pinecone/core-2020-05-10-deduplication huggingface dataset:
S.cerevisiae complex function prediction with modular multi-relational framework

Proceeding of: 23rd International Conference on Industrial Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2010, Córdoba, Spain, June 1-4, 2010Determining the functions of genes is essential for understanding how the metabolisms work, and for trying to solve their malfunctions. Genes usually work in groups rather than isolated, so functions should be assigned to gene groups and not to individual genes. Moreover, the genetic knowledge has many relations and is very frequently changeable. Thus, a propositional ad-hoc approach is not appropriate to deal with the gene group function prediction domain. We propose the Modular Multi-Relational Framework (MMRF), which faces the problem from a relational and flexible point of view. The MMRF consists of several modules covering all involved domain tasks (grouping, representing and learning using computational prediction techniques). A specific application is described, including a relational representation language, where each module of MMRF is individually instantiated and refined for obtaining a prediction under specific given conditions.This research work has been supported by CICYT, TRA 2007-67374-C02-02 project and by the expert biological knowledge of the Structural Computational Biology Group in Spanish National Cancer Research Centre (CNIO). The authors would like to thank members of Tilde tool developer
group in K.U.Leuven for providing their help and many useful suggestions.Publicad
Symmetry Matters for Sizes of Extended Formulations

In 1991, Yannakakis (J. Comput. System Sci., 1991) proved that no symmetric
extended formulation for the matching polytope of the complete graph K_n with n
nodes has a number of variables and constraints that is bounded
subexponentially in n. Here, symmetric means that the formulation remains
invariant under all permutations of the nodes of K_n. It was also conjectured
in the paper mentioned above that "asymmetry does not help much," but no
corresponding result for general extended formulations has been found so far.
In this paper we show that for the polytopes associated with the matchings in
K_n with log(n) (rounded down) edges there are non-symmetric extended
formulations of polynomial size, while nevertheless no symmetric extended
formulations of polynomial size exist. We furthermore prove similar statements
for the polytopes associated with cycles of length log(n) (rounded down). Thus,
with respect to the question for smallest possible extended formulations, in
general symmetry requirements may matter a lot. Compared to the extended
abtract that has appeared in the Proceedings of IPCO XIV at Lausanne, this
paper does not only contain proofs that had been ommitted there, but it also
presents slightly generalized and sharpened lower bounds.Comment: 24 pages; incorporated referees' comments; to appear in: SIAM Journal
  on Discrete Mathematic
A polynomial-time algorithm for optimizing over N-fold 4-block
  decomposable integer programs

In this paper we generalize N-fold integer programs and two-stage integer
programs with N scenarios to N-fold 4-block decomposable integer programs. We
show that for fixed blocks but variable N, these integer programs are
polynomial-time solvable for any linear objective. Moreover, we present a
polynomial-time computable optimality certificate for the case of fixed blocks,
variable N and any convex separable objective function. We conclude with two
sample applications, stochastic integer programs with second-order dominance
constraints and stochastic integer multi-commodity flows, which (for fixed
blocks) can be solved in polynomial time in the number of scenarios and
commodities and in the binary encoding length of the input data. In the proof
of our main theorem we combine several non-trivial constructions from the
theory of Graver bases. We are confident that our approach paves the way for
further extensions
Fault-Tolerant Facility Location: a randomized dependent LP-rounding
  algorithm

We give a new randomized LP-rounding 1.725-approximation algorithm for the
metric Fault-Tolerant Uncapacitated Facility Location problem. This improves on
the previously best known 2.076-approximation algorithm of Swamy & Shmoys. To
the best of our knowledge, our work provides the first application of a
dependent-rounding technique in the domain of facility location. The analysis
of our algorithm benefits from, and extends, methods developed for
Uncapacitated Facility Location; it also helps uncover new properties of the
dependent-rounding approach. An important concept that we develop is a novel,
hierarchical clustering scheme. Typically, LP-rounding approximation algorithms
for facility location problems are based on partitioning facilities into
disjoint clusters and opening at least one facility in each cluster. We extend
this approach and construct a laminar family of clusters, which then guides the
rounding procedure. It allows to exploit properties of dependent rounding, and
provides a quite tight analysis resulting in the improved approximation ratio.Comment: conference paper + proofs in appendice
On Column-restricted and Priority Covering Integer Programs

