OpenRaiser/Intern-Atlas huggingface dataset:
Beyond word frequency: Bursts, lulls, and scaling in the temporal distributions of words
Venue: arXiv cs.CL 2009
Year: 2009

Background: Zipf's discovery that word frequency distributions obey a power law established parallels between biological and physical processes, and language, laying the groundwork for a complex systems perspective on human communication. More recent research has also identified scaling regularities in the dynamics underlying the successive occurrences of events, suggesting the possibility of similar findings for language as well. Methodology/Principal Findings: By considering frequent words in USENET discussion groups and in disparate databases where the language has different levels of formality, here we show that the distributions of distances between successive occurrences of the same word display bursty deviations from a Poisson process and are well characterized by a stretched exponential (Weibull) scaling. The extent of this deviation depends strongly on semantic type -- a measure of the logicality of each word -- and less strongly on frequency. We develop a generative model of this behavior that fully determines the dynamics of word usage. Conclusions/Significance: Recurrence patterns of words are well described by a stretched exponential distribution of recurrence times, an empirical scaling that cannot be anticipated from Zipf's law. Because the use of words provides a uniquely precise and powerful lens on human thought and activity, our findings also have implications for other overt manifestations of collective human dynamics.
The Safe Lambda Calculus
Venue: arXiv cs.PL 2009
Year: 2009

Safety is a syntactic condition of higher-order grammars that constrains occurrences of variables in the production rules according to their type-theoretic order. In this paper, we introduce the safe lambda calculus, which is obtained by transposing (and generalizing) the safety condition to the setting of the simply-typed lambda calculus. In contrast to the original definition of safety, our calculus does not constrain types (to be homogeneous). We show that in the safe lambda calculus, there is no need to rename bound variables when performing substitution, as variable capture is guaranteed not to happen. We also propose an adequate notion of beta-reduction that preserves safety. In the same vein as Schwichtenberg's 1976 characterization of the simply-typed lambda calculus, we show that the numeric functions representable in the safe lambda calculus are exactly the multivariate polynomials; thus conditional is not definable. We also give a characterization of representable word functions. We then study the complexity of deciding beta-eta equality of two safe simply-typed terms and show that this problem is PSPACE-hard. Finally we give a game-semantic analysis of safety: We show that safe terms are denoted by `P-incrementally justified strategies'. Consequently pointers in the game semantics of safe lambda-terms are only necessary from order 4 onwards.
On some simplicial elimination schemes for chordal graphs
Venue: arXiv cs.DS 2009
Year: 2009

We present here some results on particular elimination schemes for chordal graphs, namely we show that for any chordal graph we can construct in linear time a simplicial elimination scheme starting with a pending maximal clique attached via a minimal separator maximal (resp. minimal) under inclusion among all minimal separators.
A Super-Polynomial Lower Bound for the Parity Game Strategy Improvement Algorithm as We Know it
Venue: arXiv cs.GT 2009
Year: 2009

This paper presents a new lower bound for the discrete strategy improvement algorithm for solving parity games due to Voege and Jurdziski. First, we informally show which structures are difficult to solve for the algorithm. Second, we outline a family of games of quadratic size on which the algorithm requires exponentially many strategy iterations, answering in the negative the long-standing question whether this algorithm runs in polynomial time. Additionally we note that the same family of games can be used to prove a similar result w.r.t. the strategy improvement variant by Schewe.
Sample-Align-D: A High Performance Multiple Sequence Alignment System using Phylogenetic Sampling and Domain Decomposition
Venue: arXiv cs.DC 2009
Year: 2009

Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to align, for example, 2000 homologous sequences of average length 300. Inspired by the Sample Sort approach in parallel processing, in this paper we propose a highly scalable multiprocessor solution for the MSA problem in phylogenetically diverse sequences. Our method employs an intelligent scheme to partition the set of sequences into smaller subsets using kmer count based similarity index, referred to as k-mer rank. Each subset is then independently aligned in parallel using any sequential approach. Further fine tuning of the local alignments is achieved using constraints derived from a global ancestor of the entire set. The proposed Sample-Align-D Algorithm has been implemented on a cluster of workstations using MPI message passing library. The accuracy of the proposed solution has been tested on standard benchmarks such as PREFAB. The accuracy of the alignment produced by our methods is comparable to that of well known sequential MSA techniques. We were able to align 2000 randomly selected sequences from the Methanosarcina acetivorans genome in less than 10 minutes using Sample-Align-D on a 16 node cluster, compared to over 23 hours on sequential MUSCLE system running on a single cluster node.
On the Computation of Matrices of Traces and Radicals of Ideals
Venue: arXiv cs.SC 2009
Year: 2009

Let $f_1,...,f_s \in \mathbb{K}[x_1,...,x_m]$ be a system of polynomials generating a zero-dimensional ideal $\I$, where $\mathbb{K}$ is an arbitrary algebraically closed field. We study the computation of "matrices of traces" for the factor algebra $\A := \CC[x_1, ..., x_m]/ \I$, i.e. matrices with entries which are trace functions of the roots of $\I$. Such matrices of traces in turn allow us to compute a system of multiplication matrices $\{M_{x_i}|i=1,...,m\}$ of the radical $\sqrt{\I}$. We first propose a method using Macaulay type resultant matrices of $f_1,...,f_s$ and a polynomial $J$ to compute moment matrices, and in particular matrices of traces for $\A$. Here $J$ is a polynomial generalizing the Jacobian. We prove bounds on the degrees needed for the Macaulay matrix in the case when $\I$ has finitely many projective roots in $\mathbb{P}^m_\CC$. We also extend previous results which work only for the case where $\A$ is Gorenstein to the non-Gorenstein case. The second proposed method uses Bezoutian matrices to compute matrices of traces of $\A$. Here we need the assumption that $s=m$ and $f_1,...,f_m$ define an affine complete intersection. This second method also works if we have higher dimensional components at infinity. A new explicit description of the generators of $\sqrt{\I}$ are given in terms of Bezoutians.
Scheduling in Multi-hop Wireless Networks with Priorities
Venue: arXiv cs.IT 2009
Year: 2009

In this paper we consider prioritized maximal scheduling in multi-hop wireless networks, where the scheduler chooses a maximal independent set greedily according to a sequence specified by certain priorities. We show that if the probability distributions of the priorities are properly chosen, we can achieve the optimal (maximum) stability region using an i.i.d random priority assignment process, for any set of arrival processes that satisfy Law of Large Numbers. The pre-computation of the priorities is, in general, NP-hard, but there exists polynomial time approximation scheme (PTAS) to achieve any fraction of the optimal stability region. We next focus on the simple case of static priority and specify a greedy priority assignment algorithm, which can achieve the same fraction of the optimal stability region as the state of art result for Longest Queue First (LQF) schedulers. We also show that this algorithm can be easily adapted to satisfy delay constraints in the large deviations regime, and therefore, supports Quality of Service (QoS) for each link.
An Upper Limit of AC Huffman Code Length in JPEG Compression
Venue: arXiv cs.IT 2009
Year: 2009

A strategy for computing upper code-length limits of AC Huffman codes for an 8x8 block in JPEG Baseline coding is developed. The method is based on a geometric interpretation of the DCT, and the calculated limits are as close as 14% to the maximum code-lengths. The proposed strategy can be adapted to other transform coding methods, e.g., MPEG 2 and 4 video compressions, to calculate close upper code length limits for the respective processing blocks.
Statistical analysis of the Indus script using $n$-grams
Venue: arXiv cs.CL 2009
Year: 2009

