
  via http://dx.doi.org/10.1007/978-3-319-26227-7_1
Coverage-Driven Verification - An approach to verify code for robots
  that directly interact with humans

Collaborative robots could transform several industries, such as
manufacturing and healthcare, but they present a significant challenge to
verification. The complex nature of their working environment necessitates
testing in realistic detail under a broad range of circumstances. We propose
the use of Coverage-Driven Verification (CDV) to meet this challenge. By
automating the simulation-based testing process as far as possible, CDV
provides an efficient route to coverage closure. We discuss the need, practical
considerations, and potential benefits of transferring this approach from
microelectronic design verification to the field of human-robot interaction. We
demonstrate the validity and feasibility of the proposed approach by
constructing a custom CDV testbench and applying it to the verification of an
object handover task.Comment: Accepted for publication, Haifa Verification Conference (HVC) 201
The Size of History. Coincidence, Counterfactuality and Questions

Contains fulltext :
                  159170.pdf (publisher's version ) (Open Access)Historians try to interpret the past by analysing patterns in human behaviour in earlier periods of time. In some ways, that excludes ‘coincidence’ as a mode of interpretation. Most historians view coincidences as closely related events that lack causal relationship. That type of coincidence does not fit into a historical narrative, because historians tend to focus on causality, action, and consequence.
This is noticeably linked to questions of historical scale: the choice for the scale of a specific narrative decides whether certain events are coincidental to the history which is being described, or causal factors within that history. This relation between historical coincidence and the scale of writing history is at the centre of this contribution. It focuses on different trends in writing history, and analyses the possibilities to use ‘coincidence’ as an interpretative tool in each of them. In doing so, this article discusses counterfactual historical analysis (‘what if history’), determinist views of history and their relation to speculative philosophy of history, ‘cliodynamics’ and ‘big history’. It ultimately argues for historical accounts that pay attention to both the large processes that are likely to lead to certain trajectories, and the enormous number of micro-causes that triggered the events as they happened.
Coincidence might fall outside of the analysis of (macro-) historians who are looking for a comprehensive view of historical processes, but could still play a proper role in thinking about historical trajectories
The experience of coincidence: An integrated psychological and neurocognitive perspective

Contains fulltext :
                  157551.pdf (publisher's version ) (Open Access)In this chapter, we focus on psychological and brain perspectives on the experience of coincidence. We first introduce the topic of the experience of coincidence in general. In the second section, we outline several psychological mechanisms that underlie the experience of coincidence in humans, such as cognitive biases, the role of context and the role of individual differences. In the third and final section we formulate the phenomenon of coincidence in the light of the unifying brain account of predictive coding, while arguing that the notion of coincidence provides a wonderful example of a construct that connects the Bayesian brain to folk psychology and philosophy
Exploiting the beta distribution-based reputation model in recommender system

Reputation systems are employed to measure the quality of items on the Web. Incorporating accurate reputation scores in recommender systems is useful to provide more accurate recommendations as recommenders are agnostic to reputation. The ratings aggregation process is a vital component of a reputation system. Reputation models available do not consider statistical data in the rating aggregation process. This limitation can reduce the accuracy of generated reputation scores. In this paper, we propose a new reputation model that considers previously ignored statistical data. We compare our proposed model against state-of the-art models using top-N recommender system experiment
Monte Carlo analysis of a puzzle game

When a puzzle game is created, its design parameters must be chosen to allow solvable and interesting challenges to be created for the player. We investigate the use of random sampling as a computationally inexpensive means of automated game analysis, to evaluate the BoxOff family of puzzle games. This analysis reveals useful insights into the game, such as the surprising fact that almost 100% of randomly generated challenges have a solution, but less than 10% will be solved using strictly random play, validating the inventor’s design choices. We show the 1D game to be trivial and the 3D game to be viable
Dynamic Boundary Stabilization of First Order Hyperbolic Systems

International audienceIn this chapter, we address the problem of the dynamic boundary stabilization of linear, quasilinear and LPV first-order hyperbolic systems. We provide sufficient conditions for the exponential stability for this class of infinite dimensional systems by means of Lyapunov based techniques and matrix inequalities. We develop an applicative example of a temperature boundary control in a Poiseuille flow using some of our main results and we present simulation results that illustrate the efficiency of our approach
A MAC protocol for underwater sensors networks

“The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-26401-1_37."Underwater sensor networks are becoming an important field of research, because of its everyday increasing application scope. Examples of their application areas are environmental and pollution monitoring (mainly oil spills), oceanographic data collection, support for submarine geo-localization, ocean sampling and early tsunamis alert. It is well-known the challenge that represents to perform underwater communications provided that radio signals are useless in this medium and a wired solution is too expensive. Therefore, the sensors in these network transmit their information using acoustic signals that propagate well under water. This data transmission type bring an opportunity, but also several challenges to the implementation of these networks, e.g., in terms of energy consumption, data transmission and signal interference. Few proposals are available to deal with the problem in this particular application scenario, and these proposals does not address properly the transmission of underwater acoustic signals. In order to help advance the knowledge in the design and implementation of these networks, this paper proposes a MAC protocol for acoustic communications between the nodes based on a self-organized time division multiple access mechanism. The proposal is still preliminary and it has only been evaluated in the laboratory; however, it represents a highly promising behavior that make us expect interesting results in real-world scenarios.Peer ReviewedPostprint (author's final draft