In a column-restricted covering integer program (CCIP), all the non-zero
entries of any column of the constraint matrix are equal. Such programs capture
capacitated versions of covering problems. In this paper, we study the
approximability of CCIPs, in particular, their relation to the integrality gaps
of the underlying 0,1-CIP.
  If the underlying 0,1-CIP has an integrality gap O(gamma), and assuming that
the integrality gap of the priority version of the 0,1-CIP is O(omega), we give
a factor O(gamma + omega) approximation algorithm for the CCIP. Priority
versions of 0,1-CIPs (PCIPs) naturally capture quality of service type
constraints in a covering problem.
  We investigate priority versions of the line (PLC) and the (rooted) tree
cover (PTC) problems. Apart from being natural objects to study, these problems
fall in a class of fundamental geometric covering problems. We bound the
integrality of certain classes of this PCIP by a constant. Algorithmically, we
give a polytime exact algorithm for PLC, show that the PTC problem is APX-hard,
and give a factor 2-approximation algorithm for it.Comment: 28 pages, 6 figures, extended abstract to appear in proceedings of
  IPCO 2010
On k-Column Sparse Packing Programs

We consider the class of packing integer programs (PIPs) that are column
sparse, i.e. there is a specified upper bound k on the number of constraints
that each variable appears in. We give an (ek+o(k))-approximation algorithm for
k-column sparse PIPs, improving on recent results of $k^2\cdot 2^k$ and
$O(k^2)$. We also show that the integrality gap of our linear programming
relaxation is at least 2k-1; it is known that k-column sparse PIPs are
$\Omega(k/ \log k)$-hard to approximate. We also extend our result (at the loss
of a small constant factor) to the more general case of maximizing a submodular
objective over k-column sparse packing constraints.Comment: 19 pages, v3: additional detail
Hypergraphic LP Relaxations for Steiner Trees

We investigate hypergraphic LP relaxations for the Steiner tree problem,
primarily the partition LP relaxation introduced by Koenemann et al. [Math.
Programming, 2009]. Specifically, we are interested in proving upper bounds on
the integrality gap of this LP, and studying its relation to other linear
relaxations. Our results are the following. Structural results: We extend the
technique of uncrossing, usually applied to families of sets, to families of
partitions. As a consequence we show that any basic feasible solution to the
partition LP formulation has sparse support. Although the number of variables
could be exponential, the number of positive variables is at most the number of
terminals. Relations with other relaxations: We show the equivalence of the
partition LP relaxation with other known hypergraphic relaxations. We also show
that these hypergraphic relaxations are equivalent to the well studied
bidirected cut relaxation, if the instance is quasibipartite. Integrality gap
upper bounds: We show an upper bound of sqrt(3) ~ 1.729 on the integrality gap
of these hypergraph relaxations in general graphs. In the special case of
uniformly quasibipartite instances, we show an improved upper bound of 73/60 ~
1.216. By our equivalence theorem, the latter result implies an improved upper
bound for the bidirected cut relaxation as well.Comment: Revised full version; a shorter version will appear at IPCO 2010
On Generalizations of Network Design Problems with Degree Bounds