The Indus script is one of the major undeciphered scripts of the ancient world. The small size of the corpus, the absence of bilingual texts, and the lack of definite knowledge of the underlying language has frustrated efforts at decipherment since the discovery of the remains of the Indus civilisation. Recently, some researchers have questioned the premise that the Indus script encodes spoken language. Building on previous statistical approaches, we apply the tools of statistical language processing, specifically $n$-gram Markov chains, to analyse the Indus script for syntax. Our main results are that the script has well-defined signs which begin and end texts, that there is directionality and strong correlations in the sign order, and that there are groups of signs which appear to have identical syntactic function. All these require no {\it a priori} suppositions regarding the syntactic or semantic content of the signs, but follow directly from the statistical analysis. Using information theoretic measures, we find the information in the script to be intermediate between that of a completely random and a completely fixed ordering of signs. Our study reveals that the Indus script is a structured sign system showing features of a formal language, but, at present, cannot conclusively establish that it encodes {\it natural} language. Our $n$-gram Markov model is useful for predicting signs which are missing or illegible in a corpus of Indus texts. This work forms the basis for the development of a stochastic grammar which can be used to explore the syntax of the Indus script in greater detail.
On linear balancing sets
Venue: arXiv cs.IT 2009
Year: 2009

Let n be an even positive integer and F be the field \GF(2). A word in F^n is called balanced if its Hamming weight is n/2. A subset C \subseteq F^n$ is called a balancing set if for every word y \in F^n there is a word x \in C such that y + x is balanced. It is shown that most linear subspaces of F^n of dimension slightly larger than 3/2\log_2(n) are balancing sets. A generalization of this result to linear subspaces that are "almost balancing" is also presented. On the other hand, it is shown that the problem of deciding whether a given set of vectors in F^n spans a balancing set, is NP-hard. An application of linear balancing sets is presented for designing efficient error-correcting coding schemes in which the codewords are balanced.
Self-assembly of the discrete Sierpinski carpet and related fractals
Venue: arXiv cs.OH 2009
Year: 2009

It is well known that the discrete Sierpinski triangle can be defined as the nonzero residues modulo 2 of Pascal's triangle, and that from this definition one can easily construct a tileset with which the discrete Sierpinski triangle self-assembles in Winfree's tile assembly model. In this paper we introduce an infinite class of discrete self-similar fractals that are defined by the residues modulo a prime p of the entries in a two-dimensional matrix obtained from a simple recursive equation. We prove that every fractal in this class self-assembles using a uniformly constructed tileset. As a special case we show that the discrete Sierpinski carpet self-assembles using a set of 30 tiles.
A Boundary Approximation Algorithm for Distributed Sensor Networks
Venue: arXiv cs.DC 2009
Year: 2009

We present an algorithm for boundary approximation in locally-linked sensor networks that communicate with a remote monitoring station. Delaunay triangulations and Voronoi diagrams are used to generate a sensor communication network and define boundary segments between sensors, respectively. The proposed algorithm reduces remote station communication by approximating boundaries via a decentralized computation executed within the sensor network. Moreover, the algorithm identifies boundaries based on differences between neighboring sensor readings, and not absolute sensor values. An analysis of the bandwidth consumption of the algorithm is presented and compared to two naive approaches. The proposed algorithm reduces the amount of remote communication (compared to the naive approaches) and becomes increasingly useful in networks with more nodes.
Automating Access Control Logics in Simple Type Theory with LEO-II
Venue: arXiv cs.LO 2009
Year: 2009

Garg and Abadi recently proved that prominent access control logics can be translated in a sound and complete way into modal logic S4. We have previously outlined how normal multimodal logics, including monomodal logics K and S4, can be embedded in simple type theory (which is also known as higher-order logic) and we have demonstrated that the higher-order theorem prover LEO-II can automate reasoning in and about them. In this paper we combine these results and describe a sound and complete embedding of different access control logics in simple type theory. Employing this framework we show that the off the shelf theorem prover LEO-II can be applied to automate reasoning in prominent access control logics.
Decay of Correlations in Low Density Parity Check Codes: Low Noise Regime
Venue: arXiv cs.IT 2009
Year: 2009