Iterative rounding and relaxation have arguably become the method of choice
in dealing with unconstrained and constrained network design problems. In this
paper we extend the scope of the iterative relaxation method in two directions:
(1) by handling more complex degree constraints in the minimum spanning tree
problem (namely, laminar crossing spanning tree), and (2) by incorporating
`degree bounds' in other combinatorial optimization problems such as matroid
intersection and lattice polyhedra. We give new or improved approximation
algorithms, hardness results, and integrality gaps for these problems.Comment: v2, 24 pages, 4 figure
A New Fibre Optic Pulse Oximeter Probe for Monitoring Splanchnic Organ Arterial Blood Oxygen Saturation

a new continuous method of monitoring splanchnic organ oxygen saturation (SpO2) would make the early detection of inadequate tissue oxygenation feasible, reducing the risk of hypoperfusion, severe ischaemia, and, ultimately, death. In an attempt to provide such a device, a new fiber optic based reflectance pulse oximeter probe and processing system were developed followed by an in vivo evaluation of the technology on seventeen patients undergoing elective laparotomy. Photoplethysmographic (PPG) signals of good quality were obtained from the small bowel, large bowel, liver and stomach. Simultaneous peripheral PPG signals from the finger were also obtained for comparison purposes. Analysis of the amplitudes of all acquired PPG signals indicated much larger amplitudes for those signals obtained from splanchnic organs than those obtained from the periphery. Estimated SpO2 values for splanchnic organs showed good agreement with those obtained from the peripheral fibre optic probe and those obtained from a commercial device. These preliminary results suggest that a miniaturized ‘indwelling’ fibre optic sensor may be a suitable method for pre-operative and post-operative evaluation of splanchnic organ SpO2 and their health
Potential AI Strategies to Solve the Commons Game: A Position Paper

Published version of an article from the book: Advances in Artificial Intelligence 
: 23rd Canadian Conference on Artificial Intelligence. The original publication is available at Springerlink. http://dx.doi.org/10.1007/978-3-642-13059-5_45In this paper, we propose the use of hill climbing and particle swarm optimization to find strategies in order to play the Commons Game (CG). The game, which is a non-trivial N-person non-zero-sum game, presents a simple mechanism to formulate how different parties can use shared resources. If the parties cooperate, the resources are sustainable. However, the resources get depleted if used indiscriminately. We consider the case when a single player has to determine the “optimal” solution, and when the other N − 1 players play the game by choosing the options with a fixed probability vector
InfraWatch: Data management of large systems for monitoring infrastructural performance

This paper introduces a new project, InfraWatch, that demonstrates the many challenges that a large complex data analysis application has to offer in terms of data capture, management, analysis and reporting. The project is concerned with the intelligent monitoring and analysis of large infrastructural projects in the public domain, such as public roads, highways, tunnels and bridges. As a demonstrator, the project includes the detailed measurement of traffic and weather load on one of the largest highway bridges in the Netherlands. As part of a recent renovation 
and re-enforcement effort, the bridge has been equipped with a substantial sensor network, which has been producing large amounts of sensor data for more than a year. The bridge is currently equipped with a multitude of vibration 
and stress sensors, a video camera and weather station. We propose this bridge as a challenging environment for intelligent data analysis research. In this paper we outline the reasons for monitoring infrastructural 
assets through sensors, the scientific challenges in for example data management and analysis, and we present a visualization tool for the data coming from the bridge. We think that the bridge can serve as a means to promote research and education in intelligent data analysis.status: publishe
On the number of higher order Delaunay triangulations

Higher order Delaunay triangulations are a generalization of the Delaunay triangulation which provides a class of well-shaped triangulations, over which extra criteria can be optimized. A triangulation is order-k Delaunay if the circumcircle of each triangle of the triangulation contains at most k points. In this paper we study lower and upper bounds on the number of higher order Delaunay triangulations, as well\ud
as their expected number for randomly distributed points. We show that arbitrarily large point sets can have a single higher order Delaunay triangulation, even for large orders, whereas for first order Delaunay triangulations, the maximum number is 2n−3. Next we show that uniformly distributed points have an expected number of at least 2ρ1n(1+o(1)) first order Delaunay triangulations, where ρ1 is an analytically defined constant (ρ1 ≈ 0.525785), and for k > 1, the expected number of order-k Delaunay triangulations (which are not order-i for any i < k) is at least 2ρkn(1+o(1)), where ρk can be calculated numerically.Peer ReviewedPostprint (published version
Finding consistent categorial grammars of bounded value: A parameterized approach

acceptance rate 41%Kanazawa has studied the learnability of several parameterized families of classes of categorial grammars. These classes were shown to be learnable from text, in the technical sense of identifiability in the limit from positive data. They are defined in terms of bounds on certain parameters of the grammars. Intuitively, these bounds correspond to restrictions on linguistic aspects such as the amount of lexical ambiguity of the grammar.
The time complexity of learning these classes has been studied by Costa Florêncio. It was shown that for most of these classes, selecting a grammar from the class that is consistent with the data is NP-hard. In this paper existing complexity results are sharpened by demonstrating W[2]-hardness. Additional parameters allowing FPT-results are also studied, and it is shown that if these parameters are fixed, these problems become computable in polynomial time. As far as the authors are aware, this is the first such result for learning problems.status: publishe
The Inclusion Problem for Regular Expressions

This paper presents a new polynomial-time algorithm for the
inclusion problem for certain pairs of regular expressions. The algorithm
is not based on construction of finite automata, and can therefore be
faster than the lower bound implied by the Myhill-Nerode theorem. The
algorithm automatically discards unnecessary parts of the right-hand
expression. In these cases the right-hand expression might even be 1-
ambiguous. For example, if r is a regular expression such that any DFA
recognizing r is very large, the algorithm can still, in time independent of
r, decide that the language of ab is included in that of (a+r)b. The algorithm
is based on a syntax-directed inference system. It takes arbitrary
regular expressions as input, and if the 1-ambiguity of the right-hand
expression becomes a problem, the algorithm will report this
A Simple n-Dimensional Intrinsically Universal Quantum Cellular
  Automaton

We describe a simple n-dimensional quantum cellular automaton (QCA) capable
of simulating all others, in that the initial configuration and the forward
evolution of any n-dimensional QCA can be encoded within the initial
configuration of the intrinsically universal QCA. Several steps of the
intrinsically universal QCA then correspond to one step of the simulated QCA.
The simulation preserves the topology in the sense that each cell of the
simulated QCA is encoded as a group of adjacent cells in the universal QCA.Comment: 13 pages, 7 figures. In Proceedings of the 4th International
  Conference on Language and Automata Theory and Applications (LATA 2010),
  Lecture Notes in Computer Science (LNCS). Journal version: arXiv:0907.382
Conceptualizing a bottom-up approach to service bundling

Offering service bundles to the market is a promising option for service providers to strengthen their competitive advantages, cope with dynamic market conditions and deal with heterogeneous consumer demand. Although the expected positive effects of bundling strategies and pricing considerations for bundles are covered well by the available literature, limited guidance can be found regarding the identification of potential bundle candidates and the actual process of bundling. The contribution of this paper is the positioning of bundling based on insights from both business and computer science and the proposition of a structured bundling method, which guides organizations with the composition of bundles in practice
Supporting Semantic Search on Heterogeneous Semi-structured Documents

Taux d'acceptation (13%)International audienceThis paper presents SHIRI-Querying, an approach for semantic search in semistructured documents. We propose a solution to tackle incompleteness and imprecision of annotations at querying time. This solution relies on two elementary reformulation types that use the notion of aggregation and the documents structure. We present the dynamic algorithm (DREQ) which combines these elementary transformations to construct ordered reformulations of user queries. Experimentations on two real datasets show that reformulations increase greatly the recall and that the precision is better for the first returned answers
Incorporating modules into the i* framework

When building large-scale goal-oriented models using the i* framework, the problem of scalability arises. One of the most important causes for this problem is the lack of modularity constructs in the language: just the concept of actor boundary allows grouping related model elements. In this paper, we present an approach that incorporates modules into the i* framework\ud
with the purpose of ameliorating the scalability problem. We explore the different types of modules that may be conceived in the framework, define them\ud
in terms of an i* metamodel, and introduce different model operators that support their application.Peer ReviewedPostprint (author’s final draft
Tradeoffs in process strategy games with application in the WDM reconfiguration problem