Consider transmission over a binary additive white gaussian noise channel using a fixed low-density parity check code. We consider the posterior measure over the code bits and the corresponding correlation between two codebits, averaged over the noise realizations. We show that for low enough noise variance this average correlation decays exponentially fast with the graph distance between the code bits. One consequence of this result is that for low enough noise variance the GEXIT functions (further averaged over a standard code ensemble) of the belief propagation and optimal decoders are the same.
Closures in Formal Languages and Kuratowski's Theorem
Venue: arXiv cs.CC 2009
Year: 2009

A famous theorem of Kuratowski states that in a topological space, at most 14 distinct sets can be produced by repeatedly applying the operations of closure and complement to a given set. We re-examine this theorem in the setting of formal languages, where closure is either Kleene closure or positive closure. We classify languages according to the structure of the algebra they generate under iterations of complement and closure. We show that there are precisely 9 such algebras in the case of positive closure, and 12 in the case of Kleene closure.
Remembering what we like: Toward an agent-based model of Web traffic
Venue: arXiv cs.HC 2009
Year: 2009

Analysis of aggregate Web traffic has shown that PageRank is a poor model of how people actually navigate the Web. Using the empirical traffic patterns generated by a thousand users over the course of two months, we characterize the properties of Web traffic that cannot be reproduced by Markovian models, in which destinations are independent of past decisions. In particular, we show that the diversity of sites visited by individual users is smaller and more broadly distributed than predicted by the PageRank model; that link traffic is more broadly distributed than predicted; and that the time between consecutive visits to the same site by a user is less broadly distributed than predicted. To account for these discrepancies, we introduce a more realistic navigation model in which agents maintain individual lists of bookmarks that are used as teleportation targets. The model can also account for branching, a traffic property caused by browser features such as tabs and the back button. The model reproduces aggregate traffic patterns such as site popularity, while also generating more accurate predictions of diversity, link traffic, and return time distributions. This model for the first time allows us to capture the extreme heterogeneity of aggregate traffic measurements while explaining the more narrowly focused browsing patterns of individual users.
Du corpus au dictionnaire
Venue: arXiv cs.CL 2009
Year: 2009

In this article, we propose an automatic process to build multi-lingual lexico-semantic resources. The goal of these resources is to browse semantically textual information contained in texts of different languages. This method uses a mathematical model called Atlas sémantiques in order to represent the different senses of each word. It uses the linguistic relations between words to create graphs that are projected into a semantic space. These projections constitute semantic maps that denote the sense trends of each given word. This model is fed with syntactic relations between words extracted from a corpus. Therefore, the lexico-semantic resource produced describes all the words and all their meanings observed in the corpus. The sense trends are expressed by syntactic contexts, typical for a given meaning. The link between each sense trend and the utterances used to build the sense trend are also stored in an index. Thus all the instances of a word in a particular sense are linked and can be browsed easily. And by using several corpora of different languages, several resources are built that correspond with each other through languages. It makes it possible to browse information through languages thanks to syntactic contexts translations (even if some of them are partial).
Mining for adverse drug events with formal concept analysis
Venue: arXiv cs.AI 2009
Year: 2009

The pharmacovigilance databases consist of several case reports involving drugs and adverse events (AEs). Some methods are applied consistently to highlight all signals, i.e. all statistically significant associations between a drug and an AE. These methods are appropriate for verification of more complex relationships involving one or several drug(s) and AE(s) (e.g; syndromes or interactions) but do not address the identification of them. We propose a method for the extraction of these relationships based on Formal Concept Analysis (FCA) associated with disproportionality measures. This method identifies all sets of drugs and AEs which are potential signals, syndromes or interactions. Compared to a previous experience of disproportionality analysis without FCA, the addition of FCA was more efficient for identifying false positives related to concomitant drugs.
Cross-situational and supervised learning in the emergence of communication
Venue: arXiv cs.LG 2009
Year: 2009