International audienceWe consider a variant of the graph searching games that is closely related to the routing reconfiguration problem in WDM networks. In the digraph processing game, a team of agents is aiming at clearing, or processing, the vertices of a digraph D. In this game, two important measures arise: 1) the total number of agents used, and 2) the total number of vertices occupied by an agent during the processing of D. Previous works have studied the problem of minimizing each of these parameters independently. In particular, both of these optimization problems are not in APX. In this paper, we study the tradeoff between both these conflicting objectives. More precisely, we prove that there exist some instances for which minimizing one of these objectives arbitrarily impairs the quality of the solution for the other one. We show that such bad tradeoffs may happen even in the case of basic network topologies. On the other hand, we exhibit classes of instances where good tradeoffs can be achieved. We also show that minimizing one of these parameters while the other is constrained is not in APX
A decision support system for logistics operations

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-13161-5_14Proceedings of 5th International Workshop Soft Computing Models in Industrial and Environmental ApplicationsThis paper describes an Artificial Intelligence based application for a logistic company that solves the problem of grouping by zones the packages that have to be delivered and propose the routes that the drivers should follow. The tool combines from the one hand, Case-Based Reasoning techniques to separate and learn the most frequent areas or zones that the experienced logistic operators do. These techniques allow the company to separate the daily incidents that generate noise in the routes, from the decision made based on the knowledge of the route. From the other hand, we have used Evolutionary Computation to plan optimal routes from the learning areas and evaluate those routes. The application allows the users to decide under what parameters (i.e. distance, time, etc) the route should be optimized.We want to thank Antonio Montoya for his contribution in the tool developed.
This work has been supported by the Espi & Le Barbier company and the public projects
funded by the Spanish Ministry of Science and Innovation under the projects COMPUBIODIVE
(TIN2007-65989), V-LeaF (TIN2008-02729-E/TIN) and by Castilla-La Mancha project PEII09-
0266-6640
Extending LMS to Support IRT-Based Assessment Test Calibration

Developing unambiguous and challenging assessment material for measuring educational attainment is a time-consuming, labor-intensive process. As a result Computer Aided Assessment (CAA) tools are becoming widely adopted in academic environments in an effort to improve the assessment quality and deliver reliable results of examinee performance. This paper introduces a methodological and architectural framework which embeds a CAA tool in a Learning Management System (LMS) so as to assist test developers in refining items to constitute assessment tests. An Item Response Theory (IRT) based analysis is applied to a dynamic assessment profile provided by the LMS. Test developers define a set of validity rules for the statistical indices given by the IRT analysis. By applying those rules, the LMS can detect items with various discrepancies which are then flagged for review of their content. Repeatedly executing the aforementioned procedure can improve the overall efficiency of the testing process
Technology enhanced learning for people with intellectual disabilities and cerebral parallysis: the MAS platform.

Proceedings of: First International Conference on Reforming Education, Quality of Teaching and Technology-Enhanced Learning: Learning Technologies, Quality of Education, Educational Systems, Evaluation, Pedagogies (TECH-EDUCATION 2010), Athens, Greece, May, 19-21, 2010Education for students with disabilities now takes place in a wide range of settings, thus, including a wider range of assistive tools. As a result of this, one of the most interesting application domains of technology enhanced learning is related to the adoption of learning technologies and designs for people with disabilities. Following this unstoppable trend, this paper presents MAS, a software platform aimed to help people with severe intellectual disabilities and cerebral paralysis in their learning processes. MAS, as a technology enhanced learning platform, provides several tools that supports learning and monitoring for people with special needs, including adaptative games, data processing and monitoring tools. Installed in a special needs education institution in Madrid, Spain, MAS provides special educators with a tool that improved students education processes.Publicad