Scenarios for the emergence or bootstrap of a lexicon involve the repeated interaction between at least two agents who must reach a consensus on how to name N objects using H words. Here we consider minimal models of two types of learning algorithms: cross-situational learning, in which the individuals determine the meaning of a word by looking for something in common across all observed uses of that word, and supervised operant conditioning learning, in which there is strong feedback between individuals about the intended meaning of the words. Despite the stark differences between these learning schemes, we show that they yield the same communication accuracy in the realistic limits of large N and H, which coincides with the result of the classical occupancy problem of randomly assigning N objects to H words.
On the upstream mobility scheme for two-phase flow in porous media
Venue: arXiv cs.NA 2009
Year: 2009

When neglecting capillarity, two-phase incompressible flow in porous media is modelled as a scalar nonlinear hyperbolic conservation law. A change in the rock type results in a change of the flux function. Discretizing in one-dimensional with a finite volume method, we investigate two numerical fluxes, an extension of the Godunov flux and the upstream mobility flux, the latter being widely used in hydrogeology and petroleum engineering. Then, in the case of a changing rock type, one can give examples when the upstream mobility flux does not give the right answer.
Adaptive FPGA NoC-based Architecture for Multispectral Image Correlation
Venue: arXiv cs.AR 2009
Year: 2009

An adaptive FPGA architecture based on the NoC (Network-on-Chip) approach is used for the multispectral image correlation. This architecture must contain several distance algorithms depending on the characteristics of spectral images and the precision of the authentication. The analysis of distance algorithms is required which bases on the algorithmic complexity, result precision, execution time and the adaptability of the implementation. This paper presents the comparison of these distance computation algorithms on one spectral database. The result of a RGB algorithm implementation was discussed.
Everyone is a Curator: Human-Assisted Preservation for ORE Aggregations
Venue: arXiv cs.DL 2009
Year: 2009

The Open Archives Initiative (OAI) has recently created the Object Reuse and Exchange (ORE) project that defines Resource Maps (ReMs) for describing aggregations of web resources. These aggregations are susceptible to many of the same preservation challenges that face other web resources. In this paper, we investigate how the aggregations of web resources can be preserved outside of the typical repository environment and instead rely on the thousands of interactive users in the web community and the Web Infrastructure (the collection of web archives, search engines, and personal archiving services) to facilitate preservation. Inspired by Web 2.0 services such as digg, deli.cio.us, and Yahoo! Buzz, we have developed a lightweight system called ReMember that attempts to harness the collective abilities of the web community for preservation purposes instead of solely placing the burden of curatorial responsibilities on a small number of experts.
Adaptive algorithms for identifying large flows in IP traffic
Venue: arXiv cs.NI 2009
Year: 2009

We propose in this paper an on-line algorithm based on Bloom filters for identifying large flows in IP traffic (a.k.a. elephants). Because of the large number of small flows, hash tables of these algorithms have to be regularly refreshed. Recognizing that the periodic erasure scheme usually used in the technical literature turns out to be quite inefficient when using real traffic traces over a long period of time, we introduce a simple adaptive scheme that closely follows the variations of traffic. When tested against real traffic traces, the proposed on-line algorithm performs well in the sense that the detection ratio of long flows by the algorithm over a long time period is quite high. Beyond the identification of elephants, this same class of algorithms is applied to the closely related problem of detection of anomalies in IP traffic, e.g., SYN flood due for instance to attacks. An algorithm for detecting SYN and volume flood anomalies in Internet traffic is designed. Experiments show that an anomaly is detected in less than one minute and the targeted destinations are identified at the same time.
The second weight of generalized Reed-Muller codes in most cases
Venue: arXiv cs.IT 2009
Year: 2009

The second weight of the Generalized Reed-Muller code of order $d$ over the finite field with $q$ elements is now known for $d <q$ and $d>(n-1)(q-1)$. In this paper, we determine the second weight for the other values of $d$ which are not multiple of $q-1$ plus 1. For the special case $d=a(q-1)+1$ we give an estimate.